Replace black and flake8 by ruff

.circleci/config.yml

@@ -99,8 +99,7 @@ jobs:
           name: Check style
           command: |
             isort --check .
-            black --check nigsp
-            flake8 ./nigsp
+            ruff check nigsp
 
   merge_coverage:
     working_directory: /tmp/src/nigsp

.pre-commit-config.yaml

@@ -1,38 +1,46 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
-    -   id: check-case-conflict
-    -   id: check-merge-conflict
--   repo: https://github.com/psf/black
-    rev: 24.4.0
-    hooks:
-    -   id: black
--   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-    -   id: isort
--   repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-    -   id: flake8
--   repo: https://github.com/pycqa/pydocstyle
-    rev: 6.3.0
-    hooks:
-      - id: pydocstyle
--   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-      - id: rst-backticks
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
--   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
-    hooks:
-      - id: codespell
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.6.0
+      hooks:
+          - id: end-of-file-fixer
+          - id: check-yaml
+          - id: check-added-large-files
+          - id: check-case-conflict
+          - id: check-merge-conflict
+
+    - repo: https://github.com/pycqa/isort
+      rev: 5.13.2
+      hooks:
+          - id: isort
+
+    - repo: https://github.com/pycqa/pydocstyle
+      rev: 6.3.0
+      hooks:
+          - id: pydocstyle
+
+
+    - repo: https://github.com/pre-commit/pygrep-hooks
+      rev: v1.10.0
+      hooks:
+          - id: rst-backticks
+          - id: rst-directive-colons
+          - id: rst-inline-touching-normal
+
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.2.6
+      hooks:
+          - id: codespell
+
+
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.3.7
+      hooks:
+          - id: ruff
+            name: ruff linter
+            args: [--fix]
+            files: nigsp
+          - id: ruff-format
+            name: ruff formatter
+            files: nigsp

codecov.yml

@@ -1,43 +1,25 @@
+comment: false
+github_checks:  # too noisy, even though "a" interactively disables them
+  annotations: false
+
 codecov:
-  branch: master
-  strict_yaml_branch: master
-  require_ci_to_pass: true
-  bot: "codecov-io"
-  max_report_age: 48
-  disable_default_path_fixes: false
+  notify:
+    require_ci_to_pass: false
 
 coverage:
-  precision: 2
-  round: down
-  range: "60...90"
-
-parsers:
-  gcov:
-    branch_detection:
-      conditional: yes
-      loop: yes
-      method: no
-      macro: no
-
-ignore:
-  - "docs"
-  - "tests"
-  - "_version.py"
-  - "__init__.py"
-  - "**/__init__.py"
-  - "due.py"
-  - ".*rc"
-  - "versioneer.py"
-  - "setup.py"
-  - "nigsp/tests"
-  - "nigsp/_version.py"
-  - "nigsp/__init__.py"
-  - "nigsp/**/__init__.py"
-  - "nigsp/due.py"
-  - "nigsp/.*rc"
-  - "nigsp/versioneer.py"
-  - "nigsp/setup.py"
-comment:
-  layout: "reach,diff,flags,tree"
-  behavior: default
-  require_changes: false
+  status:
+    patch:
+      default:
+        informational: true
+        target: 95%
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: error
+    project:
+      default: false
+      library:
+        informational: true
+        target: 90%
+        if_no_uploads: error
+        if_not_found: success
+        if_ci_failed: error

nigsp/_version.py

@@ -84,7 +84,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
                 stderr=(subprocess.PIPE if hide_stderr else None),
             )
             break
-        except EnvironmentError:
+        except EnvironmentError:  # noqa
             e = sys.exc_info()[1]
             if e.errno == errno.ENOENT:
                 continue
@@ -94,7 +94,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
             return None, None
     else:
         if verbose:
-            print("unable to find command, tried %s" % (commands,))
+            print(f"unable to find command, tried {commands}")
         return None, None
     stdout = p.communicate()[0].strip()
     if sys.version_info[0] >= 3:
@@ -116,7 +116,7 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
             return {
@@ -132,8 +132,8 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
 
     if verbose:
         print(
-            "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
+            f"Tried directories {str(rootdirs)} but none started with prefix "
+            f"{parentdir_prefix}"
         )
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
@@ -147,7 +147,7 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        f = open(versionfile_abs, "r")
+        f = open(versionfile_abs, "r")  # noqa: UP015
         for line in f.readlines():
             if line.strip().startswith("git_refnames ="):
                 mo = re.search(r'=\s*"(.*)"', line)
@@ -162,7 +162,7 @@ def git_get_keywords(versionfile_abs):
                 if mo:
                     keywords["date"] = mo.group(1)
         f.close()
-    except EnvironmentError:
+    except EnvironmentError:  # noqa
         pass
     return keywords
 
@@ -302,9 +302,8 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
-                full_tag,
-                tag_prefix,
+            pieces["error"] = (
+                f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'"
             )
             return pieces
         pieces["closest-tag"] = full_tag[len(tag_prefix) :]
@@ -524,7 +523,7 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split("/"):
+        for _ in cfg.versionfile_source.split("/"):
             root = os.path.dirname(root)
     except NameError:
         return {

nigsp/blocks.py

@@ -68,7 +68,7 @@ def export_metric(scgraph, outext, outprefix):
     """
     if outext in io.EXT_NIFTI:
         try:
-            import nibabel as _
+            import nibabel as _  # noqa: F401
         except ImportError:
             LGR.warning(
                 "The necessary library for nifti export (nibabel) "
@@ -118,7 +118,6 @@ def plot_metric(scgraph, outprefix, atlas=None, thr=None):
     """
     # Check that atlas format is supported.
     try:
-        atlas.header
         atlas_plot = atlas
     except AttributeError:
         try:

nigsp/cli/run.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """Parser for crispy-octo-broccoli."""
 
 import argparse

nigsp/conftest.py

@@ -59,7 +59,7 @@ def fetch_file(osf_id, path, filename):
             )
         )
         ssl._create_default_https_context = ssl._create_unverified_context
-    url = "https://osf.io/{}/download".format(osf_id)
+    url = f"https://osf.io/{osf_id}/download"
     full_path = os.path.join(path, filename)
     if not os.path.isfile(full_path):
         urlretrieve(url, full_path)

nigsp/due.py

@@ -27,7 +27,7 @@
 __version__ = "0.0.9"
 
 
-class InactiveDueCreditCollector(object):
+class InactiveDueCreditCollector:
     """Just a stub at the Collector which would not do anything"""
 
     def _donothing(self, *args, **kwargs):

nigsp/objects.py

@@ -130,15 +130,15 @@ def compute_graph_energy(self, mean=False):  # pragma: no cover
         )
         return self
 
-    def split_graph(self, index=None, keys=["low", "high"]):
+    def split_graph(self, index=None, keys=["low", "high"]):  # noqa: B006
         """Implement timeseries.median_cutoff_frequency_idx as class method."""
         if index is None:
             index = self.index
 
         if index == "median":  # pragma: no cover
             index = operations.median_cutoff_frequency_idx(self.energy)
 
-        elif type(index) is not int:
+        elif not isinstance(index, int):
             raise ValueError(
                 f"Unknown option {index} for frequency split index. "
                 "Declared index must be either an integer or 'median'"

nigsp/operations/laplacian.py

@@ -45,7 +45,8 @@ def compute_laplacian(mtx, negval="absolute", selfloops=False):
     numpy.ndarray
         The laplacian of mtx
     numpy.ndarray
-        The degree matrix of mtx as a (mtx.ndim-1)D array, updated with selfloops in case.
+        The degree matrix of mtx as a (mtx.ndim-1)D array, updated with selfloops in
+        case.
 
     Raises
     ------
@@ -104,8 +105,7 @@ def compute_laplacian(mtx, negval="absolute", selfloops=False):
 
 
 def normalisation(lapl, degree, norm="symmetric", fix_zeros=True):
-    """
-    Normalise a Laplacian (L) matrix using either symmetric or random walk normalisation.
+    """Normalise a Laplacian (L) matrix using either symmetric or random walk normalisation.
 
     Parameters
     ----------
@@ -125,8 +125,8 @@ def normalisation(lapl, degree, norm="symmetric", fix_zeros=True):
           It normalises the outflow, i.e. it is column-optimised (each column = 0).
           Normally used in e.g. physical distribution networks.
     fix_zeros : bool, optional
-        Whether to change 0 elements in the degree matrix to 1 to avoid multiplying by 0.
-        Default is to do so.
+        Whether to change 0 elements in the degree matrix to 1 to avoid multiplying by
+        0. Default is to do so.
 
     Returns
     -------
@@ -145,7 +145,7 @@ def normalisation(lapl, degree, norm="symmetric", fix_zeros=True):
     Notes
     -----
     https://en.wikipedia.org/wiki/Laplacian_matrix
-    """
+    """  # noqa: E501
     deg = deepcopy(degree)
     if lapl.ndim - deg.ndim > 1:
         raise NotImplementedError(

nigsp/operations/metrics.py

@@ -206,7 +206,8 @@ def _fc(timeseries, mean=False):
         timeseries : numpy.ndarray
             A 2- or 3-D matrix containing timeseries along axis 1.
         mean : bool, optional
-            If timeseries is 3D and this is True, return the average FC along the last axis.
+            If timeseries is 3D and this is True, return the average FC along the last
+            axis.
 
         Returns
         -------
@@ -236,7 +237,7 @@ def _fc(timeseries, mean=False):
                 fcorr = fcorr.mean(axis=2).squeeze()
             return fcorr
 
-    if type(timeseries) is dict:
+    if isinstance(timeseries, dict):
         fc = dict()
         for k in timeseries.keys():
             fc[k] = _fc(timeseries[k], mean)

nigsp/operations/nifti.py

@@ -175,9 +175,11 @@ def apply_atlas(data, atlas, mask=None):
     data : numpy.ndarray
         A 3- or 4- D matrix (normally nifti data) of timeseries.
     atlas : numpy.ndarray
-        A 2- or 3- D matrix representing the atlas, each parcel represented by a different int.
+        A 2- or 3- D matrix representing the atlas, each parcel represented by a
+        different int.
     mask : None or numpy.ndarray, optional
-        A 2- or 3- D matrix representing a mask, all voxels == 0 are excluded from the computation.
+        A 2- or 3- D matrix representing a mask, all voxels == 0 are excluded from the
+        computation.
 
     Returns
     -------
@@ -230,8 +232,8 @@ def apply_atlas(data, atlas, mask=None):
     parcels = np.empty([len(labels), data.shape[-1]], dtype="float32")
 
     # Compute averages
-    for n, l in enumerate(labels):
-        parcels[n, :] = data[atlas == l].mean(axis=0)
+    for n, label in enumerate(labels):
+        parcels[n, :] = data[atlas == label].mean(axis=0)
 
     return parcels
 
@@ -302,8 +304,8 @@ def unfold_atlas(data, atlas, mask=None):
         if data.shape[ax] > 1:
             out = out[..., np.newaxis].repeat(data.shape[ax], axis=-1)
 
-    for n, l in enumerate(labels):
-        out[atlas == l] = data[n, ...]
+    for n, label in enumerate(labels):
+        out[atlas == label] = data[n, ...]
 
     return out