ci: some ci maintenance work

.github/workflows/pylake_test.yml

@@ -36,7 +36,7 @@ jobs:
       run: python -c "import lumicks.pylake as lk; lk.benchmark(repeat=1)"
     - name: Black
       run: |
-        pip install black==23.7.0 isort==5.12.0
+        pip install black==24.4.2 isort==5.13.2
         black --check --diff --color .
         isort --check-only --diff .
     - name: flake8

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 24.4.2
+  hooks:
+  - id: black
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: end-of-file-fixer
+    exclude: ^.*\.png$ ^.*\.gif$
+  - id: requirements-txt-fixer
+  - id: trailing-whitespace
+    exclude: ^.*\.png$ ^.*\.gif$
+- repo: https://github.com/pycqa/flake8
+  rev: 7.1.0
+  hooks:
+  - id: flake8
+    language_version: python3
+    additional_dependencies:
+      - flake8-bugbear==24.4.26

setup.manifest → MANIFEST.in

@@ -1,4 +1,5 @@
-include license.md readme.md
+include license.md
+include readme.md
 global-include *.npz
 global-include *.gb
 global-include *.csv

contributing.md

@@ -59,3 +59,17 @@ Code and documentation contributions will generally proceed through a Pull Reque
 - Please set up your editor to follow PEP8 (remove trailing white space, no tabs, etc.). Use [black](https://github.com/psf/black) to format your code.
 - All public functions and classes require an informative docstring. Document these using the [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html) style.
 - Features should ideally be grouped by category in their own folder, with implementational details in a sub-folder named `detail`. Tests for each specific category should be placed in a sub-folder `tests`.
+
+### Installing pre-commit hooks
+
+To help with formatting and code-style consider installing the pre-commit hooks.
+These will check the formatting whenever you commit.
+Install `pre-commit` with:
+
+    pip install pre-commit
+
+Next, set up the hook with::
+
+    pre-commit install
+
+That's all there is to it.

docs/conf.py

@@ -256,7 +256,7 @@
     # 'pointsize': '10pt',
     # Additional stuff for the LaTeX preamble.
     "preamble": r"\definecolor{VerbatimBorderColor}{rgb}{1,1,1}"
-    r"\usepackage{etoolbox}\patchcmd{\thebibliography}{\section*{\refname}}{}{}{}"
+    r"\usepackage{etoolbox}\patchcmd{\thebibliography}{\section*{\refname}}{}{}{}",
     # Latex figure (float) alignment
     # 'figure_align': 'htbp',
 }

lumicks/pylake/calibration.py

@@ -132,9 +132,11 @@ def format_timestamp(timestamp):
                     item.kind,
                     f"{item.stiffness:.2f}" if item.stiffness else "N/A",
                     f"{item.force_sensitivity:.2f}" if item.force_sensitivity else "N/A",
-                    f"{item.displacement_sensitivity:.2f}"
-                    if item.displacement_sensitivity
-                    else "N/A",
+                    (
+                        f"{item.displacement_sensitivity:.2f}"
+                        if item.displacement_sensitivity
+                        else "N/A"
+                    ),
                     item.hydrodynamically_correct,
                     item.distance_to_surface is not None,
                     bool(

lumicks/pylake/detail/mixin.py

@@ -1,4 +1,5 @@
 """Mixin class which add properties for predefined channels"""
+
 from ..channel import Slice, empty_slice
 
 

lumicks/pylake/detail/tests/test_bead_crop.py

@@ -31,8 +31,10 @@ def test_bead_cropping_allow_negative_beads(filename, ref_edges, ref_edges_no_ne
     # because the fluorescence typically tails out wide.
     np.testing.assert_equal(edges, ref_edges)
 
-    with nullcontext() if ref_edges_no_negative else pytest.raises(
-        RuntimeError, match="Did not find two beads"
+    with (
+        nullcontext()
+        if ref_edges_no_negative
+        else pytest.raises(RuntimeError, match="Did not find two beads")
     ):
         edges = find_beads_brightness(
             np.atleast_2d(data["green"]).T,
@@ -50,7 +52,7 @@ def test_bead_cropping_failure():
 
 
 def test_plotting():
-    data = np.load(pathlib.Path(__file__).parent / "data" / f"kymo_sum0.npz")
+    data = np.load(pathlib.Path(__file__).parent / "data" / "kymo_sum0.npz")
     for allow_negative in (False, True):
         edges = find_beads_brightness(
             np.atleast_2d(data["green"]).T,

lumicks/pylake/fitting/detail/model_implementation.py

@@ -889,16 +889,8 @@ def ewlc_marko_siggia_force_jac(d, Lp, Lc, St, kT=4.11):
     denom1 = Lc**3 * (Lp * St + kT) ** 2
     denom2 = Lc * (Lp**2 * St**2 + 2.0 * Lp * St * kT + kT**2)
     dkT = d * kT
-    dc_dLc = (
-        St**3 * dkT * (1.5 * Lc**2 - 4.5 * Lc * d + 3.0 * d**2) / (Lc**4 * (Lp * St + kT))
-    )
-    dc_dSt = (
-        -(St**2)
-        * dkT
-        * (2 * Lp * St + 3 * kT)
-        * (1.5 * Lc**2 - 2.25 * Lc * d + d**2)
-        / denom1
-    )
+    dc_dLc = St**3 * dkT * (1.5 * Lc**2 - 4.5 * Lc * d + 3.0 * d**2) / (Lc**4 * (Lp * St + kT))
+    dc_dSt = -(St**2) * dkT * (2 * Lp * St + 3 * kT) * (1.5 * Lc**2 - 2.25 * Lc * d + d**2) / denom1
     dc_dLp = St**4 * dkT * (1.5 * Lc**2 - 2.25 * Lc * d + d**2) / denom1
     dc_dkT = -Lp * St**4 * d * (1.5 * Lc**2 - 2.25 * Lc * d + d**2) / denom1
     db_dLc = (
@@ -1287,9 +1279,7 @@ def ewlc_marko_siggia_distance_derivative(f, Lp, Lc, St, kT=4.11):
         )
         / (St**3 * kT)
     )
-    db_df = (
-        Lc**2 * (4 * f * Lp * St + 6 * f * kT + 2 * Lp * St**2 + 4.5 * St * kT) / (St**2 * kT)
-    )
+    db_df = Lc**2 * (4 * f * Lp * St + 6 * f * kT + 2 * Lp * St**2 + 4.5 * St * kT) / (St**2 * kT)
     da_df = -Lc * Lp / kT - 3 * Lc / St
 
     return total_dy_da * da_df + total_dy_db * db_df + total_dy_dc * dc_df

lumicks/pylake/force_calibration/calibration_models.py

@@ -866,9 +866,9 @@ def __init__(
                 bead_radius=self.bead_diameter * 1e-6 / 2.0,  # um diameter -> m radius
                 rho_sample=self.rho_sample,
                 rho_bead=self.rho_bead,
-                distance_to_surface=None
-                if self.distance_to_surface is None
-                else self.distance_to_surface * 1e-6,  # um => m
+                distance_to_surface=(
+                    None if self.distance_to_surface is None else self.distance_to_surface * 1e-6
+                ),  # um => m
             )
         else:
             self._theoretical_driving_power_model = partial(

lumicks/pylake/kymotracker/kymotracker.py

@@ -189,9 +189,11 @@ def track_greedy(
         bias_correction=bias_correction,
         filter_width=filter_width / kymograph.pixelsize_um[0] if filter_width is not None else 0.5,
         adjacency_half_width=half_width_pixels if adjacency_filter else None,
-        rect=_to_pixel_rect(rect, kymograph.pixelsize[0], kymograph.line_time_seconds)
-        if rect
-        else None,
+        rect=(
+            _to_pixel_rect(rect, kymograph.pixelsize[0], kymograph.line_time_seconds)
+            if rect
+            else None
+        ),
     )
 
     if not peaks:
@@ -389,9 +391,11 @@ def minimum_observable_time(track, min_length, min_duration):
             track._with_minimum_time(
                 max(
                     # We can't unfilter tracks.
-                    track._minimum_observable_duration
-                    if track._minimum_observable_duration is not None
-                    else 0,
+                    (
+                        track._minimum_observable_duration
+                        if track._minimum_observable_duration is not None
+                        else 0
+                    ),
                     minimum_observable_time(track, minimum_length, minimum_duration),
                 )
             )

lumicks/pylake/kymotracker/tests/test_io.py

@@ -198,13 +198,17 @@ def test_csv_version(version, read_with_version):
     )
 
     testfile = Path(__file__).parent / f"./data/tracks_v{version}.csv"
-    with pytest.warns(
-        RuntimeWarning,
-        match=(
-            "This CSV file is from a version in which the minimum observable track duration "
-            "was incorrectly rounded to an integer."
-        ),
-    ) if version == 3 else contextlib.nullcontext():
+    with (
+        pytest.warns(
+            RuntimeWarning,
+            match=(
+                "This CSV file is from a version in which the minimum observable track duration "
+                "was incorrectly rounded to an integer."
+            ),
+        )
+        if version == 3
+        else contextlib.nullcontext()
+    ):
         imported_tracks = import_kymotrackgroup_from_csv(testfile, kymo, "red", delimiter=";")
 
     data, pylake_version, csv_version = _read_txt(testfile, ";")
@@ -228,7 +232,7 @@ def test_bad_csv(filename, blank_kymo):
 
 def test_min_obs_csv_regression(tmpdir_factory, blank_kymo):
     """This tests a regression where saving a freshly imported older file does not function"""
-    testfile = Path(__file__).parent / f"./data/tracks_v0.csv"
+    testfile = Path(__file__).parent / "./data/tracks_v0.csv"
     imported_tracks = import_kymotrackgroup_from_csv(testfile, blank_kymo, "red", delimiter=";")
     out_file = f"{tmpdir_factory.mktemp('pylake')}/no_min_lengths.csv"
 

lumicks/pylake/nb_widgets/image_editing.py

@@ -59,8 +59,8 @@ def __init__(
         self.channel = channel
         self.current_frame = frame
         self.num_frames = self._current_image.num_frames
-        self.make_title = (
-            lambda: make_image_title(self._current_image, self.current_frame, show_name=False)
+        self.make_title = lambda: (
+            make_image_title(self._current_image, self.current_frame, show_name=False)
             if show_title
             else (lambda: "")
         )

lumicks/pylake/nb_widgets/kymotracker_widgets.py

@@ -760,9 +760,11 @@ def _create_algorithm_sliders(self):
         def threshold_slider_callback(change):
             self._set_label(
                 "warning",
-                ""
-                if change["new"] > min_threshold
-                else f"Tracking with threshold of {change['new']} may be slow.",
+                (
+                    ""
+                    if change["new"] > min_threshold
+                    else f"Tracking with threshold of {change['new']} may be slow."
+                ),
             )
 
         threshold_slider.observe(

lumicks/pylake/population/detail/fit_info.py

@@ -31,6 +31,7 @@ class PopulationFitInfo:
     log_likelihood: float
         log of the maximized value of the likelihood function of the fitted data
     """
+
     converged: bool
     n_iter: int
     bic: float

lumicks/pylake/tests/test_imaging_confocal/test_kymo_plotting.py

@@ -290,10 +290,14 @@ def process_binning(px_per_bin, axis):
 
     for px_per_bin in range(1, ref.image.shape[0] + 1):
         ref_counts, ref_bin_widths, msg = process_binning(px_per_bin, "position")
-        with pytest.warns(
-            UserWarning,
-            match=msg,
-        ) if msg else nullcontext():
+        with (
+            pytest.warns(
+                UserWarning,
+                match=msg,
+            )
+            if msg
+            else nullcontext()
+        ):
             kymo.plot_with_position_histogram(color_channel="red", pixels_per_bin=px_per_bin)
             counts, bin_widths = get_hist_data("position")
 

lumicks/pylake/tests/test_imaging_confocal/test_kymo_slice_crop.py

@@ -1,5 +1,3 @@
-import pathlib
-
 import numpy as np
 import pytest
 
@@ -39,43 +37,43 @@ def test_kymo_slicing(test_kymo):
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :, 0])
 
     num_lines = 2
-    sliced = kymo["0s":f"{num_lines * line_time}s"]
+    sliced = kymo["0s" :f"{num_lines * line_time}s"]
     assert sliced.get_image("red").shape == (ref_pixels, num_lines)
     assert sliced.shape == (ref_pixels, num_lines, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :num_lines, 0])
 
-    sliced = kymo["0s":f"-{line_time * 0.6}s"]
+    sliced = kymo["0s" :f"-{line_time * 0.6}s"]
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines - 1)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :-1, 0])
 
-    sliced = kymo["0s":f"-{2 * line_time}s"]
+    sliced = kymo["0s" :f"-{2 * line_time}s"]
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines - 2)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, : (ref_lines - 2), 0])
 
     # get a sliver of the next frame
     # stop needs to be > halfway the deadtime between lines
-    sliced = kymo["0s":f"-{2 * line_time - deadtime_slice_offset}s"]
+    sliced = kymo["0s" :f"-{2 * line_time - deadtime_slice_offset}s"]
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines - 1)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :-1, 0])
 
     # Two full frames
-    sliced = kymo["0s":f"{2 * line_time}s"]
+    sliced = kymo["0s" :f"{2 * line_time}s"]
     assert sliced.get_image("red").shape == (ref_pixels, 2)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :2, 0])
 
     # Two full frames plus a bit
-    sliced = kymo["0s":f"{2 * scan_time + 2 * dead_time + deadtime_slice_offset}s"]
+    sliced = kymo["0s" :f"{2 * scan_time + 2 * dead_time + deadtime_slice_offset}s"]
     assert sliced.get_image("red").shape == (ref_pixels, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :3, 0])
 
     # slice from deadtime before first line until deadtime after first line
-    sliced = kymo[f"{scan_time + dead_time / 2}s":f"{2 * line_time - dead_time / 2}s"]
+    sliced = kymo[f"{scan_time + dead_time / 2}s" :f"{2 * line_time - dead_time / 2}s"]
     assert sliced.get_image("red").shape == (ref_pixels, 1)
     assert sliced.shape == (ref_pixels, 1, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, 1:2, 0])
 
     # slice over entire kymo
-    sliced = kymo["0s":f"{line_time * (ref.metadata.lines_per_frame + 1)}s"]
+    sliced = kymo["0s" :f"{line_time * (ref.metadata.lines_per_frame + 1)}s"]
     assert sliced.get_image("red").shape == (ref_pixels, ref_lines)
     assert sliced.shape == (ref_pixels, ref_lines, 3)
     np.testing.assert_allclose(sliced.get_image("red").data, ref.image[:, :, 0])
@@ -245,7 +243,7 @@ def test_kymo_slice_crop(cropping_kymo):
     dead_time = (ref.timestamps.dt * ref.infowave.line_padding * 2) * 1e-9
     line_time = scan_time + dead_time
 
-    sliced_cropped = kymo[f"{line_time}s":f"{5 * line_time}s"].crop_by_distance(
+    sliced_cropped = kymo[f"{line_time}s" :f"{5 * line_time}s"].crop_by_distance(
         2 * px_size, 4 * px_size
     )
     np.testing.assert_equal(sliced_cropped.timestamps, ref.timestamps.data[2:4, 1:5])

lumicks/pylake/tests/test_imaging_confocal/test_scan.py

@@ -29,9 +29,11 @@ def test_scan_attrs(test_scans, test_scans_multiframe):
 
         np.testing.assert_equal(
             scan.frame_timestamp_ranges(include_dead_time=True),
-            ref.timestamps.timestamp_ranges  # For the single frame case, there is no dead time
-            if scan.num_frames == 1
-            else ref.timestamps.timestamp_ranges_deadtime,
+            (
+                ref.timestamps.timestamp_ranges  # For the single frame case, there is no dead time
+                if scan.num_frames == 1
+                else ref.timestamps.timestamp_ranges_deadtime
+            ),
         )
         np.testing.assert_equal(scan.frame_timestamp_ranges(), ref.timestamps.timestamp_ranges)
 

lumicks/pylake/tests/test_imaging_confocal/test_scan_slice_crop.py

@@ -255,22 +255,22 @@ def test_scan_slicing_by_time(test_scan_slicing):
     wiggle = 0.01
 
     # start of frame 2, until frame 2 signal stop
-    assert isinstance(multi_frame[f"{rng[2, 0]}s":f"{rng[2, 1]}s"], EmptyScan)
+    assert isinstance(multi_frame[f"{rng[2, 0]}s" :f"{rng[2, 1]}s"], EmptyScan)
 
     # start of frame 2, just over frame 2 signal stop
-    sliced = multi_frame[f"{rng[2, 0]}s":f"{rng[2, 1] + wiggle}s"]
+    sliced = multi_frame[f"{rng[2, 0]}s" :f"{rng[2, 1] + wiggle}s"]
     np.testing.assert_equal(sliced.get_image("rgb"), ref.image[2])
 
     # start of frame 2, until frame 3 signal stop
-    sliced = multi_frame[f"{rng[2, 0]}s":f"{rng[3, 1]}s"]
+    sliced = multi_frame[f"{rng[2, 0]}s" :f"{rng[3, 1]}s"]
     np.testing.assert_equal(sliced.get_image("rgb"), ref.image[2])
 
     # start of frame 2, just over frame 3 signal stop
-    sliced = multi_frame[f"{rng[2, 0]}s":f"{rng[3, 1] + wiggle}s"]
+    sliced = multi_frame[f"{rng[2, 0]}s" :f"{rng[3, 1] + wiggle}s"]
     np.testing.assert_equal(sliced.get_image("rgb"), ref.image[2:4])
 
     # start of frame 2, until start of frame 4
-    sliced = multi_frame[f"{rng[2, 0]}s":f"{rng[4, 0]}s"]
+    sliced = multi_frame[f"{rng[2, 0]}s" :f"{rng[4, 0]}s"]
     np.testing.assert_equal(sliced.get_image("rgb"), ref.image[2:4])
 
     # from start of frame 2
@@ -332,15 +332,15 @@ def test_scan_slicing_by_time_iterative(test_scan_slicing):
     wiggle = 0.01
 
     # first slice frame 2 through 5 (inclusive)
-    first_slice = multi_frame[f"{rng[2, 0]}s":f"{rng[5, 1] + wiggle}s"]
+    first_slice = multi_frame[f"{rng[2, 0]}s" :f"{rng[5, 1] + wiggle}s"]
     ref_sliced = ref.image[2:6]
 
     # start of frame 1, just over frame 3 signal stop
-    sliced = first_slice[f"{rng[1, 0]}s":f"{rng[3, 1] + wiggle}s"]
+    sliced = first_slice[f"{rng[1, 0]}s" :f"{rng[3, 1] + wiggle}s"]
     np.testing.assert_equal(sliced.get_image("rgb"), ref_sliced[1:4])
 
     # start of frame 1, until frame 3 signal stop
-    sliced = first_slice[f"{rng[1, 0]}s":f"{rng[3, 1]}s"]
+    sliced = first_slice[f"{rng[1, 0]}s" :f"{rng[3, 1]}s"]
     np.testing.assert_equal(sliced.get_image("rgb"), ref_sliced[1:3])
 
     # from start of frame 1