Chore/devtools

.github/pull_request_template.md

@@ -22,4 +22,4 @@ The optional `-- format` and `-- write` arguments (see above) attempt to correct
 ## Further checks:
 - [ ] The documentation builds: `$ nox -s docs`.
 - [ ] Code is commented, particularly in hard-to-understand areas.
-- [ ] Tests are added that prove fix is effective or that feature works.
+- [ ] Tests are added that prove fix is effective or that feature works.

.github/workflows/codecov.yml

@@ -0,0 +1,52 @@
+name: codecov
+
+on:
+  push:
+    paths-ignore:
+      - "*.md"
+      - "LICENSE"
+      - "docs/**"
+      - "images/**"
+      - ".github/ISSUE_TEMPLATE/**"
+
+  pull_request:
+    branches: [main]
+    paths-ignore:
+      - "*.md"
+      - "LICENSE"
+      - "docs/**"
+      - "images/**"
+      - ".github/ISSUE_TEMPLATE/**"
+
+jobs:
+  tests:
+    name: Collect and upload coverage
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+
+      - name: Install thevenin
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[tests]
+
+      - name: Pytest with coverage
+        run: pytest --cov=thevenin --cov-report=xml tests/
+
+      - name: Upload to codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+          flags: unittests
+          env_vars: OS,PYTHON
+          files: ./coverage.xml
+          name: codecov-umbrella
+          fail_ci_if_error: false

CHANGELOG.md

@@ -22,6 +22,7 @@
 - `initial_state` was renamed to `state0` in `sim.pre()` ([#14](https://github.com/NatLabRockies/thevenin/pull/14))
 
 ### Chores
+- Switch linter over to `ruff`, enable `codecov` workflow, update README badges ([#31](https://github.com/NatLabRockies/thevenin/pull/31))
 - Make GitHub hyperlinks reference new org name `NREL` -> `NatLabRockies` ([#30](https://github.com/NatLabRockies/thevenin/pull/30))
 - Allow single backticks for sphinx inline code (`default_role = 'literal'`) ([#28](https://github.com/NatLabRockies/thevenin/pull/28))
 - Rebrand NREL to NLR, and include name change for Alliance as well ([#27](https://github.com/NatLabRockies/thevenin/pull/27))

README.md

@@ -5,19 +5,11 @@
 
  # thevenin
 
-[![CI][ci-b]][ci-l]  
-![tests][test-b]  
-![coverage][cov-b]  
-[![pep8][pep-b]][pep-l]
-
-[ci-b]: https://github.com/NatLabRockies/thevenin/actions/workflows/ci.yml/badge.svg
-[ci-l]: https://github.com/NatLabRockies/thevenin/actions/workflows/ci.yml
-
-[test-b]: https://github.com/NatLabRockies/thevenin/blob/main/images/tests.svg?raw=true
-[cov-b]: https://github.com/NatLabRockies/thevenin/blob/main/images/coverage.svg?raw=true
-
-[pep-b]: https://img.shields.io/badge/code%20style-pep8-orange.svg
-[pep-l]: https://www.python.org/dev/peps/pep-0008
+[![ci](https://github.com/NatLabRockies/thevenin/actions/workflows/ci.yml/badge.svg)](https://github.com/NatLabRockies/thevenin/actions/workflows/ci.yml)  
+[![codecov](https://codecov.io/gh/NatLabRockies/thevenin/graph/badge.svg?token=XM2VF9JVEW)](https://codecov.io/gh/NatLabRockies/thevenin)  
+[![license](https://img.shields.io/badge/license-BSD--3-blue.svg)](https://github.com/NatLabRockies/thevenin/blob/main/LICENSE)  
+[![downloads](https://static.pepy.tech/personalized-badge/thevenin?period=total&units=INTERNATIONAL_SYSTEM&left_color=GREY&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/thevenin)  
+[![pypi](https://img.shields.io/pypi/v/thevenin)](https://pypi.org/project/thevenin)
 
 ## Summary
 This package is a wrapper for the well-known Thevenin equivalent circuit model. The model is comprised of a single series resistor followed by any number of parallel RC pairs. Figure 1 below illustrates a circuit with 2 RC pairs; however, the model can be run with as few as zero, and as many as $N$.

docs/source/development/code_style_and_linting.rst

@@ -8,11 +8,11 @@ We adhere to `PEP8 <https://peps.python.org/pep-0008/>`_ with minimal exceptions
 
 Code Formatting
 ---------------
-While `black <https://black.readthedocs.io/en/stable/>`_ is a popular auto-formatting package, we do not permit it to be used for this codebase. Although it adheres to the same PEP8 standards that we follow, the `black` styling can be a bit more opinionated at times and does not always help improve clarity. For those still looking for auto-formatting, we permit the use of `autopep8 <https://github.com/hhatto/autopep8>`_ is when paired with the `.flake8` configuration file found in `.github/linters`. IDEs supporting `autopep8` should be configured accordingly. Developers can also run the formatter manually using::
+While `black <https://black.readthedocs.io/en/stable/>`_ is a popular auto-formatting package, we do not permit it to be used for this codebase. Although it adheres to the same PEP8 standards that we follow, the `black` styling is also much more opinionated and does not always help improve clarity. For those still looking for auto-formatting, we permit the use of `autopep8 <https://github.com/hhatto/autopep8>`_ when paired with the `.flake8` configuration file found in `.github/linters`. However, we do not automatically include and configure `autopep8` as a dependency. If you'd like to use it in your IDE, you should install it and configure it with the provided `.flake8` file. We also provide a `nox` session that uses a pre-configured `ruff` linter to apply minimal fixes to the codebase that is well-aligned with our style guidelines. To run this session, use the following command::
 
     nox -s linter -- format 
 
-When used with the optional `format` argument, this `nox` command will first run the auto-formatter and then check for errors. This means that is errors persist, then `autopep8` was unable to address them and that they must be addressed manually.
+When used with the optional `format` argument, this `nox` command will run `ruff check` with the `--fix` option enabled. Note that there is also an option to run `nox -s linter -- stats` if you want to see a summary of the linting errors rather than a full report. Lastly, you can run `nox -s linter -- format-unsafe` to apply auto-fixes that the linter considers "unsafe". These fixes may potentially change the behavior of the code, so they should be used with caution and reviewed carefully. The `stats` and `format` or `format-unsafe` options can also be used together to see the summary of errors that remain after applying fixes. If you do not lint and format your code locally, the CI will catch any issues during the push process. Failed tests may result in a delayed reviewer assignments when you open pull requests.
 
 Enforcement
 -----------

noxfile.py

@@ -9,8 +9,7 @@
 
 @nox.session(name='cleanup', python=False)
 def run_cleanup(_) -> None:
-    """Use os/shutil to remove some files/directories"""
-
+    """Use os/shutil to remove some files/directories."""
     if os.path.exists('.coverage'):
         os.remove('.coverage')
 
@@ -21,34 +20,38 @@ def run_cleanup(_) -> None:
 
 
 @nox.session(name='linter', python=False)
-def run_flake8(session: nox.Session) -> None:
+def run_ruff(session: nox.Session) -> None:
     """
-    Run flake8 with the github config file
+    Run ruff to check for linting errors.
 
-    Use the optional 'format' argument to run autopep8 prior to the linter.
+    Use the optional 'format' or 'format-unsafe' arguments to run ruff with the
+    --fix or --unsafe-fixes option prior to the linter. You can also use 'stats'
+    to show a summary of the found errors rather than a full report.
 
     """
+    session.run('pip', 'install', '--upgrade', '--quiet', 'ruff')
 
-    session.run('pip', 'install', '--upgrade', '--quiet', 'flake8')
-    session.run('pip', 'install', '--upgrade', '--quiet', 'autopep8')
+    command = ['ruff', 'check']
+    if 'stats' in session.posargs:
+        command.append('--statistics')
 
     if 'format' in session.posargs:
-        session.run('autopep8', '.', '--in-place', '--recursive',
-                    '--global-config=.github/linters/.flake8')
+        command.append('--fix')
+    elif 'format-unsafe' in session.posargs:
+        command.extend(['--fix', '--unsafe-fixes'])
 
-    session.run('flake8', '--config=.github/linters/.flake8')
+    session.run(*command)
 
 
 @nox.session(name='codespell', python=False)
 def run_codespell(session: nox.Session) -> None:
     """
-    Run codespell with the github config file
+    Run codespell with the github config file.
 
     Use the optional 'write' argument to write the corrections directly into
     the files. Otherwise, you will only see a summary of the found errors.
 
     """
-
     session.run('pip', 'install', '--upgrade', '--quiet', 'codespell')
 
     command = ['codespell', '--config=.github/linters/.codespellrc']
@@ -61,13 +64,12 @@ def run_codespell(session: nox.Session) -> None:
 @nox.session(name='spellcheck', python=False)
 def run_spellcheck(session: nox.Session) -> None:
     """
-    Run codespell with docs files included
+    Run codespell with docs files included.
 
     Use the optional 'write' argument to write the corrections directly into
     the files. Otherwise, you will only see a summary of the found errors.
 
     """
-
     run_codespell(session)
 
     command = ['codespell', '--config=.github/linters/.codespellrc']
@@ -80,14 +82,13 @@ def run_spellcheck(session: nox.Session) -> None:
 @nox.session(name='tests', python=False)
 def run_pytest(session: nox.Session) -> None:
     """
-    Run pytest and generate test/coverage reports
+    Run pytest and generate test/coverage reports.
 
     Use the optional 'parallel' argument to run the tests in parallel. As just
     a flag, the number of workers will be determined automatically. Otherwise,
     you can specify the number of workers using an int, e.g., parallel=4.
 
     """
-
     package = importlib.util.find_spec('thevenin')
     coverage_folder = os.path.dirname(package.origin)
 
@@ -98,6 +99,8 @@ def run_pytest(session: nox.Session) -> None:
             'tests/',
         ]
     else:
+        os.makedirs('reports', exist_ok=True)
+
         command = [
             'pytest',
             '--cov=src/thevenin',
@@ -115,15 +118,13 @@ def run_pytest(session: nox.Session) -> None:
         elif arg.startswith('parallel'):
             command[1:1] = ['-n', 'auto']
 
+    os.environ['MPLBACKEND'] = 'Agg'
     session.run(*command)
 
-    run_cleanup(session)
-
 
 @nox.session(name='badges', python=False)
 def run_genbadge(session: nox.Session) -> None:
-    """Run genbadge to make test/coverage badges"""
-
+    """Run genbadge to make test/coverage badges."""
     session.run(
         'genbadge', 'coverage', '-l',
         '-i', 'reports/coverage.xml',
@@ -140,15 +141,14 @@ def run_genbadge(session: nox.Session) -> None:
 @nox.session(name='docs', python=False)
 def run_sphinx(session: nox.Session) -> None:
     """
-    Run spellcheck and then use sphinx to build docs
+    Run spellcheck and then use sphinx to build docs.
 
     Use the optional 'clean' argument to remove everything under the 'build'
     and 'source/api' folders prior to re-building the docs. This is important
     in cases where the api module names have been changed or when some navbars
     are not showing new pages. In general, try without 'clean' first.
 
     """
-
     if 'clean' in session.posargs:
         os.chdir('docs')
         session.run('make', 'clean')
@@ -169,14 +169,13 @@ def run_sphinx(session: nox.Session) -> None:
 @nox.session(name='pre-commit', python=False)
 def run_pre_commit(session: nox.Session) -> None:
     """
-    Run all linters/tests and make new badges
+    Run all linters/tests and make new badges.
 
-    Order of sessions: flake8, spellcheck, pytest, genbadge. Using 'format' for
+    Order of sessions: ruff, spellcheck, pytest, genbadge. Using 'format' for
     linter, 'write' for spellcheck, and/or 'parallel' for pytest is permitted.
 
     """
-
-    run_flake8(session)
+    run_ruff(session)
     run_spellcheck(session)
 
     run_pytest(session)

pyproject.toml

@@ -46,6 +46,31 @@ where = ["src"]
 [tool.setuptools.package-data]
 thevenin = ["_resources/*.yaml"]
 
+[tool.ruff]
+line-length = 80
+exclude = ["build", "docs", "images", "reports"]
+
+[tool.ruff.lint]
+preview = true
+select = [
+    "E",  # All pycodestyle errors
+    "W",  # All pycodestyle warnings
+    "F",  # All pyflakes errors
+    "B",  # All flake8-bugbear checks
+    "D",  # All pydocstyle checks
+]
+extend-select = [
+    "E302",  # Expected 2 blank lines, found 1 (requires preview=true, above)
+]
+ignore = [
+    "B007", "B009", "B028", "B905",
+    "D100", "D103", "D104", "D203", "D205", "D212", "D401",
+    "E201", "E202", "E226", "E241", "E731",
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**/*" = ["D"]
+
 [project.optional-dependencies]
 docs = [
     "sphinx",
@@ -64,8 +89,7 @@ tests = [
 ]
 dev = [
     "nox",
-    "flake8",
-    "autopep8",
+    "ruff",
     "codespell",
     "genbadge[all]",
     "thevenin[docs,tests]",

scripts/version_checker.py

@@ -27,7 +27,6 @@ def get_latest_version(package: str, prefix: str = None) -> str:
         Failed to fetch PyPI data for requested package.
 
     """
-
     url = f"https://pypi.org/pypi/{package}/json"
 
     response = requests.get(url)
@@ -72,7 +71,6 @@ def check_against_pypi(pypi: str, local: str) -> None:
         Local package is older than PyPI.
 
     """
-
     pypi = Version(pypi)
     local = Version(local)
 
@@ -103,7 +101,6 @@ def check_against_tag(tag: str, local: str) -> None:
         Version mismatch: tag differs from local.
 
     """
-
     tag = Version(tag)
     local = Version(local)
 

src/thevenin/__init__.py

@@ -15,7 +15,7 @@
 the documentation by visiting the website, hosted on Read the Docs. The website
 includes search functionality and more detailed examples.
 
-"""
+"""  # noqa: D400, D415 (ignore missing punctuation on first line)
 
 # core package
 from ._experiment import Experiment

src/thevenin/_basemodel.py

@@ -43,7 +43,6 @@ def calculated_current(voltage, ocv, hyst, eta_j, R0) -> float | np.ndarray:
         Calculated current at a single or multiple times [A].
 
     """
-
     if eta_j.ndim == 1:
         return -(voltage - ocv - hyst + np.sum(eta_j)) / R0
     elif eta_j.ndim == 2:
@@ -83,7 +82,6 @@ def calculated_voltage(current, ocv, hyst, eta_j, R0) -> float | np.ndarray:
         Calculated voltage at a single or multiple times [V].
 
     """
-
     if eta_j.ndim == 1:
         return ocv + hyst - np.sum(eta_j) - current*R0
     elif eta_j.ndim == 2:
@@ -223,7 +221,6 @@ def __repr__(self) -> str:  # pragma: no cover
             A console-readable instance representation.
 
         """
-
         keys = self._repr_keys
         values = [getattr(self, k) for k in keys]
 
@@ -253,7 +250,6 @@ def _classname(self) -> str:
     @property
     def _get_params_dict(self) -> dict:
         """Return the params dictionary needed to initialize a new instance."""
-
         params = {}
         for k in self._repr_keys:
             params[k] = getattr(self, k)
@@ -275,7 +271,6 @@ def pre(self, *args, **kwargs) -> None:  # pragma: no cover
 
     def _check_RC_pairs(self) -> None:
         """Verify correct attributes are set based on num_RC_pairs."""
-
         missing_attrs = []
         for j in range(1, self.num_RC_pairs + 1):
             if not hasattr(self, 'R' + str(j)):