Switch to pyproject.toml

.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[2:],
+        version_low_dict=get_env_version(env_content=env_content),
+        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+    )
+
+    with open('pyproject.toml', "w") as f:
+        f.writelines("".join(setup_content[:2]) + 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/coverage.yml

@@ -14,7 +14,7 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: "3.11"
@@ -23,13 +23,10 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-openmpi.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       run: |
+        pip install --no-deps .
         coverage run --omit pylammpsmpi/_version.py -m unittest discover tests
         coverage combine
     - name: Coveralls

.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

@@ -14,23 +14,21 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/pylammpsmpi
+      url: https://pypi.org/p/${{ github.event.repository.name }}
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
       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 versioneer
     - 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/format_black.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
         ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR

.github/workflows/pypicheck.yml

@@ -10,7 +10,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: "3.11"

.github/workflows/unittests-mpich.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
@@ -27,10 +27,9 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-mpich.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 5
-      run: python -m unittest discover tests
+      run: |
+        pip install --no-deps .
+        python -m unittest discover tests

.github/workflows/unittests-old.yml

@@ -14,7 +14,7 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: '3.9'
@@ -23,10 +23,9 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-old.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 5
-      run: python -m unittest discover tests
+      run: |
+        pip install --no-deps .
+        python -m unittest discover tests

.github/workflows/unittests-openmpi.yml

@@ -18,7 +18,7 @@ jobs:
         python-version: ['3.9', '3.10', '3.11']
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
@@ -27,10 +27,9 @@ jobs:
         channel-priority: strict
         use-mamba: true
         environment-file: .ci_support/environment-openmpi.yml
-    - name: Setup
-      shell: bash -l {0}
-      run: pip install --no-deps .
     - name: Test
       shell: bash -l {0}
       timeout-minutes: 5
-      run: python -m unittest discover tests
+      run: |
+        pip install --no-deps .
+        python -m unittest discover tests

MANIFEST.in

@@ -1,3 +1 @@
-include LICENSE
-include versioneer.py
-include pylammpsmpi/_version.py
+include LICENSE

pylammpsmpi/__init__.py

@@ -1,14 +1,12 @@
-from pylammpsmpi.wrapper.extended import LammpsLibrary
-from pylammpsmpi.wrapper.concurrent import LammpsConcurrent
-from pylammpsmpi.wrapper.base import LammpsBase
-
 from ._version import get_versions
 
 try:
+    from pylammpsmpi.wrapper.extended import LammpsLibrary
+    from pylammpsmpi.wrapper.concurrent import LammpsConcurrent
+    from pylammpsmpi.wrapper.base import LammpsBase
     from pylammpsmpi.wrapper.ase import LammpsASELibrary
 except ImportError:
     pass
 
 
 __version__ = get_versions()["version"]
-del get_versions

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools", "versioneer[toml]==0.29"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pylammpsmpi"
+description = "Parallel Lammps Python interface - control a mpi4py parallel LAMMPS instance from a serial python process or a Jupyter notebook"
+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 = [
+    "mpi4py==3.1.5",
+    "pympipool==0.7.5",
+    "numpy==1.26.2",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/pyiron/pylammpsmpi"
+Documentation = "https://github.com/pyiron/pylammpsmpi"
+Repository = "https://github.com/pyiron/pylammpsmpi"
+
+[project.optional-dependencies]
+ase = [
+    "ase==3.22.1",
+    "scipy==1.11.4",
+]
+
+[tool.setuptools.packages.find]
+include = ["pylammpsmpi*"]
+
+[tool.setuptools.dynamic]
+version = {attr = "pylammpsmpi.__version__"}
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440-pre"
+versionfile_source = "pylammpsmpi/_version.py"
+parentdir_prefix = "pylammpsmpi"
+tag_prefix = "pylammpsmpi-"

setup.py

@@ -1,36 +1,8 @@
-from setuptools import setup, find_packages
+from setuptools import setup
+
 import versioneer
 
 setup(
-    name="pylammpsmpi",
     version=versioneer.get_version(),
-    description="Parallel Lammps Python interface",
-    long_description="PylammpsMPI couples a serial python process to an MPI parallel LAMMPS libary.",
-    url='https://github.com/pyiron/pylammpsmpi',
-    author='Jan Janssen',
-    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 :: 3.7',
-         'Programming Language :: Python :: 3.8',
-         'Programming Language :: Python :: 3.9',
-         'Programming Language :: Python :: 3.10',
-         'Programming Language :: Python :: 3.11',
-    ],
-
-    keywords='lammps, mpi4py',
-    packages=find_packages(exclude=["*tests*"]),
-    install_requires=[
-        "mpi4py==3.1.5", "pympipool==0.7.5", "numpy==1.26.2"
-    ],
-    extras_require={
-        "ase": ["ase==3.22.1", "scipy==1.11.4"],
-    },
     cmdclass=versioneer.get_cmdclass(),
-)
+)