update: add support for ruff linter

.github/workflows/lint.yml

@@ -6,26 +6,18 @@ on:
 
 jobs:
   lint:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        python-version: ['3.11']
-
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Install Python
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: "3.11"
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install tox tox-gh-actions
-      - name: Check with flake8
-        run: |
-          tox -e flake8
-      - name: Check with codespell
-        run: |
-          tox -e codespell
+          python -m pip install --upgrade pip
+          python -m pip install tox ruff
+      - name: Run ruff
+        run: ruff check --format=github .
+      - name: Run codespell
+        run: tox -e codespell

README.md

@@ -9,6 +9,7 @@
 ![GitHub](https://img.shields.io/github/license/juaml/junifer?style=flat-square)
 ![Codecov](https://img.shields.io/codecov/c/github/juaml/junifer?style=flat-square)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/charliermarsh/ruff)
 
 ## About
 

conda-env.yml

@@ -22,13 +22,10 @@ dependencies:
   - sphinxcontrib-mermaid=0.8.*
   - tox
   - ipykernel
-  - isort
   - pytest-cov
   - pytest
   - black
-  - flake8
-  - flake8-docstrings
-  - flake8-bugbear
+  - ruff
   - codespell
   - pip
   - pip:

docs/changes/newsfragments/229.misc

@@ -0,0 +1 @@
+Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_

docs/conf.py

@@ -138,7 +138,6 @@
     "julearn": ("https://juaml.github.io/julearn/main", None),
     "nibabel": ("https://nipy.org/nibabel/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None),
     # "sqlalchemy": ("https://docs.sqlalchemy.org/en/20/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),

junifer/api/cli.py

@@ -135,6 +135,7 @@ def cli() -> None:  # pragma: no cover
 )
 def run(filepath: click.Path, element: str, verbose: Union[str, int]) -> None:
     """Run command for CLI.
+
     \f
     Parameters
     ----------
@@ -182,6 +183,7 @@ def run(filepath: click.Path, element: str, verbose: Union[str, int]) -> None:
 )
 def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
     """Collect command for CLI.
+
     \f
     Parameters
     ----------
@@ -224,6 +226,7 @@ def queue(
     verbose: Union[str, int],
 ) -> None:
     """Queue command for CLI.
+
     \f
     Parameters
     ----------
@@ -261,6 +264,7 @@ def queue(
 @click.option("--long", "long_", is_flag=True)
 def wtf(long_: bool) -> None:
     """Wtf command for CLI.
+
     \f
     Parameters
     ----------
@@ -282,6 +286,7 @@ def wtf(long_: bool) -> None:
 @click.argument("subpkg", type=str)
 def selftest(subpkg: str) -> None:
     """Selftest command for CLI.
+
     \f
     Parameters
     ----------

junifer/api/functions.py

@@ -234,19 +234,19 @@ def queue(
     # Create a folder within the CWD to store the job files / config
     cwd = Path.cwd()
     jobdir = cwd / "junifer_jobs" / jobname
-    logger.info(f"Creating job in {str(jobdir.absolute())}")
+    logger.info(f"Creating job in {jobdir.absolute()!s}")
     if jobdir.exists():
         if not overwrite:
             raise_error(
                 f"Job folder for {jobname} already exists. "
                 "This error is raised to prevent overwriting job files "
                 "that might be scheduled but not yet executed. "
-                f"Either delete the directory {str(jobdir.absolute())} "
+                f"Either delete the directory {jobdir.absolute()!s} "
                 "or set overwrite=True."
             )
         else:
             logger.info(
-                f"Deleting existing job directory at {str(jobdir.absolute())}"
+                f"Deleting existing job directory at {jobdir.absolute()!s}"
             )
             shutil.rmtree(jobdir)
     jobdir.mkdir(exist_ok=True, parents=True)
@@ -268,7 +268,7 @@ def queue(
         config["with"] = fixed_load
 
     yaml_config = jobdir / "config.yaml"
-    logger.info(f"Writing YAML config to {str(yaml_config.absolute())}")
+    logger.info(f"Writing YAML config to {yaml_config.absolute()!s}")
     yaml.dump(config, stream=yaml_config)
 
     # Get list of elements
@@ -378,11 +378,11 @@ def _queue_condor(
     """
     logger.debug("Creating HTCondor job")
     run_junifer_args = (
-        f"run {str(yaml_config.absolute())} "
+        f"run {yaml_config.absolute()!s} "
         f"--verbose {verbose} --element $(element)"
     )
     collect_junifer_args = (
-        f"collect {str(yaml_config.absolute())} --verbose {verbose} "
+        f"collect {yaml_config.absolute()!s} --verbose {verbose} "
     )
 
     if not isinstance(collect, str):
@@ -401,7 +401,7 @@ def _queue_condor(
         executable = "run_conda.sh"
         arguments = f"{env_name} junifer"
         exec_path = jobdir / executable
-        logger.info(f"Copying {executable} to {str(exec_path.absolute())}")
+        logger.info(f"Copying {executable} to {exec_path.absolute()!s}")
         shutil.copy(Path(__file__).parent / "res" / executable, exec_path)
         make_executable(exec_path)
     elif env["kind"] == "venv":
@@ -441,7 +441,7 @@ def _queue_condor(
         request_disk = {disk}
 
         # Executable
-        initial_dir = {str(jobdir.absolute())}
+        initial_dir = {jobdir.absolute()!s}
         executable = $(initial_dir)/{executable}
         transfer_executable = False
 
@@ -450,9 +450,9 @@ def _queue_condor(
         {extra_preamble}
 
         # Logs
-        log = {str(log_dir.absolute())}/junifer_run_$(log_element).log
-        output = {str(log_dir.absolute())}/junifer_run_$(log_element).out
-        error = {str(log_dir.absolute())}/junifer_run_$(log_element).err
+        log = {log_dir.absolute()!s}/junifer_run_$(log_element).log
+        output = {log_dir.absolute()!s}/junifer_run_$(log_element).out
+        error = {log_dir.absolute()!s}/junifer_run_$(log_element).err
         """
 
     submit_run_fname = jobdir / f"run_{jobname}.submit"
@@ -475,7 +475,7 @@ def _queue_condor(
         request_disk = {disk}
 
         # Executable
-        initial_dir = {str(jobdir.absolute())}
+        initial_dir = {jobdir.absolute()!s}
         executable = $(initial_dir)/{executable}
         transfer_executable = False
 
@@ -484,9 +484,9 @@ def _queue_condor(
         {extra_preamble}
 
         # Logs
-        log = {str(log_dir.absolute())}/junifer_collect.log
-        output = {str(log_dir.absolute())}/junifer_collect.out
-        error = {str(log_dir.absolute())}/junifer_collect.err
+        log = {log_dir.absolute()!s}/junifer_collect.log
+        output = {log_dir.absolute()!s}/junifer_collect.out
+        error = {log_dir.absolute()!s}/junifer_collect.err
         """
 
     # Now create the collect submit file
@@ -535,7 +535,7 @@ def _queue_condor(
         subprocess.run(["condor_submit_dag", dag_fname])
         logger.info("HTCondor job submitted")
     else:
-        cmd = f"condor_submit_dag {str(dag_fname.absolute())}"
+        cmd = f"condor_submit_dag {dag_fname.absolute()!s}"
         logger.info(
             f"HTCondor job files created, to submit the job, run `{cmd}`"
         )

junifer/api/parser.py

@@ -32,10 +32,10 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
     if not isinstance(filepath, Path):
         filepath = Path(filepath)
 
-    logger.info(f"Parsing yaml file: {str(filepath.absolute())}")
+    logger.info(f"Parsing yaml file: {filepath.absolute()!s}")
     # Filepath existence check
     if not filepath.exists():
-        raise_error(f"File does not exist: {str(filepath.absolute())}")
+        raise_error(f"File does not exist: {filepath.absolute()!s}")
     # Filepath reading
     contents = yaml.load(filepath)
     if "elements" in contents:

junifer/api/tests/test_api_utils.py

@@ -32,7 +32,7 @@ def test_get_python_information() -> None:
 def test_get_dependency_information_short() -> None:
     """Test short version of _get_dependency_information()."""
     dependency_information = _get_dependency_information(long_=False)
-    assert [key for key in dependency_information.keys()] == [
+    assert list(dependency_information.keys()) == [
         "click",
         "numpy",
         "datalad",
@@ -47,9 +47,7 @@ def test_get_dependency_information_short() -> None:
 def test_get_dependency_information_long() -> None:
     """Test long version of _get_dependency_information()."""
     dependency_information = _get_dependency_information(long_=True)
-    dependency_information_keys = [
-        key for key in dependency_information.keys()
-    ]
+    dependency_information_keys = list(dependency_information.keys())
     for key in [
         "click",
         "numpy",

junifer/api/tests/test_functions.py

@@ -718,7 +718,7 @@ def test_queue_condor_assets_generation(
             # Check junifer run submit file
             assert run_submit_file_path.is_file()
             # Read run submit file to check if resources are correct
-            with open(run_submit_file_path, "r") as f:
+            with open(run_submit_file_path) as f:
                 for line in f.read().splitlines():
                     if "request_cpus" in line:
                         assert int(line.split("=")[1].strip()) == cpus
@@ -744,7 +744,7 @@ def test_queue_condor_assets_generation(
             element_count = 0
             has_collect_job = False
             has_final_collect_job = False
-            with open(dag_file_path, "r") as f:
+            with open(dag_file_path) as f:
                 for line in f.read().splitlines():
                     if "JOB" in line:
                         element_count += 1
@@ -812,7 +812,7 @@ def test_queue_condor_extra_preamble(
         run_submit_file_path = Path(
             tmp_path / "junifer_jobs" / jobname / f"run_{jobname}.submit"
         )
-        with open(run_submit_file_path, "r") as f:
+        with open(run_submit_file_path) as f:
             for line in f.read().splitlines():
                 if "FOO" in line:
                     assert line.strip() == extra_preamble
@@ -821,7 +821,7 @@ def test_queue_condor_extra_preamble(
         collect_submit_file_path = Path(
             tmp_path / "junifer_jobs" / jobname / f"collect_{jobname}.submit"
         )
-        with open(collect_submit_file_path, "r") as f:
+        with open(collect_submit_file_path) as f:
             for line in f.read().splitlines():
                 if "FOO" in line:
                     assert line.strip() == extra_preamble

junifer/data/coordinates.py

@@ -143,7 +143,7 @@ def load_coordinates(name: str) -> Tuple[ArrayLike, List[str]]:
     if isinstance(t_coord, Path):
         df_coords = pd.read_csv(t_coord, sep="\t", header=None)
         coords = df_coords.iloc[:, [0, 1, 2]].to_numpy()
-        names = [x for x in df_coords.iloc[:, [3]].values[:, 0]]
+        names = list(df_coords.iloc[:, [3]].values[:, 0])
     else:
         coords = t_coord["coords"]
         coords = typing.cast(ArrayLike, coords)

junifer/data/parcellations.py

@@ -103,6 +103,7 @@ def register_parcellation(
     ValueError
         If the parcellation name is already registered and overwrite is set to
         False or if the parcellation name is a built-in parcellation.
+
     """
     # Check for attempt of overwriting built-in parcellations
     if name in _available_parcellations:
@@ -139,6 +140,7 @@ def list_parcellations() -> List[str]:
     -------
     list of str
         A list with all available parcellations.
+
     """
     return sorted(_available_parcellations.keys())
 
@@ -187,6 +189,7 @@ def load_parcellation(
         Parcellation labels.
     pathlib.Path
         File path to the parcellation image.
+
     """
     # Invalid parcellation name
     if name not in _available_parcellations:
@@ -209,7 +212,7 @@ def load_parcellation(
             **parcellation_definition,
         )
 
-    logger.info(f"Loading parcellation {str(parcellation_fname.absolute())}")
+    logger.info(f"Loading parcellation {parcellation_fname.absolute()!s}")
 
     parcellation_img = None
     if path_only is False:
@@ -254,12 +257,12 @@ def _retrieve_parcellation(
         available, the closest resolution will be loaded. Preferably, use a
         resolution higher than the desired one. By default, will load the
         highest one (default None).
+    **kwargs
+        Use to specify parcellation-specific keyword arguments found in the
+        following section.
 
     Other Parameters
     ----------------
-    **kwargs
-        Use to specify parcellation-specific keyword arguments:
-
     * Schaefer :
       ``n_rois`` : {100, 200, 300, 400, 500, 600, 700, 800, 900, 1000}
             Granularity of parcellation to be used.
@@ -289,6 +292,7 @@ def _retrieve_parcellation(
     ------
     ValueError
         If the parcellation's name is invalid.
+
     """
     if parcellations_dir is None:
         parcellations_dir = (
@@ -364,6 +368,7 @@ def _retrieve_schaefer(
     ValueError
         If invalid value is provided for `n_rois` or `yeo_networks` or if
         there is a problem fetching the parcellation.
+
     """
     logger.info("Parcellation parameters:")
     logger.info(f"\tn_rois: {n_rois}")
@@ -471,6 +476,7 @@ def _retrieve_tian(
     ValueError
         If invalid value is provided for `scale` or `magneticfield` or `space`
         or if there is a problem fetching the parcellation.
+
     """
     # show parameters to user
     logger.info("Parcellation parameters:")
@@ -619,7 +625,7 @@ def _retrieve_suit(
         see http://www.diedrichsenlab.org/imaging/suit.htm).
 
     Returns
-    ------
+    -------
     pathlib.Path
         File path to the parcellation image.
     list of str
@@ -630,6 +636,7 @@ def _retrieve_suit(
     ValueError
         If invalid value is provided for `space` or if there is a problem
         fetching the parcellation.
+
     """
     logger.info("Parcellation parameters:")
     logger.info(f"\tspace: {space}")

junifer/data/tests/test_parcellations.py

@@ -94,7 +94,7 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
         load_parcellation("WrongLabels")
 
     # Test wrong number of labels
-    register_parcellation("WrongLabels2", schaefer_path, labels + ["wrong"])
+    register_parcellation("WrongLabels2", schaefer_path, [*labels, "wrong"])
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 101"):
         load_parcellation("WrongLabels2")