use docval

Makefile

@@ -32,7 +32,7 @@ build_frontend:
 docs:
 	rm -rf docs/_build/
 	# pip install -e '.[doc]'
-	# sphinx-apidoc -f -o ./docs/_build/modules ./studio
+	sphinx-apidoc -f --no-toc -o ./docs/modules ./studio
 	sphinx-autobuild -b html docs docs/_build --port 8001
 
 .PHONY: dockerhub

docs/conf.py

@@ -5,6 +5,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 import os
+import sys
 from datetime import datetime
 
 # -- Path setup --------------------------------------------------------------
@@ -14,6 +15,8 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 
+sys.path.insert(0, os.path.abspath("../studio"))
+
 
 # -- Project information -----------------------------------------------------
 project = "OptiNiSt"
@@ -94,3 +97,45 @@
     "includehidden": True,
     "titles_only": False,
 }
+
+
+# include_modules = [
+#     # CaImAn
+#     "caiman_cnmf",
+#     "caiman_cnmfe",
+#     "caiman_mc",
+#     "foobar",
+#     # Suite2p
+#     "suite2p_file_convert",
+#     "suite2p_registration",
+#     "suite2p_roi",
+#     "suite2p_spike_deconv",
+#     # LCCD
+#     "lccd_detect",
+#     # OptiNiSt: Basic neural analysis
+#     "ETA",
+#     # OptiNiSt: Dimension reduction
+#     "CCA",
+#     "dpca_fit",
+#     "PCA",
+#     "TSNE",
+#     # OptiNiSt: Neural decoding
+#     "GLM",
+#     "LDA",
+#     "SVM",
+#     # OptiNiSt: Neural population analysis
+#     "correlation",
+#     "cross_correlation",
+#     "Granger",
+# ]
+
+
+# def skip(app, what, name, obj, would_skip, options):
+#     if name in include_modules:
+#         return False
+#     else:
+#         return True
+
+
+# def setup(app):
+#     app.connect("autodoc-skip-member", skip)

docs/modules/studio.app.common.core.auth.rst

@@ -0,0 +1,45 @@
+studio.app.common.core.auth package
+===================================
+
+Submodules
+----------
+
+studio.app.common.core.auth.auth module
+---------------------------------------
+
+.. automodule:: studio.app.common.core.auth.auth
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.auth.auth\_config module
+-----------------------------------------------
+
+.. automodule:: studio.app.common.core.auth.auth_config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.auth.auth\_dependencies module
+-----------------------------------------------------
+
+.. automodule:: studio.app.common.core.auth.auth_dependencies
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.auth.security module
+-------------------------------------------
+
+.. automodule:: studio.app.common.core.auth.security
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: studio.app.common.core.auth
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/modules/studio.app.common.core.experiment.rst

@@ -0,0 +1,53 @@
+studio.app.common.core.experiment package
+=========================================
+
+Submodules
+----------
+
+studio.app.common.core.experiment.experiment module
+---------------------------------------------------
+
+.. automodule:: studio.app.common.core.experiment.experiment
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.experiment.experiment\_builder module
+------------------------------------------------------------
+
+.. automodule:: studio.app.common.core.experiment.experiment_builder
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.experiment.experiment\_reader module
+-----------------------------------------------------------
+
+.. automodule:: studio.app.common.core.experiment.experiment_reader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.experiment.experiment\_utils module
+----------------------------------------------------------
+
+.. automodule:: studio.app.common.core.experiment.experiment_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.experiment.experiment\_writer module
+-----------------------------------------------------------
+
+.. automodule:: studio.app.common.core.experiment.experiment_writer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: studio.app.common.core.experiment
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/modules/studio.app.common.core.rst

@@ -0,0 +1,43 @@
+studio.app.common.core package
+==============================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   studio.app.common.core.auth
+   studio.app.common.core.experiment
+   studio.app.common.core.rules
+   studio.app.common.core.snakemake
+   studio.app.common.core.users
+   studio.app.common.core.utils
+   studio.app.common.core.workflow
+
+Submodules
+----------
+
+studio.app.common.core.logger module
+------------------------------------
+
+.. automodule:: studio.app.common.core.logger
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.mode module
+----------------------------------
+
+.. automodule:: studio.app.common.core.mode
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: studio.app.common.core
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/modules/studio.app.common.core.rules.rst

@@ -0,0 +1,45 @@
+studio.app.common.core.rules package
+====================================
+
+Submodules
+----------
+
+studio.app.common.core.rules.data module
+----------------------------------------
+
+.. automodule:: studio.app.common.core.rules.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.rules.file\_writer module
+------------------------------------------------
+
+.. automodule:: studio.app.common.core.rules.file_writer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.rules.func module
+----------------------------------------
+
+.. automodule:: studio.app.common.core.rules.func
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.rules.runner module
+------------------------------------------
+
+.. automodule:: studio.app.common.core.rules.runner
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: studio.app.common.core.rules
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/modules/studio.app.common.core.snakemake.rst

@@ -0,0 +1,69 @@
+studio.app.common.core.snakemake package
+========================================
+
+Submodules
+----------
+
+studio.app.common.core.snakemake.smk module
+-------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.smk
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.snakemake.smk\_builder module
+----------------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.smk_builder
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.snakemake.smk\_utils module
+--------------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.smk_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.snakemake.snakemake\_executor module
+-----------------------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.snakemake_executor
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.snakemake.snakemake\_reader module
+---------------------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.snakemake_reader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.snakemake.snakemake\_rule module
+-------------------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.snakemake_rule
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+studio.app.common.core.snakemake.snakemake\_writer module
+---------------------------------------------------------
+
+.. automodule:: studio.app.common.core.snakemake.snakemake_writer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: studio.app.common.core.snakemake
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/modules/studio.app.common.core.users.rst

@@ -0,0 +1,21 @@
+studio.app.common.core.users package
+====================================
+
+Submodules
+----------
+
+studio.app.common.core.users.crud\_users module
+-----------------------------------------------
+
+.. automodule:: studio.app.common.core.users.crud_users
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: studio.app.common.core.users
+   :members:
+   :undoc-members:
+   :show-inheritance: