diff --git a/.github/additional_files/environment.yml b/.github/additional_files/environment.yml index d45db0c4..ffcc5570 100644 --- a/.github/additional_files/environment.yml +++ b/.github/additional_files/environment.yml @@ -1,7 +1,9 @@ -name: SPARCSminimal +name: base channels: - conda-forge dependencies: + - numpy==1.26.4 + - numba - pip: - affine==2.4.0 - aicspylibczi==3.1.2 @@ -21,7 +23,6 @@ dependencies: - click==8.1.7 - click-plugins==1.1.1 - cligj==0.7.2 - - cloudpickle==3.0.0 - colorama==0.4.6 - contextlib2==21.6.0 - contourpy==1.2.1 @@ -59,9 +60,7 @@ dependencies: - multidict==6.0.5 - natsort==8.4.0 - networkx==3.3 - - numba==0.59.1 - numcodecs==0.12.1 - - numpy==1.26.4 - ome-zarr==0.9.0 - opencv-python==4.9.0.80 - opencv-python-headless==4.9.0.80 @@ -111,4 +110,5 @@ dependencies: - yarl==1.9.4 - zarr==2.18.2 - zict==3.0.0 - - zipp==3.19.0 \ No newline at end of file + - zipp==3.19.0 + - xarray==2024.5.0 \ No newline at end of file diff --git a/.github/workflows/generate_documentation.yml b/.github/workflows/generate_documentation.yml index 8876117e..c97cf9c3 100644 --- a/.github/workflows/generate_documentation.yml +++ b/.github/workflows/generate_documentation.yml @@ -22,7 +22,16 @@ jobs: echo $CONDA/bin >> $GITHUB_PATH - name: Install Dependencies with Mamba run: | - conda env update -n base --file .github/additional_files/environment.yml + conda env update -n base --file .github/additional_files/environment.yml - name: Install Repository Module run: | pip install ./ + - name: Install Sphinx and additional dependences + run: | + pip install sphinx sphinx-rtd-theme sphinx-autodoc-typehints sphinx-argparse nbsphinx renku-sphinx-theme + - name: Generate Documentation + run: | + cd docs_source + make clean + make html + \ No newline at end of file diff --git a/.github/workflows/unit_test.yml b/.github/workflows/unit_test.yml index 10ce296a..86ffda39 100644 --- a/.github/workflows/unit_test.yml +++ b/.github/workflows/unit_test.yml @@ -20,7 +20,7 @@ jobs: echo $CONDA/bin >> $GITHUB_PATH - name: Install dependencies run: | - conda env update --file .github/additional_files/environment.yml --name base + conda env update --file .github/additional_files/environment.yml --name SPARCSpy - name: Test with pytest run: | conda install pytest