docs: 📝 Build docs

README.md

@@ -1,6 +1,6 @@
 <img src="https://raw.githubusercontent.com/janelia-cellmap/dacapo/main/docs/source/_static/CellMapLogo.png" alt="CellMap logo" width="85%">
 
-# cellmap-data
+# CellMap-Data
 
 <!-- [![License](https://img.shields.io/pypi/l/cellmap-data.svg?color=green)](https://github.com/janelia-cellmap/cellmap-data/blob/main/LICENSE)
 [![PyPI](https://img.shields.io/pypi/v/cellmap-data.svg?color=green)](https://pypi.org/project/cellmap-data)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.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 $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/build_docs.sh

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+sphinx-apidoc -o ./source ../src/
+make clean
+make html
+# sphinx-build -M coverage source build

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/cellmap_data.CellMapDataLoader.rst

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+cellmap\_data.CellMapDataLoader
+===============================
+
+.. currentmodule:: cellmap_data
+
+.. autoclass:: CellMapDataLoader
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CellMapDataLoader.__init__
+      ~CellMapDataLoader.collate_fn
+      ~CellMapDataLoader.refresh
+
+
+
+
+
+

docs/source/cellmap_data.CellMapDataSplit.rst

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+cellmap\_data.CellMapDataSplit
+==============================
+
+.. currentmodule:: cellmap_data
+
+.. autoclass:: CellMapDataSplit
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CellMapDataSplit.__init__
+      ~CellMapDataSplit.construct
+      ~CellMapDataSplit.from_csv
+      ~CellMapDataSplit.set_arrays
+      ~CellMapDataSplit.set_raw_value_transforms
+      ~CellMapDataSplit.set_spatial_transforms
+      ~CellMapDataSplit.set_target_value_transforms
+      ~CellMapDataSplit.verify_datasets
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~CellMapDataSplit.class_counts
+      ~CellMapDataSplit.train_datasets_combined
+      ~CellMapDataSplit.validation_blocks
+      ~CellMapDataSplit.validation_datasets_combined
+
+

docs/source/cellmap_data.CellMapDataset.rst

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+cellmap\_data.CellMapDataset
+============================
+
+.. currentmodule:: cellmap_data
+
+.. autoclass:: CellMapDataset
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CellMapDataset.__init__
+      ~CellMapDataset.generate_spatial_transforms
+      ~CellMapDataset.get_empty_store
+      ~CellMapDataset.get_indices
+      ~CellMapDataset.get_label_array
+      ~CellMapDataset.get_target_array
+      ~CellMapDataset.reset_arrays
+      ~CellMapDataset.set_raw_value_transforms
+      ~CellMapDataset.set_target_value_transforms
+      ~CellMapDataset.to
+      ~CellMapDataset.verify
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~CellMapDataset.bounding_box
+      ~CellMapDataset.bounding_box_shape
+      ~CellMapDataset.center
+      ~CellMapDataset.class_counts
+      ~CellMapDataset.class_weights
+      ~CellMapDataset.device
+      ~CellMapDataset.largest_voxel_sizes
+      ~CellMapDataset.sampling_box
+      ~CellMapDataset.sampling_box_shape
+      ~CellMapDataset.size
+      ~CellMapDataset.validation_indices
+
+

docs/source/cellmap_data.CellMapImage.rst

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+cellmap\_data.CellMapImage
+==========================
+
+.. currentmodule:: cellmap_data
+
+.. autoclass:: CellMapImage
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CellMapImage.__init__
+      ~CellMapImage.apply_spatial_transforms
+      ~CellMapImage.find_level
+      ~CellMapImage.return_data
+      ~CellMapImage.rotate_coords
+      ~CellMapImage.set_spatial_transforms
+      ~CellMapImage.to
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~CellMapImage.array
+      ~CellMapImage.array_path
+      ~CellMapImage.bg_count
+      ~CellMapImage.bounding_box
+      ~CellMapImage.center
+      ~CellMapImage.class_counts
+      ~CellMapImage.coordinateTransformations
+      ~CellMapImage.full_coords
+      ~CellMapImage.group
+      ~CellMapImage.multiscale_attrs
+      ~CellMapImage.sampling_box
+      ~CellMapImage.scale_level
+      ~CellMapImage.shape
+      ~CellMapImage.translation
+
+

docs/source/cellmap_data.CellMapMultiDataset.rst

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+cellmap\_data.CellMapMultiDataset
+=================================
+
+.. currentmodule:: cellmap_data
+
+.. autoclass:: CellMapMultiDataset
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CellMapMultiDataset.__init__
+      ~CellMapMultiDataset.cumsum
+      ~CellMapMultiDataset.get_indices
+      ~CellMapMultiDataset.get_subset_random_sampler
+      ~CellMapMultiDataset.get_weighted_sampler
+      ~CellMapMultiDataset.set_raw_value_transforms
+      ~CellMapMultiDataset.set_spatial_transforms
+      ~CellMapMultiDataset.set_target_value_transforms
+      ~CellMapMultiDataset.to
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~CellMapMultiDataset.class_counts
+      ~CellMapMultiDataset.class_weights
+      ~CellMapMultiDataset.cummulative_sizes
+      ~CellMapMultiDataset.dataset_weights
+      ~CellMapMultiDataset.sample_weights
+      ~CellMapMultiDataset.validation_indices
+      ~CellMapMultiDataset.datasets
+      ~CellMapMultiDataset.cumulative_sizes
+
+

docs/source/cellmap_data.CellMapSubset.rst

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+cellmap\_data.CellMapSubset
+===========================
+
+.. currentmodule:: cellmap_data
+
+.. autoclass:: CellMapSubset
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~CellMapSubset.__init__
+      ~CellMapSubset.set_raw_value_transforms
+      ~CellMapSubset.set_target_value_transforms
+      ~CellMapSubset.to
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~CellMapSubset.class_counts
+      ~CellMapSubset.class_weights
+      ~CellMapSubset.classes
+      ~CellMapSubset.validation_indices
+      ~CellMapSubset.dataset
+      ~CellMapSubset.indices
+
+

docs/source/cellmap_data.dataloader.rst

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+cellmap\_data.dataloader
+========================
+
+.. automodule:: cellmap_data.dataloader
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      CellMapDataLoader
+

docs/source/cellmap_data.dataset.rst

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+cellmap\_data.dataset
+=====================
+
+.. automodule:: cellmap_data.dataset
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      split_target_path
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      CellMapDataset
+

docs/source/cellmap_data.datasplit.rst

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+cellmap\_data.datasplit
+=======================
+
+.. automodule:: cellmap_data.datasplit
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      CellMapDataSplit
+

docs/source/cellmap_data.image.rst

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+cellmap\_data.image
+===================
+
+.. automodule:: cellmap_data.image
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      CellMapImage
+      EmptyImage
+

docs/source/cellmap_data.multidataset.rst

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+cellmap\_data.multidataset
+==========================
+
+.. automodule:: cellmap_data.multidataset
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      CellMapMultiDataset
+