Migration docs to Sphinx.

BodenmillerGroup · Mar 16, 2021 · 639ca51 · 639ca51
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Showing 15 changed files with 107 additions and 94 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -1,9 +1,11 @@
 name: docs
+
 on:
   push:
     branches:
       - master
   workflow_dispatch:
+
 jobs:
   docs:
     name: Documentation

diff --git a/README.md b/README.md
@@ -40,13 +40,3 @@ Created and maintained by Vito Zanotelli [[email protected]](mailto:vito.zan
 ## License
 
 [MIT](https://bodenmillergroup.github.io/imctools/LICENSE.html)
-
-## Contents
-
-```{toctree}
-quickstart
-api_reference
-CONTRIBUTING
-CHANGELOG
-LICENSE
-```
diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/source/_templates/autosummary/class.rst b/docs/source/_templates/autosummary/class.rst
diff --git a/docs/source/_templates/autosummary/module.rst b/docs/source/_templates/autosummary/module.rst
diff --git a/docs/source/api_reference.rst b/docs/source/api_reference.rst
@@ -1,20 +1,10 @@
 API reference
 =============
 
-.. autosummary::
-    :nosignatures:
-    :caption: API reference
-    :toctree: stubs
+.. toctree::
+    :maxdepth: 2
 
-    imctools.cli
-    imctools.converters
-    imctools.data
-    imctools.io
-
-..
-    Indices and tables
-    ==================
-
-    * :ref:`genindex`
-    * :ref:`modindex`
-    * :ref:`search`
+    imctools.cli.rst
+    imctools.converters.rst
+    imctools.data.rst
+    imctools.io.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -29,14 +29,14 @@
 extensions = [
     'myst_parser',
     'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
+    # 'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
     'sphinx_autodoc_typehints',
     'sphinx_paramlinks'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = []
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -57,4 +57,4 @@
 
 add_module_names = False
 autodoc_member_order = 'bysource'
-autosummary_generate = True
+autosummary_generate = False
diff --git a/docs/source/stubs/imctools.cli.rst → docs/source/imctools.cli.rst b/docs/source/stubs/imctools.cli.rst → docs/source/imctools.cli.rst
@@ -2,5 +2,6 @@
 ============
 
 .. automodule:: imctools.cli
+    :imported-members:
     :members:
-    :undoc-members:
+    :undoc-members:
diff --git a/docs/source/stubs/imctools.converters.rst → docs/source/imctools.converters.rst b/docs/source/stubs/imctools.converters.rst → docs/source/imctools.converters.rst
@@ -2,5 +2,6 @@
 ===================
 
 .. automodule:: imctools.converters
+    :imported-members:
     :members:
-    :undoc-members:
+    :undoc-members:
diff --git a/docs/source/imctools.data.rst b/docs/source/imctools.data.rst
@@ -0,0 +1,38 @@
+imctools.data
+=============
+
+imctools.data.acquisition
+-------------------------
+.. automodule:: imctools.data.acquisition
+    :members:
+    :undoc-members:
+
+imctools.data.acquisitiondata
+-----------------------------
+.. automodule:: imctools.data.acquisitiondata
+    :members:
+    :undoc-members:
+
+imctools.data.channel
+---------------------
+.. automodule:: imctools.data.channel
+    :members:
+    :undoc-members:
+
+imctools.data.panorama
+----------------------
+.. automodule:: imctools.data.panorama
+    :members:
+    :undoc-members:
+
+imctools.data.session
+---------------------
+.. automodule:: imctools.data.session
+    :members:
+    :undoc-members:
+
+imctools.data.slide
+-------------------
+.. automodule:: imctools.data.slide
+    :members:
+    :undoc-members:
diff --git a/docs/source/imctools.io.rst b/docs/source/imctools.io.rst
@@ -0,0 +1,44 @@
+imctools.io
+===========
+
+imctools.io.utils
+-----------------
+.. automodule:: imctools.io.utils
+    :members:
+    :undoc-members:
+
+imctools.io.imc
+---------------
+.. automodule:: imctools.io.imc.imcparser
+    :members:
+    :undoc-members:
+
+.. automodule:: imctools.io.imc.imcwriter
+    :members:
+    :undoc-members:
+
+imctools.io.mcd
+---------------
+.. automodule:: imctools.io.mcd.mcdparser
+    :members:
+    :undoc-members:
+
+.. automodule:: imctools.io.mcd.mcdxmlparser
+    :members:
+    :undoc-members:
+
+.. automodule:: imctools.io.mcd.constants
+    :members:
+    :undoc-members:
+
+imctools.io.ometiff
+-------------------
+.. automodule:: imctools.io.ometiff.ometiffparser
+    :members:
+    :undoc-members:
+
+imctools.io.txt
+---------------
+.. automodule:: imctools.io.txt.txtparser
+    :members:
+    :undoc-members:
diff --git a/docs/source/index.md b/docs/source/index.md
@@ -1,2 +1,10 @@
 ```{include} ../../README.md
 ```
+
+```{toctree}
+quickstart
+api_reference
+CONTRIBUTING
+CHANGELOG
+LICENSE
+```
diff --git a/docs/source/quickstart.md b/docs/source/quickstart.md
@@ -1,4 +1,4 @@
-# imctools
+# Quickstart
 
 > `imctools` v2.x has many changes in IMC data output format, available CLI commands, dropped Python 2 and Fiji plugins support, etc.
 > If you are using `imctools` in pre-processing pipelines, please install v1.x version until your pipeline is modified accordingly!
@@ -79,7 +79,7 @@ ac_data.save_tiffs("/home/anton/tiffs", compression=0, bigtiff=False)
 parser.close()
 ```
 
-### Usage of previous version 1.x
+## Usage of version 1.x
 
 ```python
 import imctools.io.mcdparser as mcdparser

diff --git a/docs/source/stubs/imctools.data.rst b/docs/source/stubs/imctools.data.rst
diff --git a/docs/source/stubs/imctools.io.rst b/docs/source/stubs/imctools.io.rst