Merge branch 'main' into Py314u

Author: jan-janssen

.ci_support/environment-docs.yml

@@ -11,8 +11,8 @@ dependencies:
 - sphinx
 - sphinx_rtd_theme
 - cloudpickle =3.1.1
-- h5py =3.14.0
+- h5py =3.15.0
 - jupyter-book =1.0.0
-- mpi4py =4.1.0
+- mpi4py =4.1.1
 - python =3.12
 - pyzmq =27.1.0

.ci_support/environment-integration.yml

@@ -1,10 +1,10 @@
 channels:
 - conda-forge
 dependencies:
-- h5py
+- h5py =3.15.0
 - jupyter
-- mpi4py
-- numpy
+- mpi4py =4.1.1
+- numpy =2.3.3
 - openmpi
 - papermill
 - atomistics =0.3.0

.ci_support/environment-mini.yml

@@ -2,7 +2,7 @@ channels:
 - conda-forge
 dependencies:
 - python
-- numpy
+- numpy =2.3.3
 - cloudpickle =3.1.0
 - hatchling =1.27.0
 - hatch-vcs =0.5.0

.ci_support/environment-mpich.yml

@@ -2,14 +2,14 @@ channels:
 - conda-forge
 dependencies:
 - python
-- numpy
+- numpy =2.3.3
 - mpich
 - cloudpickle =3.1.1
-- h5py =3.14.0
+- h5py =3.15.0
 - hatchling =1.27.0
 - hatch-vcs =0.5.0
 - ipython =9.0.2
-- mpi4py =4.1.0
+- mpi4py =4.1.1
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.3.2

.ci_support/environment-openmpi.yml

@@ -2,14 +2,14 @@ channels:
 - conda-forge
 dependencies:
 - python
-- numpy
+- numpy =2.3.3
 - openmpi
 - cloudpickle =3.1.1
-- h5py =3.14.0
+- h5py =3.15.0
 - hatchling =1.27.0
 - hatch-vcs =0.5.0
 - ipython =9.0.2
-- mpi4py =4.1.0
+- mpi4py =4.1.1
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.3.2

.ci_support/environment-win.yml

@@ -2,14 +2,14 @@ channels:
 - conda-forge
 dependencies:
 - python
-- numpy
+- numpy =2.3.3
 - msmpi
 - cloudpickle =3.1.1
-- h5py =3.14.0
+- h5py =3.15.0
 - hatchling =1.27.0
 - hatch-vcs =0.5.0
 - ipython =9.0.2
-- mpi4py =4.1.0
+- mpi4py =4.1.1
 - networkx =3.4.2
 - pygraphviz =1.14
 - pyzmq =27.1.0

.github/workflows/deploy.yml

@@ -31,7 +31,7 @@ jobs:
       run: |
         cp .ci_support/environment-old.yml environment.yml
         python .ci_support/release.py; cat pyproject.toml
-        git update-index --assume-unchanged pyproject.toml executorlib/_version.py
+        git update-index --assume-unchanged pyproject.toml src/executorlib/_version.py
         hatchling build -t sdist -t wheel
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pipeline.yml

@@ -13,7 +13,7 @@ jobs:
     - uses: psf/black@stable
       with:
         options: "--check --diff"
-        src: ./${{ github.event.repository.name }}
+        src: ./src/${{ github.event.repository.name }}
 
   black_fix:  # in most cases pre-commit is faster
     needs: [black]
@@ -29,7 +29,7 @@ jobs:
       uses: psf/black@stable
       with:
         options: ""
-        src: "./${{ github.event.repository.name }}"
+        src: "./src/${{ github.event.repository.name }}"
     - name: commit
       run: |
         git config --local user.email "pyiron@mpie.de"
@@ -55,7 +55,7 @@ jobs:
       - name: Install mypy
         run: pip install mypy
       - name: Test
-        run: mypy --ignore-missing-imports ${{ github.event.repository.name }}
+        run: mypy --ignore-missing-imports src/${{ github.event.repository.name }}
 
   minimal:
     needs: [black]
@@ -457,7 +457,7 @@ jobs:
       timeout-minutes: 10
       run: |
         conda install -y pylint graphviz
-        pyreverse -o png -p ./${{ github.event.repository.name }} ./${{ github.event.repository.name }}
+        pyreverse -o png -p ./src/${{ github.event.repository.name }} ./src/${{ github.event.repository.name }}
         zip -m uml.zip *.png
     - uses: actions/upload-artifact@v4
       with:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.13.3
+    rev: v0.14.0
     hooks:
       - id: ruff
         name: ruff lint

binder/environment.yml

@@ -2,17 +2,17 @@ channels:
 - conda-forge
 dependencies:
 - python
-- numpy
+- numpy =2.3.3
 - openmpi
 - cloudpickle =3.1.1
 - flux-core =0.79.0
 - flux-pmix =0.6.0
 - hatchling =1.27.0
 - hatch-vcs =0.5.0
-- h5py =3.12.1
+- h5py =3.15.0
 - ipython =9.0.2
 - matplotlib =3.10.0
-- mpi4py =4.1.0
+- mpi4py =4.1.1
 - networkx =3.4.2
 - pygraphviz =1.14
 - pysqa =0.3.2