Merge pull request #58 from harripd/master #5
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| name: Tests | |
| on: | |
| push: | |
| branch: | |
| - master | |
| - setuptools_scm | |
| pull_request: | |
| branch: | |
| - master | |
| jobs: | |
| build: | |
| runs-on: ${{matrix.os}} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-13, macos-14, ] | |
| python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] | |
| exclude: | |
| - os: macos-14 | |
| python-version: "3.7" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| # # - name: Setup Python ${{matrix.python-version}} | |
| # # uses: actions/setup-python@v4 | |
| # # with: | |
| # # python-version: ${{matrix.python-version}} | |
| # # - name: Upgrade pip | |
| # # run: python -m pip install --upgrade pip | |
| # # - name: Windows 3.6 Oddities | |
| # # if: matrix.python-version == 3.6 && runner.os == 'Windows' | |
| # # run: python -m pip install pwintypy==1.1.6 | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge | |
| python-version: ${{matrix.python-version}} | |
| activate-environment: test | |
| - name: Apple Silicon oddities | |
| if: matrix.os == 'macos-14' | |
| shell: bash -l {0} | |
| run: | | |
| brew install c-blosc hdf5 | |
| export HDF5_DIR=/opt/homebrew/opt/hdf5 | |
| export BLOSC_DIR=/opt/homebrew/opt/c-blosc | |
| # # - name: Install Conda (old fashioned way) | |
| # # if: matrix.os == 'macos-14' | |
| # # run: | | |
| # # wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh | |
| # # bash ~/miniconda.sh -b -p $HOME/miniconda | |
| # # export PATH="$HOME/miniconda/bin:$PATH" | |
| # # source $HOME/miniconda/bin/activate | |
| # # conda config --set always_yes yes --set changeps1 no | |
| # # conda init --all | |
| # # conda create -n test python=${{matrix.python-version}} | |
| # # conda activate test | |
| - name: Install Dependencies | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install setuptools build | |
| conda install numpy cython pytest pyyaml jupyter | |
| conda install pytables matplotlib pandas numba | |
| - name: Old Python dependencies | |
| if: matrix.python-version <= 3.9 | |
| shell: bash -l {0} | |
| run: pip install importlib_resources | |
| - name: build phconvert | |
| shell: bash -l {0} | |
| run: | | |
| pip install . | |
| - name: Download files Unix | |
| shell: bash -l {0} | |
| if: runner.os!= 'Windows' | |
| run: | | |
| cd notebooks/data | |
| wget https://ndownloader.figshare.com/files/3350666 -O dsdna_d7d17_50_50_1.set | |
| wget https://ndownloader.figshare.com/files/3350669 -O dsdna_d7d17_50_50_1.spc | |
| wget https://ndownloader.figshare.com/files/3350672 -O Pre.ht3 | |
| wget https://ndownloader.figshare.com/files/3350663 -O 0023uLRpitc_NTP_20dT_0.5GndCl.sm | |
| wget https://ndownloader.figshare.com/files/6955091 -O 161128_DM1_50pM_pH74.ptu | |
| wget https://ndownloader.figshare.com/files/14828594 -O 20161027_DM1_1nM_pH7_20MHz1.ptu | |
| wget https://ndownloader.figshare.com/files/13675271 -O TestFile_2.ptu | |
| wget https://ndownloader.figshare.com/files/14850533 -O trace_T2_300s_1_coincidence.ptu | |
| wget https://ndownloader.figshare.com/files/14890535 -O nanodiamant_histo.phu | |
| wget https://github.com/dwaithe/FCS_point_correlator/raw/master/focuspoint/topfluorPE_2_1_1_1.pt3 | |
| wget https://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip | |
| unzip Cy3.Cy5_diff_PIE-FRET.ptu.zip | |
| wget https://github.com/Photon-HDF5/phconvert/files/1380341/DNA_FRET_0.5nM.pt3.zip | |
| unzip DNA_FRET_0.5nM.pt3.zip | |
| wget https://github.com/Photon-HDF5/phconvert/files/1336330/data.zip | |
| unzip data.zip | |
| cd ../.. | |
| - name: Download files Windows | |
| shell: bash -l {0} | |
| if: runner.os == 'Windows' | |
| run: | | |
| cd notebooks/data | |
| curl.exe -L --output dsdna_d7d17_50_50_1.set --url https://ndownloader.figshare.com/files/3350666 | |
| curl.exe -L --output dsdna_d7d17_50_50_1.spc --url https://ndownloader.figshare.com/files/3350669 | |
| curl.exe -L --output Pre.ht3 --url https://ndownloader.figshare.com/files/3350672 | |
| curl.exe -L --output 0023uLRpitc_NTP_20dT_0.5GndCl.sm --url https://ndownloader.figshare.com/files/3350663 | |
| curl.exe -L --output 161128_DM1_50pM_pH74.ptu --url https://ndownloader.figshare.com/files/6955091 | |
| curl.exe -L --output 20161027_DM1_1nM_pH7_20MHz1.ptu --url https://ndownloader.figshare.com/files/14828594 | |
| curl.exe -L --output TestFile_2.ptu --url https://ndownloader.figshare.com/files/13675271 | |
| curl.exe -L --output trace_T2_300s_1_coincidence.ptu --url https://ndownloader.figshare.com/files/14850533 | |
| curl.exe -L --output nanodiamant_histo.phu --url https://ndownloader.figshare.com/files/14890535 | |
| curl.exe -L --output topfluorPE_2_1_1_1.pt3 --url https://github.com/dwaithe/FCS_point_correlator/raw/master/focuspoint/topfluorPE_2_1_1_1.pt3 | |
| curl.exe -L --output Cy3.Cy5_diff_PIE-FRET.ptu.zip --url https://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip | |
| 7z e Cy3.Cy5_diff_PIE-FRET.ptu.zip | |
| curl.exe -L --output DNA_FRET_0.5nM.pt3.zip --url https://github.com/Photon-HDF5/phconvert/files/1380341/DNA_FRET_0.5nM.pt3.zip | |
| 7z e DNA_FRET_0.5nM.pt3.zip | |
| curl.exe -L --output data.zip --url https://github.com/Photon-HDF5/phconvert/files/1336330/data.zip | |
| 7z e data.zip | |
| cd .. | |
| cd .. | |
| - name: Test project | |
| shell: bash -l {0} | |
| run: | | |
| pytest | |
| cd notebooks | |
| python ../tests/nbrun.py | |