Merge pull request #148 from Dana-Farber-AIOS/readthedocs

Fix readthedocs build

.readthedocs.yaml

@@ -12,4 +12,4 @@ sphinx:
     fail_on_warning: false
 
 conda:
-    environment: environment.yml
+    environment: docs/env_readthedocs.yml

docs/env_readthedocs.yml

@@ -0,0 +1,37 @@
+# same as the main environment.yml, but without openslide or spams (which have C dependencies)
+# see: https://docs.readthedocs.io/en/stable/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
+
+name: pathml
+
+channels:
+    - conda-forge
+    - pytorch
+
+dependencies:
+    - pip==21.2.1
+    - python==3.8
+    - numpy>=1.16.4,<1.19.0
+    - scipy>=1.5.4
+    - scikit-image>=0.16.2
+    - matplotlib==3.1.3
+    - openjdk==8.0.152
+    - pytorch==1.9.0
+    - h5py==3.1.0
+    - dask==2021.7.1
+    - pydicom==2.1.2
+    - pytest>=6.2.2
+    - pre-commit==2.13.0
+    - pip:
+        - opencv-contrib-python==4.5.3.56
+        - javabridge==1.0.19
+        - python-bioformats==4.0.0
+        - scanpy==1.7.2
+        - anndata==0.7.4
+        - deepcell>=0.9.0
+        - cellpose>=0.6.1
+        - tensorly==0.6.0
+        - ipython>=7.20.0
+        - sphinx>=3.4.3
+        - nbsphinx>=0.8.1
+        - nbsphinx-link>=1.3.0
+        - sphinx-rtd-theme>=0.5.1

docs/source/conf.py

@@ -80,6 +80,10 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
+# mocking imports which require C extension for readthedocs builds
+# see: https://docs.readthedocs.io/en/stable/faq.html#i-get-import-errors-on-libraries-that-depend-on-c-modules
+autodoc_mock_imports = ["openslide", "spams"]
+
 
 def setup(app):
     app.add_css_file('css/pathml.css')