From 31cda54aafeedccfe97cfdc56054e8c0a77befb7 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 03:38:27 -0700 Subject: [PATCH 01/36] DEP: Update setup.py re: python and pandas #315 --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 9f44ceb2..ce77aa91 100644 --- a/setup.py +++ b/setup.py @@ -78,7 +78,7 @@ "biom-format[hdf5]", "click", "numpy >= 1.12.0", - "pandas >= 0.24.0, <1", + "pandas >= 1", "scikit-bio > 0.5.3", ], # Based on how Altair splits up its requirements: @@ -98,5 +98,5 @@ "console_scripts": ["qurro=qurro.scripts._plot:plot"], }, zip_safe=False, - python_requires=">=3.6,<3.8", + python_requires=">=3.6", ) From 60efe40326a39e01f1fe0bd4af32ee08374d2229 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 03:58:12 -0700 Subject: [PATCH 02/36] DEV: port CI from Travis to GH Actions: close #316 --- .github/workflows/main.yml | 54 ++++++++++++++++++++++++++++++ .travis.yml | 68 -------------------------------------- README.md | 2 +- 3 files changed, 55 insertions(+), 69 deletions(-) create mode 100644 .github/workflows/main.yml delete mode 100644 .travis.yml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 00000000..6d1551bf --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,54 @@ +# Based on +# https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml +# (which was based on EMPress' workflow); some of the Node.js stuff based on +# MetagenomeScope's JS workflow +name: Qurro CI (Python, JS, example notebooks) +on: [push, pull_request] +jobs: + build: + runs-on: ubuntu-latest + + steps: + + # Updating from v2 to v3 to match, as of writing, + # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + - name: Check out code + uses: actions/checkout@v3 + + # (See https://dev.qiime2.org/latest/quickstart, thanks @thermokarst for + # the heads up :) + - name: Download the latest QIIME 2 conda environment YAML + run: wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml + + # https://github.com/conda-incubator/setup-miniconda#example-3-other-options + - name: Hit the yoinky sploinky (install QIIME 2) + uses: conda-incubator/setup-miniconda@v2 + with: + activate-environment: qiime2-dev + environment-file: qiime2-latest-py38-linux-conda.yml + + - name: Install Qurro (and its pip dependencies) + run: conda run -n qiime2-dev pip install -e .[dev] + + - name: Install the example notebooks' dependencies + run: | + conda run -n qiime2-dev pip install songbird deicode + conda run -n qiime2-dev conda install --yes -c bioconda bioconductor-aldex2 mygene + + - name: Set up Node.js + uses: actions/setup-node@v1 + + - name: Install Qurro's Node.js development dependencies + run: npm install -g mocha-headless-chrome nyc prettier@2.0.5 jshint + + - name: Run tests + run: conda run -n qiime2-dev make test + + - name: Verify that the example notebooks can be run without crashing + run: conda run -n qiime2-dev make notebooks + + - name: Lint and stylecheck + run: conda run -n qiime2-dev make stylecheck + + - name: Upload code coverage information to Codecov + uses: codecov/codecov-action@v2 diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 152e726f..00000000 --- a/.travis.yml +++ /dev/null @@ -1,68 +0,0 @@ -language: python -python: - - "3.6" -before_install: - # Here, we install the stuff needed to test the q2-qurro plugin. - # This will cause tests to take a while, but that's an ok price to pay. - # - # 1. Install conda (commands from - # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/use-conda-with-travis-ci.html) - - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh - - bash miniconda.sh -b -p $HOME/miniconda - - export PATH="$HOME/miniconda/bin:$PATH" - - hash -r - - conda config --set always_yes yes --set changeps1 no - - conda update -q conda - - conda info -a - # 2. Install the latest QIIME 2 version - # (see https://dev.qiime2.org/latest/quickstart, thanks @thermokarst for - # the heads up :) - - wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml - - travis_retry conda env create -n qiime2-dev --file qiime2-latest-py36-linux-conda.yml - - source activate qiime2-dev - # 3. Install Songbird and DEICODE - # (this will let us rerun the Sleep Apnea, Moving Pictures, Qarcoal, and - # Red Sea example notebooks) - # These are installed using pip due to conda-forge-related problems at the - # moment: see https://github.com/biocore/songbird/issues/126. - - pip install songbird deicode - # 4. Install seaborn so we can run the colors example notebook - # (should be already installed in a QIIME 2 environment, but we may as well - # make sure that this won't break in the future) - - conda install seaborn - # 5. Install ALDEx2 and mygene - # (this will let us rerun the ALDEx2 example notebook) - - conda install -c bioconda bioconductor-aldex2 mygene - # 6. Update Node.js to the latest version, since Prettier relies on us - # having at least version 10.13 and the default on Travis as of writing is - # apparently 8.12.0. See https://github.com/nvm-sh/nvm#usage and - # https://github.com/travis-ci/travis-ci/issues/4090#issuecomment-122688955 - - nvm install node -install: - - pip install -e .[dev] - # Install various JS testing/stylechecking packages that we use for - # developing qurro, but aren't required to just use qurro - - npm install -g mocha-headless-chrome - - npm install -g jshint - # Pinning prettier to avoid having to update everything - # This is also currently done in Empress' travis YAML - - npm install -g prettier@2.0.5 - - npm install -g nyc -script: - # Just to be safe - - qiime dev refresh-cache - # Run actual Qurro tests (both Python and JavaScript) - - make test - # Verify that example notebooks can be run without crashing - - make notebooks - # Verify that code is properly formatted - - make stylecheck -after_success: - - wget -O codecov.sh https://codecov.io/bash - # Upload coverage information (see - # https://docs.codecov.io/docs/merging-reports). Fortunately, codecov's - # bash script detects both the python and JS code coverage by default -- - # so it automatically merges the reports, without us needing to run - # codecov.sh multiple times (although that should be doable also, in case - # future reports aren't automatically detected). - - bash codecov.sh -c diff --git a/README.md b/README.md index 0ac9605d..2cc9f3e1 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@
-Build Status +Qurro CI Code Coverage DOI PyPI From b9d1ac87ac8900b339ce0f26df4288df69306f9a Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 04:12:18 -0700 Subject: [PATCH 03/36] TST: For now, omit "make notebooks" from CI Maybe we can make another GitHub Actions for these later; but Songbird is causing tensorflow nonsense to pop up, and this is not the sort of thing I think we should spend time fixing (esp with the advent of birdman) --- .github/workflows/main.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6d1551bf..9d777c89 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -30,10 +30,10 @@ jobs: - name: Install Qurro (and its pip dependencies) run: conda run -n qiime2-dev pip install -e .[dev] - - name: Install the example notebooks' dependencies - run: | - conda run -n qiime2-dev pip install songbird deicode - conda run -n qiime2-dev conda install --yes -c bioconda bioconductor-aldex2 mygene + # - name: Install the example notebooks' dependencies + # run: | + # conda run -n qiime2-dev pip install songbird deicode + # conda run -n qiime2-dev conda install --yes -c bioconda bioconductor-aldex2 mygene - name: Set up Node.js uses: actions/setup-node@v1 @@ -44,8 +44,8 @@ jobs: - name: Run tests run: conda run -n qiime2-dev make test - - name: Verify that the example notebooks can be run without crashing - run: conda run -n qiime2-dev make notebooks + # - name: Verify that the example notebooks can be run without crashing + # run: conda run -n qiime2-dev make notebooks - name: Lint and stylecheck run: conda run -n qiime2-dev make stylecheck From 7aca3ced97376da0ec7edd068ee09334cc805a9e Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 04:27:33 -0700 Subject: [PATCH 04/36] DEP: pin min biom vsn and add some comments --- setup.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ce77aa91..7cfc27e5 100644 --- a/setup.py +++ b/setup.py @@ -74,10 +74,18 @@ # for details. include_package_data=True, install_requires=[ + # Updating this pin will require updating the entire JS interface to + # work with later versions of Vega-Lite, which is doable but likely not + # worth the effort at the moment; see + # https://github.com/biocore/qurro/issues/315 "altair == 3.1.0", - "biom-format[hdf5]", + # 2.1.9 is the earliest BIOM version that adds support for pandas >= 1. + # Also, it takes care of the issue where biom.Table.to_dataframe() + # produced a dense instead of a sparse DataFrame. + "biom-format[hdf5] >= 2.1.9", "click", "numpy >= 1.12.0", + # SparseDataFrame is dead, long live DataFrame "pandas >= 1", "scikit-bio > 0.5.3", ], From b90a834ba6a1e441a5a53b3f948bee456af782bf Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 04:27:48 -0700 Subject: [PATCH 05/36] DEP: Fix biom_table_to_sparse_df for pandas >= 1 See #258 and #315. not confident this is done yet (and if nothing else the rest of the code gleefully refers to "SparseDataFrame" because 2019 marcus was a schmuck), but this at least fixes a fair amount of failing tests --- qurro/_df_utils.py | 26 +++++++++----------------- 1 file changed, 9 insertions(+), 17 deletions(-) diff --git a/qurro/_df_utils.py b/qurro/_df_utils.py index 91d118d5..91b1bd82 100644 --- a/qurro/_df_utils.py +++ b/qurro/_df_utils.py @@ -112,29 +112,21 @@ def replace_nan(df, new_nan_val=None): def biom_table_to_sparse_df(table, min_row_ct=2, min_col_ct=1): - """Loads a BIOM table as a pd.SparseDataFrame. Also calls validate_df(). + """Loads a BIOM table as a (sparse) pd.DataFrame. Also calls validate_df(). - We need to use a helper function for this because old versions of BIOM - accidentally produce an effectively-dense DataFrame when using - biom.Table.to_dataframe() -- see - https://github.com/biocore/biom-format/issues/808. - - To get around this, we extract the scipy.sparse.csr_matrix data from the - BIOM table and directly convert that to a pandas SparseDataFrame. + In the past, we did this in a roundabout way to avoid a weird biom-format + issue (https://github.com/biocore/biom-format/issues/808), but now our min + biom-format version should mean that we never run into this problem. """ - logging.debug("Creating a SparseDataFrame from BIOM table.") - table_sdf = pd.SparseDataFrame(table.matrix_data, default_fill_value=0.0) + logging.debug("Creating a DataFrame from BIOM table.") - # The csr_matrix doesn't include column/index IDs, so we manually add them - # in to the SparseDataFrame. - table_sdf.index = table.ids(axis="observation") - table_sdf.columns = table.ids(axis="sample") + table_sdf = table.to_dataframe(dense=False) - # Validate the table DataFrame -- should be ok since we loaded this through - # the biom module, but might as well check + # Validate the DataFrame -- should be ok since we loaded the table through + # biom, but might as well check validate_df(table_sdf, "BIOM table", min_row_ct, min_col_ct) - logging.debug("Converted BIOM table to SparseDataFrame.") + logging.debug("Converted BIOM table to DataFrame.") return table_sdf From d0947ff7fcccb2df5ef2143bad4743e3dce74763 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 04:44:55 -0700 Subject: [PATCH 06/36] DEP: remove some warnings, docs, fix a test re: pd --- qurro/_rank_utils.py | 23 ++++++++++++++----- qurro/tests/test_filter_unextreme_features.py | 13 +++++++---- 2 files changed, 26 insertions(+), 10 deletions(-) diff --git a/qurro/_rank_utils.py b/qurro/_rank_utils.py index 6acff909..2131d2b4 100644 --- a/qurro/_rank_utils.py +++ b/qurro/_rank_utils.py @@ -103,7 +103,7 @@ def differentials_to_df(differentials_loc): def filter_unextreme_features( - table: pd.SparseDataFrame, ranks: pd.DataFrame, extreme_feature_count: int + table: pd.DataFrame, ranks: pd.DataFrame, extreme_feature_count: int ) -> None: """Returns copies of the table and ranks with "unextreme" features removed. @@ -115,8 +115,8 @@ def filter_unextreme_features( Parameters ---------- - table: pd.SparseDataFrame - A SparseDataFrame representation of a BIOM table. This can be + table: pd.DataFrame + A DataFrame representation of a BIOM table. This can be generated easily from a biom.Table object using qurro._df_utils.biom_table_to_sparse_df(). @@ -134,7 +134,7 @@ def filter_unextreme_features( Returns ------- - (table, ranks): (pandas.SparseDataFrame, pandas.DataFrame) + (table, ranks): (pandas.DataFrame, pandas.DataFrame) Filtered copies of the input table and ranks DataFrames. Behavior @@ -206,6 +206,17 @@ def filter_unextreme_features( features_to_preserve |= set(upper_extrema) features_to_preserve |= set(lower_extrema) + # In the year of our lord 2022, using a set as an indexer for .loc[] + # makes pandas raise a warning. So, now that we've made use of the fact + # that features_to_preserve has no duplicates, we convert it back to a + # list. There's probably a more efficient way to do this, but I doubt this + # will be a bottleneck. + features_to_preserve_but_as_a_list = list(features_to_preserve) + + # (NOTE FROM 2022: the below comment is old and I have no idea why I + # formatted it like that or if this benchmarking is even still accurate + # after pandas 1's changes to dataframe sparsity, idk) + # # Now, we actually filter the feature ranks and table. We do this using # .loc[]. I benchmarked it, and .loc was about 1.77x as fast as .filter -- # >>> df = pd.SparseDataFrame(np.zeros(34000000).reshape(17000, 2000)) @@ -213,8 +224,8 @@ def filter_unextreme_features( # 460 ms +/- 17.6 ms per loop # >>> %timeit df.filter(items=set([16990, 8983, 8982]), axis="index") # 818 ms +/- 25.6 ms per loop - filtered_ranks = ranks.loc[features_to_preserve] - filtered_table = table.loc[features_to_preserve] + filtered_ranks = ranks.loc[features_to_preserve_but_as_a_list] + filtered_table = table.loc[features_to_preserve_but_as_a_list] filtered_feature_ct = filtered_ranks.shape[0] print( diff --git a/qurro/tests/test_filter_unextreme_features.py b/qurro/tests/test_filter_unextreme_features.py index 42b91973..60671e89 100644 --- a/qurro/tests/test_filter_unextreme_features.py +++ b/qurro/tests/test_filter_unextreme_features.py @@ -63,10 +63,15 @@ def test_filtering_basic(): assert sid in filtered_table.columns # Check that the appropriate data is left in the table. - assert list(filtered_table.loc["F1"]) == [0, 1, 0, 3, 4] - assert list(filtered_table.loc["F2"]) == [5, 6, 0, 8, 9] - assert list(filtered_table.loc["F7"]) == [30, 31, 0, 33, 34] - assert list(filtered_table.loc["F8"]) == [35, 36, 0, 38, 39] + # Using .loc[] on DataFrames with sparse columns makes pandas get angry, + # so we can get around this by (just in this case) converting + # filtered_table to a dense DataFrame. + # See https://stackoverflow.com/q/49032856 + ftd = filtered_table.sparse.to_dense() + assert list(ftd.loc["F1"]) == [0, 1, 0, 3, 4] + assert list(ftd.loc["F2"]) == [5, 6, 0, 8, 9] + assert list(ftd.loc["F7"]) == [30, 31, 0, 33, 34] + assert list(ftd.loc["F8"]) == [35, 36, 0, 38, 39] # Check that the rank filtering worked as expected. expected_filtered_ranks = DataFrame( From e773b9573a4ba5b5840e9e46727c3bef31777142 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 04:49:26 -0700 Subject: [PATCH 07/36] TST: Fix the python tests!!! #258 The problem was using .loc[] on these sparse dataframes. whoops --- qurro/tests/testing_utilities.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/qurro/tests/testing_utilities.py b/qurro/tests/testing_utilities.py index d53582fe..694d7d7b 100644 --- a/qurro/tests/testing_utilities.py +++ b/qurro/tests/testing_utilities.py @@ -296,9 +296,12 @@ def validate_rank_plot_json( rank_json, id_field="Feature ID" ) + # Convert the table to a dense DF (the horror!) so that we can use .loc[] + dense_table = table.sparse.to_dense() + for ref_feature_id in ref_feature_ranks.index: # If this feature is empty, it should have been filtered! - if sum(table.loc[ref_feature_id]) == 0: + if sum(dense_table.loc[ref_feature_id]) == 0: assert ref_feature_id not in rank_json_feature_data continue # ...If this feature isn't empty, though, it shouldn't have been From 542d1379ad697455afa8c8d1c25e8a92e3980cde Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 04:51:46 -0700 Subject: [PATCH 08/36] STY: tiny style fixes --- qurro/tests/test_df_utils.py | 4 ++-- qurro/tests/test_qarcoal.py | 6 +++--- qurro/tests/testing_utilities.py | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/qurro/tests/test_df_utils.py b/qurro/tests/test_df_utils.py index 9767f13e..78cc816e 100644 --- a/qurro/tests/test_df_utils.py +++ b/qurro/tests/test_df_utils.py @@ -949,8 +949,8 @@ def test_vibe_check_failures(): ) in str(exception_info.value) # Test failure, with the default safe range, on a few small cases. - lower_lim = -(2 ** 53) - 1 - upper_lim = (2 ** 53) - 1 + lower_lim = -(2**53) - 1 + upper_lim = (2**53) - 1 weird_small_values = [lower_lim - 1, lower_lim * 2, lower_lim * 3] for w in weird_small_values: diff --git a/qurro/tests/test_qarcoal.py b/qurro/tests/test_qarcoal.py index 6b4dbe68..ece776db 100644 --- a/qurro/tests/test_qarcoal.py +++ b/qurro/tests/test_qarcoal.py @@ -432,9 +432,9 @@ def test_large_numbers(self): """ samps = ["S{}".format(i) for i in range(3)] feats = ["F{}".format(i) for i in range(6)] - s0 = [x ** 53 for x in (2.0, 3.2, 4.1, 6.2, 4.3, 3.7)] - s1 = [x ** 53 for x in (2.5, 2.6, 2.9, 5.2, 2.1, 2.5)] - s2 = [x ** 53 for x in (2.2, 3.5, 3.1, 3.0, 2.2, 4.0)] + s0 = [x**53 for x in (2.0, 3.2, 4.1, 6.2, 4.3, 3.7)] + s1 = [x**53 for x in (2.5, 2.6, 2.9, 5.2, 2.1, 2.5)] + s2 = [x**53 for x in (2.2, 3.5, 3.1, 3.0, 2.2, 4.0)] confidence = ["0.99"] * 6 tax_labels = [ "Charmander", diff --git a/qurro/tests/testing_utilities.py b/qurro/tests/testing_utilities.py index 694d7d7b..12b2acdb 100644 --- a/qurro/tests/testing_utilities.py +++ b/qurro/tests/testing_utilities.py @@ -298,7 +298,7 @@ def validate_rank_plot_json( # Convert the table to a dense DF (the horror!) so that we can use .loc[] dense_table = table.sparse.to_dense() - + for ref_feature_id in ref_feature_ranks.index: # If this feature is empty, it should have been filtered! if sum(dense_table.loc[ref_feature_id]) == 0: From 0a8483216a4e7ba55da0567e06ca89d104b75553 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:01:44 -0700 Subject: [PATCH 09/36] DEP: knock out some pandas warnings --- qurro/qarcoal.py | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/qurro/qarcoal.py b/qurro/qarcoal.py index 18435798..4a12aeaa 100644 --- a/qurro/qarcoal.py +++ b/qurro/qarcoal.py @@ -51,12 +51,15 @@ def filter_and_join_taxonomy(feat_table, taxonomy, num_string, denom_string): num_indices = taxonomy_joined_df["Taxon"].str.contains(num_string) denom_indices = taxonomy_joined_df["Taxon"].str.contains(denom_string) - tax_num_df = taxonomy_joined_df.loc[num_indices] - tax_denom_df = taxonomy_joined_df.loc[denom_indices] + tax_num_df_with_extra_col = taxonomy_joined_df.loc[num_indices] + tax_denom_df_with_extra_col = taxonomy_joined_df.loc[denom_indices] - # want to drop Taxon column because we want the dfs to be only numeric - tax_num_df.drop(columns="Taxon", inplace=True) - tax_denom_df.drop(columns="Taxon", inplace=True) + # We need to drop the Taxon column because we want the dfs to be numeric + # Also, we don't use in-place operations to prevent pandas warnings about + # "A value is trying to be set on a copy of a slice from a DataFrame" -- + # see https://stackoverflow.com/a/33727690 + tax_num_df = tax_num_df_with_extra_col.drop(columns="Taxon") + tax_denom_df = tax_denom_df_with_extra_col.drop(columns="Taxon") # if _q suffix was added due to sample called Taxon, change back to Taxon if "Taxon_q" in taxonomy_joined_df: @@ -89,8 +92,11 @@ def filter_and_join_taxonomy(feat_table, taxonomy, num_string, denom_string): "No samples contain both numerator and denominator features!" ) - tax_num_df = tax_num_df[samp_to_keep] - tax_denom_df = tax_denom_df[samp_to_keep] + # using a set as an indexer is now deprecated, so we convert it to a list + samp_to_keep_but_as_a_list = list(samp_to_keep) + + tax_num_df = tax_num_df[samp_to_keep_but_as_a_list] + tax_denom_df = tax_denom_df[samp_to_keep_but_as_a_list] return tax_num_df, tax_denom_df From 45bdd3a1c280493c55627d83c3e2716488a3b91e Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:03:58 -0700 Subject: [PATCH 10/36] DEP: np.matrix() -> np.array() in qarcoal tests since apparently it's deprecated, or about to be deprecated, idk --- qurro/tests/test_qarcoal.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/qurro/tests/test_qarcoal.py b/qurro/tests/test_qarcoal.py index ece776db..f8607c3a 100644 --- a/qurro/tests/test_qarcoal.py +++ b/qurro/tests/test_qarcoal.py @@ -168,7 +168,7 @@ def test_no_common_samples(self): s2 = [10, 15, 7, 0, 0, 0] s3 = [0, 0, 0, 0, 0, 0] s4 = [0, 0, 0, 6, 4, 2] - mat = np.matrix([s0, s1, s2, s3, s4]).T + mat = np.array([s0, s1, s2, s3, s4]).T table = biom.table.Table(mat, feats, samps).to_dataframe() tax_labels = [ @@ -444,7 +444,7 @@ def test_large_numbers(self): "Ivysaur", "Vensaur", ] - mat = np.matrix([s0, s1, s2]).T + mat = np.array([s0, s1, s2]).T table = biom.table.Table(mat, feats, samps) taxonomy = pd.DataFrame([feats, tax_labels, confidence]).T From c330e68551eee9597f24a6f6b23b9d428491e737 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:11:43 -0700 Subject: [PATCH 11/36] DEP/STY: Fix more warnings; remove unused import most of these warnings were just pd.DataFrame.append() being deprecated and replaced with pd.concat() --- qurro/_df_utils.py | 1 - qurro/tests/test_df_utils.py | 19 ++++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/qurro/_df_utils.py b/qurro/_df_utils.py index 91b1bd82..c5d1c756 100644 --- a/qurro/_df_utils.py +++ b/qurro/_df_utils.py @@ -8,7 +8,6 @@ # ---------------------------------------------------------------------------- import logging -import pandas as pd def ensure_df_headers_unique(df, df_name): diff --git a/qurro/tests/test_df_utils.py b/qurro/tests/test_df_utils.py index 78cc816e..00d3701d 100644 --- a/qurro/tests/test_df_utils.py +++ b/qurro/tests/test_df_utils.py @@ -1,7 +1,8 @@ import pytest +import pandas as pd +import numpy as np from pandas import DataFrame, Series from pandas.testing import assert_frame_equal, assert_series_equal -import numpy as np from qurro._df_utils import ( ensure_df_headers_unique, validate_df, @@ -339,7 +340,7 @@ def test_remove_empty_samples_and_features_both(): ftable, table[["Sample1", "Sample3"]].iloc[0:6], check_like=True ) assert_frame_equal( - fmetadata, metadata.loc[set(["Sample1", "Sample3"])], check_like=True + fmetadata, metadata.loc[["Sample1", "Sample3"]], check_like=True ) assert_frame_equal(franks, ranks.iloc[0:6]) @@ -662,7 +663,7 @@ def test_match_table_and_data_table_extra_feature(capsys): columns=table.columns, index=["FeatureInTableButNotRanks"], ) - table = table.append(new_row, verify_integrity=True) + table = pd.concat([table, new_row], verify_integrity=True) m_table, m_metadata = match_table_and_data(table, ranks, metadata) # Only features in the ranks' index should be left in the table's index, # and the table and ranks' indices should line up. @@ -715,7 +716,7 @@ def test_match_table_and_data_metadata_extra_sample(capsys): columns=metadata.columns, index=["SampleInMDButNotTable"], ) - metadata = metadata.append(new_row, verify_integrity=True) + metadata = pd.concat([metadata, new_row], verify_integrity=True) m_table, m_metadata = match_table_and_data(table, ranks, metadata) assert len(set(m_table.columns) & set(m_metadata.index)) == len( table.columns @@ -740,7 +741,7 @@ def test_match_table_and_data_ranked_features_not_in_table(): # (...because that is not a good situation.) table, metadata, ranks = get_test_data() new_feature_row = DataFrame([[9, 0]], columns=ranks.columns, index=["F9"]) - ranks_modified = ranks.append(new_feature_row, verify_integrity=True) + ranks_modified = pd.concat([ranks, new_feature_row], verify_integrity=True) with pytest.raises(ValueError) as exception_info: match_table_and_data(table, ranks_modified, metadata) expected_message = ( @@ -754,8 +755,8 @@ def test_match_table_and_data_ranked_features_not_in_table(): new_feature_row = DataFrame( [[10, -1]], columns=ranks.columns, index=["F10"] ) - ranks_modified = ranks_modified.append( - new_feature_row, verify_integrity=True + ranks_modified = pd.concat( + [ranks_modified, new_feature_row], verify_integrity=True ) with pytest.raises(ValueError) as exception_info: match_table_and_data(table, ranks_modified, metadata) @@ -789,7 +790,7 @@ def test_match_table_and_data_complex(capsys): # Add the extra feature to the table new_f_row = DataFrame([[1, 2, 3, 4]], columns=table.columns, index=["F9"]) - table = table.append(new_f_row, verify_integrity=True) + table = pd.concat([table, new_f_row], verify_integrity=True) # Add the extra sample to the table table["Sample5"] = 5 @@ -798,7 +799,7 @@ def test_match_table_and_data_complex(capsys): new_s_row = DataFrame( [[4, 3, 2, 1]], columns=metadata.columns, index=["SampleM"] ) - metadata = metadata.append(new_s_row, verify_integrity=True) + metadata = pd.concat([metadata, new_s_row], verify_integrity=True) # Ok, actually run the function! m_table, m_metadata = match_table_and_data(table, ranks, metadata) From 425cde5f6dd7930ca6336e4e2a927f9642679be1 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:13:30 -0700 Subject: [PATCH 12/36] DOC: one of the demos' JS data slightly changed looks like it's a tiny floating-point thing -- probably an artifact of working here on a new operating system, on a new python version, a new pandas version, a new biom version, etc. shouldn't make a noticeable difference --- docs/demos/q2_moving_pictures/main.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/demos/q2_moving_pictures/main.js b/docs/demos/q2_moving_pictures/main.js index 63b58fd8..e57f035d 100644 --- a/docs/demos/q2_moving_pictures/main.js +++ b/docs/demos/q2_moving_pictures/main.js @@ -42,7 +42,7 @@ requirejs( // "var *JSON = {};" lines are expected to contain that text by Qurro's // python code, which replaces the empty {}s with JSON objects that // contain all of the data needed for the Qurro visualization. - var rankPlotJSON = {"$schema": "https://vega.github.io/schema/vega-lite/v3.3.0.json", "autosize": {"resize": true}, "background": "#FFFFFF", "config": {"axis": {"gridColor": "#f2f2f2", "labelBound": true}, "mark": {"tooltip": null}, "view": {"height": 300, "width": 400}}, "data": {"name": "data-c61b56aa5bd689564a6fcbcdd39f9563"}, "datasets": {"data-c61b56aa5bd689564a6fcbcdd39f9563": [{"Axis 1": -0.07656628126254535, "Axis 2": 0.021454931533858128, "Axis 3": 0.27293792335243716, "Axis 4": 0.3570557415869906, "Axis 5": -0.25633122007078846, "Confidence": 0.9972511412166732, "Feature ID": "4b5eeb300368260019c1fbc7a3c718fc", "Taxon": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__", "qurro_classification": "None", "qurro_spc": 13.0}, {"Axis 1": 0.10805989085103826, "Axis 2": -0.2405422073411352, "Axis 3": -0.1708979267324281, "Axis 4": -0.05330127270981942, "Axis 5": -0.2217689569827807, "Confidence": 0.9799426564411076, "Feature ID": "fe30ff0f71a38a39cf1717ec2be3a2fc", "Taxon": "k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__Neisseria", "qurro_classification": "None", "qurro_spc": 16.0}, {"Axis 1": 0.1693976733516469, "Axis 2": -0.07053640212750548, "Axis 3": -0.26445904154084005, "Axis 4": 0.07650073635262021, "Axis 5": -0.2631901755626461, "Confidence": 0.9999999999716238, "Feature ID": "d29fe3c70564fc0f69f2c03e0d1e5561", "Taxon": "k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus", "qurro_classification": "None", "qurro_spc": 25.0}, {"Axis 1": -0.11291565220526853, "Axis 2": 0.20313055813596156, "Axis 3": -0.10604121194111753, "Axis 4": -0.3599545026546503, "Axis 5": -0.13358595296722264, "Confidence": 0.995585946749247, "Feature ID": "868528ca947bc57b69ffdf83e6b73bae", "Taxon": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__", "qurro_classification": "None", "qurro_spc": 10.0}, {"Axis 1": -0.12968594644949796, "Axis 2": 0.17420349991808984, "Axis 3": 0.15544628548802367, "Axis 4": 0.032277791612310015, "Axis 5": -0.2801570305640862, "Confidence": 0.9999999735454731, "Feature ID": "154709e160e8cada6bfb21115acc80f5", "Taxon": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides", "qurro_classification": "None", "qurro_spc": 13.0}, {"Axis 1": 0.07435316464216078, "Axis 2": -0.29873477983376723, "Axis 3": -0.11267376231336822, "Axis 4": -0.042195065820123924, "Axis 5": -0.18640465771725792, "Confidence": 0.9455365481961946, "Feature ID": "1d2e5f3444ca750c85302ceee2473331", "Taxon": "k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__Haemophilus; s__parainfluenzae", "qurro_classification": "None", "qurro_spc": 23.0}, {"Axis 1": -0.08330675594931562, "Axis 2": 0.12361036103529294, "Axis 3": 0.15882592068742724, "Axis 4": -0.14124028464298144, "Axis 5": -0.2672359484400899, "Confidence": 0.9909718328940056, "Feature ID": "0305a4993ecf2d8ef4149fdfc7592603", "Taxon": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__uniformis", "qurro_classification": "None", "qurro_spc": 11.0}, {"Axis 1": 0.1791786996495833, "Axis 2": 0.1465516067454795, "Axis 3": -0.18391504429737188, "Axis 4": 0.12540798059224528, "Axis 5": -0.11819322504685396, "Confidence": 0.9999999078928576, "Feature ID": "cb2fe0146e2fbcb101050edb996a0ee2", "Taxon": "k__Bacteria; p__Firmicutes; c__Bacilli", "qurro_classification": "None", "qurro_spc": 15.0}, {"Axis 1": 0.023374641599027246, "Axis 2": -0.27875661279210756, "Axis 3": 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"3c9c437f27aca05f8db167cd080ff1ec", "Taxon": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__melaninogenica", "qurro_classification": "None", "qurro_spc": 14.0}, {"Axis 1": -0.10596039317924098, "Axis 2": 0.07043004022262178, "Axis 3": 0.0661518237005731, "Axis 4": -0.06623550501122111, "Axis 5": -0.17622951528467717, "Confidence": 0.9936028877616412, "Feature ID": "bfbed36e63b69fec4627424163d20118", "Taxon": "k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Faecalibacterium; s__prausnitzii", "qurro_classification": "None", "qurro_spc": 14.0}, {"Axis 1": -0.05564270206194526, "Axis 2": 0.020738764622334437, "Axis 3": 0.1390445231864249, "Axis 4": 0.13844147586220432, "Axis 5": -0.17178493378125656, "Confidence": 0.9999875721629126, "Feature ID": "90d32ffe026535b392c0bad850f213c4", "Taxon": "k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Faecalibacterium; 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"L2S382": 2.0, "L4S137": 2.0, "L5S203": 3.0, "L5S240": 2.0, "L6S20": 2.0, "L6S68": 10.0, "L6S93": 12.0}, "fea5c05e9b8245c5ca46f6673f59e0bf": {"L1S105": 17.0, "L1S140": 11.0, "L1S208": 16.0, "L1S257": 22.0, "L1S281": 11.0, "L1S76": 6.0}, "ff3df50eea7490dd794148649c480fd3": {"L1S105": 26.0, "L1S281": 26.0, "L1S57": 64.0, "L1S76": 30.0}, "ff8c7f94f941a0c647120d4e142db316": {"L2S382": 10.0, "L4S137": 8.0}}; new display.RRVDisplay( From e54d70f151a5cb01f72f3aa74164d2e907eab792 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:18:57 -0700 Subject: [PATCH 13/36] DOC: update readme re: min Q2 vsn --- README.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 2cc9f3e1..f675cf55 100644 --- a/README.md +++ b/README.md @@ -57,8 +57,8 @@ Qurro can be used standalone (as a Python 3 script that generates a folder containing a HTML/JS/CSS visualization) or as a [QIIME 2](https://qiime2.org/) plugin (that generates a QZV file that can be visualized at [view.qiime2.org](https://view.qiime2.org/) or by using -`qiime tools view`). *Starting with Qurro v0.3.0, Qurro requires a QIIME 2 -version of at least 2019.7.* +`qiime tools view`). *Starting with Qurro v0.8.0, Qurro requires a QIIME 2 +version of at least 2020.11.* Qurro should work with most modern web browsers. Firefox or Chrome are recommended. @@ -84,7 +84,7 @@ can be viewed online [here](https://biocore.github.io/qurro/demos/red_sea/index. ## Installation and Usage -You can install Qurro using [pip](https://pip.pypa.io/en/stable/) or [conda](https://docs.conda.io/en/latest/). In either case, a python version of at least 3.6 and less than 3.8 is required to use Qurro. +You can install Qurro using [pip](https://pip.pypa.io/en/stable/) or [conda](https://docs.conda.io/en/latest/). In either case, a python version of at least 3.6 is required to use Qurro. ### Installing with `pip` ```bash @@ -203,8 +203,7 @@ For python testing/style checking, Qurro uses [flake8](http://flake8.pycqa.org/en/latest/), and [black](https://github.com/ambv/black). You'll also need to have QIIME 2 installed to run most of the python tests (your QIIME 2 version should be at -least 2019.7, due to the `FeatureData[Differential]` type being merged into -q2-types starting with this release). +least 2020.11; this is the version which switched to pandas >= 1). For JavaScript testing/style checking, Qurro uses [Mocha](https://mochajs.org/), [Chai](https://www.chaijs.com/), From 17c8e3714f0179543cb84861ad7a64bb62c4ddca Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:23:49 -0700 Subject: [PATCH 14/36] TST: matrix of qiime 2 versions nice! --- .github/workflows/main.yml | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 9d777c89..e35e6b3b 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -2,12 +2,23 @@ # https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml # (which was based on EMPress' workflow); some of the Node.js stuff based on # MetagenomeScope's JS workflow -name: Qurro CI (Python, JS, example notebooks) +name: Qurro CI on: [push, pull_request] jobs: build: runs-on: ubuntu-latest + strategy: + matrix: + # We could use a matrix of just QIIME 2 versions, but other stuff about + # the URLs change (e.g. the -py36- or -py38- thing), so it's easier to + # just have the matrix be the URLs to the YAMLs. That sentence has too + # many acronyms. Look, you get the point. + q2-yaml: [ + "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.11/release/qiime2-2020.11-py36-linux-conda.yml", + "https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml" + ] + steps: # Updating from v2 to v3 to match, as of writing, @@ -17,15 +28,15 @@ jobs: # (See https://dev.qiime2.org/latest/quickstart, thanks @thermokarst for # the heads up :) - - name: Download the latest QIIME 2 conda environment YAML - run: wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml + - name: Download the QIIME 2 conda environment YAML + run: wget -O q2-env.yml ${{ matrix.q2-yaml }} # https://github.com/conda-incubator/setup-miniconda#example-3-other-options - name: Hit the yoinky sploinky (install QIIME 2) uses: conda-incubator/setup-miniconda@v2 with: activate-environment: qiime2-dev - environment-file: qiime2-latest-py38-linux-conda.yml + environment-file: q2-env.yml - name: Install Qurro (and its pip dependencies) run: conda run -n qiime2-dev pip install -e .[dev] From 31bcaab27f3db5b109be9e3bbc1c4824c1b1a9ab Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:29:07 -0700 Subject: [PATCH 15/36] TST: more detailed comment about Q2 vsn matrix --- .github/workflows/main.yml | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e35e6b3b..fd528027 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -10,10 +10,19 @@ jobs: strategy: matrix: - # We could use a matrix of just QIIME 2 versions, but other stuff about - # the URLs change (e.g. the -py36- or -py38- thing), so it's easier to - # just have the matrix be the URLs to the YAMLs. That sentence has too - # many acronyms. Look, you get the point. + # Test on multiple QIIME 2 versions. This is a nice way of making sure + # that Qurro works on all of the QIIME 2 versions it actually, you + # know, supports. + # + # We could use a matrix of just QIIME 2 version strings (e.g. + # "2020.11", ...), but other stuff about the URLs change across QIIME 2 + # versions (e.g. the "-py36-" or "-py38-" thing). It ends up being + # easier just have the variable here be the URLs to the YAMLs. That + # sentence has too many acronyms. Look, you get the point. + # + # Worth noting: the final of these URLs (with qiime2-latest) will + # always be set to the latest version of QIIME 2. Thanks @thermokarst + # for the heads up about this :) q2-yaml: [ "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.11/release/qiime2-2020.11-py36-linux-conda.yml", "https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml" @@ -26,8 +35,6 @@ jobs: - name: Check out code uses: actions/checkout@v3 - # (See https://dev.qiime2.org/latest/quickstart, thanks @thermokarst for - # the heads up :) - name: Download the QIIME 2 conda environment YAML run: wget -O q2-env.yml ${{ matrix.q2-yaml }} From 7f34bcbdb1ff82ed8a25b16d8cb0182169aa9f12 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:43:52 -0700 Subject: [PATCH 16/36] DOC: remove the "Sparse" from "SparseDataFrame" --- qurro/_df_utils.py | 10 +++++----- qurro/generate.py | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/qurro/_df_utils.py b/qurro/_df_utils.py index c5d1c756..f05f7c5f 100644 --- a/qurro/_df_utils.py +++ b/qurro/_df_utils.py @@ -204,11 +204,11 @@ def print_if_dropped( Parameters ---------- - df_old: pd.DataFrame (or pd.SparseDataFrame) + df_old: pd.DataFrame "Unfiltered" DataFrame -- used as the reference when trying to determine if df_new has been filtered. - df_new: pd.DataFrame (or pd.SparseDataFrame) + df_new: pd.DataFrame A potentially-filtered DataFrame. axis_num: int @@ -256,7 +256,7 @@ def match_table_and_data(table, feature_ranks, sample_metadata): Parameters ---------- - table: pd.DataFrame (or pd.SparseDataFrame) + table: pd.DataFrame A DataFrame created from a BIOM table. The index of this DataFrame should correspond to observations (i.e. features), and the columns should correspond to samples. @@ -474,7 +474,7 @@ def add_sample_presence_count(feature_data, table_sdf): point in Qurro this is called, this will likely include both feature ranking information and feature metadata information. - table_sdf: pd.SparseDataFrame + table_sdf: pd.DataFrame Representation of a BIOM table containing count data. The index contains feature IDs, and the columns contain sample IDs. This table should only contain samples that will be used in the @@ -607,7 +607,7 @@ def vibe_check( to feature IDs and the columns correspond to ranking names. Critically, every entry in this should be numeric. - table_sdf: pd.DataFrame (or pd.SparseDataFrame) + table_sdf: pd.DataFrame DataFrame representation of a feature table. Similarly to the feature rankings, every entry in this should be numeric. diff --git a/qurro/generate.py b/qurro/generate.py index 4dde1582..a2fdf62a 100755 --- a/qurro/generate.py +++ b/qurro/generate.py @@ -86,7 +86,7 @@ def process_input( missing values are represented consistently with a None (which will be represented as a null in JSON/JavaScript). - 3. Converts the BIOM table to a SparseDataFrame by calling + 3. Converts the BIOM table to a DataFrame by calling biom_table_to_sparse_df(). 4. Runs vibe_check() on the feature ranks and BIOM table to ensure @@ -122,7 +122,7 @@ def process_input( feature_metadata_cols: list The feature metadata columns' names in output_ranks. - output_table: pd.SparseDataFrame + output_table: pd.DataFrame The BIOM table, post matching with the feature ranks and sample metadata and with empty samples removed. """ @@ -217,7 +217,7 @@ def gen_rank_plot(V, rank_type, ranking_ids, feature_metadata_cols, table_sdf): IDs of the "feature metadata" columns in V (if there wasn't any feature metadata provided, this can just be an empty list). - table_sdf: pd.SparseDataFrame + table_sdf: pd.DataFrame A representation of the input BIOM table containing count data. This is used to calculate qurro_spc (the number of samples a feature is present in) for each feature in V. This should ONLY contain samples From 94d512979c30f7e406dc5f1c3941dd3785a7a465 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 05:47:45 -0700 Subject: [PATCH 17/36] REL: version kick --- qurro/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qurro/__init__.py b/qurro/__init__.py index ebc94d0a..b499d00f 100644 --- a/qurro/__init__.py +++ b/qurro/__init__.py @@ -10,5 +10,5 @@ # The full license is in the file LICENSE.txt, distributed with this software. # ---------------------------------------------------------------------------- -__version__ = "0.7.1" +__version__ = "0.8.0" name = "qurro" From 07d7665792f530c69a1daaf961dde31f3bee46cd Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 06:27:08 -0700 Subject: [PATCH 18/36] TST: Add standalone CI IIRC something about how our specific altair version works makes it incompatible with python 3.10. let's test that here -- if needed, we can update the README to disallow python versions >= 3.10. (And then we can look into removing the altair pin when absolutely needed.) --- .github/workflows/{main.yml => qiime2.yml} | 2 +- .github/workflows/standalone.yml | 42 ++++++++++++++++++++++ README.md | 3 +- 3 files changed, 45 insertions(+), 2 deletions(-) rename .github/workflows/{main.yml => qiime2.yml} (99%) create mode 100644 .github/workflows/standalone.yml diff --git a/.github/workflows/main.yml b/.github/workflows/qiime2.yml similarity index 99% rename from .github/workflows/main.yml rename to .github/workflows/qiime2.yml index fd528027..813b4aac 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/qiime2.yml @@ -2,7 +2,7 @@ # https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml # (which was based on EMPress' workflow); some of the Node.js stuff based on # MetagenomeScope's JS workflow -name: Qurro CI +name: QIIME 2 CI on: [push, pull_request] jobs: build: diff --git a/.github/workflows/standalone.yml b/.github/workflows/standalone.yml new file mode 100644 index 00000000..29df9d26 --- /dev/null +++ b/.github/workflows/standalone.yml @@ -0,0 +1,42 @@ +# Based on +# https://github.com/fedarko/pyfastg/blob/master/.github/workflows/main.yml +name: Standalone CI +on: [push, pull_request] +jobs: + build: + runs-on: ubuntu-latest + + strategy: + matrix: + python-version: [3.6, 3.7, 3.8, 3.9, "3.10", "3.11-dev"] + + steps: + + - name: Check out code + uses: actions/checkout@v3 + + # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + + - name: Install Cython and NumPy + run: pip install cython "numpy >= 1.12.0" + + - name: Install Qurro (and its pip dependencies) + run: pip install -e .[dev] + + - name: Set up Node.js + uses: actions/setup-node@v1 + + - name: Install Qurro's Node.js development dependencies + run: npm install -g mocha-headless-chrome nyc prettier@2.0.5 jshint + + # Just run the tests; don't bother running stylechecking / linting, since + # that's already done in the QIIME 2 CI. + - name: Run tests + run: make test + + - name: Upload code coverage information to Codecov + uses: codecov/codecov-action@v2 diff --git a/README.md b/README.md index f675cf55..9c7f4bcd 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,8 @@
-Qurro CI +QIIME 2 CI +Standalone CI Code Coverage DOI PyPI From 418136d0729489a78f219ecab1656bd5093b3e2d Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 06:58:51 -0700 Subject: [PATCH 19/36] TST: attempt to get standalone tests working --- .github/workflows/standalone.yml | 4 +++- Makefile | 6 ++++++ ...est_metadata_utils.py => test_metadata_utils_uses_q2.py} | 5 +++++ qurro/tests/{test_qarcoal.py => test_q2_qarcoal.py} | 0 qurro/tests/testing_utilities.py | 4 ++-- 5 files changed, 16 insertions(+), 3 deletions(-) rename qurro/tests/{test_metadata_utils.py => test_metadata_utils_uses_q2.py} (97%) rename qurro/tests/{test_qarcoal.py => test_q2_qarcoal.py} (100%) diff --git a/.github/workflows/standalone.yml b/.github/workflows/standalone.yml index 29df9d26..e9dac185 100644 --- a/.github/workflows/standalone.yml +++ b/.github/workflows/standalone.yml @@ -36,7 +36,9 @@ jobs: # Just run the tests; don't bother running stylechecking / linting, since # that's already done in the QIIME 2 CI. - name: Run tests - run: make test + run: | + make pytest_standalone + make jstest - name: Upload code coverage information to Codecov uses: codecov/codecov-action@v2 diff --git a/Makefile b/Makefile index 8429f88c..97ce6ed9 100644 --- a/Makefile +++ b/Makefile @@ -18,6 +18,12 @@ test: pytest jstest pytest: python3 -B -m pytest qurro/tests --cov qurro +# Ignore test files (and functions) that have q2 in the name +# This way, we can run non-QIIME2-specific tests outside of a QIIME 2 conda +# environment +pytest_standalone: + python3 -B -m pytest qurro/tests --cov qurro -k "not q2" + jstest: @# Re-update specs for JS tests by running update_js_test_jsons.py python3 qurro/tests/update_js_test_jsons.py diff --git a/qurro/tests/test_metadata_utils.py b/qurro/tests/test_metadata_utils_uses_q2.py similarity index 97% rename from qurro/tests/test_metadata_utils.py rename to qurro/tests/test_metadata_utils_uses_q2.py index fcfd10e3..c54f5c77 100644 --- a/qurro/tests/test_metadata_utils.py +++ b/qurro/tests/test_metadata_utils_uses_q2.py @@ -8,6 +8,11 @@ from qurro._metadata_utils import read_metadata_file +# Brief note: this file tests that our metadata reading functionality matches +# QIIME 2's. For this reason, this test can only be performed in an environment +# that has access to the "qiime2" module. + + def test_read_metadata_file_basic(): """Tests that read_metadata_file() works + handles bools ok. diff --git a/qurro/tests/test_qarcoal.py b/qurro/tests/test_q2_qarcoal.py similarity index 100% rename from qurro/tests/test_qarcoal.py rename to qurro/tests/test_q2_qarcoal.py diff --git a/qurro/tests/testing_utilities.py b/qurro/tests/testing_utilities.py index 12b2acdb..79f7ccfe 100644 --- a/qurro/tests/testing_utilities.py +++ b/qurro/tests/testing_utilities.py @@ -4,8 +4,6 @@ from pytest import approx from click.testing import CliRunner from biom import load_table -from qiime2 import Artifact, Metadata -from qiime2.plugins import qurro as q2qurro import qurro.scripts._plot as rrvp from qurro._rank_utils import read_rank_file from qurro._metadata_utils import read_metadata_file @@ -52,6 +50,8 @@ def run_integration_test( rrv_qzv = result = None if use_q2: + from qiime2 import Artifact, Metadata + from qiime2.plugins import qurro as q2qurro if q2_ranking_tool == "songbird": q2_action = q2qurro.actions.differential_plot q2_rank_type = "FeatureData[Differential]" From dcc63c9dc47e4420504118e8247cad0bb1ac8870 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 07:09:47 -0700 Subject: [PATCH 20/36] TST: attempt to fix pytest q2 exclusion --- Makefile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 97ce6ed9..e336092e 100644 --- a/Makefile +++ b/Makefile @@ -20,9 +20,11 @@ pytest: # Ignore test files (and functions) that have q2 in the name # This way, we can run non-QIIME2-specific tests outside of a QIIME 2 conda -# environment +# environment. (For some reason, -k "not q2" wasn't working, even though the +# docs said that it should consider file names... well, this seems to work.) +# https://stackoverflow.com/questions/11117062/how-to-tell-py-test-to-skip-certain-directories#comment113260122_41940247 pytest_standalone: - python3 -B -m pytest qurro/tests --cov qurro -k "not q2" + python3 -B -m pytest qurro/tests --cov qurro --ignore-glob "*q2*" jstest: @# Re-update specs for JS tests by running update_js_test_jsons.py From 9e8b4645d0942981927d99ea3a4944d5dfc6ad56 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 07:21:04 -0700 Subject: [PATCH 21/36] DEP: ok py 3.10 is a no go --- .github/workflows/standalone.yml | 2 +- README.md | 2 +- setup.py | 4 +++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/standalone.yml b/.github/workflows/standalone.yml index e9dac185..fd6e50bc 100644 --- a/.github/workflows/standalone.yml +++ b/.github/workflows/standalone.yml @@ -8,7 +8,7 @@ jobs: strategy: matrix: - python-version: [3.6, 3.7, 3.8, 3.9, "3.10", "3.11-dev"] + python-version: [3.6, 3.7, 3.8, 3.9] steps: diff --git a/README.md b/README.md index 9c7f4bcd..2d12a587 100644 --- a/README.md +++ b/README.md @@ -85,7 +85,7 @@ can be viewed online [here](https://biocore.github.io/qurro/demos/red_sea/index. ## Installation and Usage -You can install Qurro using [pip](https://pip.pypa.io/en/stable/) or [conda](https://docs.conda.io/en/latest/). In either case, a python version of at least 3.6 is required to use Qurro. +You can install Qurro using [pip](https://pip.pypa.io/en/stable/) or [conda](https://docs.conda.io/en/latest/). In either case, a python version of at least 3.6 and less than 3.10 is required to use Qurro. ### Installing with `pip` ```bash diff --git a/setup.py b/setup.py index 7cfc27e5..1c1ae49a 100644 --- a/setup.py +++ b/setup.py @@ -106,5 +106,7 @@ "console_scripts": ["qurro=qurro.scripts._plot:plot"], }, zip_safe=False, - python_requires=">=3.6", + # altair 3.1.0 uses the "collections" module in a way that isn't compatible + # with Python 3.10 and up. We should eventually un-pin altair to fix this. + python_requires=">=3.6,<3.10", ) From 75a76ba043e452d2101514ce314b8518f44c2077 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 07:38:46 -0700 Subject: [PATCH 22/36] STY: fix formatting --- qurro/tests/testing_utilities.py | 1 + 1 file changed, 1 insertion(+) diff --git a/qurro/tests/testing_utilities.py b/qurro/tests/testing_utilities.py index 79f7ccfe..b0475d71 100644 --- a/qurro/tests/testing_utilities.py +++ b/qurro/tests/testing_utilities.py @@ -52,6 +52,7 @@ def run_integration_test( if use_q2: from qiime2 import Artifact, Metadata from qiime2.plugins import qurro as q2qurro + if q2_ranking_tool == "songbird": q2_action = q2qurro.actions.differential_plot q2_rank_type = "FeatureData[Differential]" From cc17180e5d2c90ef52149d67a375d2ff4f2ffbb1 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 15:34:53 -0700 Subject: [PATCH 23/36] DOC: Rerun 4 / 6 example notebooks Songbird and ALDEx2 ones will cause problems --- .../DEICODE_sleep_apnea/deicode_example.ipynb | 271 +++--------------- .../color_compositions/color_example.ipynb | 266 +++++++++-------- .../moving_pictures/data/qurro-plot.qzv | Bin 735991 -> 736282 bytes .../moving_pictures/moving_pictures.ipynb | 54 ++-- .../qarcoal/qarcoal_example.ipynb | 200 +++---------- 5 files changed, 255 insertions(+), 536 deletions(-) diff --git a/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb b/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb index aa0dc4f0..98259aa3 100644 --- a/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb +++ b/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb @@ -56,7 +56,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mImported input/qiita_10422_table.biom as BIOMV210DirFmt to output/qiita_10422_table.biom.qza\u001b[0m\r\n" + "\u001b[32mImported input/qiita_10422_table.biom as BIOMV210DirFmt to output/qiita_10422_table.biom.qza\u001b[0m\r\n", + "\u001b[0m" ] } ], @@ -85,9 +86,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[33mQIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.\u001b[0m\r\n", - "\u001b[32mSaved PCoAResults % Properties('biplot') to: output/ordination.qza\u001b[0m\r\n", - "\u001b[32mSaved DistanceMatrix to: output/dist_matrix.qza\u001b[0m\r\n" + "\u001b[33mQIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.\u001b[0m\n", + "\u001b[32mSaved PCoAResults % Properties('biplot') to: output/ordination.qza\u001b[0m\n", + "\u001b[32mSaved DistanceMatrix to: output/dist_matrix.qza\u001b[0m\n", + "\u001b[0m" ] } ], @@ -118,7 +120,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mSaved Visualization to: output/biplot.qzv\u001b[0m\r\n" + "\u001b[32mSaved Visualization to: output/biplot.qzv\u001b[0m\r\n", + "\u001b[0m" ] } ], @@ -155,30 +158,30 @@ "name": "stdout", "output_type": "stream", "text": [ - "Usage: \u001b[34mqiime qurro loading-plot\u001b[0m [OPTIONS]\r\n", + "Usage: \u001b[94mqiime qurro loading-plot\u001b[0m [OPTIONS]\r\n", "\r\n", " Generates an interactive visualization of feature loadings in tandem with\r\n", " a visualization of the log-ratios of selected features' sample abundances.\r\n", "\r\n", "\u001b[1mInputs\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--i-ranks\u001b[0m ARTIFACT \u001b[32mPCoAResults % Properties('biplot')\u001b[0m\r\n", + " \u001b[94m\u001b[4m--i-ranks\u001b[0m ARTIFACT \u001b[32mPCoAResults % Properties('biplot')\u001b[0m\r\n", " A biplot containing feature loadings. \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m\u001b[4m--i-table\u001b[0m ARTIFACT \u001b[32mFeatureTable[Frequency]\u001b[0m\r\n", + " \u001b[94m\u001b[4m--i-table\u001b[0m ARTIFACT \u001b[32mFeatureTable[Frequency]\u001b[0m\r\n", " A BIOM table describing the abundances of the ranked\r\n", " features in samples. Note that empty samples and\r\n", " features will be removed from the Qurro visualization.\r\n", " \u001b[35m[required]\u001b[0m\r\n", "\u001b[1mParameters\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--m-sample-metadata-file\u001b[0m METADATA...\r\n", + " \u001b[94m\u001b[4m--m-sample-metadata-file\u001b[0m METADATA...\r\n", " (multiple Sample metadata. In Qurro visualizations, you can use\r\n", " arguments will sample metadata fields to change the x-axis and colors\r\n", " be merged) in the sample plot. \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m--m-feature-metadata-file\u001b[0m METADATA...\r\n", + " \u001b[94m--m-feature-metadata-file\u001b[0m METADATA...\r\n", " (multiple Feature metadata (for example, if your features are\r\n", " arguments will ASVs or OTUs, this could be taxonomy). You can use\r\n", " be merged) feature metadata fields to filter features in the rank\r\n", " plot when selecting log-ratios. \u001b[35m[optional]\u001b[0m\r\n", - " \u001b[34m--p-extreme-feature-count\u001b[0m INTEGER\r\n", + " \u001b[94m--p-extreme-feature-count\u001b[0m INTEGER\r\n", " If specified, Qurro will only use this many \"extreme\"\r\n", " features from both ends of all of the rankings. This is\r\n", " useful when dealing with huge datasets (e.g. with BIOM\r\n", @@ -187,21 +190,22 @@ " crash due to memory limits. Note that the automatic\r\n", " removal of empty samples and features from the table\r\n", " will be done *after* this filtering step. \u001b[35m[optional]\u001b[0m\r\n", - " \u001b[34m--p-debug\u001b[0m / \u001b[34m--p-no-debug\u001b[0m\r\n", + " \u001b[94m--p-debug\u001b[0m / \u001b[94m--p-no-debug\u001b[0m\r\n", " If this flag is used, Qurro will output debug\r\n", " messages. Note that you'll also need to use the\r\n", " --verbose option to see these messages.\r\n", " \u001b[35m[default: False]\u001b[0m\r\n", "\u001b[1mOutputs\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--o-visualization\u001b[0m VISUALIZATION\r\n", + " \u001b[94m\u001b[4m--o-visualization\u001b[0m VISUALIZATION\r\n", " \u001b[35m[required]\u001b[0m\r\n", "\u001b[1mMiscellaneous\u001b[0m:\r\n", - " \u001b[34m--output-dir\u001b[0m PATH Output unspecified results to a directory\r\n", - " \u001b[34m--verbose\u001b[0m / \u001b[34m--quiet\u001b[0m Display verbose output to stdout and/or stderr during\r\n", + " \u001b[94m--output-dir\u001b[0m PATH Output unspecified results to a directory\r\n", + " \u001b[94m--verbose\u001b[0m / \u001b[94m--quiet\u001b[0m Display verbose output to stdout and/or stderr during\r\n", " execution of this action. Or silence output if\r\n", " execution is successful (silence is golden).\r\n", - " \u001b[34m--citations\u001b[0m Show citations and exit.\r\n", - " \u001b[34m--help\u001b[0m Show this message and exit.\r\n" + " \u001b[94m--example-data\u001b[0m PATH Write example data and exit.\r\n", + " \u001b[94m--citations\u001b[0m Show citations and exit.\r\n", + " \u001b[94m--help\u001b[0m Show this message and exit.\r\n" ] } ], @@ -218,95 +222,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "/Users/mfedarko/Dropbox/Work/KnightLab/qurro/qurro/_df_utils.py:126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " table_sdf = pd.SparseDataFrame(table.matrix_data, default_fill_value=0.0)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " sparse_index=BlockIndex(N, blocs, blens),\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return klass(values, index=self.index, name=items, fastpath=True)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_values, index=self.index, name=self.name)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_fill_value=self.default_fill_value,\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\r\n", - "689 feature(s) in the BIOM table were not present in the feature rankings.\r\n", - "These feature(s) have been removed from the visualization.\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " result = self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:1999: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(result, **d).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:745: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_fill_value=self._default_fill_value,\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:9126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_kind=self._default_kind,\r\n", - "\u001b[32mSaved Visualization to: output/qurro_plot_q2.qzv\u001b[0m\r\n" + "689 feature(s) in the BIOM table were not present in the feature rankings.\n", + "These feature(s) have been removed from the visualization.\n", + "\u001b[32mSaved Visualization to: output/qurro_plot_q2.qzv\u001b[0m\n", + "\u001b[0m" ] } ], @@ -343,42 +262,7 @@ "cell_type": "code", "execution_count": 7, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/biom/table.py:4068: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return constructor(mat, index=index, columns=columns)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " sparse_index=BlockIndex(N, blocs, blens),\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:4583: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_kind=self._default_kind,\r\n" - ] - } - ], + "outputs": [], "source": [ "!deicode auto-rpca \\\n", " --in-biom input/qiita_10422_table.biom \\\n", @@ -427,10 +311,12 @@ " loadings). When sorted numerically,\r\n", " differentials and feature loadings alike\r\n", " provide 'rankings.' [required]\r\n", + "\r\n", " -t, --table TEXT A BIOM table describing the abundances of\r\n", " the ranked features in samples. Note that\r\n", " empty samples and features will be removed\r\n", " from the Qurro visualization. [required]\r\n", + "\r\n", " -sm, --sample-metadata TEXT Sample metadata, formatted as a TSV file\r\n", " (where each row describes a sample and each\r\n", " column describes a 'metadata' field, and the\r\n", @@ -438,6 +324,7 @@ " visualizations, you can use sample metadata\r\n", " fields to change the x-axis and colors in\r\n", " the sample plot. [required]\r\n", + "\r\n", " -fm, --feature-metadata TEXT Feature metadata, formatted as a TSV file\r\n", " (where each row describes a feature and each\r\n", " column describes a 'metadata' field, and the\r\n", @@ -445,6 +332,7 @@ " visualizations, you can use feature metadata\r\n", " fields to filter features in the rank plot\r\n", " when selecting log-ratios.\r\n", + "\r\n", " -o, --output-dir TEXT Directory to write the HTML/JS/... files\r\n", " defining a Qurro visualization to. If this\r\n", " directory already exists, files/directories\r\n", @@ -455,6 +343,7 @@ " another location, without also moving the\r\n", " JS/etc. files, will break the visualization.\r\n", " [required]\r\n", + "\r\n", " -x, --extreme-feature-count INTEGER\r\n", " If specified, Qurro will only use this many\r\n", " \"extreme\" features from both ends of all of\r\n", @@ -466,8 +355,10 @@ " limits. Note that the automatic removal of\r\n", " empty samples and features from the table\r\n", " will be done *after* this filtering step.\r\n", + "\r\n", " --debug If this flag is used, Qurro will output\r\n", " debug messages.\r\n", + "\r\n", " --version Show the version and exit.\r\n", " --help Show this message and exit.\r\n" ] @@ -486,95 +377,9 @@ "name": "stdout", "output_type": "stream", "text": [ - "/Users/mfedarko/Dropbox/Work/KnightLab/qurro/qurro/_df_utils.py:126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " table_sdf = pd.SparseDataFrame(table.matrix_data, default_fill_value=0.0)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " sparse_index=BlockIndex(N, blocs, blens),\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return klass(values, index=self.index, name=items, fastpath=True)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_values, index=self.index, name=self.name)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_fill_value=self.default_fill_value,\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\r\n", - "689 feature(s) in the BIOM table were not present in the feature rankings.\r\n", - "These feature(s) have been removed from the visualization.\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " result = self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:1999: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(result, **d).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:745: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_fill_value=self._default_fill_value,\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:9126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_kind=self._default_kind,\r\n", - "Successfully generated a visualization in the folder output/qurro_plot_standalone/.\r\n" + "689 feature(s) in the BIOM table were not present in the feature rankings.\n", + "These feature(s) have been removed from the visualization.\n", + "Successfully generated a visualization in the folder output/qurro_plot_standalone/.\n" ] } ], @@ -606,7 +411,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -620,7 +425,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.8.13" } }, "nbformat": 4, diff --git a/example_notebooks/color_compositions/color_example.ipynb b/example_notebooks/color_compositions/color_example.ipynb index c159b6ae..2949f536 100644 --- a/example_notebooks/color_compositions/color_example.ipynb +++ b/example_notebooks/color_compositions/color_example.ipynb @@ -26,12 +26,19 @@ }, { "cell_type": "code", - "execution_count": 1, - "metadata": {}, + "execution_count": 6, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:14.148850Z", + "iopub.status.busy": "2022-07-05T21:46:14.147867Z", + "iopub.status.idle": "2022-07-05T21:46:15.345873Z", + "shell.execute_reply": "2022-07-05T21:46:15.343311Z" + } + }, "outputs": [], "source": [ "# Clear the output directory so we can write these files there\n", - "!rm -rf output/*\n", + "!rm -rf output\n", "# Since git doesn't keep track of empty directories, create the output/ directory if it doesn't already exist\n", "# (if it does already exist, -p ensures that an error won't be thrown)\n", "!mkdir -p output" @@ -57,8 +64,15 @@ }, { "cell_type": "code", - "execution_count": 2, - "metadata": {}, + "execution_count": 7, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:15.354818Z", + "iopub.status.busy": "2022-07-05T21:46:15.354129Z", + "iopub.status.idle": "2022-07-05T21:46:15.750792Z", + "shell.execute_reply": "2022-07-05T21:46:15.750251Z" + } + }, "outputs": [ { "data": { @@ -282,7 +296,7 @@ "[5 rows x 22 columns]" ] }, - "execution_count": 2, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -303,8 +317,32 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 8, "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/marcus/.npm-global/bin /home/marcus/Dropbox/dotfiles/cmds /home/marcus/.npm-global/bin /home/marcus/Dropbox/dotfiles/cmds /home/marcus/.npm-global/bin /home/marcus/anaconda3/bin /home/marcus/anaconda3/condabin /home/marcus/Dropbox/dotfiles/cmds /usr/local/sbin /usr/local/bin /usr/sbin /usr/bin /sbin /bin /usr/games /usr/local/games /snap/bin /home/marcus/anaconda3/envs/q2-2022.2-unfucked/bin\r\n" + ] + } + ], + "source": [ + "!echo $PATH" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:15.753021Z", + "iopub.status.busy": "2022-07-05T21:46:15.752869Z", + "iopub.status.idle": "2022-07-05T21:46:16.335861Z", + "shell.execute_reply": "2022-07-05T21:46:16.333833Z" + } + }, "outputs": [], "source": [ "!biom convert \\\n", @@ -323,8 +361,15 @@ }, { "cell_type": "code", - "execution_count": 4, - "metadata": {}, + "execution_count": 10, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:16.345322Z", + "iopub.status.busy": "2022-07-05T21:46:16.343469Z", + "iopub.status.idle": "2022-07-05T21:46:16.919444Z", + "shell.execute_reply": "2022-07-05T21:46:16.917542Z" + } + }, "outputs": [ { "name": "stdout", @@ -360,8 +405,15 @@ }, { "cell_type": "code", - "execution_count": 5, - "metadata": {}, + "execution_count": 11, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:16.927027Z", + "iopub.status.busy": "2022-07-05T21:46:16.926512Z", + "iopub.status.idle": "2022-07-05T21:46:16.967815Z", + "shell.execute_reply": "2022-07-05T21:46:16.967201Z" + } + }, "outputs": [ { "data": { @@ -476,7 +528,7 @@ "5 0.188 0.299 AitchisonGreenacre2002 " ] }, - "execution_count": 5, + "execution_count": 11, "metadata": {}, "output_type": "execute_result" } @@ -512,14 +564,21 @@ }, { "cell_type": "code", - "execution_count": 6, - "metadata": {}, + "execution_count": 12, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:16.970486Z", + "iopub.status.busy": "2022-07-05T21:46:16.970313Z", + "iopub.status.idle": "2022-07-05T21:46:18.346441Z", + "shell.execute_reply": "2022-07-05T21:46:18.345998Z" + } + }, "outputs": [ { "data": { - "image/png": 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\n", 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\n", "text/plain": [ - "" + "
" ] }, "metadata": { @@ -552,8 +611,15 @@ }, { "cell_type": "code", - "execution_count": 7, - "metadata": {}, + "execution_count": 13, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:18.348586Z", + "iopub.status.busy": "2022-07-05T21:46:18.348359Z", + "iopub.status.idle": "2022-07-05T21:46:18.354924Z", + "shell.execute_reply": "2022-07-05T21:46:18.354555Z" + } + }, "outputs": [ { "data": { @@ -625,7 +691,7 @@ "Yellow -0.153330 0.028251" ] }, - "execution_count": 7, + "execution_count": 13, "metadata": {}, "output_type": "execute_result" } @@ -643,8 +709,15 @@ }, { "cell_type": "code", - "execution_count": 8, - "metadata": {}, + "execution_count": 14, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:18.356940Z", + "iopub.status.busy": "2022-07-05T21:46:18.356770Z", + "iopub.status.idle": "2022-07-05T21:46:18.362609Z", + "shell.execute_reply": "2022-07-05T21:46:18.362116Z" + } + }, "outputs": [ { "data": { @@ -716,7 +789,7 @@ "5 -0.159943 -0.367294" ] }, - "execution_count": 8, + "execution_count": 14, "metadata": {}, "output_type": "execute_result" } @@ -735,8 +808,15 @@ }, { "cell_type": "code", - "execution_count": 9, - "metadata": {}, + "execution_count": 15, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:18.365121Z", + "iopub.status.busy": "2022-07-05T21:46:18.364917Z", + "iopub.status.idle": "2022-07-05T21:46:18.370805Z", + "shell.execute_reply": "2022-07-05T21:46:18.370205Z" + } + }, "outputs": [ { "data": { @@ -744,7 +824,7 @@ "'output/apca-ordination.txt'" ] }, - "execution_count": 9, + "execution_count": 15, "metadata": {}, "output_type": "execute_result" } @@ -765,8 +845,15 @@ }, { "cell_type": "code", - "execution_count": 10, - "metadata": {}, + "execution_count": 16, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:18.373142Z", + "iopub.status.busy": "2022-07-05T21:46:18.372949Z", + "iopub.status.idle": "2022-07-05T21:46:18.390260Z", + "shell.execute_reply": "2022-07-05T21:46:18.389692Z" + } + }, "outputs": [ { "data": { @@ -903,7 +990,7 @@ "5 -0.367294 " ] }, - "execution_count": 10, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -933,8 +1020,15 @@ }, { "cell_type": "code", - "execution_count": 11, - "metadata": {}, + "execution_count": 17, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:18.392380Z", + "iopub.status.busy": "2022-07-05T21:46:18.392196Z", + "iopub.status.idle": "2022-07-05T21:46:18.888167Z", + "shell.execute_reply": "2022-07-05T21:46:18.887080Z" + } + }, "outputs": [ { "name": "stdout", @@ -961,10 +1055,12 @@ " loadings). When sorted numerically,\r\n", " differentials and feature loadings alike\r\n", " provide 'rankings.' [required]\r\n", + "\r\n", " -t, --table TEXT A BIOM table describing the abundances of\r\n", " the ranked features in samples. Note that\r\n", " empty samples and features will be removed\r\n", " from the Qurro visualization. [required]\r\n", + "\r\n", " -sm, --sample-metadata TEXT Sample metadata, formatted as a TSV file\r\n", " (where each row describes a sample and each\r\n", " column describes a 'metadata' field, and the\r\n", @@ -972,6 +1068,7 @@ " visualizations, you can use sample metadata\r\n", " fields to change the x-axis and colors in\r\n", " the sample plot. [required]\r\n", + "\r\n", " -fm, --feature-metadata TEXT Feature metadata, formatted as a TSV file\r\n", " (where each row describes a feature and each\r\n", " column describes a 'metadata' field, and the\r\n", @@ -979,6 +1076,7 @@ " visualizations, you can use feature metadata\r\n", " fields to filter features in the rank plot\r\n", " when selecting log-ratios.\r\n", + "\r\n", " -o, --output-dir TEXT Directory to write the HTML/JS/... files\r\n", " defining a Qurro visualization to. If this\r\n", " directory already exists, files/directories\r\n", @@ -989,6 +1087,7 @@ " another location, without also moving the\r\n", " JS/etc. files, will break the visualization.\r\n", " [required]\r\n", + "\r\n", " -x, --extreme-feature-count INTEGER\r\n", " If specified, Qurro will only use this many\r\n", " \"extreme\" features from both ends of all of\r\n", @@ -1000,8 +1099,10 @@ " limits. Note that the automatic removal of\r\n", " empty samples and features from the table\r\n", " will be done *after* this filtering step.\r\n", + "\r\n", " --debug If this flag is used, Qurro will output\r\n", " debug messages.\r\n", + "\r\n", " --version Show the version and exit.\r\n", " --help Show this message and exit.\r\n" ] @@ -1029,100 +1130,21 @@ }, { "cell_type": "code", - "execution_count": 12, - "metadata": {}, + "execution_count": 18, + "metadata": { + "execution": { + "iopub.execute_input": "2022-07-05T21:46:18.892221Z", + "iopub.status.busy": "2022-07-05T21:46:18.891899Z", + "iopub.status.idle": "2022-07-05T21:46:19.418979Z", + "shell.execute_reply": "2022-07-05T21:46:19.417045Z" + } + }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "/home/marcus/Dropbox/Work/KnightLab/qurro/qurro/_df_utils.py:126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " table_sdf = pd.SparseDataFrame(table.matrix_data, default_fill_value=0.0)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " sparse_index=BlockIndex(N, blocs, blens),\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return klass(values, index=self.index, name=items, fastpath=True)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_values, index=self.index, name=self.name)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_fill_value=self.default_fill_value,\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " result = self._constructor(new_data).__finalize__(self)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/generic.py:1999: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(result, **d).__finalize__(self)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/sparse/frame.py:745: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_fill_value=self._default_fill_value,\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/generic.py:9126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/home/marcus/Software/miniconda2/envs/qiime2-2019.10/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_kind=self._default_kind,\n", - "Successfully generated a visualization in the folder output/qurro-viz/.\n" + "Successfully generated a visualization in the folder output/qurro-viz/.\r\n" ] } ], @@ -1194,9 +1216,9 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python [conda env:q2-2022.2-unfucked] *", "language": "python", - "name": "python3" + "name": "conda-env-q2-2022.2-unfucked-py" }, "language_info": { "codemirror_mode": { @@ -1208,7 +1230,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.8.13" } }, "nbformat": 4, diff --git a/example_notebooks/moving_pictures/data/qurro-plot.qzv b/example_notebooks/moving_pictures/data/qurro-plot.qzv index 4b34272ea198597d92080c122ff8f4f8511f94d3..9c796a786e38cd1b2664cc242d4aeeeb37dfcdd3 100644 GIT binary patch delta 42973 zcmb@tWmH{Tx2C&r5AN4dW#_9?r%tt7xAy+d z{V{2cALE&0yra)P-_`q=_qTKz4|KwcGGO3n0000Qz~FtLy3p>3M*Z<0<;O+$aj|k3 z85wbKn9?(HF|pCJa&d9e8*wr+(VH=wn6a@inzFMq8YK$BPy?A~S!P+bK>`02HzGuR z-3<)@#NYw|%zqQdU~FM(Z0+P?>-5>ygsn2!p14>3z!Dz17P$()f7XEtSqCj 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b/example_notebooks/moving_pictures/moving_pictures.ipynb index 31ee0d0a..2d46df15 100644 --- a/example_notebooks/moving_pictures/moving_pictures.ipynb +++ b/example_notebooks/moving_pictures/moving_pictures.ipynb @@ -62,29 +62,30 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[33mQIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.\u001b[0m\r\n", - "Usage: \u001b[34mqiime qurro\u001b[0m [OPTIONS] COMMAND [ARGS]...\r\n", - "\r\n", - " Description: This QIIME 2 plugin supports the interactive visualization of\r\n", - " feature rankings (either differentials or feature loadings -- when sorted\r\n", - " numerically these provide rankings) in tandem with feature log-ratios\r\n", - " across samples.\r\n", - "\r\n", - " Plugin website: https://github.com/biocore/qurro\r\n", - "\r\n", - " Getting user support: Please post to the QIIME 2 forum for help with this\r\n", - " plugin: https://forum.qiime2.org\r\n", - "\r\n", - "\u001b[1mOptions\u001b[0m:\r\n", - " \u001b[34m--version\u001b[0m Show the version and exit.\r\n", - " \u001b[34m--citations\u001b[0m Show citations and exit.\r\n", - " \u001b[34m--help\u001b[0m Show this message and exit.\r\n", - "\r\n", - "\u001b[1mCommands\u001b[0m:\r\n", - " \u001b[34mdifferential-plot\u001b[0m Generate a Qurro visualization from feature differentials\r\n", - " \u001b[34mloading-plot\u001b[0m Generate a Qurro visualization from feature loadings\r\n", - " \u001b[34mqarcoal\u001b[0m Compute feature log-ratios based on textual taxonomy\r\n", - " searching.\r\n" + "\u001b[33mQIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.\u001b[0m\n", + "\u001b[0mUsage: \u001b[94mqiime qurro\u001b[0m [OPTIONS] COMMAND [ARGS]...\n", + "\n", + " Description: This QIIME 2 plugin supports the interactive visualization of\n", + " feature rankings (either differentials or feature loadings -- when sorted\n", + " numerically these provide rankings) in tandem with feature log-ratios\n", + " across samples.\n", + "\n", + " Plugin website: https://github.com/biocore/qurro\n", + "\n", + " Getting user support: Please post to the QIIME 2 forum for help with this\n", + " plugin: https://forum.qiime2.org\n", + "\n", + "\u001b[1mOptions\u001b[0m:\n", + " \u001b[94m--version\u001b[0m Show the version and exit.\n", + " \u001b[94m--example-data\u001b[0m PATH Write example data and exit.\n", + " \u001b[94m--citations\u001b[0m Show citations and exit.\n", + " \u001b[94m--help\u001b[0m Show this message and exit.\n", + "\n", + "\u001b[1mCommands\u001b[0m:\n", + " \u001b[94mdifferential-plot\u001b[0m Generate a Qurro visualization from feature differentials\n", + " \u001b[94mloading-plot\u001b[0m Generate a Qurro visualization from feature loadings\n", + " \u001b[94mqarcoal\u001b[0m Compute feature log-ratios based on textual taxonomy\n", + " searching.\n" ] } ], @@ -174,7 +175,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mSaved Visualization to: data/qurro-plot.qzv\u001b[0m\r\n" + "\u001b[32mSaved Visualization to: data/qurro-plot.qzv\u001b[0m\r\n", + "\u001b[0m" ] } ], @@ -360,7 +362,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -374,7 +376,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.8.13" } }, "nbformat": 4, diff --git a/example_notebooks/qarcoal/qarcoal_example.ipynb b/example_notebooks/qarcoal/qarcoal_example.ipynb index b2c7c854..dd1bbfe9 100644 --- a/example_notebooks/qarcoal/qarcoal_example.ipynb +++ b/example_notebooks/qarcoal/qarcoal_example.ipynb @@ -57,7 +57,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mImported ../DEICODE_sleep_apnea/input/qiita_10422_table.biom as BIOMV210DirFmt to output/qiita_10422_table.biom.qza\u001b[0m\r\n" + "\u001b[32mImported ../DEICODE_sleep_apnea/input/qiita_10422_table.biom as BIOMV210DirFmt to output/qiita_10422_table.biom.qza\u001b[0m\r\n", + "\u001b[0m" ] } ], @@ -87,7 +88,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "Usage: \u001b[34mqiime qurro qarcoal\u001b[0m [OPTIONS]\r\n", + "Usage: \u001b[94mqiime qurro qarcoal\u001b[0m [OPTIONS]\r\n", "\r\n", " Compute the log-ratio of two specified feature strings by searching\r\n", " taxonomy for incidence of each string, summing all relevant feature counts\r\n", @@ -95,37 +96,38 @@ " by denominator sum.\r\n", "\r\n", "\u001b[1mInputs\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--i-table\u001b[0m ARTIFACT \u001b[32mFeatureTable[Frequency]\u001b[0m\r\n", + " \u001b[94m\u001b[4m--i-table\u001b[0m ARTIFACT \u001b[32mFeatureTable[Frequency]\u001b[0m\r\n", " Feature table describing the abundances of the\r\n", " features in samples. \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m\u001b[4m--i-taxonomy\u001b[0m ARTIFACT \u001b[32mFeatureData[Taxonomy]\u001b[0m\r\n", + " \u001b[94m\u001b[4m--i-taxonomy\u001b[0m ARTIFACT \u001b[32mFeatureData[Taxonomy]\u001b[0m\r\n", " Taxonomy information to be used for selecting\r\n", " features in log-ratio. \u001b[35m[required]\u001b[0m\r\n", "\u001b[1mParameters\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--p-num-string\u001b[0m TEXT Numerator string to search for in taxonomy.\r\n", + " \u001b[94m\u001b[4m--p-num-string\u001b[0m TEXT Numerator string to search for in taxonomy.\r\n", " \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m\u001b[4m--p-denom-string\u001b[0m TEXT Denominator string to search for in taxonomy.\r\n", + " \u001b[94m\u001b[4m--p-denom-string\u001b[0m TEXT Denominator string to search for in taxonomy.\r\n", " \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m--m-samples-to-use-file\u001b[0m METADATA...\r\n", + " \u001b[94m--m-samples-to-use-file\u001b[0m METADATA...\r\n", " (multiple Sample metadata file. If provided, log-ratios will\r\n", " arguments will be only be calculated from sample labels present in this\r\n", " merged) file. \u001b[35m[optional]\u001b[0m\r\n", - " \u001b[34m--p-allow-shared-features\u001b[0m / \u001b[34m--p-no-allow-shared-features\u001b[0m\r\n", + " \u001b[94m--p-allow-shared-features\u001b[0m / \u001b[94m--p-no-allow-shared-features\u001b[0m\r\n", " Boolean value denoting handling of features shared\r\n", " between numerator and denominator. If False, an error\r\n", " is raised if features are shared. If True, shared\r\n", " features are retained in log-ratio computation.\r\n", " \u001b[35m[default: False]\u001b[0m\r\n", "\u001b[1mOutputs\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--o-qarcoal-log-ratios\u001b[0m ARTIFACT \u001b[32mSampleData[LogRatios]\u001b[0m\r\n", + " \u001b[94m\u001b[4m--o-qarcoal-log-ratios\u001b[0m ARTIFACT \u001b[32mSampleData[LogRatios]\u001b[0m\r\n", " \u001b[35m[required]\u001b[0m\r\n", "\u001b[1mMiscellaneous\u001b[0m:\r\n", - " \u001b[34m--output-dir\u001b[0m PATH Output unspecified results to a directory\r\n", - " \u001b[34m--verbose\u001b[0m / \u001b[34m--quiet\u001b[0m Display verbose output to stdout and/or stderr\r\n", + " \u001b[94m--output-dir\u001b[0m PATH Output unspecified results to a directory\r\n", + " \u001b[94m--verbose\u001b[0m / \u001b[94m--quiet\u001b[0m Display verbose output to stdout and/or stderr\r\n", " during execution of this action. Or silence output if\r\n", " execution is successful (silence is golden).\r\n", - " \u001b[34m--citations\u001b[0m Show citations and exit.\r\n", - " \u001b[34m--help\u001b[0m Show this message and exit.\r\n" + " \u001b[94m--example-data\u001b[0m PATH Write example data and exit.\r\n", + " \u001b[94m--citations\u001b[0m Show citations and exit.\r\n", + " \u001b[94m--help\u001b[0m Show this message and exit.\r\n" ] } ], @@ -142,7 +144,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mSaved SampleData[LogRatios] to: output/allobaculum_coprococcus_log_ratios.qza\u001b[0m\r\n" + "\u001b[32mSaved SampleData[LogRatios] to: output/allobaculum_coprococcus_log_ratios.qza\u001b[0m\r\n", + "\u001b[0m" ] } ], @@ -226,34 +229,34 @@ " \n", " \n", " \n", - " 10422.20.F.8\n", - " 2.0\n", - " 113.0\n", - " -4.034241\n", + " 10422.21.F.4\n", + " 9.0\n", + " 659.0\n", + " -4.293499\n", " \n", " \n", - " 10422.29.F.11\n", - " 4.0\n", - " 27.0\n", - " -1.909543\n", + " 10422.22.F.8\n", + " 5.0\n", + " 3266.0\n", + " -6.481883\n", " \n", " \n", - " 10422.30.F.11\n", - " 2.0\n", - " 279.0\n", - " -4.938065\n", + " 10422.24.F.5\n", + " 36.0\n", + " 2028.0\n", + " -4.031286\n", " \n", " \n", - " 10422.29.F.3\n", - " 14.0\n", - " 950.0\n", - " -4.217405\n", + " 10422.17.F.9\n", + " 8.0\n", + " 50.0\n", + " -1.832581\n", " \n", " \n", - " 10422.26.F.4\n", - " 2.0\n", - " 991.0\n", - " -6.205567\n", + " 10422.18.F.12\n", + " 9.0\n", + " 141.0\n", + " -2.751535\n", " \n", " \n", "\n", @@ -262,11 +265,11 @@ "text/plain": [ " Num_Sum Denom_Sum log_ratio\n", "Sample-ID \n", - "10422.20.F.8 2.0 113.0 -4.034241\n", - "10422.29.F.11 4.0 27.0 -1.909543\n", - "10422.30.F.11 2.0 279.0 -4.938065\n", - "10422.29.F.3 14.0 950.0 -4.217405\n", - "10422.26.F.4 2.0 991.0 -6.205567" + "10422.21.F.4 9.0 659.0 -4.293499\n", + "10422.22.F.8 5.0 3266.0 -6.481883\n", + "10422.24.F.5 36.0 2028.0 -4.031286\n", + "10422.17.F.9 8.0 50.0 -1.832581\n", + "10422.18.F.12 9.0 141.0 -2.751535" ] }, "execution_count": 6, @@ -299,42 +302,7 @@ "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/biom/table.py:4068: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return constructor(mat, index=index, columns=columns)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " sparse_index=BlockIndex(N, blocs, blens),\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:4583: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_kind=self._default_kind,\n" - ] - } - ], + "outputs": [], "source": [ "from qiime2.plugins import deicode\n", "\n", @@ -367,84 +335,6 @@ "scrolled": true }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/Users/mfedarko/Dropbox/Work/KnightLab/qurro/qurro/_df_utils.py:126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " table_sdf = pd.SparseDataFrame(table.matrix_data, default_fill_value=0.0)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return klass(values, index=self.index, name=items, fastpath=True)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_values, index=self.index, name=self.name)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_fill_value=self.default_fill_value,\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " result = self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:1999: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(result, **d).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:745: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_fill_value=self._default_fill_value,\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:9126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n" - ] - }, { "data": { "text/plain": [ @@ -798,7 +688,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -812,7 +702,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.8.13" } }, "nbformat": 4, From 1e263871d1544d8f0fd8d470f5735e62fbba50b1 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 19:46:42 -0700 Subject: [PATCH 24/36] DOC: tidy/update readme refs --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 2d12a587..27885deb 100644 --- a/README.md +++ b/README.md @@ -222,7 +222,7 @@ also. ### Data Sources The test data located in `qurro/tests/input/mackerel/` were exported from -QIIME 2 artifacts in [this repository](https://github.com/knightlab-analyses/qurro-mackerel-analysis). These data are from Minich et al. 2019 [1]. +QIIME 2 artifacts in [this repository](https://github.com/knightlab-analyses/qurro-mackerel-analysis). These data are from Minich et al. 2020 [1]. The test data located in `qurro/tests/input/byrd/` are from [this repository](https://github.com/knightlab-analyses/reference-frames). @@ -291,22 +291,22 @@ Here's the BibTeX: ## References [1] Minich, J. J., Petrus, S., Michael, J. D., Michael, T. P., Knight, R., & -Allen, E. E. (2019). Temporal, environmental, and biological -drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. -_bioRxiv_, page 721555. [Link](https://www.biorxiv.org/content/10.1101/721555v1). +Allen, E. E. (2020). Temporal, environmental, and biological drivers of the +mucosal microbiome in a wild marine fish, Scomber japonicus. _mSphere, 5_(3), +e00401-20. [Link](https://journals.asm.org/doi/full/10.1128/mSphere.00401-20). -[2] Byrd, A. L., Deming, C., Cassidy, S. K., Harrison, O. J., Ng, W. I., Conlan, S., ... & NISC Comparative Sequencing Program. (2017). Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis. _Science translational medicine, 9_(397), eaal4651. +[2] Byrd, A. L., Deming, C., Cassidy, S. K., Harrison, O. J., Ng, W. I., Conlan, S., ... & NISC Comparative Sequencing Program. (2017). Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis. _Science Translational Medicine, 9_(397), eaal4651. [Link](https://www.ncbi.nlm.nih.gov/pubmed/28679656). [3] Thompson, L. R., Williams, G. J., Haroon, M. F., Shibl, A., Larsen, P., Shorenstein, J., ... & Stingl, U. (2017). Metagenomic covariation along densely -sampled environmental gradients in the Red Sea. _The ISME journal, 11_(1), 138. +sampled environmental gradients in the Red Sea. _The ISME Journal, 11_(1), 138. [Link](https://www.ncbi.nlm.nih.gov/pubmed/27420030). [4] Tripathi, A., Melnik, A. V., Xue, J., Poulsen, O., Meehan, M. J., Humphrey, G., ... & Haddad, G. (2018). Intermittent hypoxia and hypercapnia, a hallmark of obstructive sleep apnea, alters the gut microbiome and metabolome. _mSystems, 3_(3), e00020-18. [Link](https://www.ncbi.nlm.nih.gov/pubmed/29896566). -[5] Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., ... & Gordon, J. I. (2011). Moving pictures of the human microbiome. _Genome biology, 12_(5), R50. +[5] Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., ... & Gordon, J. I. (2011). Moving pictures of the human microbiome. _Genome Biology, 12_(5), R50. [Link](https://www.ncbi.nlm.nih.gov/pubmed/21624126). ## License From 380e69b6dfb060b92f996d5f0a32da6238c79688 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 19:48:56 -0700 Subject: [PATCH 25/36] DOC: update jake fish dataset ref on website --- docs/index.html | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/index.html b/docs/index.html index 0dc07e9a..f154b7a2 100644 --- a/docs/index.html +++ b/docs/index.html @@ -104,8 +104,9 @@

Demos

Songbird Here - Minich et al. 2019 (under review)Minich et al. 2020; differentials generated Date: Tue, 5 Jul 2022 21:17:07 -0700 Subject: [PATCH 26/36] DOC: Fix songbird notebook!, standardize output rm --- .../DEICODE_sleep_apnea/deicode_example.ipynb | 4 +- .../qarcoal/qarcoal_example.ipynb | 4 +- .../songbird_red_sea/songbird_example.ipynb | 385 ++++++++---------- 3 files changed, 175 insertions(+), 218 deletions(-) diff --git a/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb b/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb index 98259aa3..7eca2967 100644 --- a/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb +++ b/example_notebooks/DEICODE_sleep_apnea/deicode_example.ipynb @@ -23,12 +23,12 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "# Clear the output directory so we can write these files there\n", - "!rm -rf output/*\n", + "!rm -rf output\n", "# Since git doesn't keep track of empty directories, create the output/ directory if it doesn't already exist\n", "# (if it does already exist, -p ensures that an error won't be thrown)\n", "!mkdir -p output" diff --git a/example_notebooks/qarcoal/qarcoal_example.ipynb b/example_notebooks/qarcoal/qarcoal_example.ipynb index dd1bbfe9..32dcbfd0 100644 --- a/example_notebooks/qarcoal/qarcoal_example.ipynb +++ b/example_notebooks/qarcoal/qarcoal_example.ipynb @@ -26,12 +26,12 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 14, "metadata": {}, "outputs": [], "source": [ "# Clear the output directory so we can write these files there\n", - "!rm -rf output/*\n", + "!rm -rf output\n", "# Since git doesn't keep track of empty directories, create the output/ directory if it doesn't already exist\n", "# (if it does already exist, -p ensures that an error won't be thrown)\n", "!mkdir -p output" diff --git a/example_notebooks/songbird_red_sea/songbird_example.ipynb b/example_notebooks/songbird_red_sea/songbird_example.ipynb index 11d4a278..9da74829 100644 --- a/example_notebooks/songbird_red_sea/songbird_example.ipynb +++ b/example_notebooks/songbird_red_sea/songbird_example.ipynb @@ -7,12 +7,25 @@ "# Visualizing Songbird feature differentials with Qurro\n", "In this example, we use data from the Red Sea metagenome dataset. This particular data was obtained from [Songbird's GitHub repository in its `data/redsea` folder](https://github.com/biocore/songbird/tree/master/data/redsea), and is associated with the following paper:\n", "\n", - "Thompson, L. R., Williams, G. J., Haroon, M. F., Shibl, A., Larsen, P., Shorenstein, J., ... & Stingl, U. (2017). Metagenomic covariation along densely sampled environmental gradients in the Red Sea. _The ISME journal, 11_(1), 138.\n", + "Thompson, L. R., Williams, G. J., Haroon, M. F., Shibl, A., Larsen, P., Shorenstein, J., ... & Stingl, U. (2017). Metagenomic covariation along densely sampled environmental gradients in the Red Sea. _The ISME Journal, 11_(1), 138.\n", "\n", - "The commands for running Songbird and importing the Red Sea data are based on the example usage of this dataset in the Songbird README file on its GitHub page. **Note that here we don't explicitly monitor Songbird's diagnostics regarding model fitting**, as described in [Songbird's README](https://github.com/biocore/songbird/); when using Songbird in practice, it's important to do that. (The hyperparameters we do use were set based on experimentation with Tensorboard.)\n", + "## 2022 note on running Songbird (and also running Qurro)\n", + "\n", + "A lot has changed since we published these tools in 2019 and 2020! Notably, the [pandas](https://pandas.pydata.org/) (and, as a result, QIIME 2 versions) required by Qurro and Songbird are now incompatible, as of writing:\n", + "\n", + "| Tool | Required `pandas` version | Required QIIME 2 version |\n", + "| ---- | ---- | ---- |\n", + "| Qurro | `>= 1` | `>= 2020.11` |\n", + "| Songbird | `< 1` | `>= 2019.7, <= 2020.6` |\n", + "\n", + "This implies that installing Qurro and Songbird into the same conda environment is not feasible. However, it's possible to install them into separate conda environments; the differentials output by Songbird are still completely compatible with Qurro.\n", + "\n", + "__To get around this issue for the purposes of this tutorial__, we will run Songbird from within one QIIME 2 conda environment (version `2020.6`) and run Qurro from within another QIIME 2 conda environment (version `2022.2`). (Getting Jupyter and conda to play nicely can be a bit of a pain, but the `nb_conda_kernels` package should help make it easier to switch between conda environments within a notebook. That being said, it'll probably be easier to replicate these analyses outside of a Jupyter notebook.)\n", + "\n", + "That said, for the most up-to-date details about how to install and run Songbird, please see [its documentation](https://github.com/biocore/songbird/).\n", "\n", "## Requirements\n", - "This notebook relies on QIIME 2, Songbird, and Qurro all being installed. You should be in a QIIME 2 conda environment." + "This notebook relies on two QIIME 2 conda environments being installed, as discussed above: one containing Songbird, and one containing Qurro. See above for details on the exact versions required." ] }, { @@ -30,7 +43,7 @@ "outputs": [], "source": [ "# Clear the output directory so we can write these files there\n", - "!rm -rf output/*\n", + "!rm -rf output\n", "# Since git doesn't keep track of empty directories, create the output/ directory if it doesn't already exist\n", "# (if it does already exist, -p ensures that an error won't be thrown)\n", "!mkdir -p output" @@ -40,12 +53,14 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## 1. Using Songbird and Qurro through QIIME 2\n", - "You can use Songbird and Qurro inside or outside of QIIME 2. In this section, we'll use Songbird and Qurro from within QIIME 2; in the next section, we'll use these tools outside of QIIME 2.\n", + "## 1. Using Songbird and Qurro through QIIME 2 (using two conda environments)\n", + "\n", + "### 1. A. Using Songbird through QIIME 2 (`>= 2019.7, <= 2020.6`)\n", "\n", - "If you just installed Songbird or Qurro, it's advised that you run `qiime dev refresh-cache` on your system afterwards in order to get QIIME 2 to \"find\" these tools' QIIME 2 plugins.\n", + "__This should be run from a QIIME 2 conda environment in which Songbird (but not Qurro) is installed.__\n", + "\n", + "If you just installed Songbird, it's advised that you run `qiime dev refresh-cache` on your system afterwards in order to get QIIME 2 to \"find\" its QIIME 2 plugin.\n", "\n", - "### 1. A. Using Songbird through QIIME 2\n", "In order to use this dataset's BIOM table in QIIME 2, we need to import it as a `FeatureTable[Frequency]` QIIME 2 artifact." ] }, @@ -78,7 +93,7 @@ "Please see [Songbird's documentation](https://github.com/biocore/songbird/) for more information about how it works and how its output files are formatted.\n", "\n", "#### Why these hyperparameters?\n", - "These hyperparameters (in particular, `epochs` and `differential-prior`) were selected based on experimentation with Tensorboard. See Songbird's [FAQs](https://github.com/biocore/songbird/#faqs) for details on how to use Tensorboard and select these sort of hyperparameters for your own datasets (the scope of that is beyond this tutorial)." + "These hyperparameters (in particular, `epochs` and `differential-prior`) were selected based on experimentation with Tensorboard. See Songbird's [FAQs](https://github.com/biocore/songbird/#faqs) for details on how to use Tensorboard and select these sort of hyperparameters for your own datasets (this is important, but the question of how to do this is beyond the scope of this tutorial)." ] }, { @@ -90,9 +105,10 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mSaved FeatureData[Differential] to: output/differentials.qza\u001b[0m\r\n", - "\u001b[32mSaved SampleData[SongbirdStats] to: output/regression-stats.qza\u001b[0m\r\n", - "\u001b[32mSaved PCoAResults % Properties('biplot') to: output/regression-biplot.qza\u001b[0m\r\n" + "\u001b[33mQIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.\u001b[0m\n", + "\u001b[32mSaved FeatureData[Differential] to: output/differentials.qza\u001b[0m\n", + "\u001b[32mSaved SampleData[SongbirdStats] to: output/regression-stats.qza\u001b[0m\n", + "\u001b[32mSaved PCoAResults % Properties('biplot') to: output/regression-biplot.qza\u001b[0m\n" ] } ], @@ -112,44 +128,47 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### 1. B. Using Qurro through QIIME 2\n", + "### 1. B. Using Qurro through QIIME 2 (`>= 2020.11`)\n", + "\n", + "__At this point, you should switch to a newer QIIME 2 environment with which Qurro will be compatible.__\n", + "\n", "Since our \"feature rankings\" are the (sorted) feature differentials that Songbird just produced, we'll use the `qiime qurro differential-plot` command." ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Usage: \u001b[34mqiime qurro differential-plot\u001b[0m [OPTIONS]\r\n", + "Usage: \u001b[94mqiime qurro differential-plot\u001b[0m [OPTIONS]\r\n", "\r\n", " Generates an interactive visualization of feature differentials in tandem\r\n", " with a visualization of the log-ratios of selected features' sample\r\n", " abundances.\r\n", "\r\n", "\u001b[1mInputs\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--i-ranks\u001b[0m ARTIFACT \u001b[32mFeatureData[Differential]\u001b[0m\r\n", + " \u001b[94m\u001b[4m--i-ranks\u001b[0m ARTIFACT \u001b[32mFeatureData[Differential]\u001b[0m\r\n", " Feature differentials. \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m\u001b[4m--i-table\u001b[0m ARTIFACT \u001b[32mFeatureTable[Frequency]\u001b[0m\r\n", + " \u001b[94m\u001b[4m--i-table\u001b[0m ARTIFACT \u001b[32mFeatureTable[Frequency]\u001b[0m\r\n", " A BIOM table describing the abundances of the ranked\r\n", " features in samples. Note that empty samples and\r\n", " features will be removed from the Qurro visualization.\r\n", " \u001b[35m[required]\u001b[0m\r\n", "\u001b[1mParameters\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--m-sample-metadata-file\u001b[0m METADATA...\r\n", + " \u001b[94m\u001b[4m--m-sample-metadata-file\u001b[0m METADATA...\r\n", " (multiple Sample metadata. In Qurro visualizations, you can use\r\n", " arguments will sample metadata fields to change the x-axis and colors\r\n", " be merged) in the sample plot. \u001b[35m[required]\u001b[0m\r\n", - " \u001b[34m--m-feature-metadata-file\u001b[0m METADATA...\r\n", + " \u001b[94m--m-feature-metadata-file\u001b[0m METADATA...\r\n", " (multiple Feature metadata (for example, if your features are\r\n", " arguments will ASVs or OTUs, this could be taxonomy). You can use\r\n", " be merged) feature metadata fields to filter features in the rank\r\n", " plot when selecting log-ratios. \u001b[35m[optional]\u001b[0m\r\n", - " \u001b[34m--p-extreme-feature-count\u001b[0m INTEGER\r\n", + " \u001b[94m--p-extreme-feature-count\u001b[0m INTEGER\r\n", " If specified, Qurro will only use this many \"extreme\"\r\n", " features from both ends of all of the rankings. This is\r\n", " useful when dealing with huge datasets (e.g. with BIOM\r\n", @@ -158,21 +177,22 @@ " crash due to memory limits. Note that the automatic\r\n", " removal of empty samples and features from the table\r\n", " will be done *after* this filtering step. \u001b[35m[optional]\u001b[0m\r\n", - " \u001b[34m--p-debug\u001b[0m / \u001b[34m--p-no-debug\u001b[0m\r\n", + " \u001b[94m--p-debug\u001b[0m / \u001b[94m--p-no-debug\u001b[0m\r\n", " If this flag is used, Qurro will output debug\r\n", " messages. Note that you'll also need to use the\r\n", " --verbose option to see these messages.\r\n", " \u001b[35m[default: False]\u001b[0m\r\n", "\u001b[1mOutputs\u001b[0m:\r\n", - " \u001b[34m\u001b[4m--o-visualization\u001b[0m VISUALIZATION\r\n", + " \u001b[94m\u001b[4m--o-visualization\u001b[0m VISUALIZATION\r\n", " \u001b[35m[required]\u001b[0m\r\n", "\u001b[1mMiscellaneous\u001b[0m:\r\n", - " \u001b[34m--output-dir\u001b[0m PATH Output unspecified results to a directory\r\n", - " \u001b[34m--verbose\u001b[0m / \u001b[34m--quiet\u001b[0m Display verbose output to stdout and/or stderr during\r\n", + " \u001b[94m--output-dir\u001b[0m PATH Output unspecified results to a directory\r\n", + " \u001b[94m--verbose\u001b[0m / \u001b[94m--quiet\u001b[0m Display verbose output to stdout and/or stderr during\r\n", " execution of this action. Or silence output if\r\n", " execution is successful (silence is golden).\r\n", - " \u001b[34m--citations\u001b[0m Show citations and exit.\r\n", - " \u001b[34m--help\u001b[0m Show this message and exit.\r\n" + " \u001b[94m--example-data\u001b[0m PATH Write example data and exit.\r\n", + " \u001b[94m--citations\u001b[0m Show citations and exit.\r\n", + " \u001b[94m--help\u001b[0m Show this message and exit.\r\n" ] } ], @@ -182,14 +202,15 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "\u001b[32mSaved Visualization to: output/qurro_plot_q2.qzv\u001b[0m\r\n" + "\u001b[32mSaved Visualization to: output/qurro_plot_q2.qzv\u001b[0m\r\n", + "\u001b[0m" ] } ], @@ -216,70 +237,82 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## 2. Using Songbird and Qurro as standalone tools\n", + "## 2. Using Songbird and Qurro as standalone tools (again, using two conda environments)\n", "We don't need to use Songbird and Qurro through QIIME 2; if you want, you can run these tools outside of QIIME 2. Although this means you don't have access to some of QIIME 2's functionality (e.g. provenance tracking, or artifact semantic types), the results you get should be roughly the same. (We say \"roughly\" because some of the machine learning methods used by Songbird involve randomness.)\n", "\n", - "### 2. A. Using Songbird as a standalone tool" + "As with the QIIME 2 examples above, Songbird and Qurro are incompatible -- they have conflicting dependencies. We recommend using conda, so that you can install Songbird and Qurro into two separate environments (and switch between these as needed).\n", + "\n", + "### 2. A. Using Songbird as a standalone tool\n", + "\n", + "__This should be run from a conda environment in which Songbird (but not Qurro) is installed.__" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/bin/songbird:191: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/bin/songbird:191: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.\n", "\n", - "2020-03-10 15:54:17.429657: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7f93a910c6d0 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", - "2020-03-10 15:54:17.429683: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/bin/songbird:194: The name tf.set_random_seed is deprecated. Please use tf.compat.v1.set_random_seed instead.\n", + "2022-07-05 21:04:30.548298: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA\n", + "2022-07-05 21:04:30.572787: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 1999965000 Hz\n", + "2022-07-05 21:04:30.573710: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55feb226f620 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n", + "2022-07-05 21:04:30.573769: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/bin/songbird:194: The name tf.set_random_seed is deprecated. Please use tf.compat.v1.set_random_seed instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:70: multinomial (from tensorflow.python.ops.random_ops) is deprecated and will be removed in a future version.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:70: multinomial (from tensorflow.python.ops.random_ops) is deprecated and will be removed in a future version.\n", "Instructions for updating:\n", "Use `tf.random.categorical` instead.\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:81: The name tf.random_normal is deprecated. Please use tf.random.normal instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:81: The name tf.random_normal is deprecated. Please use tf.random.normal instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:86: Normal.__init__ (from tensorflow.python.ops.distributions.normal) is deprecated and will be removed after 2019-01-01.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:86: Normal.__init__ (from tensorflow.python.ops.distributions.normal) is deprecated and will be removed after 2019-01-01.\n", "Instructions for updating:\n", "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/python/ops/distributions/normal.py:160: Distribution.__init__ (from tensorflow.python.ops.distributions.distribution) is deprecated and will be removed after 2019-01-01.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/distributions/normal.py:160: Distribution.__init__ (from tensorflow.python.ops.distributions.distribution) is deprecated and will be removed after 2019-01-01.\n", "Instructions for updating:\n", "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:95: Multinomial.__init__ (from tensorflow.python.ops.distributions.multinomial) is deprecated and will be removed after 2019-01-01.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:95: Multinomial.__init__ (from tensorflow.python.ops.distributions.multinomial) is deprecated and will be removed after 2019-01-01.\n", "Instructions for updating:\n", "The TensorFlow Distributions library has moved to TensorFlow Probability (https://github.com/tensorflow/probability). You should update all references to use `tfp.distributions` instead of `tf.distributions`.\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:110: The name tf.summary.scalar is deprecated. Please use tf.compat.v1.summary.scalar instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:110: The name tf.summary.scalar is deprecated. Please use tf.compat.v1.summary.scalar instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:116: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:116: The name tf.train.AdamOptimizer is deprecated. Please use tf.compat.v1.train.AdamOptimizer instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/tensorflow_core/python/ops/clip_ops.py:301: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/tensorflow_core/python/ops/clip_ops.py:301: where (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version.\n", "Instructions for updating:\n", "Use tf.where in 2.0, which has the same broadcast rule as np.where\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:124: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:124: The name tf.summary.histogram is deprecated. Please use tf.compat.v1.summary.histogram instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:125: The name tf.summary.merge_all is deprecated. Please use tf.compat.v1.summary.merge_all instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:125: The name tf.summary.merge_all is deprecated. Please use tf.compat.v1.summary.merge_all instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:127: The name tf.summary.FileWriter is deprecated. Please use tf.compat.v1.summary.FileWriter instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:127: The name tf.summary.FileWriter is deprecated. Please use tf.compat.v1.summary.FileWriter instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:131: The name tf.global_variables_initializer is deprecated. Please use tf.compat.v1.global_variables_initializer instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:131: The name tf.global_variables_initializer is deprecated. Please use tf.compat.v1.global_variables_initializer instead.\n", "\n", - "WARNING:tensorflow:From /Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/songbird/multinomial.py:163: The name tf.train.Saver is deprecated. Please use tf.compat.v1.train.Saver instead.\n", + "WARNING:tensorflow:From /home/marcus/anaconda3/envs/q2-2020.6/lib/python3.6/site-packages/songbird/multinomial.py:163: The name tf.train.Saver is deprecated. Please use tf.compat.v1.train.Saver instead.\n", "\n", - " 0%| | 0/80000 [00:00>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " sparse_index=BlockIndex(N, blocs, blens),\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return klass(values, index=self.index, name=items, fastpath=True)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_values, index=self.index, name=self.name)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_fill_value=self.default_fill_value,\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\n", - "Use a Series with sparse values instead.\n", - "\n", - " >>> series = pd.Series(pd.SparseArray(...))\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " result = self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:1999: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(result, **d).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:745: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_fill_value=self._default_fill_value,\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:9126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " return self._constructor(new_data).__finalize__(self)\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\n", - "\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\n", - "\n", - " default_kind=self._default_kind,\n", - "Successfully generated a visualization in the folder output/qurro_plot_standalone/.\n" + "Successfully generated a visualization in the folder output/qurro_plot_standalone/.\r\n" ] } ], @@ -511,9 +468,9 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python [conda env:q2-2022.2-unfucked] *", "language": "python", - "name": "python3" + "name": "conda-env-q2-2022.2-unfucked-py" }, "language_info": { "codemirror_mode": { @@ -525,7 +482,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.8.13" } }, "nbformat": 4, From 40c8081cdeeb675f81305fd6e5c8f3d40ca38770 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 21:18:26 -0700 Subject: [PATCH 27/36] BLD: rm (now-)unused comments from q2 ci --- .github/workflows/qiime2.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/.github/workflows/qiime2.yml b/.github/workflows/qiime2.yml index 813b4aac..19abcd59 100644 --- a/.github/workflows/qiime2.yml +++ b/.github/workflows/qiime2.yml @@ -48,11 +48,6 @@ jobs: - name: Install Qurro (and its pip dependencies) run: conda run -n qiime2-dev pip install -e .[dev] - # - name: Install the example notebooks' dependencies - # run: | - # conda run -n qiime2-dev pip install songbird deicode - # conda run -n qiime2-dev conda install --yes -c bioconda bioconductor-aldex2 mygene - - name: Set up Node.js uses: actions/setup-node@v1 @@ -62,9 +57,6 @@ jobs: - name: Run tests run: conda run -n qiime2-dev make test - # - name: Verify that the example notebooks can be run without crashing - # run: conda run -n qiime2-dev make notebooks - - name: Lint and stylecheck run: conda run -n qiime2-dev make stylecheck From bb449739959e030d3e476443d37c11d9a55c9ef7 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 21:28:10 -0700 Subject: [PATCH 28/36] DOC: fix transcriptomics ntbk :) --- .../transcriptomic_example.ipynb | 208 ++++++------------ 1 file changed, 68 insertions(+), 140 deletions(-) diff --git a/example_notebooks/ALDEx2_TCGA_LUSC/transcriptomic_example.ipynb b/example_notebooks/ALDEx2_TCGA_LUSC/transcriptomic_example.ipynb index c73f5821..90018f4d 100644 --- a/example_notebooks/ALDEx2_TCGA_LUSC/transcriptomic_example.ipynb +++ b/example_notebooks/ALDEx2_TCGA_LUSC/transcriptomic_example.ipynb @@ -11,12 +11,15 @@ "\n", "**Please note that this example is primarily intended to demonstrate how to use Qurro**, rather than to demonstrate \"best practices\" in using ALDEx2 or in analyzing transcriptomic data. We designed Qurro in the context of microbiome / metabolome data, but it should be applicable to arbitrary compositional datasets :)\n", "\n", - "[1] Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., ... & Cancer Genome Atlas Research Network. (2013). The cancer genome atlas pan-cancer analysis project. *Nature genetics, 45*(10), 1113.\n", - "\n", + "[1] Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., ... & Cancer Genome Atlas Rese to arch Network. (2013). The cancer genome atlas pan-cancer analysis project. *Nature Genetics, 45*(10), 1113.\n", "\n", "## Requirements:\n", "\n", - "This notebook requires **qurro**, **pandas (>= 0.24.0 and < 1.0.0)**, **mygene**, and **biom-format** to be installed on the Python side of things. The R package [ALDEx2](http://bioconductor.org/packages/release/bioc/html/ALDEx2.html) is also required for the `run_aldex.R` script." + "This notebook requires **qurro** and **mygene** to be installed on the Python side of things. The R package [ALDEx2](http://bioconductor.org/packages/release/bioc/html/ALDEx2.html) is also required for the `run_aldex.R` script.\n", + "\n", + "### 2022 note on running this notebook\n", + "\n", + "In previous years, we installed ALDEx2 through conda using the [`bioconductor-aldex2`](https://anaconda.org/bioconda/bioconductor-aldex2) conda package. However, it no longer seems easily possible to install this package (at least on my laptop). Therefore, we now recommend installing ALDEx2 directly through Bioconductor in R; see [ALDEx2's Bioconductor documentation](https://bioconductor.org/packages/release/bioc/html/ALDEx2.html) for details." ] }, { @@ -34,7 +37,7 @@ "outputs": [], "source": [ "# Clear the output directory so we can write these files there\n", - "!rm -rf output/*\n", + "!rm -rf output\n", "# Since git doesn't keep track of empty directories, create the output/ directory if it doesn't already exist\n", "# (if it does already exist, -p ensures that an error won't be thrown)\n", "!mkdir -p output" @@ -1785,7 +1788,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -1809,35 +1812,47 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[1] \"aldex.clr: generating Monte-Carlo instances and clr values\"\r\n", - "[1] \"operating in serial mode\"\r\n", - "[1] \"removed rows with sums equal to zero\"\r\n", - "[1] \"computing center with all features\"\r\n", - "[1] \"data format is OK\"\r\n", - "[1] \"dirichlet samples complete\"\r\n", - "[1] \"clr transformation complete\"\r\n", - "[1] \"aldex.ttest: doing t-test\"\r\n", - "[1] \"running tests for each MC instance:\"\r\n", - "|------------(25%)----------(50%)----------(75%)----------|\r\n", - "[1] \"aldex.effect: calculating effect sizes\"\r\n", - "[1] \"operating in serial mode\"\r\n", - "[1] \"sanity check complete\"\r\n", - "[1] \"rab.all complete\"\r\n", - "[1] \"rab.win complete\"\r\n", - "[1] \"rab of samples complete\"\r\n", - "[1] \"within sample difference calculated\"\r\n", - "[1] \"between group difference calculated\"\r\n", - "[1] \"group summaries calculated\"\r\n", - "[1] \"effect size calculated\"\r\n", - "[1] \"summarizing output\"\r\n", - "[1] \"ALDEx2 results written to output/TCGA_LUSC_aldex_results.tsv\"\r\n" + "Loading required package: zCompositions\n", + "Loading required package: MASS\n", + "Loading required package: NADA\n", + "Loading required package: survival\n", + "\n", + "Attaching package: ‘NADA’\n", + "\n", + "The following object is masked from ‘package:stats’:\n", + "\n", + " cor\n", + "\n", + "Loading required package: truncnorm\n", + "aldex.clr: generating Monte-Carlo instances and clr values\n", + "operating in serial mode\n", + "removed rows with sums equal to zero\n", + "computing center with all features\n", + "data format is OK\n", + "dirichlet samples complete\n", + "transformation complete\n", + "aldex.ttest: doing t-test\n", + "running tests for each MC instance:\n", + "|------------(25%)----------(50%)----------(75%)----------|\n", + "aldex.effect: calculating effect sizes\n", + "operating in serial mode\n", + "sanity check complete\n", + "rab.all complete\n", + "rab.win complete\n", + "rab of samples complete\n", + "within sample difference calculated\n", + "between group difference calculated\n", + "group summaries calculated\n", + "effect size calculated\n", + "summarizing output\n", + "[1] \"ALDEx2 results written to output/TCGA_LUSC_aldex_results.tsv\"\n" ] } ], @@ -1847,7 +1862,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 18, "metadata": {}, "outputs": [], "source": [ @@ -1870,7 +1885,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 19, "metadata": {}, "outputs": [], "source": [ @@ -1894,7 +1909,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 20, "metadata": {}, "outputs": [ { @@ -1912,7 +1927,7 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 21, "metadata": {}, "outputs": [ { @@ -1981,7 +1996,7 @@ " \n", " \n", " ENSG00000198886\n", - " NADH dehydrogenase, subunit 4 (complex I)\n", + " NADH dehydrogenase subunit 4\n", " ND4\n", " MT\n", " \n", @@ -1990,24 +2005,16 @@ "

" ], "text/plain": [ - " name symbol \\\n", - "feature-id \n", - "ENSG00000168484 surfactant protein C SFTPC \n", - "ENSG00000185303 surfactant protein A2 SFTPA2 \n", - "ENSG00000198804 cytochrome c oxidase subunit I COX1 \n", - "ENSG00000122852 surfactant protein A1 SFTPA1 \n", - "ENSG00000198886 NADH dehydrogenase, subunit 4 (complex I) ND4 \n", - "\n", - " genomic_pos.chr \n", - "feature-id \n", - "ENSG00000168484 8 \n", - "ENSG00000185303 10 \n", - "ENSG00000198804 MT \n", - "ENSG00000122852 10 \n", - "ENSG00000198886 MT " + " name symbol genomic_pos.chr\n", + "feature-id \n", + "ENSG00000168484 surfactant protein C SFTPC 8\n", + "ENSG00000185303 surfactant protein A2 SFTPA2 10\n", + "ENSG00000198804 cytochrome c oxidase subunit I COX1 MT\n", + "ENSG00000122852 surfactant protein A1 SFTPA1 10\n", + "ENSG00000198886 NADH dehydrogenase subunit 4 ND4 MT" ] }, - "execution_count": 20, + "execution_count": 21, "metadata": {}, "output_type": "execute_result" } @@ -2023,7 +2030,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 22, "metadata": {}, "outputs": [], "source": [ @@ -2043,99 +2050,13 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "/Users/mfedarko/Dropbox/Work/KnightLab/qurro/qurro/_df_utils.py:126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " table_sdf = pd.SparseDataFrame(table.matrix_data, default_fill_value=0.0)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:257: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " sparse_index=BlockIndex(N, blocs, blens),\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/frame.py:3471: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return klass(values, index=self.index, name=items, fastpath=True)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/ops/__init__.py:1641: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_values, index=self.index, name=self.name)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:339: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_fill_value=self.default_fill_value,\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:6289: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:5884: FutureWarning: SparseSeries is deprecated and will be removed in a future version.\r\n", - "Use a Series with sparse values instead.\r\n", - "\r\n", - " >>> series = pd.Series(pd.SparseArray(...))\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:785: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_arrays, index=index, columns=columns).__finalize__(\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:3606: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " result = self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:1999: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(result, **d).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:745: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_fill_value=self._default_fill_value,\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/generic.py:9126: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " return self._constructor(new_data).__finalize__(self)\r\n", - "/Users/mfedarko/anaconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/pandas/core/sparse/frame.py:854: FutureWarning: SparseDataFrame is deprecated and will be removed in a future version.\r\n", - "Use a regular DataFrame whose columns are SparseArrays instead.\r\n", - "\r\n", - "See http://pandas.pydata.org/pandas-docs/stable/user_guide/sparse.html#migrating for more.\r\n", - "\r\n", - " default_kind=self._default_kind,\r\n", "Successfully generated a visualization in the folder output/qurro.\r\n" ] } @@ -2151,7 +2072,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 24, "metadata": {}, "outputs": [], "source": [ @@ -2240,11 +2161,18 @@ "\n", "If you've made it this far, thanks for reading! As always, please feel free to [open an issue](https://github.com/biocore/qurro/issues) in Qurro's repository (or ask a question on the [QIIME 2 forums](https://forum.qiime2.org/)) if you have any questions, comments, or suggestions." ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -2258,7 +2186,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.7" + "version": "3.8.13" } }, "nbformat": 4, From 54b5d0a1dee8a9d84d966831de6587f4c371295f Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 21:42:34 -0700 Subject: [PATCH 29/36] REL: update changelog --- CHANGELOG.md | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b80fc841..9bb3deb8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,43 @@ # Qurro changelog +## Qurro 0.8.0 (date TBD) +### Features added +- Add an option to Qurro's visualization interface to exclude metadata columns + from the "sample plot data" output TSV + ([#306](https://github.com/biocore/qurro/issues/306), + [#313](https://github.com/biocore/qurro/pull/313)). + - This should make it easier to merge the sample log-ratios exported from + Qurro with a sample metadata file -- since now these metadata columns won't + be duplicated, which would cause problems. (This problem comes up in + [Gemelli](https://github.com/biocore/gemelli)'s tutorials.) +### Backward-incompatible changes +- Switched to supporting `pandas >= 1`, and thus QIIME 2 >= `2020.11`. + This change makes Qurro now compatible with newer QIIME 2 versions, at the + cost of removing compatibility with older QIIME 2 versions. + (Notably, Songbird has not yet made this shift, so Songbird and Qurro will + need to be installed into separate environments; the "Red Sea" example + notebook details this process.) +- TODO FINISH +### Bug fixes +### Performance enhancements +### Miscellaneous +- Improve various parts of Qurro's code to remove various warnings (for + example, about certain things being deprecated). +- Update Qurro's example notebooks: + - Updated the "Red Sea" notebook to explain how to use + Songbird and Qurro in different conda environments. + - Updated the "ALDEx2" notebook to explain how we recommend installing ALDEx2 + nowadays. +- Updated the documentation to refer to the published version of the Mackerel + data's paper ([Minich et al. 2020](https://journals.asm.org/doi/full/10.1128/mSphere.00401-20)). +- Ported Qurro's continuous integration from Travis CI to GitHub Actions + ([#316](https://github.com/biocore/qurro/issues/316)). +- Improved Qurro's continuous integration in multiple ways: + - Test on multiple QIIME 2 versions. + - Test the standalone Qurro functionality on multiple Python versions. + - Test the standalone Qurro functionality in a non-QIIME-2 environment + (similar to EMPress' "standalone" CI). + ## Qurro 0.7.1 (May 22, 2020) ### Features added ### Backward-incompatible changes From 87599119950c1a27cd89292dea7f455e261e9c70 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 21:53:09 -0700 Subject: [PATCH 30/36] REL: update changelog --- CHANGELOG.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9bb3deb8..0b2d3352 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,13 +11,14 @@ be duplicated, which would cause problems. (This problem comes up in [Gemelli](https://github.com/biocore/gemelli)'s tutorials.) ### Backward-incompatible changes -- Switched to supporting `pandas >= 1`, and thus QIIME 2 >= `2020.11`. - This change makes Qurro now compatible with newer QIIME 2 versions, at the - cost of removing compatibility with older QIIME 2 versions. - (Notably, Songbird has not yet made this shift, so Songbird and Qurro will - need to be installed into separate environments; the "Red Sea" example - notebook details this process.) -- TODO FINISH +- Switched the required pandas version from `>= 0.24.0, <1` to `>= 1`. + This makes Qurro now compatible with QIIME 2 versions `>= 2020.11`! + - However, this change removes support for older QIIME 2 versions. (It may be + possible to get this version of Qurro installed into an older QIIME 2, but + we do not explicitly support this.) + - Notably, Songbird has not yet made the shift to pandas `>= 1`, so Songbird + and Qurro will need to be installed into separate environments; the "Red + Sea" example notebook details this process.) ### Bug fixes ### Performance enhancements ### Miscellaneous From 5627e2a52ef8cad45b1db9b7f385d2646450d54e Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 21:54:03 -0700 Subject: [PATCH 31/36] TST: see if we can finagle q2 2020.6 / 2020.8? since i thiiiink these versions mighta worked with the pandas >= 1 syntax that being said, i don't think it makes sense to devote time/energy to officially supporting them; just wanna check --- .github/workflows/qiime2.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/qiime2.yml b/.github/workflows/qiime2.yml index 19abcd59..490ebbdb 100644 --- a/.github/workflows/qiime2.yml +++ b/.github/workflows/qiime2.yml @@ -24,6 +24,8 @@ jobs: # always be set to the latest version of QIIME 2. Thanks @thermokarst # for the heads up about this :) q2-yaml: [ + "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.6/release/qiime2-2020.6-py36-linux-conda.yml", + "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.8/release/qiime2-2020.8-py36-linux-conda.yml", "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.11/release/qiime2-2020.11-py36-linux-conda.yml", "https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml" ] From 7edaa099ff2ccc555caff0fc1bb1aad16108f384 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 22:04:08 -0700 Subject: [PATCH 32/36] TST: remove Q2 2020.6 / 2020.8 in CI Looks like the tests themselves pass for these versions, but the style-checking with black fails due to incompatibility with click. yeah this is enough for me to not bother supporting these versions imo --- .github/workflows/qiime2.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/qiime2.yml b/.github/workflows/qiime2.yml index 490ebbdb..19abcd59 100644 --- a/.github/workflows/qiime2.yml +++ b/.github/workflows/qiime2.yml @@ -24,8 +24,6 @@ jobs: # always be set to the latest version of QIIME 2. Thanks @thermokarst # for the heads up about this :) q2-yaml: [ - "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.6/release/qiime2-2020.6-py36-linux-conda.yml", - "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.8/release/qiime2-2020.8-py36-linux-conda.yml", "https://raw.githubusercontent.com/qiime2/environment-files/master/2020.11/release/qiime2-2020.11-py36-linux-conda.yml", "https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml" ] From 141fe1a10638d6e60ab8fbb70189b04912321324 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 22:06:31 -0700 Subject: [PATCH 33/36] DOC: songbird compatibility deets --- example_notebooks/songbird_red_sea/songbird_example.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/example_notebooks/songbird_red_sea/songbird_example.ipynb b/example_notebooks/songbird_red_sea/songbird_example.ipynb index 9da74829..1d88d558 100644 --- a/example_notebooks/songbird_red_sea/songbird_example.ipynb +++ b/example_notebooks/songbird_red_sea/songbird_example.ipynb @@ -11,7 +11,7 @@ "\n", "## 2022 note on running Songbird (and also running Qurro)\n", "\n", - "A lot has changed since we published these tools in 2019 and 2020! Notably, the [pandas](https://pandas.pydata.org/) (and, as a result, QIIME 2 versions) required by Qurro and Songbird are now incompatible, as of writing:\n", + "A lot has changed since we published these tools in 2019 and 2020! Notably, the [pandas](https://pandas.pydata.org/) (and, as a result, QIIME 2 versions) required by Qurro (version 0.8.0 and higher) and Songbird are now incompatible, as of writing:\n", "\n", "| Tool | Required `pandas` version | Required QIIME 2 version |\n", "| ---- | ---- | ---- |\n", @@ -22,7 +22,7 @@ "\n", "__To get around this issue for the purposes of this tutorial__, we will run Songbird from within one QIIME 2 conda environment (version `2020.6`) and run Qurro from within another QIIME 2 conda environment (version `2022.2`). (Getting Jupyter and conda to play nicely can be a bit of a pain, but the `nb_conda_kernels` package should help make it easier to switch between conda environments within a notebook. That being said, it'll probably be easier to replicate these analyses outside of a Jupyter notebook.)\n", "\n", - "That said, for the most up-to-date details about how to install and run Songbird, please see [its documentation](https://github.com/biocore/songbird/).\n", + "For the most up-to-date details about how to install and run Songbird, please see [its documentation](https://github.com/biocore/songbird/).\n", "\n", "## Requirements\n", "This notebook relies on two QIIME 2 conda environments being installed, as discussed above: one containing Songbird, and one containing Qurro. See above for details on the exact versions required." From 519d40637d73ccfcf6698007983069a6d83c95fb Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 22:39:18 -0700 Subject: [PATCH 34/36] DEV/DOC: update dev docs re: 2022 the apocalypse came and all i got was this pull request --- CONTRIBUTING.md | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 1dba82cd..cf51afb9 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -14,12 +14,12 @@ in this repository or email the Qurro development team 1. Clone your fork of Qurro's source code to your computer. 2. Create a development conda environment for Qurro: 1. Install the latest version of QIIME 2 natively, - [as you would normally](https://docs.qiime2.org/2019.7/install/native/). - _You'll need to install a QIIME 2 version of at least 2019.7._ + [as you would normally](https://docs.qiime2.org/2022.2/install/native/). + _You'll need to install a QIIME 2 version of at least 2020.11._ 2. In a terminal, navigate to the folder to which you cloned your fork of Qurro's source code above. Run `pip install -e .[dev]` inside this folder to install Qurro along with its normal and development Python dependencies. - 4. Install the various Node.js requirements for testing Qurro's JavaScript + 3. Install the various Node.js requirements for testing Qurro's JavaScript code. This can be done by running `npm install -g mocha-headless-chrome jshint prettier@2.0.5 nyc`. Note that this will install these programs globally on your system. @@ -53,6 +53,23 @@ generated by Qurro's Python tests, and is used to populate some of the JavaScript tests. Long story short, you'll just need to run `make test` (or just `make pytest`) before running `make jstest`. +### When running QIIME 2, Qurro, etc. I get `TypeError: __init__() got multiple values for argument 'obj'` + +This happens due to a [Click](https://click.palletsprojects.com/en/8.1.x/) +version being installed that is unsupported by +QIIME 2. See [this q2cli issue](https://github.com/qiime2/q2cli/issues/259) for +context. This can come up in development because one of Qurro's development +dependencies is +[Black](https://github.com/psf/black), and later versions of Black can rely +on Click 8 (and as of writing QIIME 2 doesn't seem to support Click 8 yet). + +If you run into this error, you can probably get around it by installing an +older version of Black, although earlier versions of Click might disagree with +the later versions that we use in the CI. There isn't a great solution for this +yet that I know of (short of pinning Black to an earlier version and +reformatting all the Python code accordingly...), but hopefully when QIIME 2 +supports Click 8 the problem will vanish. + ## Acknowledgements This document was loosely based on Emperor's [CONTRIBUTING.md file](https://github.com/biocore/emperor/blob/new-api/CONTRIBUTING.md). From 3ae4216b4bc1db97ee14d0ce50e0bd0cc20b9170 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Tue, 5 Jul 2022 22:41:10 -0700 Subject: [PATCH 35/36] REL: update changelog about updating contributing about about about about aboot --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0b2d3352..720f7566 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,6 +38,8 @@ - Test the standalone Qurro functionality on multiple Python versions. - Test the standalone Qurro functionality in a non-QIIME-2 environment (similar to EMPress' "standalone" CI). +- Updated the development documentation regarding the minimum QIIME 2 version, + incompatibilities between `black` and `click`, etc. ## Qurro 0.7.1 (May 22, 2020) ### Features added From 994cc1865a1d27eb301383401e8e1260a7c80fb2 Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Wed, 6 Jul 2022 11:21:25 -0700 Subject: [PATCH 36/36] REL: minor chglog tidying --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 720f7566..74b589b2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,11 +14,11 @@ - Switched the required pandas version from `>= 0.24.0, <1` to `>= 1`. This makes Qurro now compatible with QIIME 2 versions `>= 2020.11`! - However, this change removes support for older QIIME 2 versions. (It may be - possible to get this version of Qurro installed into an older QIIME 2, but - we do not explicitly support this.) + possible to get this version of Qurro installed into an older QIIME 2 + environment, but we do not explicitly support this.) - Notably, Songbird has not yet made the shift to pandas `>= 1`, so Songbird and Qurro will need to be installed into separate environments; the "Red - Sea" example notebook details this process.) + Sea" example notebook details this process. ### Bug fixes ### Performance enhancements ### Miscellaneous