Attempt to fix #86 (#87)

* install patched reticulate * add tdqm and ipywidgets * Update linux anaconda environment * update windows environment * Revert "update windows environment" This reverts commit bdccdd9. * cleanup * remove if
kevinrue · Sep 9, 2024 · af016a7 · af016a7
1 parent 08a5447
commit af016a7
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diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -216,6 +216,11 @@ jobs:
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
+      - name: Install reticulate patch
+        run: |
+          remotes::install_github("rstudio/reticulate")
+        shell: Rscript {0}
+
       - name: Install BiocGenerics
         if:  env.has_RUnit == 'true'
         run: |

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.8
+Version: 1.15.9
 Date: 2024-08-30
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="[email protected]", comment = c(ORCID = '0000-0002-3564-4813')),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# velociraptor 1.15.9
+
+* Update Conda environment for Linux and MacOSX Arm.
+* Patch GitHub Action to use GitHub version of `remotes`.
+
 # velociraptor 1.15.8
 
 * Update Conda environment using micromamba for MacOSX Arm.

diff --git a/R/basilisk.R b/R/basilisk.R
@@ -165,6 +165,7 @@
     'anndata==0.10.9',
     'aom==3.9.1',
     'array-api-compat==1.8',
+    'asttokens==2.4.1',
     'blosc==1.21.6',
     'brotli==1.1.0',
     'brotli-bin==1.1.0',
@@ -174,25 +175,28 @@
     'ca-certificates==2024.8.30',
     'cached-property==1.5.2',
     'cached_property==1.5.2',
-    'certifi==2024.7.4',
-    'cffi==1.17.0',
+    'certifi==2024.8.30',
+    'cffi==1.17.1',
     'charset-normalizer==3.3.2',
     'chex==0.1.86',
     'click==8.1.7',
     'colorama==0.4.6',
+    'comm==0.2.2',
     'contextlib2==21.6.0',
     'contourpy==1.3.0',
     'cycler==0.12.1',
     'dav1d==1.2.1',
+    'decorator==5.1.1',
     'docrep==0.3.2',
     'et_xmlfile==1.1.0',
-    'etils==1.9.2',
+    'etils==1.9.4',
     'exceptiongroup==1.2.2',
-    'filelock==3.15.4',
+    'executing==2.1.0',
+    'filelock==3.16.0',
     'flax==0.9.0',
     'fonttools==4.53.1',
     'freetype==2.12.1',
-    'fsspec==2024.6.1',
+    'fsspec==2024.9.0',
     'get-annotations==0.1.2',
     'gmp==6.3.0',
     'gmpy2==2.1.5',
@@ -204,13 +208,16 @@
     'icu==75.1',
     'idna==3.8',
     'importlib-metadata==8.4.0',
-    'importlib_metadata==8.4.0',
     'importlib_resources==6.4.4',
+    'ipython==8.27.0',
+    'ipywidgets==8.1.5',
     'jax==0.4.31',
     'jaxlib==0.4.31',
+    'jedi==0.19.1',
     'jinja2==3.1.4',
     'joblib==1.4.2',
-    'kiwisolver==1.4.5',
+    'jupyterlab_widgets==3.0.13',
+    'kiwisolver==1.4.7',
     'krb5==1.21.3',
     'lcms2==2.16',
     'legacy-api-wrap==1.4',
@@ -228,7 +235,7 @@
     'libdeflate==1.21',
     'libedit==3.1.20191231',
     'libev==4.33',
-    'libexpat==2.6.2',
+    'libexpat==2.6.3',
     'libffi==3.4.2',
     'libgfortran==5.0.0',
     'libgfortran5==13.2.0',
@@ -243,7 +250,7 @@
     'libpng==1.6.43',
     'libprotobuf==4.25.3',
     'libre2-11==2023.09.01',
-    'libsqlite==3.46.0',
+    'libsqlite==3.46.1',
     'libssh2==1.11.0',
     'libtiff==4.6.0',
     'libtorch==2.4.0',
@@ -253,14 +260,15 @@
     'libxml2==2.12.7',
     'libzlib==1.3.1',
     'lightning==2.4.0',
-    'lightning-utilities==0.11.6',
+    'lightning-utilities==0.11.7',
     'llvm-openmp==18.1.8',
     'llvmlite==0.43.0',
     'loompy==3.0.6',
     'lz4-c==1.9.4',
     'markdown-it-py==3.0.0',
     'markupsafe==2.1.5',
     'matplotlib-base==3.9.2',
+    'matplotlib-inline==0.1.7',
     'mdurl==0.1.2',
     'ml-collections==0.1.1',
     'ml_dtypes==0.4.0',
@@ -282,18 +290,24 @@
     'numpyro==0.15.2',
     'openjpeg==2.5.2',
     'openpyxl==3.1.5',
-    'openssl==3.3.1',
+    'openssl==3.3.2',
     'opt-einsum==3.3.0',
     'opt_einsum==3.3.0',
     'optax==0.2.2',
     'orbax-checkpoint==0.4.4',
     'packaging==24.1',
     'pandas==2.2.2',
+    'parso==0.8.4',
     'patsy==0.5.6',
+    'pexpect==4.9.0',
+    'pickleshare==0.7.5',
     'pillow==10.4.0',
     'pip==24.2',
+    'prompt-toolkit==3.0.47',
     'protobuf==4.25.3',
     'pthread-stubs==0.4',
+    'ptyprocess==0.7.0',
+    'pure_eval==0.2.3',
     'pybind11-abi==4',
     'pycparser==2.22',
     'pygments==2.18.0',
@@ -324,28 +338,32 @@
     'seaborn==0.13.2',
     'seaborn-base==0.13.2',
     'session-info==1.0.0',
-    'setuptools==72.2.0',
+    'setuptools==73.0.1',
     'six==1.16.0',
     'sleef==3.6.1',
     'snappy==1.2.1',
     'sparse==0.15.4',
+    'stack_data==0.6.2',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
     'svt-av1==2.2.1',
     'sympy==1.13.2',
-    'tbb==2021.12.0',
+    'tbb==2021.13.0',
     'tensorstore==0.1.62',
     'threadpoolctl==3.5.0',
     'tk==8.6.13',
     'toolz==0.12.1',
     'torchmetrics==1.4.0.post0',
     'tqdm==4.66.5',
+    'traitlets==5.14.3',
     'typing-extensions==4.12.2',
     'typing_extensions==4.12.2',
     'tzdata==2024a',
     'umap-learn==0.5.6',
     'urllib3==2.2.2',
+    'wcwidth==0.2.13',
     'wheel==0.44.0',
+    'widgetsnbextension==4.0.13',
     'xarray==2024.7.0',
     'xorg-libxau==1.0.11',
     'xorg-libxdmcp==1.1.3',
@@ -561,73 +579,81 @@
 ## Linux ----
 
 .scvelo.dependencies.Linux <- list(
-  channels = c("anaconda", "conda-forge", "bioconda"),
+  channels = c("anaconda", "conda-forge"),
   packages = c(
     '_libgcc_mutex==0.1',
-    '_openmp_mutex==4.5',
+    '_openmp_mutex==5.1',
     'absl-py==2.1.0',
     'anndata==0.10.9',
     'array-api-compat==1.8',
+    'asttokens==2.0.5',
     'blas==1.0',
     'bottleneck==1.3.7',
     'brotli==1.0.9',
     'brotli-bin==1.0.9',
+    'brotli-python==1.0.9',
     'bzip2==1.0.8',
     'c-ares==1.19.1',
     'ca-certificates==2024.7.2',
+    'certifi==2024.8.30',
+    'charset-normalizer==3.3.2',
     'chex==0.1.5',
     'click==8.1.7',
+    'comm==0.2.1',
     'contextlib2==21.6.0',
     'contourpy==1.2.0',
     'cycler==0.11.0',
+    'decorator==5.1.1',
     'dm-tree==0.1.7',
     'docrep==0.3.2',
     'et_xmlfile==1.1.0',
     'exceptiongroup==1.2.0',
+    'executing==0.8.3',
     'filelock==3.13.1',
     'flax==0.6.1',
     'fonttools==4.51.0',
     'freetype==2.12.1',
-    'fsspec==2024.3.1',
+    'fsspec==2024.6.1',
     'get-annotations==0.1.2',
     'gmp==6.2.1',
     'gmpy2==2.1.2',
     'h5py==3.11.0',
     'hdf5==1.12.1',
+    'idna==3.7',
+    'ipython==8.25.0',
+    'ipywidgets==8.1.2',
     'jax==0.3.25',
     'jaxlib==0.3.25',
+    'jedi==0.19.1',
     'jinja2==3.1.4',
     'joblib==1.4.2',
     'jpeg==9e',
+    'jupyterlab_widgets==3.0.10',
     'kiwisolver==1.4.4',
     'krb5==1.20.1',
     'lcms2==2.12',
     'ld_impl_linux-64==2.38',
     'legacy-api-wrap==1.4',
     'lerc==3.0',
-    'libblas==3.9.0',
     'libbrotlicommon==1.0.9',
     'libbrotlidec==1.0.9',
     'libbrotlienc==1.0.9',
-    'libcblas==3.9.0',
     'libcurl==7.88.1',
     'libdeflate==1.17',
     'libedit==3.1.20230828',
     'libev==4.33',
     'libffi==3.4.4',
-    'libgcc==14.1.0',
-    'libgcc-ng==14.1.0',
+    'libgcc-ng==11.2.0',
     'libgfortran-ng==11.2.0',
     'libgfortran5==11.2.0',
-    'libgomp==14.1.0',
+    'libgomp==11.2.0',
     'libllvm14==14.0.6',
     'libnghttp2==1.57.0',
     'libopenblas==0.3.21',
     'libpng==1.6.39',
     'libprotobuf==3.20.3',
     'libssh2==1.11.0',
-    'libstdcxx==14.1.0',
-    'libstdcxx-ng==14.1.0',
+    'libstdcxx-ng==11.2.0',
     'libtiff==4.5.1',
     'libuuid==1.41.5',
     'libwebp-base==1.3.2',
@@ -637,74 +663,89 @@
     'lz4-c==1.9.4',
     'markdown-it-py==2.2.0',
     'markupsafe==2.1.3',
-    'matplotlib-base==3.8.4',
+    'matplotlib-base==3.9.2',
+    'matplotlib-inline==0.1.6',
     'mdurl==0.1.0',
     'ml-collections==0.1.1',
     'mpc==1.1.0',
     'mpfr==4.0.2',
     'mpmath==1.3.0',
     'msgpack-python==1.0.3',
-    'mudata==0.3.0',
+    'mudata==0.3.1',
     'multipledispatch==0.6.0',
     'natsort==7.1.1',
     'ncurses==6.4',
     'networkx==3.3',
     'numba==0.60.0',
     'numexpr==2.8.7',
-    'numpy==1.26.4',
-    'numpy-base==1.26.4',
+    'numpy==1.23.5',
+    'numpy-base==1.23.5',
     'numpy_groupies==0.11.2',
     'numpyro==0.13.2',
     'openjpeg==2.5.2',
     'openpyxl==3.1.5',
-    'openssl==3.0.14',
+    'openssl==3.0.15',
     'opt_einsum==3.3.0',
     'optax==0.1.4',
     'packaging==24.1',
     'pandas==2.2.2',
+    'parso==0.8.3',
     'patsy==0.5.6',
+    'pexpect==4.8.0',
     'pillow==10.4.0',
     'pip==24.2',
-    'pybind11-abi==4',
+    'platformdirs==3.10.0',
+    'pooch==1.7.0',
+    'prompt-toolkit==3.0.43',
+    'prompt_toolkit==3.0.43',
+    'ptyprocess==0.7.0',
+    'pure_eval==0.2.2',
     'pygments==2.15.1',
     'pynndescent==0.5.10',
-    'pyparsing==3.0.9',
+    'pyparsing==3.1.2',
     'pyro-api==0.1.2',
     'pyro-ppl==1.9.1',
+    'pysocks==1.7.1',
     'python==3.11.9',
     'python-dateutil==2.9.0post0',
     'python-tzdata==2023.3',
-    'python_abi==3.11',
     'pytorch==2.3.0',
     'pytorch-lightning==1.9.5',
     'pytz==2024.1',
     'pyyaml==6.0.1',
     'readline==8.2',
+    'requests==2.32.3',
     'rich==13.7.1',
     'scanpy==1.10.2',
     'scikit-learn==1.1.3',
-    'scipy==1.13.1',
+    'scipy==1.10.0',
     'scvelo==0.3.2',
     'scvi-tools==0.20.3',
     'seaborn==0.13.2',
     'session-info==1.0.0',
     'setuptools==72.1.0',
     'six==1.16.0',
     'sqlite==3.45.3',
+    'stack_data==0.2.0',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
-    'sympy==1.12',
+    'sympy==1.13.2',
+    'tbb==2021.8.0',
     'threadpoolctl==3.5.0',
     'tk==8.6.14',
     'toolz==0.12.0',
     'torchmetrics==1.4.0.post0',
-    'tqdm==4.66.4',
+    'tqdm==4.66.5',
+    'traitlets==5.14.3',
     'typing-extensions==4.11.0',
     'typing_extensions==4.11.0',
     'tzdata==2024a',
-    'umap-learn==0.5.3',
+    'umap-learn==0.5.4',
     'unicodedata2==15.1.0',
+    'urllib3==2.2.2',
+    'wcwidth==0.2.5',
     'wheel==0.43.0',
+    'widgetsnbextension==4.0.10',
     'xz==5.4.6',
     'yaml==0.2.5',
     'zlib==1.2.13',