tooling update (bye black)

.ruff.toml

@@ -0,0 +1,141 @@
+line-length = 120
+target-version = "py38"
+
+[lint]
+select = [
+    # pyflakes
+    "F",
+    # pycodestyle
+    "E",
+    "W",
+    # mccabe
+    "C90",
+    # isort
+    "I",
+    # pydocstyle
+    "D",
+    # pyupgrade
+    "UP",
+    # pep8-naming
+    "N",
+    # flake8-blind-except
+    "BLE",
+    # flake8-2020
+    "YTT",
+    # flake8-builtins
+    "A",
+    # flake8-comprehensions
+    "C4",
+    # flake8-debugger
+    "T10",
+    # flake8-errmsg
+    "EM",
+    # flake8-implicit-str-concat
+    "ISC",
+    # flake8-pytest-style
+    "PT",
+    # flake8-return
+    "RET",
+    # flake8-simplify
+    "SIM",
+    # flake8-unused-arguments
+    "ARG",
+    # pandas-vet
+    "PD",
+    # pygrep-hooks
+    "PGH",
+    # flake8-bugbear
+    "B",
+    # flake8-quotes
+    "Q",
+    # pylint
+    "PL",
+    # flake8-pie
+    "PIE",
+    # flake8-type-checking
+    "TCH",
+    # tryceratops
+    "TRY",
+    # flake8-use-pathlib
+    "PTH",
+    "RUF",
+    # Numpy rules
+    "NPY",
+    # Implicit namespace packages
+    "INP",
+    # No relative imports
+    "TID252",
+    # f-strings over string concatenation
+    "FLY",
+    # Annotations
+    # No enforced annotations
+#    "ANN"
+
+
+]
+
+ignore = [
+    # controversial
+    "B006",
+    # controversial
+    "B008",
+    "B010",
+    # Magic constants
+    "PLR2004",
+    # Strings in error messages
+    "EM101",
+    "EM102",
+    "EM103",
+    # Exception strings
+    "TRY003",
+    # Varaibles before return
+    "RET504",
+    # Abstract raise into inner function
+    "TRY301",
+    # df as varaible name
+    "PD901",
+    # melt over stack
+    "PD013",
+    # No Any annotations
+    "ANN401",
+    # Self annotation
+    "ANN101",
+    # To many arguments
+    "PLR0913",
+    # Class attribute shadows builtin
+    "A003",
+    # No typing for `cls`
+    "ANN102",
+    # Ignore because of formatting
+    "ISC001",
+    # Use type-checking block
+    "TCH001",
+    "TCH002",
+    "TCH003",
+    # No stacklevel
+    "B028",
+    # Overwriting loop variable
+    "PLW2901"
+
+]
+
+
+exclude = [
+    "doc/sphinxext/*.py",
+    "doc/build/*.py",
+    "doc/temp/*.py",
+    ".eggs/*.py",
+    "example_data",
+]
+
+
+[lint.per-file-ignores]
+# https://github.com/astral-sh/ruff/issues/8925
+"examples/**/*.py" = ["D400"]
+
+
+[lint.pydocstyle]
+convention = "numpy"
+
+[format]
+docstring-code-format = true

_tasks.py

@@ -1,5 +1,5 @@
-import platform
 import re
+import shutil
 import subprocess
 import sys
 from pathlib import Path
@@ -9,18 +9,18 @@
 HERE = Path(__file__).parent
 
 
-def task_docs():
+def task_docs(clean=False, builder="html") -> None:
     """Build the html docs using Sphinx."""
     # Delete Autogenerated files from previous run
-    # shutil.rmtree(str(HERE / "docs/modules/generated"), ignore_errors=True)
+    if clean:
+        shutil.rmtree(str(HERE / "docs/modules/generated"), ignore_errors=True)
+        shutil.rmtree(str(HERE / "docs/_build"), ignore_errors=True)
+        shutil.rmtree(str(HERE / "docs/auto_examples"), ignore_errors=True)
 
-    if platform.system() == "Windows":
-        subprocess.run([HERE / "docs/make.bat", "html"], shell=False, check=True)
-    else:
-        subprocess.run(["make", "-C", HERE / "docs", "html"], shell=False, check=True)
+    subprocess.run(f"sphinx-build -b {builder} -j auto -d docs/_build docs docs/_build/html", shell=True, check=True)
 
 
-def update_version_strings(file_path, new_version):
+def update_version_strings(file_path, new_version) -> None:
     # taken from:
     # https://stackoverflow.com/questions/57108712/replace-updated-version-strings-in-files-via-python
     version_regex = re.compile(r"(^_*?version_*?\s*=\s*\")(\d+\.\d+\.\d+-?\S*)\"", re.M)
@@ -37,7 +37,7 @@ def update_version_strings(file_path, new_version):
         f.truncate()
 
 
-def update_version(version):
+def update_version(version) -> None:
     subprocess.run(["poetry", "version", version], shell=False, check=True)
     new_version = (
         subprocess.run(["poetry", "version"], shell=False, check=True, capture_output=True)
@@ -51,11 +51,11 @@ def update_version(version):
     update_version_strings(HERE / "gaitmap_mad/gaitmap_mad/__init__.py", new_version)
 
 
-def task_update_version():
+def task_update_version() -> None:
     update_version(sys.argv[1])
 
 
-def task_bump_all_dev():
+def task_bump_all_dev() -> None:
     """Bump all dev dependencies."""
     pyproject = toml.load(HERE.joinpath("pyproject.toml"))
     try:

docs/conf.py

@@ -16,7 +16,7 @@
 from datetime import datetime
 from inspect import getsourcefile
 from pathlib import Path
-from typing import List
+from typing import List, Optional
 
 import toml
 from sphinx_gallery.sorting import ExplicitOrder
@@ -32,7 +32,7 @@
 def replace_gitlab_links(base_url, text):
     regex = base_url + r"-/(merge_requests|issues|commit)/(\w+)"
 
-    def substitute(matchobj):
+    def substitute(matchobj) -> str:
         tokens = {"merge_requests": "!", "issues": "#"}
         if matchobj.group(1) == "commit":
             return f"[mad-gitlab: {matchobj.group(2)[:5]}]({matchobj.group(0)})"
@@ -45,7 +45,7 @@ def substitute(matchobj):
 def convert_github_links(base_url, text):
     regex = base_url + r"(pull|issues|commit)/(\w+)"
 
-    def substitute(matchobj):
+    def substitute(matchobj) -> str:
         if matchobj.group(1) == "commit":
             return f"[{matchobj.group(2)[:5]}]({matchobj.group(0)})"
         return f"[#{matchobj.group(2)}]({matchobj.group(0)})"
@@ -229,10 +229,11 @@ def get_nested_attr(obj, attr):
 )
 
 
-def skip_properties(app, what, name, obj, skip, options):
+def skip_properties(app, what, name, obj, skip, options) -> Optional[bool]:
     """This removes all properties from the documentation as they are expected to be documented in the docstring."""
     if isinstance(obj, property):
         return True
+    return None
 
 
 GAITMAP_MAD_TEST = """
@@ -244,7 +245,7 @@ def skip_properties(app, what, name, obj, skip, options):
 """
 
 
-def add_info_about_origin(app, what, name, obj, options, lines: List[str]):
+def add_info_about_origin(app, what, name, obj, options, lines: List[str]) -> None:
     """Add a short info text to all algorithms that are only available via gaitmap_mad."""
     if what != "class":
         return
@@ -259,6 +260,6 @@ def add_info_about_origin(app, what, name, obj, options, lines: List[str]):
             lines.insert(2, l)
 
 
-def setup(app):
+def setup(app) -> None:
     app.connect("autodoc-skip-member", skip_properties)
     app.connect("autodoc-process-docstring", add_info_about_origin)

docs/image_src/create_coordinate_definition_template_plots.py

@@ -32,8 +32,9 @@
 
 colors = [docs_red, docs_green, docs_blue]
 
+
 # helper to plot different coordinate frames
-def plot_stride(data, column_names, sensor_id, stride_id, export_name):
+def plot_stride(data, column_names, sensor_id, stride_id, export_name) -> None:
     fig, axs = plt.subplots(2, figsize=(7, 7))
     start = dtw.stride_list_[sensor_id].iloc[stride_id].start
     end = dtw.stride_list_[sensor_id].iloc[stride_id].end
@@ -61,12 +62,12 @@ def plot_stride(data, column_names, sensor_id, stride_id, export_name):
     fig.savefig(sensor_id + col[3:] + ".pdf", bbox_inches="tight")
 
 
-#%%
+# %%
 # Plot "Stride-Template" in Sensor Frame
 plot_stride(dataset_sf, SF_COLS, "left_sensor", 5, "left_sensor_sensor_frame_template.pdf")
 plot_stride(dataset_sf, SF_COLS, "right_sensor", 18, "right_sensor_sensor_frame_template.pdf")
 
-#%%
+# %%
 # Plot "Stride-Template" in Body Frame
 plot_stride(dataset_bf, BF_COLS, "left_sensor", 5, "left_sensor_body_frame_template.pdf")
 plot_stride(dataset_bf, BF_COLS, "right_sensor", 18, "right_sensor_body_frame_template.pdf")

docs/sphinxext/githublink.py

@@ -30,12 +30,13 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     This is called by sphinx.ext.linkcode
 
     An example with a long-untouched module that everyone has
-    >>> _linkcode_resolve('py', {'module': 'tty',
-    ...                          'fullname': 'setraw'},
-    ...                   package='tty',
-    ...                   url_fmt='http://hg.python.org/cpython/file/'
-    ...                           '{revision}/Lib/{package}/{path}#L{lineno}',
-    ...                   revision='xxxx')
+    >>> _linkcode_resolve(
+    ...     "py",
+    ...     {"module": "tty", "fullname": "setraw"},
+    ...     package="tty",
+    ...     url_fmt="http://hg.python.org/cpython/file/" "{revision}/Lib/{package}/{path}#L{lineno}",
+    ...     revision="xxxx",
+    ... )
     'http://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
     """
     if revision is None:
@@ -85,6 +86,4 @@ def make_linkcode_resolve(package, url_fmt):
                                    '{path}#L{lineno}')
     """
     revision = _get_git_revision()
-    return partial(
-        _linkcode_resolve, revision=revision, package=package, url_fmt=url_fmt
-    )
+    return partial(_linkcode_resolve, revision=revision, package=package, url_fmt=url_fmt)

example_data/extract_example_data.py

@@ -73,10 +73,7 @@ def normalize(v: np.ndarray) -> np.ndarray:
     If a 2D array is provided, each row is considered a vector, which is normalized independently.
     """
     v = np.array(v)
-    if len(v.shape) == 1:
-        ax = 0
-    else:
-        ax = 1
+    ax = 0 if len(v.shape) == 1 else 1
     return (v.T / np.linalg.norm(v, axis=ax)).T
 
 
@@ -130,8 +127,8 @@ def normalize(v: np.ndarray) -> np.ndarray:
     rotation_from_angle(np.array([0, 0, 1]), np.deg2rad(-90))
     * rotation_from_angle(np.array([1, 0, 0]), np.deg2rad(-90))
 ).inv()
-rotations = dict(left_sensor=left_rot, right_sensor=right_rot)
-test_df = test_df.rename(columns={"l_{}".format(sensor): "left_sensor", "r_{}".format(sensor): "right_sensor"})
+rotations = {"left_sensor": left_rot, "right_sensor": right_rot}
+test_df = test_df.rename(columns={f"l_{sensor}": "left_sensor", f"r_{sensor}": "right_sensor"})
 test_df.columns = test_df.columns.set_names(("sensor", "axis"))
 test_df.sort_index(axis=1).to_csv("./imu_sample_not_rotated.csv")
 
@@ -147,7 +144,7 @@ def normalize(v: np.ndarray) -> np.ndarray:
 test_df.to_csv("./imu_sample.csv")
 
 # Example events
-test_events = test_borders = pd.read_csv(get_subject_mocap_folder(subject) / "{}_steps.csv".format(test), index_col=0)
+test_events = test_borders = pd.read_csv(get_subject_mocap_folder(subject) / f"{test}_steps.csv", index_col=0)
 test_events = test_events.rename(columns={"hs": "ic", "to": "tc", "ms": "min_vel"})
 # convert to 204.8 Hz
 test_events[["ic", "tc", "min_vel"]] *= 204.8 / 100
@@ -172,8 +169,8 @@ def normalize(v: np.ndarray) -> np.ndarray:
 # Back to 100 Hz
 test_events[["start", "end"]] *= 100 / 204.8
 
-test_orientation = dict()
-test_position = dict()
+test_orientation = {}
+test_position = {}
 for sensor, short in [("left_sensor", "L"), ("right_sensor", "R")]:
     normal_vectors = find_plane_from_points(
         test_mocap[f"{short}_FCC"], test_mocap[f"{short}_TOE"], test_mocap[f"{short}_FM5"]
@@ -182,8 +179,8 @@ def normalize(v: np.ndarray) -> np.ndarray:
     sidewards = np.cross(normal_vectors, forward_vector, axis=1)
     rot_mat = np.hstack([forward_vector, sidewards, normal_vectors]).reshape((-1, 3, 3))
     ori = pd.DataFrame(Rotation.from_matrix(rot_mat).inv().as_quat(), columns=["q_x", "q_y", "q_z", "q_w"])
-    ori_per_stride = dict()
-    pos_per_stride = dict()
+    ori_per_stride = {}
+    pos_per_stride = {}
     for _, s in test_events[test_events["foot"] == sensor.split("_")[0]].iterrows():
         ori_per_stride[s["s_id"]] = ori.iloc[int(s["start"]) : int(s["end"])].reset_index(drop=True)
         pos = test_mocap[short + "_FCC"].iloc[int(s["start"]) : int(s["end"])].reset_index(drop=True)

examples/advanced_features/algo_serialize.py

@@ -17,6 +17,7 @@
             reproducibility.
             This means you should save the exact library version together with the json version of the used algorithms.
 """
+
 from pprint import pprint
 
 # %%

examples/advanced_features/caching.py

@@ -32,7 +32,6 @@
 # ----------------
 # We will simply copy the stride segmentation example to have some data to work with.
 from gaitmap.example_data import get_healthy_example_imu_data
-from gaitmap.stride_segmentation import BarthOriginalTemplate
 from gaitmap.utils.coordinate_conversion import convert_to_fbf
 
 data = get_healthy_example_imu_data().iloc[:2000]

examples/advanced_features/multi_process.py

@@ -30,6 +30,7 @@
 Other Python helpers to spawn multiple processes will of course work as well.
 
 """
+
 from pprint import pprint
 from typing import Any, Dict