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tests.yml
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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://github.com/Photon-HDF5/phconvert/files/231343/Cy3.Cy5_diff_PIE-FRET.ptu.zip
unzip Cy3.Cy5_diff_PIE-FRET.ptu.zip
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/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 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 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 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
cd ..
cd ..
- name: Test project
shell: bash -l {0}
run: |
pytest
cd notebooks
python ../tests/nbrun.py