Add deploy task for gh-pages

.github/workflows/docs.yml

@@ -0,0 +1,51 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main]
+    tags: ["*"]
+  pull_request:
+    # Check all PR
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: setup rust
+        uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+      - name: setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: install dependencies
+        run: |
+          python -m pip install tox
+      - name: build documentation
+        run: tox -e docs
+
+      - name: put documentation in the website
+        run: |
+          git clone https://github.com/$GITHUB_REPOSITORY --branch gh-pages gh-pages
+          rm -rf gh-pages/.git
+          cd gh-pages
+
+          REF_KIND=$(echo $GITHUB_REF | cut -d / -f2)
+          if [[ "$REF_KIND" == "tags" ]]; then
+              TAG=${GITHUB_REF#refs/tags/}
+              mv ../docs/build/html $TAG
+          else
+              rm -rf latest
+              mv ../docs/build/html latest
+          fi
+
+      - name: deploy to gh-pages
+        if: github.event_name == 'push'
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./gh-pages/
+          force_orphan: true

.github/workflows/lint.yml

@@ -1,7 +1,7 @@
 # Lint tests run on PR
 # but should not run after push to main because reporting
 # these after push is meaningless to the building of the package
-name: lint
+name: Lint
 
 on:
   pull_request:

README.rst

@@ -1,7 +1,8 @@
 COSMO Software Cookbook
 =======================
 
-`COSMO Software Cookbook <https://software-cookbook.rtfd.io/>`_
+The source code for the COSMO cookbook is maintained as a GitHub pages site. The home
+page is accessible at https://lab-cosmo.github.io/software-cookbook/latest.
 
 .. marker-intro-start
 

docs/requirements-rascal.txt

@@ -1,5 +1,5 @@
 # rascal needs to be in a separate requirements file because we need to specify
-# the packages index-url for it te use the prebuilt from 
+# the packages index-url for it te use the prebuilt from
 # from https://github.com/Luthaf/nightly-wheels
 # extra-url does not work here because there is another rascal package on pypi
 --index-url https://luthaf.fr/nightly-wheels/

docs/requirements.txt

@@ -1,4 +1,3 @@
---extra-index-url https://luthaf.fr/nightly-wheels/
 # Sphinx
 sphinx
 sphinx_rtd_theme
@@ -20,7 +19,7 @@ scipy
 scikit-learn
 skmatter
 chemiscope
-equisolve @ git+https://github.com/lab-cosmo/equisolve.git@71b3dfd
+equisolve @ https://github.com/lab-cosmo/equisolve/archive/63c9c54.zip
 
 metatensor
-rascaline
+rascaline @ https://github.com/luthaf/rascaline/archive/581d0ca.zip

examples/lode_linear/lode_tutorial.py

@@ -169,10 +169,10 @@
 # For linear models only: Sum features up over atoms (``samples``) in the same
 # structure.
 
-samples_names_to_sum = ["center", "species_center"]
+sample_names_to_sum = ["center", "species_center"]
 
-ps_sr = metatensor.sum_over_samples(ps_sr, samples_names=samples_names_to_sum)
-ps_lr = metatensor.sum_over_samples(ps_lr, samples_names=samples_names_to_sum)
+ps_sr = metatensor.sum_over_samples(ps_sr, sample_names=sample_names_to_sum)
+ps_lr = metatensor.sum_over_samples(ps_lr, sample_names=sample_names_to_sum)
 
 
 # %%
@@ -188,7 +188,7 @@
 descriptor_co = calculator_co.compute(frames, gradients=["positions"])
 
 co = descriptor_co.keys_to_properties(["species_center"])
-co = metatensor.sum_over_samples(co, samples_names=["center"])
+co = metatensor.sum_over_samples(co, sample_names=["center"])
 
 # %%
 #

examples/roy_gch/roy_gch.py

@@ -153,7 +153,7 @@
 rho2i = rho2i.keys_to_samples(["species_center"]).keys_to_properties(
     ["species_neighbor_1", "species_neighbor_2"]
 )
-rho2i_structure = mean_over_samples(rho2i, samples_names=["center", "species_center"])
+rho2i_structure = mean_over_samples(rho2i, sample_names=["center", "species_center"])
 np.savez("roy_features.npz", feats=rho2i_structure.block(0).values)