Adding pre-commit-ci (#35)

* Adding pre-commit-ci config

* bump CI -- pre-commit-ci enabled

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update black version

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* pre-commit-ci happy with builtin type constructor use

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+ci:
+ autoupdate_schedule: "quarterly"
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.5.0
+ hooks:
+ - id: check-yaml
+ - id: debug-statements
+ - id: trailing-whitespace
+ - id: check-builtin-literals
+ - id: check-executables-have-shebangs
+ - id: check-json
+- repo: https://github.com/psf/black
+ rev: 24.2.0
+ hooks:
+ - id: black
+- repo: https://github.com/asottile/pyupgrade
+ rev: 'v3.15.0'
+ hooks:
+ - id: pyupgrade
+ args:
+ - --py39-plus

README.md

@@ -15,5 +15,5 @@ Copyright (c) 2023, ChoderaLab
 #### Acknowledgements
 [Choderalab -- Perses](https://github.com/choderalab/perses)
 [Open Free energy Consortium](https://openfree.energy/)
-Project based on the 
+Project based on the
 [Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.

devtools/README.md

@@ -1,14 +1,14 @@
 # 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.
 
 
 ## Manifest
 
 ### Continuous Integration
 
-You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and 
+You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and
 Windows testing if you only plan to deploy on specific platforms. These are just to help you get started.
 
 ### Conda Environment:
@@ -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. `feflow-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. `feflow-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

@@ -6,9 +6,11 @@
 import subprocess as sp
 from tempfile import TemporaryDirectory
 from contextlib import contextmanager
+
 # YAML imports
 try:
  import yaml # PyYAML
+
  loader = yaml.safe_load
 except ImportError:
  try:
@@ -17,19 +19,30 @@
  try:
  # Load Ruamel YAML from the base conda environment
  from importlib import util as import_util
- CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE'])
- ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..',
- 'lib', 'python*.*', 'site-packages',
- 'ruamel_yaml', '__init__.py'))[0]
+
+ CONDA_BIN = os.path.dirname(os.environ["CONDA_EXE"])
+ ruamel_yaml_path = glob.glob(
+ os.path.join(
+ CONDA_BIN,
+ "..",
+ "lib",
+ "python*.*",
+ "site-packages",
+ "ruamel_yaml",
+ "__init__.py",
+ )
+ )[0]
  # Based on importlib example, but only needs to load_module since its the whole package, not just
  # a module
- spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path)
+ spec = import_util.spec_from_file_location("ruamel_yaml", ruamel_yaml_path)
  yaml = spec.loader.load_module()
  except (KeyError, ImportError, IndexError):
- raise ImportError("No YAML parser could be found in this or the conda environment. "
- "Could not find PyYAML or Ruamel YAML in the current environment, "
- "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. " 
- "Environment not created!")
+ raise ImportError(
+ "No YAML parser could be found in this or the conda environment. "
+ "Could not find PyYAML or Ruamel YAML in the current environment, "
+ "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. "
+ "Environment not created!"
+ )
  loader = yaml.YAML(typ="safe").load # typ="safe" avoids odd typing on output
 
 
@@ -46,50 +59,60 @@ def temp_cd():
 
 
 # Args
-parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.')
-parser.add_argument('-n', '--name', type=str,
- help='The name of the created Python environment')
-parser.add_argument('-p', '--python', type=str,
- help='The version of the created Python environment')
-parser.add_argument('conda_file',
- help='The file for the created Python environment')
+parser = argparse.ArgumentParser(
+ description="Creates a conda environment from file for a given Python version."
+)
+parser.add_argument(
+ "-n", "--name", type=str, help="The name of the created Python environment"
+)
+parser.add_argument(
+ "-p", "--python", type=str, help="The version of the created Python environment"
+)
+parser.add_argument("conda_file", help="The file for the created Python environment")
 
 args = parser.parse_args()
 
 # Open the base file
-with open(args.conda_file, "r") as handle:
+with open(args.conda_file) as handle:
  yaml_script = loader(handle.read())
 
-python_replacement_string = "python {}*".format(args.python)
+python_replacement_string = f"python {args.python}*"
 
 try:
- for dep_index, dep_value in enumerate(yaml_script['dependencies']):
- if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value): # Match explicitly 'python' and its formats
- yaml_script['dependencies'].pop(dep_index)
+ for dep_index, dep_value in enumerate(yaml_script["dependencies"]):
+ if re.match(
+ "python([ ><=*]+[0-9.*]*)?$", dep_value
+ ): # Match explicitly 'python' and its formats
+ yaml_script["dependencies"].pop(dep_index)
  break # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse
 except (KeyError, TypeError):
  # Case of no dependencies key, or dependencies: None
- yaml_script['dependencies'] = []
+ yaml_script["dependencies"] = []
 finally:
  # Ensure the python version is added in. Even if the code does not need it, we assume the env does
- yaml_script['dependencies'].insert(0, python_replacement_string)
+ yaml_script["dependencies"].insert(0, python_replacement_string)
 
 # Figure out conda path
 if "CONDA_EXE" in os.environ:
  conda_path = os.environ["CONDA_EXE"]
 else:
  conda_path = shutil.which("conda")
 if conda_path is None:
- raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path")
+ raise RuntimeError(
+ "Could not find a conda binary in CONDA_EXE variable or in executable search path"
+ )
 
-print("CONDA ENV NAME {}".format(args.name))
-print("PYTHON VERSION {}".format(args.python))
-print("CONDA FILE NAME {}".format(args.conda_file))
-print("CONDA PATH {}".format(conda_path))
+print(f"CONDA ENV NAME {args.name}")
+print(f"PYTHON VERSION {args.python}")
+print(f"CONDA FILE NAME {args.conda_file}")
+print(f"CONDA PATH {conda_path}")
 
 # Write to a temp directory which will always be cleaned up
 with temp_cd():
  temp_file_name = "temp_script.yaml"
- with open(temp_file_name, 'w') as f:
+ with open(temp_file_name, "w") as f:
  f.write(yaml.dump(yaml_script))
- sp.call("{} env create -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True)
+ sp.call(
+ f"{conda_path} env create -n {args.name} -f {temp_file_name}",
+ shell=True,
+ )

docs/README.md

@@ -5,7 +5,7 @@ To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are inst
 
 
 ```bash
-conda install sphinx sphinx_rtd_theme 
+conda install sphinx sphinx_rtd_theme
 ```
 
 
@@ -14,7 +14,7 @@ Once installed, you can use the `Makefile` in this directory to compile static H
 make html
 ```
 
-The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself 
+The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself
 be inside a directory called `html/` depending on what version of Sphinx is installed).
 
 

docs/_static/README.md

@@ -1,11 +1,11 @@
 # Static Doc Directory
 
 Add any paths that contain custom static files (such as style sheets) here,
-relative to the `conf.py` file's directory. 
+relative to the `conf.py` file's directory.
 They are copied after the builtin static files,
 so a file named "default.css" will overwrite the builtin "default.css".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 templates_path = ['_static']
 ```

docs/_templates/README.md

@@ -1,11 +1,11 @@
 # Templates Doc Directory
 
-Add any paths that contain templates here, relative to 
+Add any paths that contain templates here, relative to
 the `conf.py` file's directory.
 They are copied after the builtin template files,
 so a file named "page.html" will overwrite the builtin "page.html".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 html_static_path = ['_templates']
 ```