Merge branch 'main' of github.com:materialsproject/atomate2 into abinit_workflows_dfpt_shg_new_review-PR

pull trunk main

Author: VicTrqt

Diff for: .github/workflows/testing.yml

@@ -71,6 +71,9 @@ jobs:
         if: github.event_name == 'repository_dispatch' && github.event.action == 'pymatgen-ci-trigger'
         run: pip install --upgrade 'git+https://github.com/materialsproject/pymatgen@${{ github.event.client_payload.pymatgen_ref }}'
 
+      - name: Test Notebooks
+        run: pytest --nbmake ./tutorials
+
       - name: Test
         env:
           MP_API_KEY: ${{ secrets.MP_API_KEY }}

Diff for: .gitignore

@@ -66,3 +66,5 @@ docs/reference/atomate2.*
 
 # see https://github.com/materialsproject/atomate2/issues/345
 *.doctrees*
+
+.ipynb_checkpoints

Diff for: .pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.4.10
+  rev: v0.5.2
   hooks:
   - id: ruff
     args: [--fix]
@@ -17,7 +17,7 @@ repos:
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/asottile/blacken-docs
-  rev: 1.16.0
+  rev: 1.18.0
   hooks:
   - id: blacken-docs
     additional_dependencies: [black]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.10.0
+  rev: v1.10.1
   hooks:
   - id: mypy
     files: ^src/
@@ -44,3 +44,12 @@ repos:
     stages: [commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.7.1
+  hooks:
+    - id: nbstripout
+      args: [
+        --drop-empty-cells,
+        --strip-init-cells,
+        --extra-keys=metadata.kernelspec,
+        ]

Diff for: docs/_static/docs_store_Si_relax.json

@@ -1,5 +1,4 @@
-License
-=======
+# License
 
 `atomate2` is developed under a modified BSD license, reproduced below:
 

Diff for: docs/_static/example_flow.png

@@ -72,7 +72,7 @@
 napoleon_use_ivar = True
 
 # The suffix(es) of source filenames.
-source_suffix = [".rst", ".md"]
+source_suffix = {".rst": "restructuredtext", ".md": "restructuredtext"}
 
 mathjax3_config = {
     "tex": {
@@ -92,10 +92,10 @@
 """
 }
 language = "en"
-html_extra_path = ["images/badge.svg"]
+# html_extra_path = ["images/badge.svg"]
 html_static_path = ["_static"]
 html_css_files = ["custom.css", "github.css"]
-suppress_warnings = "etoc.toctree"
+suppress_warnings = ["etoc.toctree"]
 
 # autodoc options
 autosummary_imported_members = False
@@ -172,6 +172,5 @@
     "python": ("https://docs.python.org/3.8", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable/", None),
-    "monty": ("https://materialsvirtuallab.github.io/monty/", None),
     "jobflow": ("https://materialsproject.github.io/jobflow", None),
 }

Diff for: docs/about/license.md

@@ -4,7 +4,9 @@
 user/index
 user/install
 user/running-workflows
+user/docs-schemas-emmet
 user/fireworks
+user/atomate-1-vs-2
 user/codes/index
 ```
 
@@ -20,6 +22,7 @@ reference/index
 dev/dev_install
 dev/workflow_tutorial
 dev/vasp_tests
+dev/abinit_tests
 ```
 
 ```{toctree}

Diff for: docs/conf.py

@@ -12,9 +12,15 @@ This section gives an overview of the API for atomate2.
     :toctree:
     :nosignatures:
 
+    abinit
+    aims
     amset
+    cli
     common
+    cp2k
+    forcefields
     lobster
+    qchem
     settings
     utils
     vasp