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ci: Use --no-build-isolation to instal cgat #77

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ci: Use --no-build-isolation to instal cgat #77

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b1dd115
ci: Use --no-build-isolation to install cgat
ns-rse Nov 27, 2024
e26cf63
ci: install cgat from GitHub v0.7.4
ns-rse Nov 27, 2024
d858c9f
ci: Remove Windows from os matrix of tests.yaml
ns-rse Nov 27, 2024
a0c94e5
ci: trying newer cgatcore package setup
ns-rse Nov 28, 2024
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9 changes: 8 additions & 1 deletion .github/workflows/sphinx_docs_to_gh_pages.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,14 @@ jobs:
python-version: 3.11
- name: Installing the Documentation requirements
run: |
pip3 install .[docs]
# Install build dependencies for now (see
# https://github.com/cgat-developers/cgat-apps/issues/134#issuecomment-2503431974)
pip install numpy
pip install Cython
pip install pysam
pip install wheel
pip install --no-build-isolation git+https://github.com/cgat-developers/cgat-apps@AC-modifybuild
pip3 install --no-build-isolation .[docs]
- name: Running Sphinx to gh-pages Action
# Uncomment if only tagged releases are to have documentation built
# if: startsWith(github.ref, 'refs/tags')
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14 changes: 9 additions & 5 deletions .github/workflows/tests.yaml
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Expand Up @@ -27,7 +27,7 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest", "macos-latest", "windows-latest"]
os: ["ubuntu-latest", "macos-latest"] # "windows-latest"]
python-version: ["3.9", "3.10", "3.11", "3.12"]
steps:
- uses: actions/checkout@v4
Expand All @@ -40,11 +40,15 @@ jobs:
pip install --upgrade virtualenv
pip install --upgrade pip setuptools
virtualenv --upgrade-embed-wheels
# Install build dependencies for now (see
# https://github.com/cgat-developers/cgat-apps/issues/134#issuecomment-2503431974)
pip install numpy
pip show numpy
pip install cgatcore
pip install cgat
pip install -e .[tests]
pip install Cython
pip install pysam
pip install wheel
pip install --no-build-isolation cgatcore
pip install --no-build-isolation git+https://github.com/cgat-developers/cgat-apps@AC-modifybuild
pip install --no-build-isolation -e .[tests]
- name: Test with pytest
run: |
pytest --cov=isoslam --cov-report=xml --mpl -x
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