[REFACTOR] [METEOR-1119] Refactor overview / tiled acquisition code #1624
Workflow file for this run
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| # This workflow will install Python dependencies, and run a selection of tests from the Odemis repository. | |
| # The selection is picked such that they do not require a back-end and are known to pass with this github workflow. | |
| # Test cases that will pass with this workflow can be added to this document. | |
| # It uses the python 3 system interpreter to run test cases. | |
| name: Unit testing | |
| on: | |
| [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-20.04, ubuntu-22.04] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Odemis dependencies | |
| run: | | |
| sudo add-apt-repository ppa:delmic-soft/odemis | |
| sudo apt-get -y update | |
| sudo apt-get -y install python3-pil python3-yaml python3-serial python3-zmq \ | |
| python3-scipy python3-decorator \ | |
| python3-libtiff python3-comedilib python3-h5py libtiff5-dev python3-future \ | |
| python3-pkg-resources python3-netifaces python3-cairo python3-numpy python3-scipy \ | |
| python3-decorator python3-xdg python3-suds python3-matplotlib python3-opencv \ | |
| python3-wxgtk4.0 python3-serial python3-evdev python3-notify2 python3-psutil \ | |
| graphicsmagick cgroup-tools authbind python3-setuptools cython3 python3-pyro4-delmic | |
| sudo mkdir /var/run/odemisd | |
| sudo chmod a+rw /var/run/odemisd | |
| python3 setup.py build_ext --inplace | |
| - name: Run tests from odemis.dataio | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest discover -s src/odemis/dataio/test -p "*_test.py" --verbose | |
| - name: Run tests from odemis.acq.drift | |
| # Run this step if the previous step passed or failed, but not if it was canceled. | |
| # continue-on-error prevents the pipeline from failing, with this `if` the pipeline | |
| # still reports a fail, and the next steps are also executed. | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest discover -s src/odemis/acq/drift/test -p "*_test.py" --verbose | |
| - name: Run tests from odemis.util.conversion | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/conversion_test.py --verbose | |
| - name: Run tests from odemis.util.dataio | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/dataio_test.py --verbose | |
| - name: Run tests from odemis.util.filename | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/filename_test.py --verbose | |
| - name: Run tests from odemis.util.fluo | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/fluo_test.py --verbose | |
| - name: Run tests from odemis.util.graph | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/graph_test.py --verbose | |
| - name: Run tests from odemis.util.img | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/img_test.py --verbose | |
| - name: Run tests from odemis.util.linalg | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/linalg_test.py --verbose | |
| - name: Run tests from odemis.util.peak_local_max | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/peak_local_max_test.py --verbose | |
| - name: Run tests from odemis.util.peak | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/peak_test.py --verbose | |
| - name: Run tests from odemis.util.registration | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/registration_test.py --verbose | |
| - name: Run tests from odemis.util.spectrum | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/spectrum_test.py --verbose | |
| - name: Run tests from odemis.util.transform | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/transform_test.py --verbose | |
| - name: Run tests from odemis.util.units | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/units_test.py --verbose | |
| - name: Run tests from odemis.util.__init__.py | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/util/test/util_test.py --verbose | |
| - name: Run tests from odemis.acq.stitching except tiled_acq | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/acq/stitching/test/registrar_test.py --verbose | |
| python3 -m unittest src/odemis/acq/stitching/test/stitching_test.py --verbose | |
| python3 -m unittest src/odemis/acq/stitching/test/weaver_test.py --verbose | |
| - name: Run tests from odemis.acq.calibration | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/acq/test/calibration_test.py --verbose | |
| - name: Run tests from odemis.acq.feature | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/acq/test/feature_test.py --verbose | |
| - name: Run tests from odemis.gui.conf | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src.odemis.gui.conf.test.conf_test.AcquisitionConfigTest --verbose | |
| python3 -m unittest src.odemis.gui.conf.test.conf_test.CalibrationConfigTest --verbose | |
| python3 -m unittest src.odemis.gui.conf.test.conf_test.GeneralConfigTest.test_save --verbose | |
| python3 -m unittest src.odemis.gui.conf.test.conf_test.GeneralConfigTest.test_save_unicode --verbose | |
| python3 -m unittest src.odemis.gui.conf.test.conf_test.GeneralConfigTest.test_simple --verbose | |
| # test_default fails on CI, because the manual path does not exist on the server | |
| # python3 -m unittest src.odemis.gui.conf.test.conf_test.GeneralConfigTest.test_default --verbose | |
| - name: Run tests from odemis.gui.util.conversion | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/gui/util/test/conversion_test.py --verbose | |
| - name: Run tests from odemis.gui.win | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src/odemis/gui/win/test/acquisition_test.py --verbose | |
| - name: Run mocked tests from odemis.acq.fastem | |
| if: ${{ !cancelled() }} | |
| run: | | |
| export PYTHONPATH="$PWD/src:$PYTHONPATH" | |
| python3 -m unittest src.odemis.acq.test.fastem_test.TestFastEMAcquisitionTaskMock --verbose |