Switch to pyproject.toml

.ci_support/environment_mini.yml

@@ -3,6 +3,6 @@ channels:
 dependencies:
 - ase =3.22.1
 - coverage
-- matplotlib-base =3.7.2
+- matplotlib-base =3.8.2
 - numpy =1.26.2
 - scipy =1.11.4

.ci_support/release.py

@@ -0,0 +1,61 @@
+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(',')
+            for dep in lst:
+                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
+
+
+def get_env_version(env_content):
+    read_flag = False
+    depend_lst, version_lst = [], []
+    for l in env_content:
+        if 'dependencies:' in l:
+            read_flag = True
+        elif read_flag:
+            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)}
+
+
+def update_dependencies(setup_content, version_low_dict, version_high_dict):
+    version_combo_dict = {}
+    for dep, ver in version_high_dict.items():
+        if dep in version_low_dict.keys() and version_low_dict[dep] != ver:
+            version_combo_dict[dep] = dep + ">=" + version_low_dict[dep] + ",<=" + ver
+        else:
+            version_combo_dict[dep] = dep + "==" + ver
+
+    setup_content_new = ""
+    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
+    return setup_content_new
+
+
+if __name__ == "__main__":
+    with open('pyproject.toml', "r") as f:
+        setup_content = f.readlines()
+
+    with open('environment.yml', "r") as f:
+        env_content = f.readlines()
+
+    setup_content_new = update_dependencies(
+        setup_content=setup_content,
+        version_low_dict=get_env_version(env_content=env_content),
+        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content),
+    )
+
+    with open('pyproject.toml', "w") as f:
+        f.writelines(setup_content_new)

.github/workflows/black.yml

@@ -12,7 +12,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: psf/black@stable
       with:
         options: "--check --diff"

.github/workflows/dependabot.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     if: (github.actor == 'dependabot[bot]')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
           fetch-depth: 0 # otherwise, you will fail to push refs to dest repo

.github/workflows/deploy.yml

@@ -22,15 +22,13 @@ jobs:
     - uses: actions/setup-python@v2
       with:
         python-version: "3.11"
-
     - name: Install dependencies
-      run: >-
-        python -m pip install --user --upgrade setuptools wheel
+      run: python -m pip install --user --upgrade setuptools wheel
     - name: Convert dependencies
-      run: >-
-        sed -i 's/==/>=/g' setup.py; cat setup.py
+      run: |
+        cp .ci_support/environment-old.yml environment.yml
+        python .ci_support/release.py; cat pyproject.toml
     - name: Build
-      run: >-
-        python setup.py sdist bdist_wheel
+      run: python setup.py sdist bdist_wheel
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/mini.yml

@@ -17,9 +17,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
-      run: cp .ci_support/environment_mini.yml environment.yml
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -28,14 +26,11 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: .ci_support/environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
-      run: python -m unittest discover tests
+      run: |
+        python -m pip install --no-deps .
+        python -m unittest discover tests

.github/workflows/pypicheck.yml

@@ -14,9 +14,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
-      run: cp .ci_support/environment.yml environment.yml
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -25,12 +23,10 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: .ci_support/environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-      if: steps.cache.outputs.cache-hit != 'true'
     - name: Pip check
       shell: bash -l {0}
       run: |
-        pip install --no-deps .
-        pip check
+        python -m pip install --no-deps .
+        python -m pip check

.github/workflows/unittests.yml

@@ -45,9 +45,7 @@ jobs:
           prefix: /usr/share/miniconda3/envs/my-env
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup environment
-      run: cp .ci_support/environment.yml environment.yml
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -56,17 +54,13 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: .ci_support/environment.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f environment.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
       run: |
+        python -m pip install --no-deps .
         coverage run --omit structuretoolkit/_version.py -m unittest discover tests
     - name: Coverage
       if:  matrix.label == 'linux-64-py-3-10'

.github/workflows/unittests_old.yml

@@ -13,7 +13,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -22,13 +22,11 @@ jobs:
         channels: conda-forge
         channel-priority: strict
         activate-environment: my-env
+        environment-file: .ci_support/environment-old.yml
         use-mamba: true
-    - name: Update environment
-      run: mamba env update -n my-env -f .ci_support/environment-old.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 30
-      run: python -m unittest discover tests
+      run: |
+        python -m pip install --no-deps .
+        python -m unittest discover tests

pyproject.toml

@@ -0,0 +1,70 @@
+[build-system]
+requires = ["ase", "matplotlib", "numpy", "setuptools", "scipy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "structuretoolkit"
+description = "build, analyse and visualise atomistic structures for materials science"
+authors = [
+    { name = "Jan Janssen", email = "janssen@mpie.de" },
+]
+readme = "README.md"
+license = { file = "LICENSE" }
+keywords = ["pyiron"]
+requires-python = ">=3.8"
+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",
+]
+dependencies = [
+    "ase==3.22.1",
+    "matplotlib==3.8.2",
+    "numpy==1.26.2",
+    "scipy==1.11.4",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/pyiron/structuretoolkit"
+Documentation = "https://github.com/pyiron/structuretoolkit"
+Repository = "https://github.com/pyiron/structuretoolkit"
+
+[project.optional-dependencies]
+grainboundary = [
+    "aimsgb==1.1.0",
+    "pymatgen==2023.11.12",
+]
+pyscal = ["pyscal2==2.10.18"]
+nglview = ["nglview==3.0.8"]
+plotly = ["plotly==5.18.0"]
+clusters = ["scikit-learn==1.3.2"]
+symmetry = ["spglib==2.1.0"]
+surface = [
+    "spglib==2.1.0",
+    "pymatgen==2023.11.12",
+]
+phonopy = [
+    "phonopy==2.20.0",
+    "spglib==2.1.0",
+]
+pyxtal = ["pyxtal==0.6.1"]
+
+[tool.setuptools]
+packages = ["structuretoolkit"]
+
+[tool.setuptools.dynamic]
+version = {attr = "structuretoolkit.__version__"}
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440-pre"
+versionfile_source = "structuretoolkit/_version.py"
+parentdir_prefix = "structuretoolkit"
+tag_prefix = "structuretoolkit-"

setup.py

@@ -1,50 +1,3 @@
-"""
-Setuptools based setup module
-"""
-from setuptools import setup, find_packages
-import versioneer
+from setuptools import setup
 
-setup(
-    name='structuretoolkit',
-    version=versioneer.get_version(),
-    description='structuretoolkit - to analyse, build and visualise atomistic structures.',
-    long_description='http://pyiron.org',
-
-    url='https://github.com/pyiron/structuretoolkit',
-    author='Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department',
-    author_email='janssen@mpie.de',
-    license='BSD',
-
-    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'
-    ],
-
-    keywords='pyiron',
-    packages=find_packages(exclude=["*tests*", "*docs*", "*binder*", "*conda*", "*notebooks*", "*.ci_support*"]),
-    install_requires=[
-        'ase==3.22.1',
-        'matplotlib==3.8.2',  # ase already requires matplotlib
-        'numpy==1.26.2',  # ase already requires numpy
-        'scipy==1.11.4',  # ase already requires scipy
-    ],
-    extras_require={
-        "grainboundary": ['aimsgb==1.1.0', 'pymatgen==2023.11.12'],
-        "pyscal": ['pyscal2==2.10.18'],
-        "nglview": ['nglview==3.0.8'],
-        "plotly": ['plotly==5.18.0'],
-        "clusters": ['scikit-learn==1.3.2'],
-        "symmetry": ['spglib==2.1.0'],
-        "surface": ['spglib==2.1.0', 'pymatgen==2023.11.12'],
-        "phonopy": ['phonopy==2.20.0', 'spglib==2.1.0'],
-        "pyxtal": ['pyxtal==0.6.1']
-    },
-    cmdclass=versioneer.get_cmdclass(),
-)
+setup()

structuretoolkit/__init__.py

@@ -1,3 +1,5 @@
+from . import _version
+
 # Analyse
 from structuretoolkit.analyse import (
     find_mic,
@@ -73,3 +75,5 @@
     grainboundary as grainboundary_build,
     sqs_structures as get_sqs_structures,
 )
+
+__version__ = _version.get_versions()["version"]