Merge pull request #20 from RobinEnjalbert/doc_fix

Migrate the documentation page from RTD to GHP.
mimesis-inria · Nov 27, 2024 · 4ee3295 · 4ee3295
2 parents 298b0d6 + abe6a68
commit 4ee3295
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -0,0 +1,27 @@
+name: documentation
+
+on: [push, pull_request, workflow_dispatch]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx_rtd_theme sphinx-tabs sphinx_copybutton myst_parser numpy torch
+      - name: Sphinx build
+        run: |
+          sphinx-build docs/src docs/build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/
+          force_orphan: true
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 ## DeepPhysX
 
-![logo](docs/source/_static/image/logo.png)
+![logo](docs/src/_static/image/logo.png)
 
 ### Interfacing AI with simulation
 
@@ -20,7 +20,7 @@ Then other packages are compatible with this **Core** and a specific **simulatio
 * Train an artificial neural network with a synthetic dataset;
 * Use the predictions of a trained network in a numerical simulation.
 
-The full list of features is detailed in the [**documentation**](https://deepphysx.readthedocs.io).
+The full list of features is detailed in the [**documentation**](https://mimesis-inria.github.io/DeepPhysX/).
 
 
 ### Quick install
@@ -31,7 +31,7 @@ Thus, **DeepPhysX** is mainly designed for these frameworks, but obviously **oth
 The packages corresponding to these frameworks will therefore be used for the default installation.
 
 The easiest way to install is using `pip`, but there are a several way to install and configure a **DeepPhysX**
-environment (refer to the [**documentation**](https://deepphysx.readthedocs.io/en/latest/presentation/install.html) 
+environment (refer to the [**documentation**](https://mimesis-inria.github.io/DeepPhysX/) 
 for further instructions).
 
 ``` bash
@@ -54,7 +54,7 @@ $ DPX --run <demo>      # Run one of the demo scripts
 
 |          **Armadillo**<br>`DPX -r armadillo`          |          **Beam**<br>`DPX -r beam`          |          **Liver**<br>`DPX -r liver`          |
 |:-----------------------------------------------------:|:-------------------------------------------:|:---------------------------------------------:|
-| ![armadillo](docs/source/_static/image/armadillo.png) | ![beam](docs/source/_static/image/beam.png) | ![liver](docs/source/_static/image/liver.png) |
+| ![armadillo](docs/src/_static/image/armadillo.png) | ![beam](docs/src/_static/image/beam.png) | ![liver](docs/src/_static/image/liver.png) |
 
 
 ### References

diff --git a/docs/Makefile b/docs/Makefile
@@ -5,7 +5,7 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = source
+SOURCEDIR     = src
 BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".

diff --git a/docs/make.bat b/docs/make.bat
@@ -7,7 +7,7 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=source
+set SOURCEDIR=src
 set BUILDDIR=build
 
 if "%1" == "" goto help

diff --git a/...tatic/image/about_classical_pipelines.png → ...tatic/image/about_classical_pipelines.png b/...tatic/image/about_classical_pipelines.png → ...tatic/image/about_classical_pipelines.png
diff --git a/...rce/_static/image/about_dpx_pipelines.png → ...src/_static/image/about_dpx_pipelines.png b/...rce/_static/image/about_dpx_pipelines.png → ...src/_static/image/about_dpx_pipelines.png
diff --git a/docs/source/_static/image/about_tree.png → docs/src/_static/image/about_tree.png b/docs/source/_static/image/about_tree.png → docs/src/_static/image/about_tree.png
diff --git a/docs/source/_static/image/armadillo.png → docs/src/_static/image/armadillo.png b/docs/source/_static/image/armadillo.png → docs/src/_static/image/armadillo.png
diff --git a/docs/source/_static/image/beam.png → docs/src/_static/image/beam.png b/docs/source/_static/image/beam.png → docs/src/_static/image/beam.png
diff --git a/docs/source/_static/image/database.png → docs/src/_static/image/database.png b/docs/source/_static/image/database.png → docs/src/_static/image/database.png
diff --git a/...urce/_static/image/environment_tcp_ip.png → .../src/_static/image/environment_tcp_ip.png b/...urce/_static/image/environment_tcp_ip.png → .../src/_static/image/environment_tcp_ip.png
diff --git a/docs/source/_static/image/liver.png → docs/src/_static/image/liver.png b/docs/source/_static/image/liver.png → docs/src/_static/image/liver.png
diff --git a/docs/source/_static/image/logo.png → docs/src/_static/image/logo.png b/docs/source/_static/image/logo.png → docs/src/_static/image/logo.png
diff --git a/...rce/_static/image/overview_components.png → ...src/_static/image/overview_components.png b/...rce/_static/image/overview_components.png → ...src/_static/image/overview_components.png
diff --git a/...ource/_static/image/overview_packages.png → docs/src/_static/image/overview_packages.png b/...ource/_static/image/overview_packages.png → docs/src/_static/image/overview_packages.png
diff --git a/docs/source/_static/theme.css → docs/src/_static/theme.css b/docs/source/_static/theme.css → docs/src/_static/theme.css
diff --git a/docs/source/api/core.rst → docs/src/api/core.rst b/docs/source/api/core.rst → docs/src/api/core.rst
diff --git a/docs/source/api/core/asyncsocket.rst → docs/src/api/core/asyncsocket.rst b/docs/source/api/core/asyncsocket.rst → docs/src/api/core/asyncsocket.rst
diff --git a/docs/source/api/core/dataset.rst → docs/src/api/core/dataset.rst b/docs/source/api/core/dataset.rst → docs/src/api/core/dataset.rst
diff --git a/docs/source/api/core/environment.rst → docs/src/api/core/environment.rst b/docs/source/api/core/environment.rst → docs/src/api/core/environment.rst
diff --git a/docs/source/api/core/manager.rst → docs/src/api/core/manager.rst b/docs/source/api/core/manager.rst → docs/src/api/core/manager.rst
diff --git a/docs/source/api/core/network.rst → docs/src/api/core/network.rst b/docs/source/api/core/network.rst → docs/src/api/core/network.rst
diff --git a/docs/source/api/core/pipeline.rst → docs/src/api/core/pipeline.rst b/docs/source/api/core/pipeline.rst → docs/src/api/core/pipeline.rst
diff --git a/docs/source/api/core/visualizer.rst → docs/src/api/core/visualizer.rst b/docs/source/api/core/visualizer.rst → docs/src/api/core/visualizer.rst
diff --git a/docs/source/api/sofa.rst → docs/src/api/sofa.rst b/docs/source/api/sofa.rst → docs/src/api/sofa.rst
diff --git a/docs/source/api/torch.rst → docs/src/api/torch.rst b/docs/source/api/torch.rst → docs/src/api/torch.rst
diff --git a/docs/source/component/dataset.rst → docs/src/component/dataset.rst b/docs/source/component/dataset.rst → docs/src/component/dataset.rst
diff --git a/docs/source/component/environment.rst → docs/src/component/environment.rst b/docs/source/component/environment.rst → docs/src/component/environment.rst
diff --git a/docs/source/component/network.rst → docs/src/component/network.rst b/docs/source/component/network.rst → docs/src/component/network.rst
diff --git a/docs/source/component/pipelines.rst → docs/src/component/pipelines.rst b/docs/source/component/pipelines.rst → docs/src/component/pipelines.rst
diff --git a/docs/source/component/stats.rst → docs/src/component/stats.rst b/docs/source/component/stats.rst → docs/src/component/stats.rst
diff --git a/docs/source/component/visualizer.rst → docs/src/component/visualizer.rst b/docs/source/component/visualizer.rst → docs/src/component/visualizer.rst
diff --git a/docs/source/conf.py → docs/src/conf.py b/docs/source/conf.py → docs/src/conf.py
@@ -10,17 +10,10 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
-from os.path import abspath, join, pardir
+import os
 import sys
 
-# DeepPhysX root
-root = abspath(join(abspath(__file__), pardir, pardir, pardir, 'src', 'Core'))
-all_modules = ['AsyncSocket', 'Database', 'Environment', 'Manager', 'Network', 'Pipelines', 'Visualization']
-
-# Import all modules
-sys.path.append(root)
-for module in all_modules:
-    sys.path.append(join(root, module))
+sys.path.insert(0, os.path.abspath('../../src'))
 
 # -- Project information -----------------------------------------------------
 
@@ -51,8 +44,8 @@
 # Add any paths that contain templates here, relative to this directory.
 # templates_path = ['_templates']
 
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
+# List of patterns, relative to src directory, that match files and
+# directories to ignore when looking for src files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 

diff --git a/docs/source/index.rst → docs/src/index.rst b/docs/source/index.rst → docs/src/index.rst
diff --git a/docs/source/presentation/about.rst → docs/src/presentation/about.rst b/docs/source/presentation/about.rst → docs/src/presentation/about.rst
diff --git a/docs/source/presentation/install.rst → docs/src/presentation/install.rst b/docs/source/presentation/install.rst → docs/src/presentation/install.rst
diff --git a/docs/source/presentation/overview.rst → docs/src/presentation/overview.rst b/docs/source/presentation/overview.rst → docs/src/presentation/overview.rst
diff --git a/docs/source/requirements.txt → docs/src/requirements.txt b/docs/source/requirements.txt → docs/src/requirements.txt
diff --git a/examples/demos/Liver/FC/Environment/utils.py b/examples/demos/Liver/FC/Environment/utils.py
@@ -7,7 +7,7 @@ def get_nb_nodes(source_file):
     """
     Get the number of node of the object.
 
-    :param source_file: Filename of the source object
+    :param source_file: Filename of the src object
     :return: Number of node
     """
 
@@ -18,7 +18,7 @@ def find_center(source_file, scale):
     """
     Find the center of mass of the object.
 
-    :param source_file: Filename of the source object
+    :param source_file: Filename of the src object
     :param scale: Scaling to apply to the objects
     :return: Center of mass of the object
     """
@@ -30,8 +30,8 @@ def find_boundaries(source_file, objects_files_list, scale):
     """
     Find the boundary conditions of the liver.
 
-    :param source_file: Filename of the source object
-    :param objects_files_list: List of filenames of objects which intersect the source object
+    :param source_file: Filename of the src object
+    :param objects_files_list: List of filenames of objects which intersect the src object
     :param scale: Scaling to apply to the objects
     :return: Boundary box defined by [xmin, ymin, zmin, xmax, ymax, zmax]
     """

diff --git a/examples/demos/Liver/UNet/Environment/utils.py b/examples/demos/Liver/UNet/Environment/utils.py
@@ -28,7 +28,7 @@ def find_center(source_file, scale):
     """
     Find the center of mass of the object.
 
-    :param source_file: Filename of the source object
+    :param source_file: Filename of the src object
     :param scale: Scaling to apply to the objects
     :return: Center of mass of the object
     """

diff --git a/src/Core/Utils/Visualizer/barycentric_mapping.py b/src/Core/Utils/Visualizer/barycentric_mapping.py
@@ -8,7 +8,7 @@ class BarycentricMapping:
 
     def __init__(self, source: Mesh, target: Mesh):
         """
-        Python implementation of a barycentric mapping between a source mesh and a target mesh.
+        Python implementation of a barycentric mapping between a src mesh and a target mesh.
 
         :param source: Source mesh
         :param target: Target mesh
@@ -23,7 +23,7 @@ def __init__(self, source: Mesh, target: Mesh):
 
     def init_mapping(self):
         """
-        Compute barycentric coordinates of target to map source.
+        Compute barycentric coordinates of target to map src.
         """
 
         # 1. CONVERT SOURCE TO VTK
@@ -84,7 +84,7 @@ def init_mapping(self):
 
     def apply(self, source_positions):
         """
-        Apply mapping between new source positions and target with barycentric coordinates.
+        Apply mapping between new src positions and target with barycentric coordinates.
         """
 
         ABC = np.array(source_positions)[np.array(self.source.cells())[self.index]]

diff --git a/src/Core/Utils/path.py b/src/Core/Utils/path.py
@@ -80,7 +80,7 @@ def create_dir(session_dir: str, session_name: str) -> str:
 
 def copy_dir(src_dir: str, dest_dir: str, dest_name: Optional[str] = None, sub_folders: Optional[str] = None) -> str:
     """
-    Copy the source directory to the destination directory.
+    Copy the src directory to the destination directory.
 
     :param src_dir: Source directory to copy.
     :param dest_dir: Parent of the destination directory to copy.
@@ -103,7 +103,7 @@ def copy_dir(src_dir: str, dest_dir: str, dest_name: Optional[str] = None, sub_f
         dest_name += f'{max_id + 1}'
 
     dest = join(dest_dir, dest_name) if dest_name is not None else dest_dir
-    print(f"Copying the source directory {src_dir} to {dest} for this session.")
+    print(f"Copying the src directory {src_dir} to {dest} for this session.")
     if sub_folders is None:
         copytree(src_dir, dest)
     else: