Add makefile to simplify common commands

Such as linting, testing, type-checking etc. Also reformat the code
to pass the linting and type-checking requirements.

.github/CONTRIBUTING.md

@@ -1,7 +1,6 @@
 # How to contribute
 
-We welcome contributions from external contributors, and this document
-describes how to merge code changes into this EnsEquil. 
+We welcome contributions from external contributors, and this document describes how to merge code changes into this repository.
 
 ## Getting Started
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,4 +9,4 @@ Notable points that this PR has either accomplished or will accomplish.
 - [ ] Question1
 
 ## Status
-- [ ] Ready to go
+- [ ] Ready to go

.github/workflows/CI.yaml

@@ -36,8 +36,8 @@ jobs:
 
       - uses: mamba-org/setup-micromamba@v1
         with:
-          environment-file: devtools/conda-envs/test_env.yaml
-          environment-name: test
+          environment-file: devtools/conda-envs/test.yaml
+          environment-name: red
           create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces
             python=${{ matrix.python-version }}
 

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+
+-   repo: local
+    hooks:
+    -   id: ruff
+        name: Autoformat python code
+        language: system
+        entry: bash
+        args: [-c, "make format"]
+
+-   repo: local
+    hooks:
+    -   id: ruff
+        name: Lint python code
+        language: system
+        entry: bash
+        args: [-c, "make lint"]
+
+-   repo: local
+    hooks:
+    -   id: mypy
+        name: Type check python code
+        language: system
+        entry: bash
+        args: [-c, "make type-check"]

MANIFEST.in

@@ -1,3 +1,3 @@
 include CODE_OF_CONDUCT.md
 
-global-exclude *.py[cod] __pycache__ *.so
+global-exclude *.py[cod] __pycache__ *.so

Makefile

@@ -0,0 +1,36 @@
+PACKAGE_NAME := red
+PACKAGE_DIR  := red
+
+CONDA_ENV_RUN   = conda run --no-capture-output --name $(PACKAGE_NAME)
+
+TEST_ARGS := -v --cov=$(PACKAGE_NAME) --cov-report=term --cov-report=xml --junitxml=unit.xml --color=yes
+
+.PHONY: env lint format test type-check docs-build docs-deploy
+
+env:
+	mamba create     --name $(PACKAGE_NAME)
+	mamba env update --name $(PACKAGE_NAME) --file devtools/conda-envs/test.yaml
+	$(CONDA_ENV_RUN) pip install --no-deps -e .
+	$(CONDA_ENV_RUN) pre-commit install || true
+
+lint:
+	$(CONDA_ENV_RUN) ruff check $(PACKAGE_DIR)
+
+format:
+	$(CONDA_ENV_RUN) ruff format $(PACKAGE_DIR)
+	$(CONDA_ENV_RUN) ruff check --fix --select I $(PACKAGE_DIR)
+
+test:
+	$(CONDA_ENV_RUN) pytest -v $(TEST_ARGS) $(PACKAGE_DIR)/tests/
+
+type-check:
+	$(CONDA_ENV_RUN) mypy --follow-imports=silent --ignore-missing-imports --strict $(PACKAGE_DIR)
+
+docs-build:
+	$(CONDA_ENV_RUN) mkdocs build
+
+docs-deploy:
+ifndef VERSION
+	$(error VERSION is not set)
+endif
+	$(CONDA_ENV_RUN) mike deploy --push --update-aliases $(VERSION)

README.md

@@ -11,11 +11,11 @@ Robust Equilibration Detection
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
-A Python package for detecting equilibration in timeseries data where an initial transient is followed by a stationary distribution. Two main methods are implemented, which differ in the way they account for autocorrelation: 
+A Python package for detecting equilibration in timeseries data where an initial transient is followed by a stationary distribution. Two main methods are implemented, which differ in the way they account for autocorrelation:
 
   - `detect_equilibration_init_seq`: This uses the initial sequence methods of Geyer ([Geyer, 1992](https://www.jstor.org/stable/2246094)) to determine the truncation point of the sum of autocovariances.
-  - `detect_equilibration_window`: This uses window methods (see [Geyer](https://www.jstor.org/stable/2246094) again) when calculating the 
-autocorrelation. 
+  - `detect_equilibration_window`: This uses window methods (see [Geyer](https://www.jstor.org/stable/2246094) again) when calculating the
+autocorrelation.
 
 For both, the equilibration point can be determined either according to the minimum of the squared standard error (the default), or the maximum effective sample size, by specifying `method="min_sse"` or `method="max_ess"`.
 
@@ -40,7 +40,7 @@ my_timeseries = ...
 # Detect equilibration based on the minimum squared standard error
 # using Geyer's initial convex sequence method to account for
 # autocorrelation. idx is the index of the first sample after
-# equilibration, g is the statistical inefficiency of the equilibrated 
+# equilibration, g is the statistical inefficiency of the equilibrated
 # sample, and ess is the effective sample size of the equilibrated sample.
 idx, g, ess = red.detect_equilibration_init_seq(my_timeseries, method="min_sse", plot=True)
 
@@ -58,6 +58,6 @@ Copyright (c) 2023, Finlay Clark
 
 
 #### Acknowledgements
- 
-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. `red-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. `red-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/conda-envs/base.yaml

@@ -0,0 +1,15 @@
+name: red
+
+channels:
+  - conda-forge
+  - defaults
+
+dependencies:
+    # Base depends
+  - python
+  - pip
+  - numpy
+  - numba
+  - scipy
+  - matplotlib
+  - statsmodels

devtools/conda-envs/test_env.yaml → devtools/conda-envs/test.yaml

@@ -1,9 +1,9 @@
-name: test
-channels:
+name: red
 
+channels:
   - conda-forge
-
   - defaults
+
 dependencies:
     # Base depends
   - python
@@ -14,8 +14,12 @@ dependencies:
   - matplotlib
   - statsmodels
 
-    # Testing
+    # Testing / Development
   - pytest
   - pytest-cov
   - pytest-env
   - codecov
+  - ruff
+  - pre-commit
+  - mypy
+  - types-PyYAML

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 +19,31 @@
         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]
-            # 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)
+
+            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)
             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(  # noqa: B904
+                "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
 
 
@@ -46,13 +60,14 @@ 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()
 
@@ -63,24 +78,31 @@ def temp_cd():
 python_replacement_string = "python {}*".format(args.python)
 
 try:
-    for dep_index, dep_value in enumerate(yaml_script['dependencies']):
-        if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value):  # Match explicitly 'python' and its formats
-            yaml_script['dependencies'].pop(dep_index)
-            break  # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse
+    for dep_index, dep_value in enumerate(yaml_script["dependencies"]):
+        if re.match(
+            "python([ ><=*]+[0-9.*]*)?$", dep_value
+        ):  # Match explicitly 'python' and its formats
+            yaml_script["dependencies"].pop(dep_index)
+            # Making the assumption there is only one Python entry, also avoids
+            # need to enumerate in reverse
+            break
 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)
+    # 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)
 
 # 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))
@@ -90,6 +112,6 @@ def temp_cd():
 # 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)

docs/Makefile

@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

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
 ```
 
 
@@ -14,11 +14,10 @@ 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).
 
 
 A configuration file for [Read The Docs](https://readthedocs.org/) (readthedocs.yaml) is included in the top level of the repository. To use Read the Docs to host your documentation, go to https://readthedocs.org/ and connect this repository. You may need to change your default branch to `main` under Advanced Settings for the project.
 
 If you would like to use Read The Docs with `autodoc` (included automatically) and your package has dependencies, you will need to include those dependencies in your documentation yaml file (`docs/requirements.yaml`).
-

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']
 ```