Merge branch 'main' into dependabot/pip/numpy-2.0.1

.ci_support/environment-lammps.yml

@@ -1,4 +1,5 @@
 channels:
 - conda-forge
 dependencies:
-- lammps =2024.02.07
+- lammps =2024.06.27=*openmpi*
+- openmpi =4.1.6

.ci_support/environment.yml

@@ -6,16 +6,16 @@ dependencies:
 - ase =3.23.0
 - coverage
 - dscribe =2.1.1
-- matplotlib-base =3.9.1
+- matplotlib-base =3.9.2
 - nglview =3.1.2
 - notebook
 - numpy =2.1.1
 - phonopy =2.26.6
-- plotly =5.22.0
-- pymatgen =2024.6.10
-- pyscal3 =3.2.6
-- pyxtal =0.6.7
-- scikit-learn =1.5.1
-- scipy =1.14.0
+- plotly =5.24.0
+- pymatgen =2024.9.10
+- pyscal3 =3.2.7
+- pyxtal =1.0.3
+- scikit-learn =1.5.2
+- scipy =1.14.1
 - spglib =2.5.0
 - sqsgenerator =0.3

.ci_support/environment_mini.yml

@@ -4,4 +4,4 @@ dependencies:
 - ase =3.23.0
 - coverage
 - numpy =2.1.1
-- scipy =1.14.0
+- scipy =1.14.1

.github/workflows/deploy.yml

@@ -19,22 +19,19 @@ jobs:
       id-token: write
     steps:
     - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: "3.12"
-        mamba-version: "*"
-        channels: conda-forge
-        miniforge-variant: Mambaforge
-        channel-priority: strict
-        auto-update-conda: true
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment.yml
-    - name: Convert dependencies
-      run: |
-        cp .ci_support/environment-old.yml environment.yml
-        python .ci_support/release.py; cat pyproject.toml
     - name: Build
       shell: bash -l {0}
       run: |
+        cp .ci_support/environment-old.yml environment.yml
+        python .ci_support/release.py; cat pyproject.toml
         pip install versioneer[toml]==0.29
         python setup.py sdist bdist_wheel
     - name: Publish distribution 📦 to PyPI

.github/workflows/mini.yml

@@ -17,16 +17,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.12'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment_mini.yml
-        use-mamba: true
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30

.github/workflows/pypicheck.yml

@@ -14,16 +14,15 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.12'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment.yml
-        use-mamba: true
     - name: Pip check
       shell: bash -l {0}
       run: |

.github/workflows/unittests.yml

@@ -48,16 +48,16 @@ jobs:
     - name: Merge conda environment
       if:  matrix.operating-system != 'windows-latest'
       run: tail --lines=+4 .ci_support/environment-lammps.yml >> .ci_support/environment.yml
+    - name: Conda config
+      shell: bash -l {0}
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment.yml
-        use-mamba: true
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30

.github/workflows/unittests_old.yml

@@ -13,16 +13,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+    - name: Conda config
+      run: echo -e "channels:\n  - conda-forge\n" > .condarc
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.9'
-        miniforge-variant: Mambaforge
-        channels: conda-forge
-        channel-priority: strict
-        activate-environment: my-env
+        miniforge-version: latest
+        condarc-file: .condarc
         environment-file: .ci_support/environment-old.yml
-        use-mamba: true
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.2
+    rev: v0.6.4
     hooks:
       - id: ruff
         name: ruff lint

pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 dependencies = [
     "ase==3.23.0",
     "numpy==2.1.1",
-    "scipy==1.14.0",
+    "scipy==1.14.1",
 ]
 dynamic = ["version"]
 
@@ -39,23 +39,23 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.1"]
 grainboundary = [
     "aimsgb==1.1.1",
-    "pymatgen==2024.6.10",
+    "pymatgen==2024.9.10",
 ]
-pyscal = ["pyscal3==3.2.6"]
+pyscal = ["pyscal3==3.2.7"]
 nglview = ["nglview==3.1.2"]
-matplotlib = ["matplotlib==3.9.1"]
-plotly = ["plotly==5.22.0"]
-clusters = ["scikit-learn==1.5.1"]
+matplotlib = ["matplotlib==3.9.2"]
+plotly = ["plotly==5.24.0"]
+clusters = ["scikit-learn==1.5.2"]
 symmetry = ["spglib==2.5.0"]
 surface = [
     "spglib==2.5.0",
-    "pymatgen==2024.6.10",
+    "pymatgen==2024.9.10",
 ]
 phonopy = [
     "phonopy==2.26.6",
     "spglib==2.5.0",
 ]
-pyxtal = ["pyxtal==0.6.7"]
+pyxtal = ["pyxtal==1.0.3"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]

structuretoolkit/analyse/distance.py

@@ -10,7 +10,7 @@ def get_distances_array(
     p2: Optional[np.ndarray] = None,
     mic: bool = True,
     vectors: bool = False,
-):
+) -> np.ndarray:
     """
     Return distance matrix of every position in p1 with every position in
     p2. If p2 is not set, it is assumed that distances between all
@@ -19,13 +19,14 @@ def get_distances_array(
     returned.
 
     Args:
-        p1 (numpy.ndarray/list): Nx3 array of positions
-        p2 (numpy.ndarray/list): Nx3 array of positions
-        mic (bool): minimum image convention
-        vectors (bool): return vectors instead of distances
+        structure (ase.atoms.Atoms): The structure object
+        p1 (numpy.ndarray/list, optional): Nx3 array of positions. Defaults to None.
+        p2 (numpy.ndarray/list, optional): Nx3 array of positions. Defaults to None.
+        mic (bool, optional): Minimum image convention. Defaults to True.
+        vectors (bool, optional): Return vectors instead of distances. Defaults to False.
+
     Returns:
         numpy.ndarray: NxN if vector=False and NxNx3 if vector=True
-
     """
     if p1 is None and p2 is not None:
         p1 = p2
@@ -48,16 +49,18 @@ def get_distances_array(
     return find_mic(structure=structure, v=diff_relative, vectors=vectors)
 
 
-def find_mic(structure: Atoms, v: np.ndarray, vectors: bool = True):
+def find_mic(structure: Atoms, v: np.ndarray, vectors: bool = True) -> np.ndarray:
     """
     Find vectors following minimum image convention (mic). In principle this
     function does the same as ase.geometry.find_mic
 
     Args:
-        v (list/numpy.ndarray): 3d vector or a list/array of 3d vectors
+        structure (ase.atoms.Atoms): The structure object
+        v (numpy.ndarray/list): 3d vector or a list/array of 3d vectors
         vectors (bool): Whether to return vectors (distances are returned if False)
 
-    Returns: numpy.ndarray of the same shape as input with mic
+    Returns:
+        numpy.ndarray: numpy.ndarray of the same shape as input with mic
     """
     if any(structure.pbc):
         v = np.einsum("ji,...j->...i", np.linalg.inv(structure.cell), v)

structuretoolkit/analyse/dscribe.py

@@ -23,6 +23,31 @@ def soap_descriptor_per_atom(
     only_physical_cores: bool = False,
     verbose: bool = False,
 ) -> np.ndarray:
+    """
+    Calculates the SOAP descriptor for each atom in the given structure.
+
+    Args:
+        structure (ase.atoms.Atoms): The atomic structure.
+        r_cut (float, optional): The cutoff radius. Defaults to None.
+        n_max (int, optional): The maximum number of radial basis functions. Defaults to None.
+        l_max (int, optional): The maximum degree of spherical harmonics. Defaults to None.
+        sigma (float, optional): The width parameter for the Gaussian-type orbital. Defaults to 1.0.
+        rbf (str, optional): The radial basis function. Defaults to "gto".
+        weighting (np.ndarray, optional): The weighting coefficients for the radial basis functions. Defaults to None.
+        average (str, optional): The type of averaging. Defaults to "off".
+        compression (dict, optional): The compression settings. Defaults to {"mode": "off", "species_weighting": None}.
+        species (list, optional): The list of chemical symbols. Defaults to None.
+        periodic (bool, optional): Whether the system is periodic. Defaults to True.
+        sparse (bool, optional): Whether to use sparse matrices. Defaults to False.
+        dtype (str, optional): The data type of the output. Defaults to "float64".
+        centers (np.ndarray, optional): The centers for the descriptor calculation. Defaults to None.
+        n_jobs (int, optional): The number of parallel jobs. Defaults to 1.
+        only_physical_cores (bool, optional): Whether to use only physical cores. Defaults to False.
+        verbose (bool, optional): Whether to print verbose output. Defaults to False.
+
+    Returns:
+        np.ndarray: The SOAP descriptor for each atom.
+    """
     from dscribe.descriptors import SOAP
 
     if species is None: