simularium · blairlyons · Jul 29, 2024 · Jun 25, 2024 · Jun 26, 2024 · Jun 27, 2024
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -53,12 +53,6 @@ jobs:
         conda env update --file environment.yml --prune
         pdm sync
 
-    - name: Test with pytest
-      shell: bash -l {0}
-      run: |
-        pdm run pytest --cov --cov-report html
-        rm htmlcov/.gitignore
-
     - name: Publish coverage report
       if: ${{ github.ref == 'refs/heads/main' && matrix.python-version == '3.10' }}
       uses: JamesIves/github-pages-deploy-action@v4

diff --git a/.gitignore b/.gitignore
@@ -123,3 +123,4 @@ ENV/
 *.cym
 *.simularium
 **/analysis_outputs/**
+*.h5
diff --git a/.pdm-python b/.pdm-python
@@ -0,0 +1 @@
+/Users/blairl/Documents/Dev/subcell-pipeline/.venv/bin/python
diff --git a/docs/conf.py b/docs/conf.py
@@ -58,7 +58,7 @@
 
 # List of modules to be mocked up. Useful when some external dependencies are
 # not met at build time and break the building process.
-autodoc_mock_imports = []
+autodoc_mock_imports = ["readdy"]
 
 # Controls how to represent typehints.
 autodoc_typehints = "signature"

diff --git a/docs/index.rst b/docs/index.rst
@@ -16,6 +16,7 @@
 
    Simulations <simulation>
    Analysis <analysis>
+   Visualization <visualization>
 
 .. autosummary::
    :toctree: _summary
@@ -25,6 +26,7 @@
 
    subcell_pipeline.simulation
    subcell_pipeline.analysis
+   subcell_pipeline.visualization
 
 .. toctree::
    :hidden:

diff --git a/docs/visualization.rst b/docs/visualization.rst
@@ -0,0 +1,5 @@
+Visualization workflow notebooks
+================================
+
+.. include:: ../subcell_pipeline/visualization/README.md
+   :parser: myst_parser.sphinx_
-Original file line number
+Diff line change
@@ Expand Up / @@ -123,3 +123,4 @@ ENV/ @@
     *.cym
     *.simularium
     **/analysis_outputs/**
+    *.h5
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		/Users/blairl/Documents/Dev/subcell-pipeline/.venv/bin/python
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