update workflows

.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
+      - zipp==3.19.0
+      - xarray==2024.5.0

.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
+      

.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