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Documentation update
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‎README.md‎

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

‎docs/Makefile‎

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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SPHINXAPIDOC = sphinx-apidoc
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SOURCEDIR = source
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BUILDDIR = build
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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html: api
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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livehtml:
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sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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api:
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@$(SPHINXAPIDOC) -f -T -M -o "$(SOURCEDIR)/generated" ../src/scip
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livehtml: api
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sphinx-autobuild --watch ../src "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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clean:
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rm -r "$(SOURCEDIR)/generated" $(BUILDDIR)

‎docs/source/conf.py‎

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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.napoleon',
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'sphinx.ext.autosummary',
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'sphinx_copybutton'
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]
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‎docs/source/generated/scip.export.rst‎

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scip.export package
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===================
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.. automodule:: scip.export
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: scip.export
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/generated/scip.features.rst‎

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scip.features package
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=====================
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.. automodule:: scip.features
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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:undoc-members:
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:show-inheritance:
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scip.features.raw\_intensity module
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-----------------------------------
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.. automodule:: scip.features.raw_intensity
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:members:
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:undoc-members:
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:show-inheritance:
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scip.features.shape module
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--------------------------
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: scip.features
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/generated/scip.filter.rst‎

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scip.filter package
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===================
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.. automodule:: scip.filter
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: scip.filter
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/generated/scip.illumination_correction.rst‎

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scip.illumination\_correction package
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=====================================
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.. automodule:: scip.illumination_correction
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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Module contents
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---------------
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.. automodule:: scip.illumination_correction
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/generated/scip.loading.rst‎

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scip.loading package
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====================
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.. automodule:: scip.loading
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:members:
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:undoc-members:
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:show-inheritance:
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:members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: scip.loading
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/generated/scip.masking.filters.rst‎

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scip.masking.filters package
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============================
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.. automodule:: scip.masking.filters
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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scip.masking.filters.normaltest module
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--------------------------------------
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.. automodule:: scip.masking.filters.normaltest
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:members:
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:undoc-members:
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:show-inheritance:
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scip.masking.filters.std module
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-------------------------------
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.. automodule:: scip.masking.filters.std
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:members:
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:undoc-members:
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:show-inheritance:
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scip.masking.filters.value\_range module
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----------------------------------------
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.. automodule:: scip.masking.filters.value_range
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/generated/scip.masking.rst‎

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scip.masking package
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====================
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.. automodule:: scip.masking
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:members:
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:undoc-members:
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:show-inheritance:
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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scip.masking.filters
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Submodules
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----------
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scip.masking.sobel module
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-------------------------
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scip.masking.li module
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----------------------
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.. automodule:: scip.masking.sobel
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.. automodule:: scip.masking.li
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scip.masking.spot module
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scip.masking.otsu module
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------------------------
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.. automodule:: scip.masking.spot
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.. automodule:: scip.masking.otsu
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scip.masking.threshold module
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-----------------------------
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scip.masking.sobel module
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-------------------------
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.. automodule:: scip.masking.sobel
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scip.masking.watershed module
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-----------------------------
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scip.masking.spot module
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------------------------
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.. automodule:: scip.masking.spot
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Module contents
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scip.masking.watershed module
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-----------------------------
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.. automodule:: scip.masking.watershed
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:show-inheritance:

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