Package modernization

.github/workflows/CI.yaml

@@ -22,8 +22,23 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.9"
+          cache: pip
+          cache-dependency-path: pyproject.toml
+
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --files solvation_analysis/*
+
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+    name: pip install on ${{ matrix.os }}, Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -34,71 +49,21 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Additional info about the build
-      shell: bash
-      run: |
-        uname -a
-        df -h
-        ulimit -a
-
-
-    # More info on options: https://github.com/conda-incubator/setup-miniconda
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-        environment-file: devtools/conda-envs/test_env.yaml
-
-        channels: conda-forge,defaults
-
-        activate-environment: test
-        auto-update-conda: false
-        auto-activate-base: false
-        show-channel-urls: true
 
     - name: Install package
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
       run: |
-        python -m pip install . --no-deps
-        conda list
-
+        python -m pip install .
 
     - name: Run tests
-
-      # conda setup requires this special shell
-      shell: bash -l {0}
-
       run: |
-        pytest -v --cov=solvation_analysis --cov-report=xml --color=yes solvation_analysis/tests/
+        pytest -v --color=yes solvation_analysis/tests/
 
     - name: CodeCov
       uses: codecov/codecov-action@v1
       with:
         file: ./coverage.xml
         flags: unittests
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-
-  test_pip_install:
-    name: pip (PEP517) install on ${{ matrix.os }}, Python ${{ matrix.python-version }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: [3.9, "3.10", 3.11, 3.12]
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install package
-      run: |
-        python -m pip install .
-
-    - name: Run tests
-      run: |
-        pytest -v --color=yes solvation_analysis/tests/

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+default_language_version:
+  python: python3
+repos:
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.4.2
+  hooks:
+  - id: ruff
+    args: [--fix]
+  - id: ruff-format
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+  - id: check-yaml
+  - id: fix-encoding-pragma
+    args: [--remove]
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.10.0
+  hooks:
+  - id: python-use-type-annotations
+  - id: rst-backticks
+  - id: rst-directive-colons
+  - id: rst-inline-touching-normal
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.10.0
+  hooks:
+  - id: mypy
+    files: ^src/
+    additional_dependencies:
+    - tokenize-rt==4.1.0
+    - types-paramiko
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.6
+  hooks:
+  - id: codespell
+    stages: [commit, commit-msg]
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
+    types_or: [python, rst, markdown]

README.md

@@ -37,17 +37,20 @@ conda install -c conda-forge solvation_analysis
 
 ### Contributing
 
-Contributions, both issues and PRs, are welcome. If you'd like to contribute, we ask that you 
+Contributions, both issues and PRs, are welcome. If you'd like to contribute, we ask that you
 follow the community guidelines outlined in the [MDAnalysis Code of Conduct](https://www.mdanalysis.org/pages/conduct/).
 
+Solvation Analysis uses [pre-commit](https://pre-commit.com/) for linting. Make sure to install
+the pre-commit hooks if you are working on a contribution.
+
 ### Citation
 
 This work is described in [JOSS](https://doi.org/10.21105/joss.05183), please cite it if you make
 use of this package in published work.
 
 ---
 
-Project based on the 
+Project based on the
 [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.
 
 

docs/requirements.yaml

@@ -14,8 +14,8 @@ dependencies:
   - ipython
   - plotly
   - sphinx_rtd_theme
+  - scipy==1.12.0
 
 
     # Pip-only installs
   #- pip:
-

docs/tutorials/basics_tutorial.ipynb

@@ -80,7 +80,7 @@
    "outputs": [],
    "source": [
     "# instantiate solute\n",
-    "from solvation_analysis.solute import Solute\n",
+    "from solvation_analysis import Solute\n",
     "\n",
     "solute = Solute.from_atoms(li_atoms, {'PF6': PF6, 'BN': BN, 'FEC': FEC}, solute_name=\"Li\")"
    ]
@@ -239,14 +239,16 @@
     "    li_atoms,\n",
     "    {'PF6': PF6, 'BN': BN, 'FEC': FEC},\n",
     "    solute_name=\"Li\",\n",
-    "    radii={\"PF6\": 2.6}\n",
+    "    radii={\"PF6\": 2.6},\n",
+    "    kernel_kwargs={\"default\": 3.0}\n",
     ")\n",
     "\n",
     "solute.run()"
    ],
    "metadata": {
     "collapsed": false
-   }
+   },
+   "id": "e7a6367c65eaded3"
   },
   {
    "cell_type": "code",

docs/tutorials/clustering_and_residence_tutorial.ipynb

@@ -35,7 +35,7 @@
    "source": [
     "# imports\n",
     "import MDAnalysis as mda\n",
-    "from solvation_analysis.solute import Solute\n",
+    "from solvation_analysis import Solute\n",
     "\n",
     "# we will use a trajectory supplied by the package\n",
     "from solvation_analysis.tests import datafiles\n",

docs/tutorials/multi_atom_solutes.ipynb

@@ -27,7 +27,7 @@
    "outputs": [],
    "source": [
     "import MDAnalysis as mda\n",
-    "from solvation_analysis.solute import Solute\n",
+    "from solvation_analysis import Solute\n",
     "\n",
     "from solvation_analysis.tests.datafiles import iba_data, iba_dcd\n",
     "\n",

docs/tutorials/plotting_tutorial.ipynb

@@ -21,7 +21,7 @@
     "\n",
     "import plotly.io\n",
     "plotly.io.renderers.default = 'svg'\n",
-    "from solvation_analysis.solute import Solute\n",
+    "from solvation_analysis import Solute\n",
     "# this is a dict of dicts, {solute_name: {group_name: atom_group}}\n",
     "from setup_eax_solutes import u_eax_atom_groups"
    ]

docs/tutorials/rdf_fitting_demo.ipynb

@@ -24,7 +24,7 @@
     "\n",
     "from solvation_analysis.rdf_parser import plot_scipy_find_peaks_troughs, identify_cutoff_scipy\n",
     "from solvation_analysis.tests import datafiles\n",
-    "from solvation_analysis.solute import Solute\n",
+    "from solvation_analysis import Solute\n",
     "\n",
     "from scipy.signal import find_peaks"
    ]

docs/tutorials/visualization_tutorial.ipynb

@@ -21,7 +21,7 @@
    "source": [
     "# imports\n",
     "import MDAnalysis as mda\n",
-    "from solvation_analysis.solute import Solute\n",
+    "from solvation_analysis import Solute\n",
     "from solvation_analysis.tests import datafiles\n",
     "\n",
     "from IPython.display import Image\n",

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     'pytest',
     'matplotlib',
     'setuptools',
-    'scipy',
+    'scipy==1.12.0',
     'statsmodels',
     'plotly',
     'rdkit'

requirements.txt

@@ -1,11 +1,11 @@
 setuptools
 numpy>=1.20.0
 pandas>=2.2
-mdanalysis>=2.0.0
+mdanalysis>=2.7.0
 pytest
 pathlib
 matplotlib
-scipy
+scipy==1.12.0
 statsmodels
 plotly
 rdkit

setup.py

@@ -2,57 +2,54 @@
 SolvationAnalysis
 An MDAnalysis rmodule for solvation analysis.
 """
+
 import sys
 from setuptools import setup, find_packages
 import versioneer
 
 short_description = __doc__.split("\n")
 
 # from https://github.com/pytest-dev/pytest-runner#conditional-requirement
-needs_pytest = {'pytest', 'test', 'ptr'}.intersection(sys.argv)
-pytest_runner = ['pytest-runner'] if needs_pytest else []
+needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
+pytest_runner = ["pytest-runner"] if needs_pytest else []
 
 try:
     with open("README.md", "r") as handle:
         long_description = handle.read()
-except:
+except:  # noqa
     long_description = "\n".join(short_description[2:])
 
 
 setup(
     # Self-descriptive entries which should always be present
-    name='solvation_analysis',
-    author='Orion Cohen',
-    author_email='[email protected]',
+    name="solvation_analysis",
+    author="Orion Cohen",
+    author_email="[email protected]",
     description=short_description[0],
     long_description=long_description,
     long_description_content_type="text/markdown",
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    license='GNU Public License v3',
-
+    license="GNU Public License v3",
     # Which Python importable modules should be included when your package is installed
     # Handled automatically by setuptools. Use 'exclude' to prevent some specific
     # subpackage(s) from being added, if needed
     packages=find_packages(),
-
     # Optional include package data to ship with your package
     # Customize MANIFEST.in if the general case does not suit your needs
     # Comment out this line to prevent the files from being packaged with your software
     include_package_data=True,
-
     # Allows `setup.py test` to work correctly with pytest
     setup_requires=[] + pytest_runner,
-
     install_requires=[
-        'numpy>=1.20.0',
-        'mdanalysis>=2.7.0',
-        'pandas',
-        'matplotlib',
-        'scipy',
-        'statsmodels',
-        'plotly',
-        'rdkit'
+        "numpy>=1.20.0",
+        "mdanalysis>=2.7.0",
+        "pandas",
+        "matplotlib",
+        "scipy==1.12.0",
+        "statsmodels",
+        "plotly",
+        "rdkit",
     ],
     # Additional entries you may want simply uncomment the lines you want and fill in the data
     # url='http://www.my_package.com',  # Website
@@ -62,8 +59,6 @@
     #            'Unix',
     #            'Windows'],            # Valid platforms your code works on, adjust to your flavor
     # python_requires=">=3.5",          # Python version restrictions
-
     # Manual control if final package is compressible or not, set False to prevent the .egg from being made
     # zip_safe=False,
-
 )

solvation_analysis/__init__.py

@@ -3,12 +3,17 @@
 An MDAnalysis rmodule for solvation analysis.
 """
 
+from . import _version
+from solvation_analysis.solute import Solute
+
 # Handle versioneer
 from ._version import get_versions
+
 versions = get_versions()
-__version__ = versions['version']
-__git_revision__ = versions['full-revisionid']
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
 del get_versions, versions
 
-from . import _version
-__version__ = _version.get_versions()['version']
+
+__version__ = _version.get_versions()["version"]
+__all__ = ["Solute"]

solvation_analysis/_column_names.py

@@ -8,7 +8,6 @@
 1. change the variable name in all files
 """
 
-
 # for solvation_data
 FRAME = "frame"
 SOLUTE_IX = "solute_ix"