mdtanker · mdtanker · Aug 2, 2024 · Jul 11, 2024 · Jul 11, 2024 · Jul 12, 2024
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -7,4 +7,7 @@ updates:
       interval: "monthly"
     commit-message:
       prefix: "chore"
-      include:
+    groups:
+      actions:
+        patterns:
+          - "*"
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,29 +16,17 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
 # Use bash by default in all jobs
 defaults:
   run:
     shell: bash -el {0}
 
 jobs:
-  # run pre-commit which includes many formatting and linting tools
-  pre-commit:
-    name: Format
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.x"
-      - uses: pre-commit/[email protected]
-        with:
-          extra_args: --hook-stage manual --all-files
-      - name: Run PyLint
-        run: pipx run nox -s pylint -- --output-format=github
-
   # Run tests and upload to codecov
   test:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
@@ -47,7 +35,6 @@ jobs:
     if: |
       ${{!startsWith(github.event.head_commit.message, 'docs:') }} ||
       ${{!startsWith(github.event.head_commit.message, 'style:') }}
-    needs: [pre-commit]
     strategy:
       # Otherwise, the workflow would stop if a single job fails. We want to
       # run all of them to catch failures in different combinations.
@@ -57,10 +44,9 @@ jobs:
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     env:
-      FORCE_COLOR: 3
       NUMBA_DISABLE_JIT: "1"
 
-    timeout-minutes: 30
+    timeout-minutes: 10
     steps:
       # Checkout current git repository
       - name: Checkout

diff --git a/.gitignore b/.gitignore
@@ -160,3 +160,6 @@ Thumbs.db
 *.pickle
 *.log
 *.lock
+
+# tmp data folders
+tmp/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -19,6 +19,7 @@ exclude: |
       docs/api/invert4geom.cross_validation.rst|
       docs/api/invert4geom.regional.rst|
       docs/api/invert4geom.optimization.rst|
+      docs/api/invert4geom.uncertainty.rst|
       docs/_invert4geom_refs.bib|
       CHANGELOG.md|
       .github/ISSUE_TEMPLATE/feature_request.md|
@@ -30,11 +31,6 @@ exclude: |
   )$
 
 repos:
-  # - repo: https://github.com/psf/black-pre-commit-mirror
-  #   rev: "23.9.1"
-  #   hooks:
-  #     - id: black-jupyter
-
   - repo: https://github.com/adamchainz/blacken-docs
     rev: "1.18.0"
     hooks:
@@ -118,3 +114,16 @@ repos:
         language: pygrep
         entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
         exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.18"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.29.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs
diff --git a/Makefile b/Makefile
@@ -75,19 +75,30 @@ clean:
 	find . -name '*.pickle' -delete
 	find . -name '*.log' -delete
 	find . -name '*.lock' -delete
+	find . -name '*.pkl' -delete
+	find . -name '*.sqlite3' -delete
+	find . -name '*.coverage' -delete
 
 ####
 ####
 # doc commands
 ####
 ####
 
-run_gallery:
-	jupyter nbconvert --ExecutePreprocessor.allow_errors=True --execute --inplace docs/gallery/*.ipynb
+clear_gallery_outputs:
+	jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace docs/gallery/*.ipynb
 
-run_user_guide:
-	jupyter nbconvert --ExecutePreprocessor.allow_errors=True --execute --inplace docs/user_guide/*.ipynb
+run_gallery: clear_gallery_outputs
+	jupyter nbconvert --ExecutePreprocessor.allow_errors=False --execute --inplace docs/gallery/*.ipynb
 
-run_doc_files:
-	jupyter nbconvert --ExecutePreprocessor.allow_errors=True --execute --inplace docs/*.ipynb
-	jupyter nbconvert --ExecutePreprocessor.allow_errors=True --execute --inplace docs/*/*.ipynb
+clear_user_guide_outputs:
+	jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace docs/user_guide/*.ipynb
+
+run_user_guide: clear_user_guide_outputs
+	jupyter nbconvert --ExecutePreprocessor.allow_errors=False --execute --inplace docs/user_guide/*.ipynb
+
+clear_docs_outputs:
+	jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace docs/**/*.ipynb
+
+run_doc_files: clear_docs_outputs
+	jupyter nbconvert --ExecutePreprocessor.allow_errors=False --execute --inplace docs/**/*.ipynb
diff --git a/RELEASE.md b/RELEASE.md
diff --git a/binder/environment.yml b/binder/environment.yml
@@ -3,21 +3,4 @@ channels:
   - conda-forge
 dependencies:
   - python==3.11
-  - invert4geom==0.7
-  # optimization
-  - optuna>=3.1.0 # need JournalStorage
-  - optuna-integration
-  - botorch>=0.4.0
-  - joblib
-  - psutil
-  # visualization
-  - pyvista
-  - trame
-  - ipywidgets
-  - matplotlib
-  - seaborn
-  - plotly
-  - ipython
-  - pip
-  - pip:
-    - tqdm_joblib
+  - invert4geom==0.7
diff --git a/docs/api.md b/docs/api.md
diff --git a/docs/api/invert4geom.cross_validation.rst b/docs/api/invert4geom.cross_validation.rst
@@ -0,0 +1,7 @@
+invert4geom.cross\_validation module
+====================================
+
+.. automodule:: invert4geom.cross_validation
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.inversion.rst b/docs/api/invert4geom.inversion.rst
@@ -0,0 +1,7 @@
+invert4geom.inversion module
+============================
+
+.. automodule:: invert4geom.inversion
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.optimization.rst b/docs/api/invert4geom.optimization.rst
@@ -0,0 +1,7 @@
+invert4geom.optimization module
+===============================
+
+.. automodule:: invert4geom.optimization
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.plotting.rst b/docs/api/invert4geom.plotting.rst
@@ -0,0 +1,7 @@
+invert4geom.plotting module
+===========================
+
+.. automodule:: invert4geom.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.regional.rst b/docs/api/invert4geom.regional.rst
@@ -0,0 +1,7 @@
+invert4geom.regional module
+===========================
+
+.. automodule:: invert4geom.regional
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.rst b/docs/api/invert4geom.rst
@@ -0,0 +1,22 @@
+invert4geom package
+===================
+
+.. automodule:: invert4geom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   invert4geom.cross_validation
+   invert4geom.inversion
+   invert4geom.optimization
+   invert4geom.plotting
+   invert4geom.regional
+   invert4geom.synthetic
+   invert4geom.uncertainty
+   invert4geom.utils
diff --git a/docs/api/invert4geom.synthetic.rst b/docs/api/invert4geom.synthetic.rst
@@ -0,0 +1,7 @@
+invert4geom.synthetic module
+============================
+
+.. automodule:: invert4geom.synthetic
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.uncertainty.rst b/docs/api/invert4geom.uncertainty.rst
@@ -0,0 +1,7 @@
+invert4geom.uncertainty module
+==============================
+
+.. automodule:: invert4geom.uncertainty
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/invert4geom.utils.rst b/docs/api/invert4geom.utils.rst
@@ -0,0 +1,7 @@
+invert4geom.utils module
+========================
+
+.. automodule:: invert4geom.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -71,7 +71,12 @@ or
 ### Building docs
 You can build the docs using:
 ```bash
-    nox -s docs -- serve
+    nox -s docs
+```
+
+or if you don't want them to automatically update
+```bash
+    nox -s docs --non-interactive
 ```
 
 ## What Can I Do?
@@ -259,12 +264,6 @@ You can build the docs using, but this will require pandoc to be install on your
 nox -s docs
 ```
 
-You can see a preview with:
-
-```bash
-nox -s docs -- --serve
-```
-
 #### Automatically build the docs
 
 Add, commit, and push all changes to GitHub in a Pull Request, and `RTD` should automatically build the docs.
@@ -329,6 +328,7 @@ Now, when submitting a PR, `RTD` will automatically build the docs and update th
 
 ## Release Checklist
 * re-run any relevant notebooks
+* add any new dependencies to the binder env
 * check docs are building correctly using the GitHub actions link within the PR
 * merge the PR
 * wait for `PyPI` to publish the new version [here](https://pypi.python.org/pypi/invert4geom)