Move more metadata and build flags from setup.py to pyproject.toml (mne-tools#12060)

hoechenberger · pre-commit-ci[bot] · larsoner · snwnde · commit 7b35fdeebace · 2024-03-20T10:48:21.000+01:00
Co-authored-by: pre-commit-ci[bot] &lt;66853113+pre-commit-ci[bot]@users.noreply.github.com&gt;
Co-authored-by: Eric Larson &lt;larson.eric.d@gmail.com&gt;
diff --git a/mne/_ola.py b/mne/_ola.py
@@ -281,7 +281,7 @@ def __init__(
         window="hann",
         tol=1e-10,
         *,
-        verbose=None
+        verbose=None,
     ):
         n_samples = _ensure_int(n_samples, "n_samples")
         n_overlap = _ensure_int(n_overlap, "n_overlap")
diff --git a/mne/beamformer/_lcmv.py b/mne/beamformer/_lcmv.py
@@ -207,7 +207,7 @@ def make_lcmv(
         noise_cov=noise_cov,
         rank=rank,
         pca=False,
-        **depth
+        **depth,
     )
     ch_names = list(info["ch_names"])
 
diff --git a/mne/datasets/brainstorm/bst_auditory.py b/mne/datasets/brainstorm/bst_auditory.py
@@ -33,7 +33,7 @@ def data_path(
     download=True,
     accept=False,
     *,
-    verbose=None
+    verbose=None,
 ):  # noqa: D103
     return _download_mne_dataset(
         name="bst_auditory",
diff --git a/mne/datasets/brainstorm/bst_phantom_ctf.py b/mne/datasets/brainstorm/bst_phantom_ctf.py
@@ -22,7 +22,7 @@ def data_path(
     download=True,
     accept=False,
     *,
-    verbose=None
+    verbose=None,
 ):  # noqa: D103
     return _download_mne_dataset(
         name="bst_phantom_ctf",
diff --git a/mne/datasets/brainstorm/bst_phantom_elekta.py b/mne/datasets/brainstorm/bst_phantom_elekta.py
@@ -22,7 +22,7 @@ def data_path(
     download=True,
     accept=False,
     *,
-    verbose=None
+    verbose=None,
 ):  # noqa: D103
     return _download_mne_dataset(
         name="bst_phantom_elekta",
diff --git a/mne/datasets/brainstorm/bst_raw.py b/mne/datasets/brainstorm/bst_raw.py
@@ -38,7 +38,7 @@ def data_path(
     download=True,
     accept=False,
     *,
-    verbose=None
+    verbose=None,
 ):  # noqa: D103
     return _download_mne_dataset(
         name="bst_raw",
diff --git a/mne/datasets/brainstorm/bst_resting.py b/mne/datasets/brainstorm/bst_resting.py
@@ -25,7 +25,7 @@ def data_path(
     download=True,
     accept=False,
     *,
-    verbose=None
+    verbose=None,
 ):  # noqa: D103
     return _download_mne_dataset(
         name="bst_resting",
diff --git a/mne/datasets/sleep_physionet/age.py b/mne/datasets/sleep_physionet/age.py
@@ -29,7 +29,7 @@ def fetch_data(
     base_url=BASE_URL,
     on_missing="raise",
     *,
-    verbose=None
+    verbose=None,
 ):  # noqa: D301, E501
     """Get paths to local copies of PhysioNet Polysomnography dataset files.
 
@@ -134,12 +134,12 @@ def fetch_data(
                 psg_fname, pdl = _fetch_one(
                     psg_records["fname"][idx].decode(),
                     psg_records["sha"][idx].decode(),
-                    *params
+                    *params,
                 )
                 hyp_fname, hdl = _fetch_one(
                     hyp_records["fname"][idx].decode(),
                     hyp_records["sha"][idx].decode(),
-                    *params
+                    *params,
                 )
                 fnames.append([psg_fname, hyp_fname])
                 if pdl:
diff --git a/mne/datasets/sleep_physionet/temazepam.py b/mne/datasets/sleep_physionet/temazepam.py
@@ -104,12 +104,12 @@ def fetch_data(
                 psg_fname, pdl = _fetch_one(
                     records["psg fname"][idx].decode(),
                     records["psg sha"][idx].decode(),
-                    *params
+                    *params,
                 )
                 hyp_fname, hdl = _fetch_one(
                     records["hyp fname"][idx].decode(),
                     records["hyp sha"][idx].decode(),
-                    *params
+                    *params,
                 )
                 fnames.append([psg_fname, hyp_fname])
                 if pdl:
diff --git a/mne/datasets/tests/test_datasets.py b/mne/datasets/tests/test_datasets.py
@@ -205,7 +205,7 @@ def test_fetch_parcellations(tmp_path):
         labels,
         parc="HCPMMP1_round",
         table_name="./left.fsaverage164.label.gii",
-        **kwargs
+        **kwargs,
     )
     orig = op.join(this_subjects_dir, "fsaverage", "label", "lh.HCPMMP1.annot")
     first = hashfunc(orig)
diff --git a/mne/decoding/base.py b/mne/decoding/base.py
@@ -419,7 +419,7 @@ def _fit_and_score(
     error_score="raise",
     *,
     verbose=None,
-    position=0
+    position=0,
 ):
     """Fit estimator and compute scores for a given dataset split."""
     #  This code is adapted from sklearn
diff --git a/mne/decoding/csp.py b/mne/decoding/csp.py
@@ -281,7 +281,7 @@ def plot_patterns(
         name_format="CSP%01d",
         nrows=1,
         ncols="auto",
-        show=True
+        show=True,
     ):
         """Plot topographic patterns of components.
 
@@ -412,7 +412,7 @@ def plot_filters(
         name_format="CSP%01d",
         nrows=1,
         ncols="auto",
-        show=True
+        show=True,
     ):
         """Plot topographic filters of components.
 
diff --git a/mne/decoding/transformer.py b/mne/decoding/transformer.py
@@ -383,7 +383,7 @@ def __init__(
         n_jobs=None,
         normalization="length",
         *,
-        verbose=None
+        verbose=None,
     ):  # noqa: D102
         self.sfreq = sfreq
         self.fmin = fmin
@@ -512,7 +512,7 @@ def __init__(
         iir_params=None,
         fir_design="firwin",
         *,
-        verbose=None
+        verbose=None,
     ):  # noqa: D102
         self.info = info
         self.l_freq = l_freq
@@ -838,7 +838,7 @@ def __init__(
         fir_window="hamming",
         fir_design="firwin",
         *,
-        verbose=None
+        verbose=None,
     ):  # noqa: D102
         self.l_freq = l_freq
         self.h_freq = h_freq
diff --git a/mne/minimum_norm/resolution_matrix.py b/mne/minimum_norm/resolution_matrix.py
@@ -78,7 +78,7 @@ def _get_psf_ctf(
     norm,
     return_pca_vars,
     vector=False,
-    verbose=None
+    verbose=None,
 ):
     """Get point-spread (PSFs) or cross-talk (CTFs) functions."""
     # check for consistencies in input parameters
@@ -302,7 +302,7 @@ def get_point_spread(
     norm=False,
     return_pca_vars=False,
     vector=False,
-    verbose=None
+    verbose=None,
 ):
     """Get point-spread (PSFs) functions for vertices.
 
@@ -351,7 +351,7 @@ def get_cross_talk(
     norm=False,
     return_pca_vars=False,
     vector=False,
-    verbose=None
+    verbose=None,
 ):
     """Get cross-talk (CTFs) function for vertices.
 
diff --git a/mne/preprocessing/ecg.py b/mne/preprocessing/ecg.py
@@ -530,7 +530,7 @@ def _make_ecg(inst, start, stop, reject_by_annotation=False, verbose=None):
             picks,
             return_times=True,
             **kwargs,
-            reject_by_annotation=reject_by_annotation
+            reject_by_annotation=reject_by_annotation,
         )
     elif isinstance(inst, BaseEpochs):
         ecg = np.hstack(inst.copy().get_data(picks, **kwargs))
diff --git a/mne/time_frequency/multitaper.py b/mne/time_frequency/multitaper.py
@@ -336,7 +336,7 @@ def psd_array_multitaper(
     n_jobs=None,
     *,
     max_iter=150,
-    verbose=None
+    verbose=None,
 ):
     r"""Compute power spectral density (PSD) using a multi-taper method.
 
@@ -475,7 +475,7 @@ def tfr_array_multitaper(
     output="complex",
     n_jobs=None,
     *,
-    verbose=None
+    verbose=None,
 ):
     """Compute Time-Frequency Representation (TFR) using DPSS tapers.
 
diff --git a/mne/viz/montage.py b/mne/viz/montage.py
@@ -20,7 +20,7 @@ def plot_montage(
     sphere=None,
     *,
     axes=None,
-    verbose=None
+    verbose=None,
 ):
     """Plot a montage.
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,3 +1,90 @@
+[project]
+name = "mne"
+description = "MNE-Python project for MEG and EEG data analysis."
+maintainers = [
+    { name = "Alexandre Gramfort", email = "alexandre.gramfort@inria.fr" },
+]
+dynamic = ["version"]
+license = { text = "BSD-3-Clause" }
+readme = { file = "README.rst", content-type = "text/x-rst" }
+requires-python = ">=3.8"
+keywords = [
+    "neuroscience",
+    "neuroimaging",
+    "MEG",
+    "EEG",
+    "ECoG",
+    "fNIRS",
+    "brain",
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved",
+    "Programming Language :: Python",
+    "Topic :: Software Development",
+    "Topic :: Scientific/Engineering",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
+    "Programming Language :: Python :: 3",
+]
+
+[project.scripts]
+mne = "mne.commands.utils:main"
+
+[project.urls]
+Homepage = "https://mne.tools/"
+Download = "https://pypi.org/project/scikit-learn/#files"
+"Bug Tracker" = "https://github.com/mne-tools/mne-python/issues/"
+Documentation = "https://mne.tools/"
+Forum = "https://mne.discourse.group/"
+"Source Code" = "https://github.com/mne-tools/mne-python/"
+
+[build-system]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "mne/_version.py"
+version_scheme = "release-branch-semver"
+
+[options]
+zip_safe = false            # the package can run out of an .egg file
+include_package_data = true
+
+[tool.setuptools.package-data]
+"mne" = [
+    "data/eegbci_checksums.txt",
+    "data/*.sel",
+    "data/icos.fif.gz",
+    "data/coil_def*.dat",
+    "data/helmets/*.fif.gz",
+    "data/FreeSurferColorLUT.txt",
+    "data/image/*gif",
+    "data/image/*lout",
+    "data/fsaverage/*.fif",
+    "channels/data/layouts/*.lout",
+    "channels/data/layouts/*.lay",
+    "channels/data/montages/*.sfp",
+    "channels/data/montages/*.txt",
+    "channels/data/montages/*.elc",
+    "channels/data/neighbors/*.mat",
+    "datasets/sleep_physionet/SHA1SUMS",
+    "datasets/_fsaverage/*.txt",
+    "datasets/_infant/*.txt",
+    "datasets/_phantom/*.txt",
+    "html/*.js",
+    "html/*.css",
+    "html_templates/repr/*.jinja",
+    "html_templates/report/*.jinja",
+    "icons/*.svg",
+    "icons/*.png",
+    "io/artemis123/resources/*.csv",
+    "io/edf/gdf_encodes.txt",
+]
+
 [tool.codespell]
 ignore-words = "ignore_words.txt"
 builtin = "clear,rare,informal,names,usage"
@@ -19,12 +106,12 @@ ignore-decorators = [
     "setter",
     "mne.utils.copy_function_doc_to_method_doc",
     "mne.utils.copy_doc",
-    "mne.utils.deprecated"
+    "mne.utils.deprecated",
 ]
 
 [tool.ruff.per-file-ignores]
 "tutorials/time-freq/10_spectrum_class.py" = [
-    "E501" # line too long
+    "E501", # line too long
 ]
 "mne/datasets/*/*.py" = [
     "D103", # Missing docstring in public function
@@ -52,4 +139,4 @@ junit_family = "xunit2"
 exclude = "(dist/)|(build/)|(.*\\.ipynb)"
 
 [tool.bandit.assert_used]
-skips = ["*/test_*.py"]  # assert statements are good practice with pytest
+skips = ["*/test_*.py"] # assert statements are good practice with pytest
diff --git a/setup.py b/setup.py
diff --git a/tutorials/inverse/50_beamformer_lcmv.py b/tutorials/inverse/50_beamformer_lcmv.py
diff --git a/tutorials/preprocessing/25_background_filtering.py b/tutorials/preprocessing/25_background_filtering.py
diff --git a/tutorials/preprocessing/45_projectors_background.py b/tutorials/preprocessing/45_projectors_background.py
diff --git a/tutorials/stats-sensor-space/20_erp_stats.py b/tutorials/stats-sensor-space/20_erp_stats.py

Original file line number	Diff line number	Diff line change
`@@ -207,7 +207,7 @@ def make_lcmv(`
`207`	`207`	`noise_cov=noise_cov,`
`208`	`208`	`rank=rank,`
`209`	`209`	`pca=False,`
`210`		`- **depth`
	`210`	`+ **depth,`
`211`	`211`	`)`
`212`	`212`	`ch_names = list(info["ch_names"])`
`213`	`213`
Original file line number	Diff line number	Diff line change
`@@ -205,7 +205,7 @@ def test_fetch_parcellations(tmp_path):`
`205`	`205`	`labels,`
`206`	`206`	`parc="HCPMMP1_round",`
`207`	`207`	`table_name="./left.fsaverage164.label.gii",`
`208`		`- **kwargs`
	`208`	`+ **kwargs,`
`209`	`209`	`)`
`210`	`210`	`orig = op.join(this_subjects_dir, "fsaverage", "label", "lh.HCPMMP1.annot")`
`211`	`211`	`first = hashfunc(orig)`