[WIP] Upgrading dependencies

.python-version

@@ -0,0 +1 @@
+3.12

MANIFEST.in

@@ -1,7 +1,6 @@
-include LICENSE
+include LICENSE.md
 include README.md
 
-recursive-include tests *
 recursive-include phylib/electrode/probes *.prb
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

Makefile

@@ -12,19 +12,19 @@ clean-pyc:
 clean: clean-build clean-pyc
 
 lint:
-	flake8 phylib
+	uv run flake8 --jobs=1 phylib
 
 test: lint
-	py.test --cov-report term-missing --cov=phylib phylib
+	uv run pytest --cov-report term-missing --cov=phylib phylib
 
 coverage:
-	coverage --html
+	uv run coverage html
 
 apidoc:
-	python tools/api.py
+	uv run python tools/api.py
 
 build:
-	python setup.py sdist --formats=zip
+	uv build
 
 upload:
-	python setup.py sdist --formats=zip upload
+	@echo "Build artifacts with 'uv build' and upload them with twine."

README.md

@@ -5,15 +5,14 @@
 Electrophysiological data analysis library used by [phy](https://github.com/kwikteam/phy/), a spike sorting visualization software, and [ibllib](https://github.com/int-brain-lab/ibllib/).
 
 
-## Contribution
-
-- run all tests using pytest `pytest phylib`
-- PR to main
-- update `CHANGELOG.md` and version in `phylib\__init__.py`
-- publish to pypi:
-```shell
-rm -R dist
-rm -R build 
-python setup.py sdist bdist_wheel
-twine upload dist/*
-```
+## Contribution
+
+- create a local environment with `uv venv --python 3.12` and `uv sync --extra dev`
+- run all tests using `uv run pytest phylib`
+- PR to main
+- update `CHANGELOG.md` and version in `phylib\__init__.py`
+- publish to pypi:
+```shell
+uv build
+twine upload dist/*
+```

phylib/io/alf.py

@@ -373,10 +373,11 @@ def get_waveforms_amp(templates):
         cha = np.max(templates, axis=1) - np.min(templates, axis=1)
         return np.max(cha, axis=1)
 
-    # we unwhiten the templates waveforms, this will expand the templates to the original non-sparse size
+    # Unwhiten templates and expand them to the original non-sparse size.
     templates_phy = np.zeros([nclu, templates['waveforms'].shape[1], nch], dtype=np.float32)
     for i in np.arange(templates_phy.shape[0]):
-        templates_phy[i] = np.matmul(templates['waveforms'][i], wm[templates['waveformsChannels'][i], :])
+        templates_phy[i] = np.matmul(
+            templates['waveforms'][i], wm[templates['waveformsChannels'][i], :])
 
     # the original templates have a rms of 1.0, so here we just need to normalize by rms
     rms_templates = np.sum(np.sum(templates['waveforms'] ** 2, axis=1), axis=1) ** 0.5
@@ -390,7 +391,10 @@ def get_waveforms_amp(templates):
     np.save(target_path.joinpath('channel_map.npy'), np.arange(nch))
     np.save(target_path.joinpath('templates.npy'), templates_phy)
 
-    np.save(target_path.joinpath('templates_ind.npy'), np.tile(np.arange(nclu)[np.newaxis, :], reps=[nch, 1]))
+    np.save(
+        target_path.joinpath('templates_ind.npy'),
+        np.tile(np.arange(nclu)[np.newaxis, :], reps=[nch, 1]),
+    )
 
     # if we have metrics information, output the ks2_label information
     if alf_path.joinpath('cluster.metrics.pqt').exists():

phylib/io/model.py

@@ -328,7 +328,8 @@ def __init__(self, **kwargs):
         elif not isinstance(self.dat_path, (list, tuple)):
             self.dat_path = [self.dat_path]
         assert isinstance(self.dat_path, (list, tuple))
-        self.dat_path = [Path(p).resolve() if not Path(p).is_symlink() else p for p in self.dat_path]
+        self.dat_path = [
+            Path(p).resolve() if not Path(p).is_symlink() else p for p in self.dat_path]
 
         self.dtype = getattr(self, 'dtype', np.int16)
         if not self.sample_rate:  # pragma: no cover
@@ -973,14 +974,15 @@ def get_waveforms(self, spike_ids, channel_ids=None):
             # Load from precomputed spikes.
             try:
                 return get_spike_waveforms(
-                spike_ids, channel_ids, spike_waveforms=self.spike_waveforms,
-                n_samples_waveforms=nsw)
+                    spike_ids, channel_ids, spike_waveforms=self.spike_waveforms,
+                    n_samples_waveforms=nsw)
             except AssertionError:
-              logger.warning(
-                  "Error when loading waveforms from precomputed waveforms, trying to load the raw data.")
-              spike_samples = self.spike_samples[spike_ids]
-              return extract_waveforms(
-                  self.traces, spike_samples, channel_ids, n_samples_waveforms=nsw)
+                logger.warning(
+                    "Error when loading waveforms from precomputed waveforms, "
+                    "trying to load the raw data.")
+                spike_samples = self.spike_samples[spike_ids]
+                return extract_waveforms(
+                    self.traces, spike_samples, channel_ids, n_samples_waveforms=nsw)
         else:
             # Or load directly from raw data (slower).
             spike_samples = self.spike_samples[spike_ids]

phylib/io/tests/test_alf.py

@@ -41,7 +41,10 @@ def __init__(self, tempdir):
         np.save(p / 'amplitudes.npy', nr.uniform(low=0.5, high=1.5, size=self.ns))
         np.save(p / 'channel_positions.npy', np.c_[np.arange(self.nc), np.zeros(self.nc)])
         templates = np.random.normal(size=(self.nt, 50, self.nc))
-        templates = templates / (np.sum(np.sum(templates ** 2, axis=1), axis=1) ** .5)[:, np.newaxis, np.newaxis]
+        templates = (
+            templates /
+            (np.sum(np.sum(templates ** 2, axis=1), axis=1) ** .5)[:, np.newaxis, np.newaxis]
+        )
         np.save(p / 'templates.npy', templates)
         np.save(p / 'similar_templates.npy', np.tile(np.arange(self.nt), (self.nt, 1)))
         np.save(p / 'channel_map.npy', np.c_[np.arange(self.nc)])

phylib/io/tests/test_datasets.py

@@ -141,10 +141,10 @@ def test_download_file(tempdir, mock_urls):
 
     assert_succeeds = (data_here and data_valid and
                        ((checksum_here == checksum_valid) or
-                        (not(checksum_here) and checksum_valid)))
+                        (not (checksum_here) and checksum_valid)))
 
     download_succeeds = (assert_succeeds or (data_here and
-                                             (not(data_valid) and not(checksum_here))))
+                                             (not (data_valid) and not (checksum_here))))
 
     if download_succeeds:
         data = _dl(path)

phylib/utils/event.py

@@ -69,9 +69,9 @@ def silent(self):
         """Prevent all callbacks to be called if events are raised
         in the context manager.
         """
-        self.is_silent = not(self.is_silent)
+        self.is_silent = not (self.is_silent)
         yield
-        self.is_silent = not(self.is_silent)
+        self.is_silent = not (self.is_silent)
 
     def connect(self, func=None, event=None, sender=None, **kwargs):
         """Register a callback function to a given event.

pyproject.toml

@@ -0,0 +1,79 @@
+[build-system]
+requires = ["setuptools>=69", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "phylib"
+dynamic = ["version"]
+description = "Ephys data analysis for thousands of channels"
+readme = "README.md"
+requires-python = ">=3.10"
+license = "BSD-3-Clause"
+license-files = ["LICENSE.md"]
+authors = [
+  {name = "Cyrille Rossant", email = "cyrille.rossant@gmail.com"},
+]
+keywords = ["phy", "data analysis", "electrophysiology", "neuroscience"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Developers",
+  "Natural Language :: English",
+  "Framework :: IPython",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+dependencies = [
+  "joblib",
+  "mtscomp",
+  "numpy",
+  "requests",
+  "scipy",
+  "tqdm",
+]
+
+[project.optional-dependencies]
+dev = [
+  "coverage",
+  "coveralls",
+  "flake8",
+  "pytest",
+  "pytest-cov",
+  "responses",
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "phylib.__version__"}
+
+[tool.setuptools.packages.find]
+include = ["phylib", "phylib.*"]
+
+[tool.setuptools.package-data]
+phylib = [
+  "*.vert",
+  "*.frag",
+  "*.glsl",
+  "*.npy",
+  "*.gz",
+  "*.txt",
+  "*.html",
+  "*.css",
+  "*.js",
+  "*.prb",
+]
+
+[tool.pytest.ini_options]
+norecursedirs = [
+  ".git",
+  ".venv",
+  ".uv-cache",
+  "build",
+  "dist",
+]
+filterwarnings = [
+  "default",
+  "ignore::DeprecationWarning:responses|cookies|socks|matplotlib",
+  "ignore:numpy.ufunc",
+]

setup.cfg

@@ -1,13 +1,3 @@
-[wheel]
-universal = 1
-
-[tool:pytest]
-norecursedirs =
-filterwarnings =
-    default
-    ignore::DeprecationWarning:responses|cookies|socks|matplotlib
-    ignore:numpy.ufunc
-
 [flake8]
 ignore=E265,E731,E741,W504,W605
 max-line-length=99