Fix ci

.github/workflows/CI.yaml

@@ -21,16 +21,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: ["3.8", "3.9"]
+        os: [macOS-latest, ubuntu-latest, macOS-13]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     # Cache our conda packages.
     # More info: https://github.com/conda-incubator/setup-miniconda#caching-packages
     - name: Cache conda environment
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       env:
         # Increase this value to reset cache if environment.yml has not changed
         CACHE_NUMBER: 0
@@ -41,15 +41,15 @@ jobs:
 
     # More info on options: https://github.com/conda-incubator/setup-miniconda
     - name: Set up Anaconda environment
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
         environment-file: environment.yml
-        channels: psi4,conda-forge,defaults
+        channels: conda-forge,defaults
         activate-environment: mdsapt
         auto-update-conda: false
         auto-activate-base: false
-        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          #use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
     # TODO: make pyright happier someday in the future
     # - name: Type-check
@@ -83,8 +83,8 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [macOS-13, ubuntu-latest]
+        python-version: [3.9, 3.10, 3.11, 3.12]
         include:
           - os: macOS-latest
             output-folder: osx-64
@@ -116,7 +116,7 @@ jobs:
         activate-environment: mdsapt-build
         auto-update-conda: false
         auto-activate-base: false
-        use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          #use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
 
     - name: Build MDSAPT conda package
       # conda requires this special shell
@@ -139,8 +139,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [macOS-latest, ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        os: [macOS-latest, macOS-13, ubuntu-latest]
+        python-version: [3.9, 3.10, 3.11, 3.12]
 
     steps:
     - uses: actions/checkout@v2

README.md

@@ -3,8 +3,8 @@ MD-SAPT
 SAPT Calculations for MDAnalysis
 
 [//]: # (Badges)
-[![GitHub Actions Build Status](https://github.com/alescoulie/MDSAPT/workflows/CI/badge.svg)](https://github.com/alescolie/MDSAPT/actions?query=workflow%3ACI)
-[![codecov](https://codecov.io/gh/alescoulie/MDSAPT/branch/master/graph/badge.svg)](https://codecov.io/gh/alescoulie/MDSAPT/branch/master)
+[![GitHub Actions Build Status](https://github.com/calpolyccg/MDSAPT/workflows/CI/badge.svg)](https://github.com/alescolie/MDSAPT/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/calpolyccg/MDSAPT/branch/master/graph/badge.svg)](https://codecov.io/gh/alescoulie/MDSAPT/branch/master)
 [![Documentation Status](https://readthedocs.org/projects/mdsapt/badge/?version=latest)](https://mdsapt.readthedocs.io/en/latest/?badge=latest)
 [![Launch binder demo](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/calpolyccg/MDSAPT_demo/master?labpath=MD-SAPT_demo.ipynb)
 

flake.nix

@@ -62,7 +62,7 @@
 
         devEnv = pkgs.mkShell {
           propagatedBuildInputs = [ poetryEnv];
-          buildInputs = with pkgs; [pkgs.qchem.psi4 pkgs.qchem.openmm pkgs.qchem.pdbfixer ];
+          buildInputs = with pkgs; [pkgs.qchem.psi4 pkgs.qchem.openmm pkgs.qchem.pdbfixer pkgs.act ];
         };
 
         # DON'T FORGET TO PUT YOUR PACKAGE NAME HERE, REMOVING `throw`

mdsapt/__init__.py

@@ -1,5 +1,6 @@
 # pylint: skip-file
 """An MDA-kit for calcuating quantum interactions in psi4."""
+from . import _version
 import logging
 
 from . import log
@@ -34,5 +35,4 @@ def log_banner() -> None:
 logger = create_logger()
 log_banner()
 
-from . import _version
 __version__ = _version.get_versions()['version']

mdsapt/_version.py

@@ -1,4 +1,3 @@
-
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
@@ -19,6 +18,9 @@
 from typing import Any, Callable, Dict, List, Optional, Tuple
 import functools
 
+# pylint: disable=consider-using-f-string
+# pylint: disable=invalid-name
+
 
 def get_keywords() -> Dict[str, str]:
     """Get the keywords needed to look up the version information."""
@@ -162,7 +164,7 @@ def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
     # _version.py.
     keywords: Dict[str, str] = {}
     try:
-        with open(versionfile_abs, "r") as fobj:
+        with open(versionfile_abs, "r") as fobj:  # pylint: disable=unspecified-encoding
             for line in fobj:
                 if line.strip().startswith("git_refnames ="):
                     mo = re.search(r'=\s*"(.*)"', line)

mdsapt/cli.py

@@ -1,9 +1,9 @@
+# pylint: disable=missing-module-docstring
 import logging
 import os
 import sys
 
 import click
-from mdsapt.config import RangeFrameSelection
 
 # Note that we do not import MDSAPT. This is a speed optimization; it is imported later.
 
@@ -16,11 +16,13 @@
 
 @click.group()
 def cli():
+    # pylint: disable=line-too-long
     """
     MDSAPT - Molecular Dynamics Symmetry-Adapted Perturbation Theory, by Alia Lescoulie, Astrid Yu, and Ashley Ringer McDonald.
 
     This command-line interface lets you easily do common MDSAPT-related tasks.
     """
+    # pylint: disable=line-too-long
 
 
 @cli.command()
@@ -43,17 +45,19 @@ def generate(filename: str, template: str, force: bool):
     """
     Generate a template input file at filename.
     """
+    # pylint: disable=fixme
     ensure_safe_to_overwrite(filename, force)
 
     # TODO: make a wizard for these templates
     template_path = os.path.join(_dir_path, 'data', f'{template}_template.yaml')
 
-    with open(template_path, 'r') as template:
+    with open(template_path, 'r', encoding='utf-8') as template:
         template_data = template.read()
-    with open(filename, 'w') as new_file:
+    with open(filename, 'w', encoding='utf-8') as new_file:
         new_file.write(template_data)
 
-    logger.info(f'Generated template input file {filename}')
+    logger.info('Generated template input file %s', filename)
+    # pylint: enable=fixme
 
 
 @cli.command()
@@ -75,7 +79,7 @@ def run(in_file: str, out_file: str, force: bool):
     Run a SAPT calculation using the configuration in in_file. Outputs will be written to
     out_file.
     """
-    import mdsapt
+    import mdsapt  # pylint: disable=import-outside-toplevel
 
     ensure_safe_to_overwrite(out_file, force)
 

mdsapt/config.py

@@ -43,15 +43,17 @@ class Psi4Config(BaseModel):
     Attributes:
         method:
             The SAPT method to use.
-            NOTE: You can use any valid Psi4 method, but it might fail if you don't use a SAPT method.
+            NOTE: You can use any valid Psi4 method, but it might fail
+            if you don't use a SAPT method.
         basis:
             The basis to use.
             NOTE: We do not verify if this is a valid basis set or not.
         save_output:
             Whether to save the raw output of Psi4. May be useful for debugging.
         settings:
             Other Psi4 settings you would like to provide. These will be passed into
-            `psi4.set_options <https://psicode.org/psi4manual/master/api/psi4.driver.set_options.html>`_.
+            `psi4.set_options 
+            <https://psicode.org/psi4manual/master/api/psi4.driver.set_options.html>`_.
     """
 
     method: str
@@ -97,10 +99,12 @@ class TopologySelection(BaseModel):
     Attributes:
         path: Where the topology file is located.
         topology_format: If specified, overrides the format to import with.
-        charge_overrides: An optional dictionary, where keys are atom numbers and values are their charges.
+        charge_overrides: An optional dictionary, where keys are atom numbers and 
+        values are their charges.
 
     .. seealso::
-        `List of topology formats that MDAnalysis supports <https://docs.mdanalysis.org/1.1.1/documentation_pages/topology/init.html>`_
+        `List of topology formats that MDAnalysis supports 
+        <https://docs.mdanalysis.org/1.1.1/documentation_pages/topology/init.html>`_
     """
 
     path: Path
@@ -164,16 +168,25 @@ class TrajectoryAnalysisConfig(BaseModel):
     type: Literal['trajectory']
     topology: TopologySelection
     trajectories: List[FilePath]
-    pairs: List[Tuple[Annotated[int, Field(strict=True, ge=0)], Annotated[int, Field(strict=True, ge=0)]
-                      ]]
+    pairs: List[
+        Tuple[
+            Annotated[
+                int,
+                Field(strict=True, ge=0)],
+            Annotated[int, Field(strict=True, ge=0)]
+        ]
+    ]
     frames: RangeFrameSelection
     output: str
 
     def create_universe(self, **universe_kwargs) -> mda.Universe:
         """
         Loads a universe from the given topology and trajectory
         """
-        return self.topology.create_universe([str(p) for p in self.trajectories], **universe_kwargs)
+        return self.topology.create_universe(
+            [str(p) for p in self.trajectories],
+            **universe_kwargs
+        )
 
     def get_selections(self) -> Set[int]:
         """
@@ -209,6 +222,10 @@ def get_invalid_residue_selections(residues: Iterable[int], unv: mda.Universe) -
 
 
 def get_individual_topologies(sel: TopologyGroupSelection) -> List[TopologySelection]:
+    """
+    Gets a list of :class:`mdsapt.config.TopolgoySelections` from a 
+    :class:`mdsapt.config.TopologyGroupSelection`
+    """
     if isinstance(sel, list):
         return sel
 
@@ -257,12 +274,27 @@ class DockingAnalysisConfig(BaseModel):
 
     @model_validator(mode='after')
     def ensure_presence_of_args(self) -> 'DockingAnalysisConfig':
-        provided_args = (self.combined_topologies is not None, self.protein is not None, self.ligands is not None)
+        """
+        Checks that arguments are correct
+        """
+        provided_args = (
+            self.combined_topologies is not None,
+            self.protein is not None,
+            self.ligands is not None
+        )
+
         if provided_args not in [(True, False, False), (False, True, True)]:
-            raise ValueError('Must provide `protein` and `ligands` keys, or only `combined_topologies`')
+            raise ValueError(
+                'Must provide `protein` and `ligands` keys, or only `combined_topologies`'
+            )
+
         return self
 
     def build_ensemble(self) -> Ensemble:
+        """
+        Creates an Ensemble containing the set of topologies used to analyze docking.
+
+        """
         return self._build_ensemble(combined_topologies=self.combined_topologies,
                                     protein=self.protein,
                                     ligands=self.ligands)
@@ -275,7 +307,9 @@ def _build_ensemble(
             protein: Optional[TopologySelection],
             ligands: Optional[TopologyGroupSelection],
     ) -> Ensemble:
-        """Fails if the wrong types of arguments are provided."""
+        """
+        Fails if the wrong types of arguments are provided.
+        """
         if combined_topologies is not None and (protein, ligands) == (None, None):
             return Ensemble.build_from_files(
                 [top.path for top in get_individual_topologies(combined_topologies)]
@@ -289,7 +323,9 @@ def _build_ensemble(
             ens = ens.merge(protein_mol)
             return ens
 
-        raise ValueError('Must provide `protein` and `ligands` keys, or only `combined_topologies`')
+        raise ValueError(
+            'Must provide `protein` and `ligands` keys, or only `combined_topologies`'
+        )
 
     def get_selections(self) -> Set[int]:
         """

mdsapt/repair.py

@@ -57,6 +57,9 @@ def get_spin_multiplicity(molecule: Chem.Mol) -> int:
 
 
 def is_amino(unv: mda.Universe, resid: int) -> bool:
+    """
+    Checks resnames aganst list of anmino acids, returns boolean if its in the list.
+    """
     std_resids: Set[str] = {
         'ALA',
         'ARG',
@@ -80,7 +83,7 @@ def is_amino(unv: mda.Universe, resid: int) -> bool:
         'VAL'
     }
 
-    resname_atr = unv._topology.resnames
+    resname_atr = unv._topology.resnames  # pylint: disable=protected-access
     return resname_atr.values[resid - 1] in std_resids
 
 

mdsapt/sapt.py

@@ -206,6 +206,10 @@ class DockingSAPT:
         'SAPT DISP ENERGY'
     ]
 
+    _res_dict: Dict[str, List[float]]
+    _key_names: Dict[str, str]
+    results: pd.DataFrame
+
     def __init__(self, config: Config) -> None:
         """
         Sets up ligand topology systems.
@@ -247,7 +251,7 @@ def _single_system(self) -> None:
 
             coords = xyz_dict[pair[0]] + '\n--\n' + xyz_dict[pair[1]] + '\nunits angstrom'
 
-            logger.info(f'Starting SAPT for {pair}')
+            logger.info(f'Starting SAPT for {pair}')  # pylint: disable=logging-fstring-interpolation
 
             if self._cfg.psi4.save_output:
                 outfile = f'sapt_{self._key_names[self._key]}_{self._pair_names[pair]}.out'

mdsapt/tests/test_config.py

@@ -5,7 +5,6 @@
 from tempfile import mktemp
 from typing import Dict, Any
 
-import pydantic
 import pytest
 
 from pydantic import ValidationError

mdsapt/tests/test_sapt.py

@@ -3,22 +3,22 @@
 """
 import os
 
-import MDAnalysis
 from MDAnalysis.topology.guessers import guess_types
 
-from ..config import Config, load_from_yaml_file
+from ..config import load_from_yaml_file
 from ..sapt import TrajectorySAPT, DockingSAPT
 
 traj_settings = load_from_yaml_file(
     os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'test_input.yaml'))
 
 dock_settings = load_from_yaml_file(
-            os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'docking_in.yaml'))
+    os.path.join(os.getcwd(), 'mdsapt', 'tests', 'testing_resources', 'docking_in.yaml'))
 
 unv = traj_settings.analysis.create_universe()
 elements = guess_types(unv.atoms.names)
 unv.add_TopologyAttr('elements', elements)
 
+
 class TestSAPT:
     """
     Test object for SAPT analysis