From 3b5bb0b502eb6d1b3dc0e30ecb31650e4d048306 Mon Sep 17 00:00:00 2001 From: Eric Talevich Date: Sun, 6 Aug 2023 14:25:09 -0700 Subject: [PATCH 1/6] Add Apache 2.0 license text --- LICENSE | 202 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 202 insertions(+) create mode 100644 LICENSE diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..d645695 --- /dev/null +++ b/LICENSE @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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From 0dd98ce244940c66633390e746b7f7c63b577cd0 Mon Sep 17 00:00:00 2001 From: Eric Talevich Date: Mon, 7 Aug 2023 10:58:51 -0700 Subject: [PATCH 2/6] Add newer dependencies 'parasail' and 'tidyverse' to conda environment --- AAV.conda_env.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/AAV.conda_env.yml b/AAV.conda_env.yml index 585c800..bfae3e3 100644 --- a/AAV.conda_env.yml +++ b/AAV.conda_env.yml @@ -10,8 +10,10 @@ dependencies: - r>=3.6.0 - minimap2 - biopython + - parasail-python>=1.3.4 - pysam - r-dplyr - r-ggplot2 - r-gridbase - r-gridextra + - r-tidyverse From f7f35c3e822e78676bbb1a8770145388a2615f18 Mon Sep 17 00:00:00 2001 From: Eric Talevich Date: Mon, 7 Aug 2023 10:59:19 -0700 Subject: [PATCH 3/6] Add Dockerfile to capture conda environment and scripts Include 'less' so the R interpreter's docs work. --- Dockerfile | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..70a2eff --- /dev/null +++ b/Dockerfile @@ -0,0 +1,25 @@ +FROM --platform=linux/amd64 continuumio/miniconda3 + +RUN apt-get update \ + && apt-get install -y \ + apt-transport-https \ + ca-certificates \ + less \ + pigz \ + samtools \ + && rm -rf /var/lib/apt/lists/* + +# Conda environment has the name AAV.env +COPY AAV.conda_env.yml ./AAV.conda_env.yml +RUN conda install -n base conda-libmamba-solver && conda config --set solver libmamba +RUN conda env create -v -f AAV.conda_env.yml +RUN echo "conda activate AAV.env" >> ~/.bashrc + +# Executable scripts for the pipeline +COPY *.py *.R /usr/local/bin +RUN chmod +x /usr/local/bin/*.py /usr/local/bin/*.R +ENV PATH "/usr/local/bin:$PATH" + +WORKDIR /data/ + +CMD ["bash"] From a314165345f060389d7c20c03902139546ba4eed Mon Sep 17 00:00:00 2001 From: Eric Talevich Date: Mon, 7 Aug 2023 20:59:42 -0700 Subject: [PATCH 4/6] Add GHA config for CI testing and dev conda environment Configure static error-checking with lintr for R and flake8 for Python. Streamline CI conda environment to reduce dependency conflicts. --- .github/workflows/ci.yaml | 62 +++++++++++++++++++++++++++++++++++++++ CI.conda_env.yml | 21 +++++++++++++ dev.conda_env.yml | 23 +++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 .github/workflows/ci.yaml create mode 100644 CI.conda_env.yml create mode 100644 dev.conda_env.yml diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml new file mode 100644 index 0000000..d40bd64 --- /dev/null +++ b/.github/workflows/ci.yaml @@ -0,0 +1,62 @@ +name: Tests +on: + push: + branches: + - master + paths-ignore: + - 'docs/**' + - '*.md' + - '*.rst' + pull_request: + paths-ignore: + - 'docs/**' + - '*.md' + - '*.rst' +jobs: + tests: + name: Lint with R and Python ${{ matrix.python }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + os: ['ubuntu-latest'] + python: ['3.11', '3.10', '3.9', '3.8', '3.7'] + defaults: + run: + # Enable the conda environment via ~/.bashrc and ~/.profile + shell: bash -el {0} + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python }} + - name: Cache conda + uses: actions/cache@v3 + env: + # Increase this value to reset cache if dev.conda_env.yml has not changed + CACHE_NUMBER: 0 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('dev.conda_env.yml') }} + - uses: conda-incubator/setup-miniconda@v2 + with: + activate-environment: AAV.ci.env + auto-activate-base: false + auto-update-conda: true + #channel-priority: strict + environment-file: CI.conda_env.yml + python-version: ${{ matrix.python }} + use-only-tar-bz2: true # Required for caching + - name: Show conda environment + run: | + conda info + conda list + - name: Lint Python scripts + run: | + # Stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + #pylint -E pylint -E -d E1101,E1136,E1138 *.py + - name: Lint R script + run: | + Rscript -e 'library(lintr); options(lintr.error_on_lint=TRUE); lint_dir(".", linters=linters_with_tags("correctness"))' diff --git a/CI.conda_env.yml b/CI.conda_env.yml new file mode 100644 index 0000000..b69f482 --- /dev/null +++ b/CI.conda_env.yml @@ -0,0 +1,21 @@ +name: AAV.ci.env +channels: + - conda-forge + - bioconda + - anaconda + - r + - defaults +dependencies: + - python>=3.7.6 + - r>=3.6.0 + - minimap2 + - biopython + - flake8 + - parasail-python>=1.3.4 + - pysam + - r-dplyr + - r-ggplot2 + - r-gridbase + - r-gridextra + - r-lintr + - r-tidyverse diff --git a/dev.conda_env.yml b/dev.conda_env.yml new file mode 100644 index 0000000..904f1bb --- /dev/null +++ b/dev.conda_env.yml @@ -0,0 +1,23 @@ +name: AAV.dev.env +channels: + - conda-forge + - bioconda + - anaconda + - r + - defaults +dependencies: + - python>=3.7.6 + - r>=3.6.0 + - minimap2 + - biopython + - flake8 + - parasail-python>=1.3.4 + - pylint + - pysam + - pytest + - r-dplyr + - r-ggplot2 + - r-gridbase + - r-gridextra + - r-lintr + - r-tidyverse From cf4c301017748c2ec4c3ca546a225a8378ca9f05 Mon Sep 17 00:00:00 2001 From: Eric Talevich Date: Wed, 30 Aug 2023 11:13:28 -0700 Subject: [PATCH 5/6] Reduce dependencies for CI conda packages In GHA, drop Python 3.7 and 3.11 from test matrix because: - pysam isn't available for Python 3.11 yet - parasail-python>=1.3.4 isn't available for Python 3.7 CI conda env: - Remove 'anaconda' and 'r' channels -- they weren't used - Remove explicit r-dplyr and r-ggplot2 -- included with r-tidyverse - Specify r-base instead of r per official guidance --- .github/workflows/ci.yaml | 5 ++--- CI.conda_env.yml | 6 +----- 2 files changed, 3 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index d40bd64..2be7d9e 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -20,7 +20,7 @@ jobs: fail-fast: false matrix: os: ['ubuntu-latest'] - python: ['3.11', '3.10', '3.9', '3.8', '3.7'] + python: ['3.10', '3.9', '3.8'] defaults: run: # Enable the conda environment via ~/.bashrc and ~/.profile @@ -44,7 +44,7 @@ jobs: activate-environment: AAV.ci.env auto-activate-base: false auto-update-conda: true - #channel-priority: strict + channel-priority: strict environment-file: CI.conda_env.yml python-version: ${{ matrix.python }} use-only-tar-bz2: true # Required for caching @@ -56,7 +56,6 @@ jobs: run: | # Stop the build if there are Python syntax errors or undefined names flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - #pylint -E pylint -E -d E1101,E1136,E1138 *.py - name: Lint R script run: | Rscript -e 'library(lintr); options(lintr.error_on_lint=TRUE); lint_dir(".", linters=linters_with_tags("correctness"))' diff --git a/CI.conda_env.yml b/CI.conda_env.yml index b69f482..aa43596 100644 --- a/CI.conda_env.yml +++ b/CI.conda_env.yml @@ -2,19 +2,15 @@ name: AAV.ci.env channels: - conda-forge - bioconda - - anaconda - - r - defaults dependencies: - python>=3.7.6 - - r>=3.6.0 + - r-base>=3.6.0 - minimap2 - biopython - flake8 - parasail-python>=1.3.4 - pysam - - r-dplyr - - r-ggplot2 - r-gridbase - r-gridextra - r-lintr From 8d062384c6672e8ba32c4499f6edd13b12359ba7 Mon Sep 17 00:00:00 2001 From: Eric Talevich Date: Wed, 30 Aug 2023 11:46:31 -0700 Subject: [PATCH 6/6] AAV,dev.conda_env.yml: clean up like CI environment --- AAV.conda_env.yml | 4 +--- dev.conda_env.yml | 8 +++----- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/AAV.conda_env.yml b/AAV.conda_env.yml index bfae3e3..7f7a5ac 100644 --- a/AAV.conda_env.yml +++ b/AAV.conda_env.yml @@ -7,13 +7,11 @@ channels: - defaults dependencies: - python>=3.7.6 - - r>=3.6.0 + - r-base>=3.6.0 - minimap2 - biopython - parasail-python>=1.3.4 - pysam - - r-dplyr - - r-ggplot2 - r-gridbase - r-gridextra - r-tidyverse diff --git a/dev.conda_env.yml b/dev.conda_env.yml index 904f1bb..7db3ad9 100644 --- a/dev.conda_env.yml +++ b/dev.conda_env.yml @@ -2,22 +2,20 @@ name: AAV.dev.env channels: - conda-forge - bioconda - - anaconda - - r - defaults dependencies: - python>=3.7.6 - - r>=3.6.0 + - r-base>=3.6.0 - minimap2 - biopython + - black - flake8 - parasail-python>=1.3.4 - pylint - pysam - pytest - - r-dplyr - - r-ggplot2 - r-gridbase - r-gridextra - r-lintr + - r-styler - r-tidyverse