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Merge branch 'main' into fix_metadata_cleanup
2 parents 9d1f9e0 + 87dec8f commit 6bd7b6e

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‎.gitattributes‎

Lines changed: 3 additions & 1 deletion
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@@ -6,4 +6,6 @@ tests/test_issue1046/expected-results/test_report.html linguist-vendored=true
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tests/test_report/report.html linguist-vendored=true
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tests/test_report/expected-results/report.html linguist-vendored=true
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tests/test_report/custom-stylesheet.css linguist-vendored=true
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tests/**/*.html linguist-vendored=true
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# SCM syntax highlighting & preventing 3-way merges
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pixi.lock merge=binary linguist-language=YAML linguist-generated=true
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tests/**/*.html linguist-vendored=true

‎.github/workflows/main.yml‎

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@@ -21,15 +21,16 @@ jobs:
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steps:
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- uses: actions/checkout@v4
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- uses: mamba-org/setup-micromamba@v1
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- name: Install Pixi
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uses: prefix-dev/[email protected]
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with:
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environment-name: black
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create-args: black
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cache-environment: false
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environments: "quality"
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pixi-version: v0.42.1
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cache: false # no pixi.lock
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locked: false
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- name: Check formatting
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shell: bash -el {0}
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run: black --check --diff .
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- name: Run black
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run: pixi run -e quality format --check --diff .
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- name: Comment PR
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if: github.event_name == 'pull_request' && failure()
@@ -38,181 +39,103 @@ jobs:
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message: "Please format your code with [black](https://black.readthedocs.io): `black snakemake tests/*.py`."
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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testing:
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################################################################################################
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# Testing: Run tests using Pixi
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################################################################################################
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tests:
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if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
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strategy:
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fail-fast: false
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matrix:
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test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
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py_ver:
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- "3.11"
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- "3.12"
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# see pyprojec.toml: [tool.pixi.feature.test] for available test types
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os: [ubuntu-latest, windows-latest] # macos-latest, macos-13 not supported yet
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env: ["py311", "py312"]
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shell:
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- bash
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#- dash # for py 3.12 also test dash as default shell (snakemake will still use bash for shell commands)
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exclude: []
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#- shell: dash
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# py_ver: "3.11"
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runs-on: ubuntu-latest
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needs: formatting
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runs-on: ${{ matrix.os }}
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env:
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AWS_AVAILABLE: "${{ secrets.AWS_ACCESS_KEY_ID }}"
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GCP_AVAILABLE: "${{ secrets.GCP_SA_KEY }}"
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ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}"
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CI: true
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Modify python version in test env
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shell: bash -el {0}
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run: |
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cp test-environment.yml test-environment-${{ matrix.py_ver }}.yml
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sed -E -i 's/- python.+/- python =${{ matrix.py_ver }}/' test-environment-${{ matrix.py_ver }}.yml
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- name: Setup snakemake environment
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uses: conda-incubator/setup-miniconda@v3
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- name: Install Pixi
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uses: prefix-dev/[email protected]
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with:
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miniforge-version: latest
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environment-file: test-environment-${{ matrix.py_ver }}.yml
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environment-name: snakemake
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auto-update-conda: true
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- name: Install snakemake from source
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shell: bash -el {0}
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run: |
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conda config --set channel_priority strict
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pip install -e .
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# - name: Configure fast APT mirror
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# uses: vegardit/[email protected]
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- name: Setup apt dependencies
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run: |
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sudo add-apt-repository -y ppa:apptainer/ppa
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sudo apt-get update
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sudo apt install -y git wget openmpi-bin libopenmpi-dev apptainer dash
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environments: ${{ matrix.env }}
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pixi-version: v0.42.1
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cache: false # no pixi.lock
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locked: false
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# See https://github.com/apptainer/apptainer/pull/2262
96-
- name: Disable apparmor namespace restrictions for apptainer
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- name: Disable apparmor namespace restrictions for apptainer (os='Linux')
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if: runner.os == 'Linux'
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run: |
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sudo sh -c 'echo kernel.apparmor_restrict_unprivileged_userns=0 \
9983
>/etc/sysctl.d/90-disable-userns-restrictions.conf'
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sudo sysctl -p /etc/sysctl.d/90-disable-userns-restrictions.conf
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- name: Setup minio
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- name: Setup MinIO for AWS S3 testing (os='Linux', for AWS S3 testing)
87+
if: runner.os == 'Linux'
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uses: comfuture/minio-action@v1
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with:
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access_key: minio
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secret_key: minio123
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port: 9000
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109-
- name: Test minio
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- name: Test MinIO (os='Linux')
95+
if: runner.os == 'Linux'
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run: |
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export AWS_ACCESS_KEY_ID=minio
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export AWS_SECRET_ACCESS_KEY=minio123
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export AWS_EC2_METADATA_DISABLED=true
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aws --endpoint-url http://127.0.0.1:9000/ s3 mb s3://test
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- name: Test local
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env:
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CI: true
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ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}"
120-
#PYTHONTRACEMALLOC: 10
121-
shell: bash -el {0}
102+
- name: Run Tests for Linux (os= 'Linux')
103+
if: runner.os == 'Linux'
122104
run: |
123-
if [ "${{ matrix.shell }}" == "dash" ]; then
124-
sudo chsh -s /usr/bin/dash $(whoami)
125-
fi
126-
127-
pytest -v -x --show-capture=stderr \
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--splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration \
129-
tests/tests.py \
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tests/tests_using_conda.py \
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tests/test_expand.py \
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tests/test_io.py \
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tests/test_schema.py \
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tests/test_linting.py \
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tests/test_executor_test_suite.py \
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tests/test_api.py \
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tests/test_internals.py
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139-
- name: Run tests/test_report/Snakefile to generate report
140-
shell: bash -el {0}
105+
pixi run --environment ${{matrix.env}} test-all \
106+
--splits 10 \
107+
--group ${{ matrix.test_group }} \
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--splitting-algorithm=least_duration
109+
110+
- name: Run Tests for Windows (os='Windows')
111+
if: runner.os == 'Windows'
141112
run: |
142-
cd tests/test_report
143-
snakemake --use-conda --cores 1 --report report.zip
113+
pixi run --environment ${{matrix.env}} test-simple --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration
144114
145-
- name: List directory structure
115+
- name: Run Report Generation Tests (os='Linux')
116+
if: runner.os == 'Linux'
117+
shell: bash -el {0}
146118
run: |
147-
ls -R
148-
149-
- name: Upload report
150-
if: ${{ matrix.test_group == 1 && matrix.shell == 'dash'}}
151-
uses: actions/upload-artifact@v4
152-
with:
153-
name: report-${{ matrix.py_ver }}.zip
154-
path: tests/test_report/report.zip
119+
cd tests/test_report
120+
pixi run -e ${{ matrix.env }} snakemake \
121+
--use-conda \
122+
--cores 1 \
123+
--report report.zip
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156125
build-container-image:
157126
if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
158127
runs-on: ubuntu-latest
159-
needs: testing
128+
needs: tests
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steps:
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- uses: actions/checkout@v4
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163132
- name: Build container image
164133
run: docker build .
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testing-windows:
167-
if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
168-
strategy:
169-
matrix:
170-
test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
171-
runs-on: windows-latest
172-
needs: formatting
173-
steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
177-
- name: Remove unix-only dependencies
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shell: python
179-
run: |
180-
import fileinput
181-
excluded_on_win = [ "environment-modules",
182-
"cwltool",
183-
"cwl-utils",
184-
"apptainer",
185-
"squashfuse",
186-
"stress-ng" ]
187-
for line in fileinput.input("test-environment.yml", inplace=True):
188-
if all(pkg not in line for pkg in excluded_on_win):
189-
print(line, end="")
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191-
- name: Setup snakemake environment
192-
uses: conda-incubator/setup-miniconda@v3
193-
with:
194-
miniforge-version: latest
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environment-file: test-environment.yml
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environment-name: snakemake
197-
auto-update-conda: true
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199-
- name: Install snakemake from source
200-
run: |
201-
202-
pip install .
203-
204-
- name: Run tests
205-
env:
206-
CI: true
207-
ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}"
208-
run: |
209-
python -m pytest --show-capture=stderr -v -x --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration tests/tests.py
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211135
testing-done:
212136
if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
213137
needs:
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- testing
215-
- testing-windows
138+
- tests
216139
runs-on: ubuntu-latest
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steps:
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- run: echo "All tests passed."
141+
- run: echo "All tests passed."

‎.gitignore‎

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@@ -31,3 +31,8 @@ playground/*
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tutorial/*
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snakemake/assets/data
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# pixi environments
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.pixi
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*.egg-info
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pixi.lock

‎apidocs/requirements.txt‎

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@@ -9,4 +9,5 @@ appdirs
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sphinxawesome-theme
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snakemake-interface-common
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snakemake-interface-executor-plugins
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snakemake-interface-storage-plugins
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snakemake-interface-storage-plugins
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snakemake-interface-logger-plugins

‎doc-environment.yml‎

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@@ -19,6 +19,7 @@ dependencies:
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- snakemake-interface-executor-plugins >=9.1.0
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- snakemake-interface-storage-plugins >=3.2.3
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- sphinx-argparse
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- sphinx-tabs
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- sphinx_rtd_theme
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- sphinxawesome-theme
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- docutils

‎docs/_static/custom.css‎

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code {
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font-family: monospace !important;
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}
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/* Dark mode styles for Sphinx tabs */
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html.dark .sphinx-tabs .sphinx-tabs-tab {
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background-color: #333 !important;
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color: #fff !important;
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border-color: #555 !important;
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}
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html.dark .sphinx-tabs .sphinx-tabs-tab[aria-selected="true"] {
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background-color: #444 !important;
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border-bottom-color: #444 !important;
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}
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html.dark .sphinx-tabs-panel {
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background-color: #333 !important;
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color: #fff !important;
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border-color: #555 !important;
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}

‎docs/conf.py‎

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"sphinx.ext.napoleon",
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"sphinxarg.ext",
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"sphinx.ext.autosectionlabel",
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"sphinx_tabs.tabs",
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"myst_parser",
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]
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‎docs/requirements.txt‎

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sphinx >=3
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sphinxcontrib-napoleon
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sphinx-argparse
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sphinx-tabs
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docutils
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myst-parser
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configargparse
@@ -11,4 +12,5 @@ snakemake-interface-common
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snakemake-interface-executor-plugins
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snakemake-interface-storage-plugins
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snakemake-interface-report-plugins
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snakemake-interface-logger-plugins
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humanfriendly

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