Documentation update

ScalableCytometryImageProcessing · Nov 2, 2022 · 22cfb7c · 22cfb7c
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diff --git a/README.md b/README.md
@@ -8,19 +8,26 @@ Scalable Cytometry Image Processing (SCIP) is an open-source tool that implement
 an image processing pipeline on top of Dask, a distributed computing framework written in Python.
 SCIP performs normalization, image segmentation and masking, and feature extraction.
 
-Check the docs for installation and usage instructions.
+Check the [docs](https://readthedocs.org/projects/scalable-cytometry-image-processing) for
+installation and usage instructions, and API documentation.
 
 ## Development
 
 ### Generating documentation
+
+For publishing online:
 ```
 cd docs
-rm -r source/generated/
-sphinx-apidoc -f -T -o source/generated/ ../src/scip
 make clean
 make html
 ```
 
+For development with live reloading:
+```
+cd docs
+make livehtml
+```
+
 ### Generate release changelog
 ```
 git log v{previous version tag}..HEAD --oneline | xclip -sel clip

diff --git a/docs/Makefile b/docs/Makefile
@@ -5,6 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
+SPHINXAPIDOC  = sphinx-apidoc
 SOURCEDIR     = source
 BUILDDIR      = build
 
@@ -14,10 +15,14 @@ help:
 
 .PHONY: help Makefile
 
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
+html: api
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-livehtml:
-	sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+api:
+	@$(SPHINXAPIDOC) -f -T -M -o "$(SOURCEDIR)/generated" ../src/scip
+
+livehtml: api
+	sphinx-autobuild --watch ../src "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -r "$(SOURCEDIR)/generated" $(BUILDDIR)
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -28,9 +28,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
     'sphinx.ext.napoleon',
-    'sphinx.ext.autosummary',
     'sphinx_copybutton'
 ]
 

diff --git a/docs/source/generated/scip.export.rst b/docs/source/generated/scip.export.rst
@@ -1,6 +1,11 @@
 scip.export package
 ===================
 
+.. automodule:: scip.export
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -19,11 +24,3 @@ scip.export.parquet module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.export
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.features.rst b/docs/source/generated/scip.features.rst
@@ -1,6 +1,11 @@
 scip.features package
 =====================
 
+.. automodule:: scip.features
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -20,6 +25,14 @@ scip.features.intensity module
    :undoc-members:
    :show-inheritance:
 
+scip.features.raw\_intensity module
+-----------------------------------
+
+.. automodule:: scip.features.raw_intensity
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 scip.features.shape module
 --------------------------
 
@@ -35,11 +48,3 @@ scip.features.texture module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.features
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.filter.rst b/docs/source/generated/scip.filter.rst
@@ -1,6 +1,11 @@
 scip.filter package
 ===================
 
+.. automodule:: scip.filter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -11,11 +16,3 @@ scip.filter.threshold module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.filter
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.illumination_correction.rst b/docs/source/generated/scip.illumination_correction.rst
@@ -1,6 +1,11 @@
 scip.illumination\_correction package
 =====================================
 
+.. automodule:: scip.illumination_correction
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -11,11 +16,3 @@ scip.illumination\_correction.jones\_2006 module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.illumination_correction
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.loading.rst b/docs/source/generated/scip.loading.rst
@@ -1,6 +1,11 @@
 scip.loading package
 ====================
 
+.. automodule:: scip.loading
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -43,11 +48,3 @@ scip.loading.zarr module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.loading
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.masking.filters.rst b/docs/source/generated/scip.masking.filters.rst
@@ -0,0 +1,34 @@
+scip.masking.filters package
+============================
+
+.. automodule:: scip.masking.filters
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+scip.masking.filters.normaltest module
+--------------------------------------
+
+.. automodule:: scip.masking.filters.normaltest
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scip.masking.filters.std module
+-------------------------------
+
+.. automodule:: scip.masking.filters.std
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+scip.masking.filters.value\_range module
+----------------------------------------
+
+.. automodule:: scip.masking.filters.value_range
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/generated/scip.masking.rst b/docs/source/generated/scip.masking.rst
@@ -1,6 +1,19 @@
 scip.masking package
 ====================
 
+.. automodule:: scip.masking
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   scip.masking.filters
+
 Submodules
 ----------
 
@@ -12,42 +25,42 @@ scip.masking.circle module
    :undoc-members:
    :show-inheritance:
 
-scip.masking.sobel module
--------------------------
+scip.masking.li module
+----------------------
 
-.. automodule:: scip.masking.sobel
+.. automodule:: scip.masking.li
    :members:
    :undoc-members:
    :show-inheritance:
 
-scip.masking.spot module
+scip.masking.otsu module
 ------------------------
 
-.. automodule:: scip.masking.spot
+.. automodule:: scip.masking.otsu
    :members:
    :undoc-members:
    :show-inheritance:
 
-scip.masking.threshold module
------------------------------
+scip.masking.sobel module
+-------------------------
 
-.. automodule:: scip.masking.threshold
+.. automodule:: scip.masking.sobel
    :members:
    :undoc-members:
    :show-inheritance:
 
-scip.masking.watershed module
------------------------------
+scip.masking.spot module
+------------------------
 
-.. automodule:: scip.masking.watershed
+.. automodule:: scip.masking.spot
    :members:
    :undoc-members:
    :show-inheritance:
 
-Module contents
----------------
+scip.masking.watershed module
+-----------------------------
 
-.. automodule:: scip.masking
+.. automodule:: scip.masking.watershed
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/source/generated/scip.normalization.rst b/docs/source/generated/scip.normalization.rst
@@ -1,6 +1,11 @@
 scip.normalization package
 ==========================
 
+.. automodule:: scip.normalization
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -11,11 +16,3 @@ scip.normalization.quantile\_normalization module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.normalization
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.projection.rst b/docs/source/generated/scip.projection.rst
@@ -1,6 +1,11 @@
 scip.projection package
 =======================
 
+.. automodule:: scip.projection
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
@@ -11,11 +16,3 @@ scip.projection.op module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip.projection
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/generated/scip.rst b/docs/source/generated/scip.rst
@@ -1,6 +1,11 @@
 scip package
 ============
 
+.. automodule:: scip
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Subpackages
 -----------
 
@@ -28,11 +33,3 @@ scip.main module
    :members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: scip
-   :members:
-   :undoc-members:
-   :show-inheritance: