better control automatic gen of docs

.github/workflows/build_docs.yml

@@ -25,11 +25,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install -e .
           pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
 
       - name: Build documentation
         run: |
-          sphinx-apidoc -o docs/source bird
           cd docs
           make html
 

.github/workflows/deploy_docs.yml

@@ -6,6 +6,11 @@ on:
     paths:
       - 'docs/**'
       - '.github/workflows/deploy_docs.yml'
+  pull_request:
+    branches: [ main ]
+    paths:
+      - 'docs/**'
+      - '.github/workflows/deploy_docs.yml'
 
 jobs:
 
@@ -26,11 +31,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install -e .
           pip install sphinx sphinx_rtd_theme sphinx-autodoc-typehints
 
       - name: Build documentation
         run: |
-          sphinx-apidoc -o docs/source bird
           cd docs
           make html
 

docs/source/bird.calibration.rst

@@ -0,0 +1,29 @@
+bird.calibration package
+========================
+
+Submodules
+----------
+
+bird.calibration.param\_nn module
+---------------------------------
+
+.. automodule:: bird.calibration.param_nn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.calibration.scaling module
+-------------------------------
+
+.. automodule:: bird.calibration.scaling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: bird.calibration
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/bird.meshing.rst

@@ -0,0 +1,37 @@
+bird.meshing package
+====================
+
+Submodules
+----------
+
+bird.meshing.block\_cyl\_mesh module
+------------------------------------
+
+.. automodule:: bird.meshing.block_cyl_mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.meshing.block\_rect\_mesh module
+-------------------------------------
+
+.. automodule:: bird.meshing.block_rect_mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.meshing.stirred\_tank\_mesh module
+---------------------------------------
+
+.. automodule:: bird.meshing.stirred_tank_mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: bird.meshing
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/bird.postprocess.rst

@@ -0,0 +1,53 @@
+bird.postprocess package
+========================
+
+Submodules
+----------
+
+bird.postprocess.conditional\_mean module
+-----------------------------------------
+
+.. automodule:: bird.postprocess.conditional_mean
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.postprocess.early\_pred module
+-----------------------------------
+
+.. automodule:: bird.postprocess.early_pred
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.postprocess.kla\_utils module
+----------------------------------
+
+.. automodule:: bird.postprocess.kla_utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.postprocess.post\_quantities module
+----------------------------------------
+
+.. automodule:: bird.postprocess.post_quantities
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.postprocess.stats module
+-----------------------------
+
+.. automodule:: bird.postprocess.stats
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: bird.postprocess
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/bird.preprocess.rst

@@ -0,0 +1,10 @@
+bird.preprocess package
+=======================
+
+Module contents
+---------------
+
+.. automodule:: bird.preprocess
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/bird.rst

@@ -0,0 +1,15 @@
+BiRD API
+============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 1
+
+   bird.calibration
+   bird.meshing
+   bird.postprocess
+   bird.preprocess
+   bird.utilities
+

docs/source/bird.utilities.rst

@@ -0,0 +1,61 @@
+bird.utilities package
+======================
+
+Submodules
+----------
+
+bird.utilities.folderManagement module
+--------------------------------------
+
+.. automodule:: bird.utilities.folderManagement
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.utilities.label\_plot module
+---------------------------------
+
+.. automodule:: bird.utilities.label_plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.utilities.mathtools module
+-------------------------------
+
+.. automodule:: bird.utilities.mathtools
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.utilities.ofio module
+--------------------------
+
+.. automodule:: bird.utilities.ofio
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.utilities.parser module
+----------------------------
+
+.. automodule:: bird.utilities.parser
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bird.utilities.stl\_plotting module
+-----------------------------------
+
+.. automodule:: bird.utilities.stl_plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: bird.utilities
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -29,6 +29,7 @@ We provide a solver ``birdmultiphaseEulerFoam`` that contains custom models adde
    uq
    python_interface
    tutorials
+   bird
    contribute
    references
    troubleshoot

docs/source/modules.rst

@@ -0,0 +1,7 @@
+bird
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   bird