Merge #48

Author: C-Achard

.github/workflows/build_docs.yml

@@ -1,19 +1,38 @@
-name: Deploy Sphinx documentation to Pages
+name: deploy
 
 on:
   push:
     branches: # branch to trigger deployment
       - main
 
+# This job installs dependencies, build the book, and pushes it to `gh-pages`
 jobs:
-  pages:
-    runs-on: ubuntu-20.04
+  build-and-deploy-book:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.8]
     steps:
-    - id: deployment
-      uses: sphinx-notes/pages@v3
+    - uses: actions/checkout@v2
+
+    # Install dependencies
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
       with:
-        publish: false
-    - uses: peaceiris/actions-gh-pages@v3
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install jupyter-book
+
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build docs/
+
+    # Deploy the book's HTML to gh-pages branch
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ${{ steps.deployment.outputs.artifact }}
+        publish_dir: docs/_build/html

.gitignore

@@ -93,14 +93,17 @@ venv/
 # written by setuptools_scm
 **/_version.py
 
+# WANDB
+/wandb/
 
 
 ########
 #project specific
 #dataset, weights, old logos, requirements
 /napari_cellseg3d/code_models/models/dataset/
 /napari_cellseg3d/code_models/models/saved_weights/
-/docs/res/logo/old_logo/
+/docs/source/logo/old_logo/
+/docs/source/code/_autosummary/
 /reqs/
 /loss_plots/
 /wandb/
@@ -111,7 +114,7 @@ notebooks/full_plot.html
 notebooks/instance_test.ipynb
 *.prof
 /docs/_build/
-/docs/source/code/_autosummary/
+/docs/source/code/_autosummary/*.rst
 
 #include test data
 !napari_cellseg3d/_tests/res/test.tif
@@ -121,3 +124,8 @@ notebooks/instance_test.ipynb
 !napari_cellseg3d/_tests/res/wnet_test/lab/*.tif
 !napari_cellseg3d/_tests/res/wnet_test/vol/*.tif
 cov.syspath.txt
+
+#include docs images
+!docs/source/logo/*
+!docs/source/images/*
+napari_cellseg3d/dev_scripts/wandb

.pre-commit-config.yaml

@@ -7,18 +7,19 @@ repos:
       - id: trailing-whitespace
       - id: check-yaml
       - id: check-added-large-files
+        args: [--maxkb=5000]
       - id: check-toml
 #  - repo: https://github.com/pycqa/isort
 #    rev: 5.12.0
 #    hooks:
 #      - id: isort
 #        args: ["--profile", "black", --line-length=79]
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    # Ruff version.
-    rev: 'v0.0.262'
-    hooks:
-      - id: ruff
-        args: [ --fix, --exit-non-zero-on-fix ]
+  # - repo: https://github.com/charliermarsh/ruff-pre-commit
+  #   # Ruff version.
+  #   rev: 'v0.0.262'
+  #   hooks:
+  #     - id: ruff
+  #       args: [ --fix, --exit-non-zero-on-fix ]
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:

conda/napari_cellseg3d_m1.yml

@@ -16,7 +16,7 @@ dependencies:
         - tifffile>=2022.2.9
         - imageio-ffmpeg>=0.4.5
         - torch>=1.11
-        - monai[nibabel,einops]>=0.9.0
+        - monai>=0.9.0
         - tqdm
         - nibabel
         - scikit-image

docs/Makefile

@@ -0,0 +1,8 @@
+[//]: # (
+TODO:
+- [ ] Add a way to get the current version of the library
+- [x] Update all modules
+- [x] Better WNet tutorial
+- [x] Setup GH Actions
+- [ ] Add a bibliography
+)

docs/TODO.md

@@ -0,0 +1,51 @@
+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: napari-cellseg3d Documentation
+author: Cyril Achard, Maxime Vidal, Timokleia Kousi, Mackenzie Mathis | Mathis Laboratory
+logo: source/logo/logo_alpha.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/AdaptiveMotorControlLab/CellSeg3d  # Online location of your book
+  path_to_book: docs  # Optional path to your book, relative to the repository root
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+
+# Add auto-generated API docs
+sphinx:
+  extra_extensions:
+  - 'sphinx.ext.napoleon'
+  - 'sphinx.ext.autodoc'
+  - 'sphinx.ext.autosummary'
+  - 'sphinx.ext.viewcode'
+  - 'sphinx.ext.autosectionlabel'
+  config:
+    add_module_names: False
+    autosectionlabel_prefix_document: True
+    autosummary_generate: True
+    autoclass_content: "both"
+    # templates_path: ['_templates']
+    exclude_patterns:
+      - '_build'
+      - '_templates'
+    #   - 'napari_cellseg3d/__pycache__'