Iss51 (#53)

* Adding versioneer in build time dependency mode * Removed versioneer and added setuptools-scm for build time versioning. Added Version flag to the CLI and a log line with the version. * added support for qual scores up to 92, made modules more pep compliant, updated install docs, updated docker, gh actions and and conda for python 3.9 since Qiime updated to 3.9. * changed python version in dockerfile * added events for action * modified gh action to test itsxpress * workflow updates * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * actions test * Updates to tests, readme, changelog, and citations
USDA-ARS-GBRU · Sep 19, 2024 · 8d28768 · 8d28768
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diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1 @@
+itsxpress/_version.py export-subst
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
@@ -2,66 +2,51 @@ name: GitHub Actions Weekly Build (V2)
 
 on:
   push:
-    branches:
-      - main
+  pull_request:
   schedule:
     - cron: "0 0 */7 * *"
 
 jobs:
   build-linux:
-    runs-on: ubuntu-latest
     strategy:
-      max-parallel: 5
+      max-parallel: 4
+      matrix:
+        os: [ubuntu-latest]
+    runs-on: ${{matrix.os}}
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Check out Repo
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.8
-    - name: Install dependencies
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-    - run:   |
-        #sudo apt update
-        #sudo apt install gcc-10 g++-10
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-        echo $CONDA_PREFIX
-        $CONDA/bin/conda list
-        $CONDA/bin/conda info --base
-        conda create --name testenv python=3.8.16
-        #CONDA_PREFIX=/usr/share/miniconda/envs/testenv
-        $CONDA/bin/conda info
-        $CONDA/bin/conda list
-        
+        python-version: 3.9.19
     - name: Initiate conda channels
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         channels: conda-forge,bioconda,default
-        activate-environment: testenv
-        auto-activate-base: false
-
-
-    - name: Set up environment
+        auto-activate-base: true
+    - name: Initialize conda
       run: |
-        wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2023.9-py38-linux-conda.yml
-        $CONDA/bin/conda env update --file qiime2-amplicon-2023.9-py38-linux-conda.yml --name testenv
+        conda info
+    - name: Set up QIIME Conda environment
+      run: |
+        conda env create -n testenv --file=https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
     - name: Install Dependencies
       run: |
-        echo $CONDA_PREFIX
-        source activate testenv
-        $CONDA/bin/conda install biopython
+        conda activate testenv 
+        conda install biopython=1.84
         pip install pyzstd
         pip install pytest
         pip install .
-        qiime
-        #itsxpress
-        #qiime itsxpress
-        #ls
-
     - name: Test with pytest
       run: |
-        source activate testenv
-        pytest
+        conda activate testenv
+        pytest 
+    - name: Test qiime install
+      run: |
+        conda activate testenv
+        #qiime dev refresch-cache
+        qiime itsxpress --help
+
diff --git a/README.rst b/README.rst
@@ -25,9 +25,14 @@ Author
 * Adam R. Rivers, US Department of Agriculture, Agricultural Research Service
 * Sveinn V. Einarsson, US Department of Agriculture, Agricultural Research Service
 
-Citation
---------
-Rivers AR, Weber KC, Gardner TG et al. ITSxpress: Software to rapidly trim
+Citations
+---------
+
+Einarsson, SV and Rivers, AR. ITSxpress Version 2: Software to rapidly trim internal
+ transcribed spacer sequences with quality scores for amplicon sequencing. 
+Microbiology Spectrum. In press, 2024.
+
+Rivers AR, Weber KC, Gardner TG, Liu, S, Armstrong, SD. ITSxpress: Software to rapidly trim
 internally transcribed spacer sequences with quality scores for marker gene
 analysis [version 1; referees: awaiting peer review]. F1000Research 2018, 7:1418
 (doi: `10.12688/f1000research.15704.1`_)
@@ -65,39 +70,35 @@ Installing ITSxpress for use as a QIIME2 Plugin
 ----------------------------------------------------
 
 To install ITSxpress as a plugin for QIIME 2 first install QIIME 2 as a separate Conda/Mamba environemnt using thier instructions 
-https://docs.qiime2.org/2024.2/install/ then add ITSxress to the QIIME 2 Conda environment. The examples below are for QIIME2 2 
-version 2024.2 an so please update the commands if you want a newer release.
+https://docs.qiime2.org/2024.5/install/ then add ITSxress to the QIIME 2 Conda environment. The examples below are for QIIME2 2 
+version 2024.5 an so please update the commands if you want a newer release.
 
 
 For Linux:
 
 .. code-block:: bash
 
-    wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml
-    mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml
-    mamba activate qiime2-amplicon-2024.2
-    mamba install ITSxpress
+    conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
+    conda activate qiime2-amplicon-2024.5
+    conda install -c bioconda -c conda-forge ITSxpress
     qiime dev refresh-cache
 
 For maxOS (Intel) and OS X:
 
 .. code-block:: bash
 
-    wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml
-    mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml
-    mamba activate qiime2-amplicon-2024.2
-    mamba install ITSxpress
+    conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
+     conda activate qiime2-amplicon-2024.5
+    conda install -c bioconda -c conda-forge ITSxpress
     qiime dev refresh-cache
 
 For macOS (Arm / Apple Silicon):
 
 .. code-block:: bash
-
-    wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml
-    CONDA_SUBDIR=osx-64 mamba create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml
-    mamba activate qiime2-amplicon-2024.2
-    mamba config --env --set subdir osx-64
-    mamba install ITSxpress
+    CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
+    conda activate qiime2-amplicon-2024.5
+    conda config --env --set subdir osx-64
+    CONDA_SUBDIR=osx-64 conda install -c bioconda -c conda-forge ITSxpress
     qiime dev refresh-cache
 
 

diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,14 @@
+2.1.1 (2024-9-19)
+------------------
+- Changed settings to allow FASTQ quality scores up to 93. This prevents an error in processing some reads from PacBio, Nanopore and Element Biosciences AVITI sequencers with quality scores over 41.
+- Updated from manual software versioning to automated versioning based on git tag metadata and `setuptools-scm`.
+- Updated Github action workflow for QIIME 2024.5 and Python 3.9.19
+- Improved and updated installation instructions in the README file
+- Updated tests for FASTQs with high qual scores
+- Added citation information for forthcoming ITSXpress version 2 publication
+- Cleaned up some PEP formatting 
+
+
 2.1.0 (2024-4-10)
 ------------------
 - HMMs are updated to version 2 of the HMM database curated by Henrik Nilson at the University of Gothenburg.  

diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
diff --git a/docker-images/Dockerfile b/docker-images/Dockerfile
@@ -1,4 +1,4 @@
-FROM condaforge/mambaforge:4.10.3-5
+FROM condaforge/mambaforge:24.7.1-0
 
 # # Install system dependencies
 RUN apt-get update && \
@@ -9,7 +9,7 @@ RUN apt-get update && \
 LABEL org.opencontainers.image.source="https://github.com/usda-ars-gbru/itsxpress"
 # Install conda dependencies
 RUN conda update mamba -c conda-forge
-RUN mamba install -c conda-forge python>3.8
+RUN mamba install -c conda-forge python>=3.9
 RUN mamba install -c bioconda vsearch=2.22.1 hmmer=3.1b2
 
 # Copy the itsxpress package files and install dependencies