Merge branch 'main' into Py314u

Author: jan-janssen

.ci_support/environment-docs.yml

@@ -2,18 +2,19 @@ channels:
 - conda-forge
 dependencies:
 - flux-core
-- hatchling
-- hatch-vcs
+- hatchling =1.30.1
+- hatch-vcs =0.5.0
 - myst-parser
 - nbsphinx
 - numpy
 - openmpi
 - sphinx
+- sphinxcontrib-mermaid
 - sphinx_rtd_theme
 - cloudpickle =3.1.2
-- h5py =3.15.1
+- h5py =3.16.0
 - jupyter-book =1.0.0
-- mpi4py =4.1.1
+- mpi4py =4.1.2
 - python =3.12
-- pydantic =2.12.5
+- pydantic =2.13.4
 - pyzmq =27.1.0

.ci_support/environment-integration.yml

@@ -1,24 +1,24 @@
 channels:
 - conda-forge
 dependencies:
-- h5py =3.15.1
+- h5py =3.16.0
 - jupyter
-- mpi4py =4.1.1
+- mpi4py =4.1.2
 - numpy =2.3.5
 - openmpi
 - papermill
-- atomistics =0.3.4
+- atomistics =0.3.6
 - cloudpickle =3.1.2
 - flux-core =0.81.0
 - flux-pmix =0.6.0
 - gpaw =25.7.0
-- hatchling =1.28.0
+- hatchling =1.30.1
 - hatch-vcs =0.5.0
 - ipython =9.9.0
 - matplotlib =3.10.8
 - networkx =3.6.1
-- pydantic =2.12.5
+- pydantic =2.13.4
 - pygraphviz =1.14
-- pysqa =0.3.5
+- pysqa =0.4.2
 - pyzmq =27.1.0
 - qe =7.5

.ci_support/environment-mini.yml

@@ -4,6 +4,6 @@ dependencies:
 - python
 - numpy =2.4.2
 - cloudpickle =3.1.0
-- hatchling =1.28.0
+- hatchling =1.30.1
 - hatch-vcs =0.5.0
 - pyzmq =27.1.0

.ci_support/environment-mpich.yml

@@ -5,13 +5,13 @@ dependencies:
 - numpy =2.4.2
 - mpich
 - cloudpickle =3.1.2
-- h5py =3.15.1
-- hatchling =1.28.0
+- h5py =3.16.0
+- hatchling =1.30.1
 - hatch-vcs =0.5.0
 - ipython =9.9.0
-- mpi4py =4.1.1
+- mpi4py =4.1.2
 - networkx =3.6.1
-- pydantic =2.12.5
+- pydantic =2.13.4
 - pygraphviz =1.14
-- pysqa =0.3.5
+- pysqa =0.4.2
 - pyzmq =27.1.0

.ci_support/environment-openmpi.yml

@@ -5,13 +5,13 @@ dependencies:
 - numpy =2.4.2
 - openmpi
 - cloudpickle =3.1.2
-- h5py =3.15.1
-- hatchling =1.28.0
+- h5py =3.16.0
+- hatchling =1.30.1
 - hatch-vcs =0.5.0
 - ipython =9.9.0
-- mpi4py =4.1.1
+- mpi4py =4.1.2
 - networkx =3.6.1
-- pydantic =2.12.5
+- pydantic =2.13.4
 - pygraphviz =1.14
-- pysqa =0.3.5
+- pysqa =0.4.2
 - pyzmq =27.1.0

.ci_support/environment-win.yml

@@ -5,12 +5,12 @@ dependencies:
 - numpy =2.4.2
 - msmpi
 - cloudpickle =3.1.2
-- h5py =3.15.1
-- hatchling =1.28.0
+- h5py =3.16.0
+- hatchling =1.30.1
 - hatch-vcs =0.5.0
 - ipython =9.9.0
-- mpi4py =4.1.1
+- mpi4py =4.1.2
 - networkx =3.6.1
-- pydantic =2.12.5
+- pydantic =2.13.4
 - pygraphviz =1.14
 - pyzmq =27.1.0

.github/workflows/pipeline.yml

@@ -3,7 +3,11 @@ name: Pipeline
 on:
   push:
     branches: [ main ]
+    paths-ignore:
+      - 'docs/**'
   pull_request:
+    paths-ignore:
+      - 'docs/**'
 
 jobs:
   black:
@@ -98,6 +102,18 @@ jobs:
         pip install . --no-deps --no-build-isolation
         pip check
 
+  uv_check:
+    needs: [black]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v7
+    - name: Install the project and pip check
+      shell: bash -l {0}
+      run: |
+        uv sync --all-extras --dev
+        pip check
+
   benchmark:
     needs: [black]
     runs-on: ${{ matrix.operating-system }}
@@ -164,7 +180,7 @@ jobs:
           papermill notebooks/1-single-node.ipynb notebooks/1-single-node-out.ipynb -k python3
           flux start papermill notebooks/2-hpc-cluster.ipynb notebooks/2-hpc-cluster-out.ipynb -k python3
           flux start papermill notebooks/3-hpc-job.ipynb notebooks/3-hpc-job-out.ipynb -k python3
-          papermill notebooks/4-developer.ipynb notebooks/4-developer-out.ipynb -k python3
+          papermill notebooks/5-developer.ipynb notebooks/5-developer-out.ipynb -k python3
 
   notebooks_integration:
     needs: [black]
@@ -186,8 +202,8 @@ jobs:
         shell: bash -l {0}
         timeout-minutes: 20
         run: |
-          flux start papermill notebooks/5-1-gpaw.ipynb notebooks/5-1-gpaw-out.ipynb -k python3
-          flux start papermill notebooks/5-2-quantum-espresso.ipynb notebooks/5-2-quantum-espresso-out.ipynb -k python3
+          flux start papermill notebooks/4-1-gpaw.ipynb notebooks/4-1-gpaw-out.ipynb -k python3
+          flux start papermill notebooks/4-2-quantum-espresso.ipynb notebooks/4-2-quantum-espresso-out.ipynb -k python3
 
   unittest_flux_mpich:
     needs: [black]
@@ -442,7 +458,7 @@ jobs:
           GH_TOKEN: ${{secrets.GITHUB_TOKEN}}
 
   uml:
-    needs: [unittest_slurm_mpich, unittest_old, unittest_win, unittest_openmpi, unittest_mpich, unittest_flux_openmpi, unittest_flux_mpich, notebooks, benchmark, minimal, pip_check, mypy]
+    needs: [uv_check, unittest_slurm_mpich, unittest_old, unittest_win, unittest_openmpi, unittest_mpich, unittest_flux_openmpi, unittest_flux_mpich, notebooks, benchmark, minimal, pip_check, mypy]
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4