Merge remote-tracking branch 'refs/remotes/origin/main' into standardize

# Conflicts:
#	structuretoolkit/analyse/symmetry.py

Author: jan-janssen

.ci_support/environment-lammps.yml

@@ -0,0 +1,4 @@
+channels:
+- conda-forge
+dependencies:
+- lammps =2024.02.07

.ci_support/environment-old.yml

@@ -9,7 +9,7 @@ dependencies:
 - phonopy =2.16.2
 - plotly =4.14.3
 - pymatgen =2022.2.1
-- pyscal =2.10.4
+- pyscal3 =3.2.5
 - pyxtal =0.5.5
 - scikit-learn =1.2.1
 - scipy =1.9.3

.ci_support/environment.yml

@@ -1,19 +1,21 @@
+name: pyiron-structuretoolkit
 channels:
 - conda-forge
 dependencies:
-- aimsgb =1.1.0
-- ase =3.22.1
+- aimsgb =1.1.1
+- ase =3.23.0
 - coverage
-- matplotlib-base =3.8.2
-- nglview =3.1.1
+- dscribe =2.1.1
+- matplotlib-base =3.9.1
+- nglview =3.1.2
 - notebook
 - numpy =1.26.4
-- phonopy =2.21.0
-- plotly =5.18.0
-- pymatgen =2024.2.8
-- pyscal =2.10.18
-- pyxtal =0.6.2
-- scikit-learn =1.4.0
-- scipy =1.12.0
-- spglib =2.3.1
+- phonopy =2.26.5
+- 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
+- spglib =2.5.0
 - sqsgenerator =0.3

.ci_support/environment_mini.yml

@@ -1,7 +1,7 @@
 channels:
 - conda-forge
 dependencies:
-- ase =3.22.1
+- ase =3.23.0
 - coverage
 - numpy =1.26.4
-- scipy =1.12.0
+- scipy =1.14.0

.ci_support/release.py

@@ -1,12 +1,19 @@
 def get_setup_version_and_pattern(setup_content):
     depend_lst, version_lst = [], []
     for l in setup_content:
-        if '==' in l:
-            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+        if "==" in l:
+            lst = (
+                l.split("[")[-1]
+                .split("]")[0]
+                .replace(" ", "")
+                .replace('"', "")
+                .replace("'", "")
+                .split(",")
+            )
             for dep in lst:
-                if dep != '\n':
-                    version_lst.append(dep.split('==')[1])
-                    depend_lst.append(dep.split('==')[0])
+                if dep != "\n":
+                    version_lst.append(dep.split("==")[1])
+                    depend_lst.append(dep.split("==")[0])
 
     version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
     return version_high_dict
@@ -16,14 +23,14 @@ def get_env_version(env_content):
     read_flag = False
     depend_lst, version_lst = [], []
     for l in env_content:
-        if 'dependencies:' in l:
+        if "dependencies:" in l:
             read_flag = True
         elif read_flag:
-            lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=")
+            lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=")
             if len(lst) == 2:
                 depend_lst.append(lst[0])
                 version_lst.append(lst[1])
-    return {d:v for d, v in zip(depend_lst, version_lst)}
+    return {d: v for d, v in zip(depend_lst, version_lst)}
 
 
 def update_dependencies(setup_content, version_low_dict, version_high_dict):
@@ -35,27 +42,29 @@ def update_dependencies(setup_content, version_low_dict, version_high_dict):
             version_combo_dict[dep] = dep + "==" + ver
 
     setup_content_new = ""
-    pattern_dict = {d:d + "==" + v for d, v in version_high_dict.items()}
+    pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()}
     for l in setup_content:
         for k, v in pattern_dict.items():
             if v in l:
                 l = l.replace(v, version_combo_dict[k])
-        setup_content_new +=l
+        setup_content_new += l
     return setup_content_new
 
 
 if __name__ == "__main__":
-    with open('pyproject.toml', "r") as f:
+    with open("pyproject.toml", "r") as f:
         setup_content = f.readlines()
 
-    with open('environment.yml', "r") as f:
+    with open("environment.yml", "r") as f:
         env_content = f.readlines()
 
     setup_content_new = update_dependencies(
         setup_content=setup_content[2:],
         version_low_dict=get_env_version(env_content=env_content),
-        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+        version_high_dict=get_setup_version_and_pattern(
+            setup_content=setup_content[2:]
+        ),
     )
 
-    with open('pyproject.toml', "w") as f:
+    with open("pyproject.toml", "w") as f:
         f.writelines("".join(setup_content[:2]) + setup_content_new)

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @jan-janssen

.github/workflows/black.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 jobs:
   build:

.github/workflows/deploy.yml

@@ -19,9 +19,9 @@ jobs:
       id-token: write
     steps:
     - uses: actions/checkout@v4
-    - uses: conda-incubator/setup-miniconda@v2.2.0
+    - uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: 3.11
+        python-version: "3.12"
         mamba-version: "*"
         channels: conda-forge
         miniforge-variant: Mambaforge

.github/workflows/mini.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -19,7 +18,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.12'
         miniforge-variant: Mambaforge

.github/workflows/pypicheck.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 jobs:
   build:
@@ -16,9 +15,9 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: '3.11'
+        python-version: '3.12'
         miniforge-variant: Mambaforge
         channels: conda-forge
         channel-priority: strict
@@ -30,4 +29,4 @@ jobs:
       run: |
         pip install versioneer[toml]==0.29
         pip install . --no-deps --no-build-isolation
-        python -m pip check
+        python -m pip check

.github/workflows/unittests.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -20,15 +19,20 @@ jobs:
       matrix:
         include:
         - operating-system: windows-latest
-          python-version: '3.11'
-          label: win-64-py-3-11
+          python-version: '3.12'
+          label: win-64-py-3-12
           prefix: C:\Miniconda3\envs\my-env
 
         - operating-system: macos-latest
-          python-version: '3.11'
-          label: osx-64-py-3-11
+          python-version: '3.12'
+          label: osx-64-py-3-12
           prefix: /Users/runner/miniconda3/envs/my-env
 
+        - operating-system: ubuntu-latest
+          python-version: '3.12'
+          label: linux-64-py-3-12
+          prefix: /usr/share/miniconda3/envs/my-env
+
         - operating-system: ubuntu-latest
           python-version: '3.11'
           label: linux-64-py-3-11
@@ -39,15 +43,13 @@ jobs:
           label: linux-64-py-3-10
           prefix: /usr/share/miniconda3/envs/my-env
 
-        - operating-system: ubuntu-latest
-          python-version: '3.9'
-          label: linux-64-py-3-9
-          prefix: /usr/share/miniconda3/envs/my-env
-
     steps:
     - uses: actions/checkout@v4
+    - name: Merge conda environment
+      if:  matrix.operating-system != 'windows-latest'
+      run: tail --lines=+4 .ci_support/environment-lammps.yml >> .ci_support/environment.yml
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         miniforge-variant: Mambaforge
@@ -62,7 +64,8 @@ jobs:
       run: |
         pip install versioneer[toml]==0.29
         pip install . --no-deps --no-build-isolation
-        coverage run --omit structuretoolkit/_version.py -m unittest discover tests
+        coverage run  --omit="structuretoolkit/_version.py,tests/*" -m unittest discover tests
+        coverage xml
     - name: Coverage
-      if:  matrix.label == 'linux-64-py-3-10'
+      if:  matrix.label == 'linux-64-py-3-12'
       uses: coverallsapp/github-action@v2

.github/workflows/unittests_old.yml

@@ -6,7 +6,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 jobs:
   build:
@@ -15,7 +14,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup Mambaforge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: '3.9'
         miniforge-variant: Mambaforge

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.2
+    hooks:
+      - id: ruff
+        name: ruff lint
+        args: ["--select", "I", "--fix"]
+        files: ^structuretoolkit/
+      - id: ruff-format
+        name: ruff format

pyproject.toml

@@ -11,22 +11,22 @@ authors = [
 readme = "README.md"
 license = { file = "LICENSE" }
 keywords = ["pyiron"]
-requires-python = ">=3.8"
+requires-python = ">=3.9, <3.13"
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Topic :: Scientific/Engineering :: Physics",
     "License :: OSI Approved :: BSD License",
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-    "ase==3.22.1",
+    "ase==3.23.0",
     "numpy==1.26.4",
-    "scipy==1.12.0",
+    "scipy==1.14.0",
 ]
 dynamic = ["version"]
 
@@ -36,25 +36,26 @@ Documentation = "https://github.com/pyiron/structuretoolkit"
 Repository = "https://github.com/pyiron/structuretoolkit"
 
 [project.optional-dependencies]
+dscribe = ["dscribe==2.1.1"]
 grainboundary = [
-    "aimsgb==1.1.0",
-    "pymatgen==2024.2.8",
+    "aimsgb==1.1.1",
+    "pymatgen==2024.6.10",
 ]
-pyscal = ["pyscal2==2.10.18"]
-nglview = ["nglview==3.1.1"]
-matplotlib = ["matplotlib==3.8.2"]
-plotly = ["plotly==5.18.0"]
-clusters = ["scikit-learn==1.4.0"]
-symmetry = ["spglib==2.3.1"]
+pyscal = ["pyscal3==3.2.6"]
+nglview = ["nglview==3.1.2"]
+matplotlib = ["matplotlib==3.9.1"]
+plotly = ["plotly==5.22.0"]
+clusters = ["scikit-learn==1.5.1"]
+symmetry = ["spglib==2.5.0"]
 surface = [
-    "spglib==2.3.1",
-    "pymatgen==2024.2.8",
+    "spglib==2.5.0",
+    "pymatgen==2024.6.10",
 ]
 phonopy = [
-    "phonopy==2.21.0",
-    "spglib==2.3.1",
+    "phonopy==2.26.5",
+    "spglib==2.5.0",
 ]
-pyxtal = ["pyxtal==0.6.2"]
+pyxtal = ["pyxtal==0.6.7"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]

setup.py

@@ -1,8 +1,7 @@
-from setuptools import setup
-
 import versioneer
+from setuptools import setup
 
 setup(
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-)
+)