Uniformly lint (#89)

* Lint

* Lint

* Lint

* Specify tolerances

* Re-lint

* Fix bad merge

* Show changes to OFFXML files

* Still error out

Author: mattwthompson

.github/ISSUE_TEMPLATE/bug_report.md

@@ -32,7 +32,7 @@ The full error message (may be large, that's fine. Better to paste too much than
 
 **Computing environment (please complete the following information):**
  - Operating system
- - Output of running `conda list` 
+ - Output of running `conda list`
 
 **Additional context**
 Add any other context about the problem here.

.github/workflows/CI.yml

@@ -89,6 +89,8 @@ jobs:
         run: |
           if test "$( git diff openforcefields/offxml/ | wc | awk '{print $1}' )" -gt 0
           then
+            echo 'The following changes in OFFXML files were detected:'
+            git diff openforcefields/offxml/
             exit 1
           else
             echo 'no files differ'

.pre-commit-config.yaml

@@ -0,0 +1,25 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: check-yaml
+  - id: end-of-file-fixer
+  - id: trailing-whitespace
+  - id: debug-statements
+- repo: https://github.com/psf/black
+  rev: 23.10.1
+  hooks:
+  - id: black
+- repo: https://github.com/PyCQA/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+- repo: https://github.com/PyCQA/flake8
+  rev: 6.1.0
+  hooks:
+  - id: flake8
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.0
+  hooks:
+  - id: pyupgrade
+    exclude: openforcefields/_version.py|setup.py

LICENSE

@@ -51,7 +51,7 @@ exhaustive, and do not form part of our licenses.
      such as asking that all changes be marked or described.
      Although not required by our licenses, you are encouraged to
      respect those requests where reasonable. More considerations
-     for the public: 
+     for the public:
 	wiki.creativecommons.org/Considerations_for_licensees
 
 =======================================================================
@@ -395,4 +395,3 @@ the avoidance of doubt, this paragraph does not form part of the
 public licenses.
 
 Creative Commons may be contacted at creativecommons.org.
-

README.md

@@ -1,6 +1,6 @@
 # OpenFF Force Fields
 
-[![Build Status](https://github.com/openforcefield/openff-forcefields/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-forcefields/actions?query=branch%3Amaster+workflow%3ACI) 
+[![Build Status](https://github.com/openforcefield/openff-forcefields/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-forcefields/actions?query=branch%3Amaster+workflow%3ACI)
 
 
 This repository contains force fields released by the [Open Force Field Initiative](https://openforcefield.org).
@@ -151,15 +151,15 @@ Force fields moving forward will be called `name-X.Y.Z`
 
 - `v2.0.0 Sage`: This major release contains the same physical parameters as `v2.0.0-rc.2 Sage`, but has the parameter ids changed. For more information see the [openff-sage repository](https://github.com/openforcefield/openff-sage).
 
-- `2023.02.1`: This release switches to a calendar-versioning system and adds `tip3p-1.0.0.offxml` and `tip3p-fb-1.0.0.offxml`, as well as `tip3p.offxml` and `tip3p-fb.offxml`, which will always point to the latest files in their respective lines. 
+- `2023.02.1`: This release switches to a calendar-versioning system and adds `tip3p-1.0.0.offxml` and `tip3p-fb-1.0.0.offxml`, as well as `tip3p.offxml` and `tip3p-fb.offxml`, which will always point to the latest files in their respective lines.
 
 - `2023.04.1`: This release adds `openff-2.1.0-rc.1.offxml` Sage 2.1.0 Release Candidate 1, with several small parameter fixes and improvements.
 
 - `2023.05.0`: This release adds the `opc-1.0.0.offxml`, our initial port of the OPC water model.
 
 - `2023.05.1`: This release adds `openff-2.1.0.offxml`, Sage 2.1.0, with identical physics parameters to `openff-2.1.0-rc.1.offxml`.
 
-- `2023.06.0`: This release adds `opc-1.0.1.offxml`, standardizing the use of the string "kilocalorie_per_mole". It also adds `tip3p-fb-1.1.0.offxml`, which fixes a unit error in the geometric constraints and adds additional ion parameters. Finally, it adds `opc3-1.0.0.offxml` and `tip4p_fb-1.0.0.offxml`. 
+- `2023.06.0`: This release adds `opc-1.0.1.offxml`, standardizing the use of the string "kilocalorie_per_mole". It also adds `tip3p-fb-1.1.0.offxml`, which fixes a unit error in the geometric constraints and adds additional ion parameters. Finally, it adds `opc3-1.0.0.offxml` and `tip4p_fb-1.0.0.offxml`.
 
 #### Acknowledgements
 

canary/scripts/test_hmr.py

@@ -1,13 +1,11 @@
+import importlib.resources
 import sys
-from pathlib import Path
 
 import numpy as np
 from openff.toolkit.topology import Molecule
 from openmmforcefields.generators import SystemGenerator
 from simtk import openmm, unit
 from simtk.openmm import app
-import importlib.resources
-
 
 DATA_PATH = importlib.resources.files("openforcefields") / "canary" / "data"
 coverage_mols = DATA_PATH / "coverage.smi"
@@ -22,7 +20,7 @@ class CanaryError(Exception):
     """Base exception for canary"""
 
     def __init__(self, message, runs):
-        super(CanaryError, self).__init__(message)
+        super().__init__(message)
         self.message = message
         self.runs = runs
 
@@ -36,7 +34,8 @@ class HMRCanaryError(CanaryError):
 
 def hmr_driver(mol, ff_name):
     """Given an OpenFF Molecule, run a short 4 fs HMR simulation. This function is adapted from
-    https://github.com/openforcefield/openforcefields/issues/19#issuecomment-689816995"""
+    https://github.com/openforcefield/openforcefields/issues/19#issuecomment-689816995
+    """
     print(
         f"Running HMR with force field {ff_name} and molecule with SMILES {mol.to_smiles()}"
     )
@@ -45,8 +44,7 @@ def hmr_driver(mol, ff_name):
         "constraints": app.HBonds,
         "rigidWater": True,
         "removeCMMotion": False,
-        "hydrogenMass": 4
-        * unit.amu,  # Does this also _subtract_ mass from heavy atoms?:w
+        "hydrogenMass": 4 * unit.amu,
     }
 
     system_generator = SystemGenerator(

codecov.yml

@@ -12,4 +12,4 @@ comment:
   branches: null
   behavior: default
   flags: null
-  paths: null
+  paths: null

devtools/README.md

@@ -1,6 +1,6 @@
 # Development, testing, and deployment tools
 
-This directory contains a collection of tools for running Continuous Integration (CI) tests, 
+This directory contains a collection of tools for running Continuous Integration (CI) tests,
 conda installation, and other development tools not directly related to the coding process.
 
 
@@ -17,7 +17,7 @@ This directory contains the files to setup the Conda environment for testing pur
 
 * `conda-envs`: directory containing the YAML file(s) which fully describe Conda Environments, their dependencies, and those dependency provenance's
   * `test_env.yaml`: Simple test environment file with base dependencies. Channels are not specified here and therefore respect global Conda configuration
-  
+
 ### Additional Scripts:
 
 This directory contains OS agnostic helper scripts which don't fall in any of the previous categories
@@ -40,17 +40,17 @@ This directory contains OS agnostic helper scripts which don't fall in any of th
 - [ ] Make sure there is an/are issue(s) opened for your specific update
 - [ ] Create the PR, referencing the issue
 - [ ] Debug the PR as needed until tests pass
-- [ ] Tag the final, debugged version 
+- [ ] Tag the final, debugged version
    *  `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags`
 - [ ] Get the PR merged in
 
 ## Versioneer Auto-version
-[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version 
-is installed by looking at the `git` tags and how many commits ahead this version is. The format follows 
+[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version
+is installed by looking at the `git` tags and how many commits ahead this version is. The format follows
 [PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of:
 ```regexp
 \d+.\d+.\d+(?\+\d+-[a-z0-9]+)
 ```
-If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, 
-e.g. `openforcefield-forcefields-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits 
+If the version of this commit is the same as a `git` tag, the installed version is the same as the tag,
+e.g. `openforcefield-forcefields-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits
 ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash.

devtools/scripts/create_conda_env.py

@@ -18,7 +18,7 @@ The OPC, OPC3, TIP3P-FB, and TIP4P-FB files includes the 12-6 hydration free ene
 These files are not original force fields made by Open Force Field.
 Instead they are ports of existing force fields into the [SMIRNOFF](https://openforcefield.github.io/standards/standards/smirnoff/) force field format.
 
-**Note**: Current mainline SMIRNOFF force fields already contain a water model and ion parameters. If you intend to use a mainline OpenFF force field for most molecules in a topology while using an alternate force field specifically for water and ions, ensure that the water-and-ions force field is loaded _last_, so that its parameters take precedence over those from the main-line force field.  
+**Note**: Current mainline SMIRNOFF force fields already contain a water model and ion parameters. If you intend to use a mainline OpenFF force field for most molecules in a topology while using an alternate force field specifically for water and ions, ensure that the water-and-ions force field is loaded _last_, so that its parameters take precedence over those from the main-line force field.
 
 ## Versioning
 
@@ -30,7 +30,7 @@ To eliminate this possibility, use a versioned file name, i.e. `ForceField("tip3
 
 The first version of each file is given version number 1.0.0 and is associated with a best-effort attempt at reproducing the parameters from the original source.
 These parameters may not precisely match what is packaged elsewhere, such as those bundled alongside of MD engines. Such files often do not agree with each other to the last significant digit.
-The SMIRNOFF format also requires definitions of some terms that affect the total energy of a system, but are either not relevant or not clearly defined for these water models, such as 1-4 scaling factors and nonbonded cutoffs. We make an effort here to choose values for these settings to ensure compatibility with the most recent mainline OpenFF force field, but when using other force fields users may need to update these values manually to ensure compatibility. 
+The SMIRNOFF format also requires definitions of some terms that affect the total energy of a system, but are either not relevant or not clearly defined for these water models, such as 1-4 scaling factors and nonbonded cutoffs. We make an effort here to choose values for these settings to ensure compatibility with the most recent mainline OpenFF force field, but when using other force fields users may need to update these values manually to ensure compatibility.
 
 
 If errors in these files are discovered, changes may be made and released in new versions of these files, i.e. `tip3p_1.0.1.offxml`.