xarray-behave 0.37.2__tar.gz → 0.37.4__tar.gz

xarray_behave-0.37.4/.github/workflows/test_install.yaml

@@ -0,0 +1,46 @@
+name: Test install
+
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: 'Log level'
+        required: true
+        default: 'warning'
+      tags:
+        description: 'manual run'
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: False
+      matrix:
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+    defaults:  # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup miniconda # https://github.com/marketplace/actions/setup-miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        auto-activate-base: true
+        channels: conda-forge
+        python-version: 3.13
+    - name: Install OpenGL dependencies
+      run: sudo apt-get update && sudo apt-get install -qq -y libx11-dev libgl1-mesa-dev libxkbcommon-x11-0
+      if: runner.os == 'Linux'
+    - name: Test
+      run: |
+        conda env create -n xb_test -y -f https://raw.githubusercontent.com/janclemenslab/xarray-behave/refs/heads/master/env/xb.yml
+        conda activate xb_test
+        python -c "import xarray_behave; print(xarray_behave.__version__)"
+        python -c "import xarray_behave.gui.app"
+        python tests/test_imports.py
+        python tests/test_io.py
+        python tests/test_sampstamps.py

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/PKG-INFO

@@ -1,17 +1,18 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: xarray-behave
-Version: 0.37.2
+Version: 0.37.4
 Summary: xarray tools for behavioral data.
 Author-email: Jan Clemens <clemensjan@googlemail.com>
-Requires-Python: >3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: Apache Software License
+License-File: LICENSE
 Requires-Dist: defopt==6.3
 Requires-Dist: rich
 Requires-Dist: flammkuchen
 Requires-Dist: h5py
 Requires-Dist: pyyaml
-Requires-Dist: zarr
+Requires-Dist: zarr<3
 Requires-Dist: dask
 Requires-Dist: pandas
 Requires-Dist: xarray
@@ -25,20 +26,23 @@ Requires-Dist: soundfile
 Requires-Dist: librosa>0.8
 Requires-Dist: opencv-python-headless
 Requires-Dist: pyvideoreader
-Requires-Dist: PySide6-Essentials
+Requires-Dist: PySide6-Essentials==6.8.*
 Requires-Dist: pyqtgraph>0.12.2
 Requires-Dist: qtpy
 Requires-Dist: superqt
 Requires-Dist: colorcet
+Requires-Dist: pytest ; extra == "dev"
+Requires-Dist: flit ; extra == "dev"
 Project-URL: documentation, https://janclemenslab.org/das/
 Project-URL: source, https://github.com/janclemenslab/xarray-behave
+Provides-Extra: dev
 
 # xarray-behave
 
-Install a working conda installation (see [here](https://docs.conda.io/en/latest/miniconda.html)). 
+Install a working conda installation (see [here](https://docs.conda.io/en/latest/miniconda.html)).
 
 ```shell
-conda create -c conda-forge -c ncb -n xb python=3.12 xarray-behave
+conda env create -n xb -y -f https://raw.githubusercontent.com/janclemenslab/xarray-behave/refs/heads/master/env/xb.yml
 ```
 
 See `demo.ipynb` for usage examples.

xarray_behave-0.37.4/README.md

@@ -0,0 +1,9 @@
+# xarray-behave
+
+Install a working conda installation (see [here](https://docs.conda.io/en/latest/miniconda.html)).
+
+```shell
+conda env create -n xb -y -f https://raw.githubusercontent.com/janclemenslab/xarray-behave/refs/heads/master/env/xb.yml
+```
+
+See `demo.ipynb` for usage examples.

xarray_behave-0.37.4/env/xb.yml

@@ -0,0 +1,10 @@
+name: xb
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - python>=3.10
+  - pip
+  - ffmpeg
+  - pip:
+    - xarray-behave

xarray_behave-0.37.4/pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["flit_core >=3.2"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "xarray-behave"
+authors = [{ name = "Jan Clemens", email = "clemensjan@googlemail.com" }]
+classifiers = ["License :: OSI Approved :: Apache Software License"]
+dynamic = ["version", "description"]
+requires-python = ">=3.10"
+dependencies = [
+       'defopt==6.3',
+       'rich',
+       'flammkuchen',
+       'h5py',
+       'pyyaml',
+       'zarr<3',
+       'dask',
+       'pandas',
+       'xarray',
+       'scikit-image',
+       'peakutils',
+       'numba',
+       'numpy',
+       'scipy>1.9',
+       'sounddevice',
+       'soundfile',
+       'librosa>0.8',
+       'opencv-python-headless',
+       'pyvideoreader',
+       'PySide6-Essentials==6.8.*',
+       'pyqtgraph>0.12.2',
+       'qtpy',
+       'superqt',
+       'colorcet',
+]
+readme = "README.md"
+
+[project.optional-dependencies]
+dev = ["pytest", "flit"]
+
+[project.urls]
+source = "https://github.com/janclemenslab/xarray-behave"
+documentation = "https://janclemenslab.org/das/"
+
+[tool.flit.module]
+name = "xarray_behave"
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = ["tests"]
+
+[tool.ruff]
+extend-select = ["C4", "NPY", "PD", "TCH"]
+ignore = ["E501"]
+show-fixes = true
+line-length = 196

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/setup.py

@@ -7,7 +7,7 @@ here = os.path.abspath(os.path.dirname(__file__))
 
 
 def read(*parts):
-    with codecs.open(os.path.join(here, *parts), 'r') as fp:
+    with codecs.open(os.path.join(here, *parts), "r") as fp:
         return fp.read()
 
 
@@ -20,6 +20,6 @@ def find_version(*file_paths):
 
 
 setup(
-    name='xarray-behave',
+    name="xarray-behave",
     version=find_version("src/xarray_behave/__init__.py"),
-)
+)

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/src/xarray_behave/__init__.py

@@ -1,6 +1,6 @@
 """xarray tools for behavioral data."""
 
-__version__ = "0.37.2"
+__version__ = "0.37.4"
 
 from .xarray_behave import assemble, assemble_metrics, load, save
 import os

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/src/xarray_behave/gui/app.py

@@ -15,6 +15,7 @@ import defopt
 import yaml
 import h5py
 import functools
+import rich
 
 import numpy as np
 import scipy.interpolate
@@ -45,7 +46,9 @@ except ImportError:
 try:
     from . import das
 except Exception:
-    logger.warning("Failed to import the das module.\nIgnore if you do not want to use das.\n" "Otherwise follow these instructions to install:\n" "https://janclemenslab.org/das/install.html")
+    logger.warning(
+        "Failed to import the das module.\nIgnore if you do not want to use das.\nOtherwise follow these instructions to install:\nhttps://janclemenslab.org/das/install.html"
+    )
 
 sys.setrecursionlimit(10**6)  # increase recursion limit to avoid errors when keeping key pressed for a long time
 package_dir: str = xarray_behave.__path__[0]
@@ -154,7 +157,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def save_swaps(self, qt_keycode=None):
         savefilename = self._get_filename_from_ds(suffix="_idswaps.txt")
-        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save swaps to", str(savefilename), filter="txt files (*.txt);;all files (*)")
+        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, "Save swaps to", str(savefilename), filter="txt files (*.txt);;all files (*)"
+        )
         if len(savefilename):
             logger.info(f"   Saving list of swap indices to {savefilename}.")
             os.makedirs(os.path.dirname(savefilename), exist_ok=True)
@@ -163,7 +168,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def save_definitions(self, qt_keycode=None):
         savefilename = self._get_filename_from_ds(suffix="_definitions.csv")
-        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, caption="Save definitions to", dir=str(savefilename), filter="CSV files (*_definitions.csv);;all files (*)")
+        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, caption="Save definitions to", dir=str(savefilename), filter="CSV files (*_definitions.csv);;all files (*)"
+        )
         if len(savefilename):
             # get defs from annot and save them to csv
             logger.info(f"   Saving definitions to {savefilename}.")
@@ -403,7 +410,9 @@ class MainWindow(QtWidgets.QMainWindow):
                 self.export_to_h5(savefilename_trunk + ".h5", start_seconds, end_seconds)  # , form_data["scale_audio"])
 
             logger.info(f"   annotations to CSV: {savefilename_trunk + '.csv'}.")
-            self.export_to_csv(savefilename_trunk + "_annotations.csv", start_seconds, end_seconds, which_events, match_to_samples=True)
+            self.export_to_csv(
+                savefilename_trunk + "_annotations.csv", start_seconds, end_seconds, which_events, match_to_samples=True
+            )
             logger.info("Done.")
 
     def das_make(self, qt_keycode=None):
@@ -504,7 +513,9 @@ class MainWindow(QtWidgets.QMainWindow):
             return form_data
 
         def save(arg):
-            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save configuration to", "", filter="yaml files (*.yaml);;all files (*)")
+            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+                self, "Save configuration to", "", filter="yaml files (*.yaml);;all files (*)"
+            )
             if len(savefilename):
                 data = dialog.form.get_form_data()
                 logger.info(f"   Saving form fields to {savefilename}.")
@@ -515,7 +526,9 @@ class MainWindow(QtWidgets.QMainWindow):
         def make_cli(arg):
             script_ext = "cmd" if os.name == "nt" else "sh"
             savefilename = "train." + script_ext
-            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Script name", savefilename, filter=f"script (*.{script_ext};;all files (*)")
+            savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+                self, "Script name", savefilename, filter=f"script (*.{script_ext};;all files (*)"
+            )
             if len(savefilename):
                 form_data = dialog.form.get_form_data()
                 form_data = _filter_form_data(form_data, is_cli=True)
@@ -523,7 +536,7 @@ class MainWindow(QtWidgets.QMainWindow):
                 cmd = "python3 -m das.train"
                 # FIXME formatting
                 for key, val in form_data.items():
-                    cmd += f" --{key.replace('_','-')} {val}"
+                    cmd += f" --{key.replace('_', '-')} {val}"
                 with open(savefilename, "w") as f:
                     f.write(cmd)
 
@@ -704,27 +717,23 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 params = das.utils.load_params(model_path)
                 if audio.shape[0] < params["nb_hist"]:
-                    logger.warning(f"   Aborting. Audio has fewer samples ({audio.shape[0]}) shorter" f"    than network chunk size ({params['nb_hist']})." "    Fix by select longer audio.")
+                    logger.warning(
+                        f"   Aborting. Audio has fewer samples ({audio.shape[0]}) shorter    than network chunk size ({params['nb_hist']}).    Fix by select longer audio."
+                    )
                     return
 
                 # select batch size so that at least 10 batches are run
                 # minimizes loss of annotations from batch size "quantization" errors
                 batch_size = 32
-                nb_batches = int(np.floor((audio.shape[0] - ((batch_size - 1) + params["nb_hist"])) / (params["stride"] * (batch_size))))
+                nb_batches = int(
+                    np.floor((audio.shape[0] - ((batch_size - 1) + params["nb_hist"])) / (params["stride"] * (batch_size)))
+                )
                 while nb_batches < 10 and batch_size > 1:
                     batch_size -= 1
 
                 logger.info("   Running inference on audio.")
                 logger.info(f"   Model from {model_path}.")
                 params = das.utils.load_params(model_path)
-                fs_model = params["samplerate_x_Hz"]
-                fs_audio = self.ds.song_raw.attrs["sampling_rate_Hz"]
-
-                if form_data["resample"] and fs_audio and fs_audio != fs_model:
-                    logger.info(f"   Resampling. Audio rate is {fs_audio}Hz but model was trained on data with {fs_model}Hz.")
-                    audio = das.utils.resample(audio, fs_audio, fs_model)
-
-                import rich
 
                 rich.print(form_data)
                 events, segments, _, _ = das.predict.predict(
@@ -742,7 +751,7 @@ class MainWindow(QtWidgets.QMainWindow):
                     bandpass_low_freq=form_data["bandpass_low_freq"],
                     bandpass_up_freq=form_data["bandpass_up_freq"],
                     resample=form_data["resample"],
-                    fs_audio=fs_audio,
+                    fs_audio=self.fs_song,
                 )
 
                 # Process detected song
@@ -780,7 +789,11 @@ class MainWindow(QtWidgets.QMainWindow):
                     # segments['sequence'] = [s for s in segments['sequence'] if s is not None]
                     detected_segment_names = np.unique(segments["sequence"])
                     # if these are indices, get corresponding names
-                    if len(detected_segment_names) and type(detected_segment_names[0]) is not str and type(detected_segment_names[0]) is not np.str_:
+                    if (
+                        len(detected_segment_names)
+                        and type(detected_segment_names[0]) is not str
+                        and type(detected_segment_names[0]) is not np.str_
+                    ):
                         detected_segment_names = [segments["names"][ii] for ii in detected_segment_names]
 
                 if len(detected_segment_names) > 0:  # and detected_segment_names[0] is not None:
@@ -796,7 +809,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                     onsets_seconds = self.ds.sampletime[onsets_samples]
                     offsets_seconds = self.ds.sampletime[offsets_samples]
-                    for name_or_index, onset_seconds, offset_seconds in zip(segments["sequence"], onsets_seconds, offsets_seconds):
+                    for name_or_index, onset_seconds, offset_seconds in zip(
+                        segments["sequence"], onsets_seconds, offsets_seconds
+                    ):
                         if type(name_or_index) is not str and type(detected_segment_names[0]) is not np.str_:
                             segment_name = segments["names"][name_or_index]
                         else:
@@ -845,8 +860,15 @@ class MainWindow(QtWidgets.QMainWindow):
                             except KeyError:
                                 pass
                 except KeyError:
-                    logger.info(f"{filename} no sample rate info in NPZ file." f"Need to save 'samplerate' variable with the audio data. Defaulting to {samplerate}")
-            elif filename.endswith(".h5") or filename.endswith(".hdfs") or filename.endswith(".hdf5") or filename.endswith(".mat"):
+                    logger.info(
+                        f"{filename} no sample rate info in NPZ file.Need to save 'samplerate' variable with the audio data. Defaulting to {samplerate}"
+                    )
+            elif (
+                filename.endswith(".h5")
+                or filename.endswith(".hdfs")
+                or filename.endswith(".hdf5")
+                or filename.endswith(".mat")
+            ):
                 # infer data set (for hdf5) and populate form
                 try:
                     # list all data sets in file and add to list
@@ -950,7 +972,9 @@ class MainWindow(QtWidgets.QMainWindow):
         if not dirname:
             dirname = QtWidgets.QFileDialog.getExistingDirectory(parent=None, caption="Select data directory")
         if dirname:
-            dialog = YamlDialog(yaml_file=package_dir + "/gui/forms/from_dir.yaml", title=f"Dataset from data directory {dirname}")
+            dialog = YamlDialog(
+                yaml_file=package_dir + "/gui/forms/from_dir.yaml", title=f"Dataset from data directory {dirname}"
+            )
 
             # initialize form data with cli args
             dialog.form["pixel_size_mm"] = pixel_size_mm  # and un-disable
@@ -1025,7 +1049,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 # add event categories if they are missing in the dataset
                 if "song_events" in ds and "event_categories" not in ds:
-                    event_categories = ["segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values]
+                    event_categories = [
+                        "segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values
+                    ]
                     ds = ds.assign_coords({"event_categories": (("event_types"), event_categories)})
 
                 # add missing song types
@@ -1083,7 +1109,9 @@ class MainWindow(QtWidgets.QMainWindow):
         if not filename:
             filename, _ = QtWidgets.QFileDialog.getOpenFileName(parent=None, caption="Select dataset")
         if filename:
-            dialog = YamlDialog(yaml_file=package_dir + "/gui/forms/from_zarr.yaml", title=f"Load dataset from zarr file {filename}")
+            dialog = YamlDialog(
+                yaml_file=package_dir + "/gui/forms/from_zarr.yaml", title=f"Load dataset from zarr file {filename}"
+            )
 
             # initialize form data with cli args
             if spec_freq_min is not None:
@@ -1121,7 +1149,9 @@ class MainWindow(QtWidgets.QMainWindow):
 
                 # add event categories if they are missing in the dataset
                 if "song_events" in ds and "event_categories" not in ds:
-                    event_categories = ["segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values]
+                    event_categories = [
+                        "segment" if "sine" in evt or "syllable" in evt else "event" for evt in ds.event_types.values
+                    ]
                     ds = ds.assign_coords({"event_categories": (("event_types"), event_categories)})
                 logger.info(ds)
                 vr = None
@@ -1166,11 +1196,15 @@ class MainWindow(QtWidgets.QMainWindow):
 
     def save_dataset(self, qt_keycode=None):
         try:
-            savefilename = Path(self.ds.attrs["root"], self.ds.attrs["dat_path"], self.ds.attrs["datename"], f"{self.ds.attrs['datename']}.zarr")
+            savefilename = Path(
+                self.ds.attrs["root"], self.ds.attrs["dat_path"], self.ds.attrs["datename"], f"{self.ds.attrs['datename']}.zarr"
+            )
         except KeyError:
             savefilename = ""
 
-        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(self, "Save dataset to", str(savefilename), filter="zarr files (*.zarr);;all files (*)")
+        savefilename, _ = QtWidgets.QFileDialog.getSaveFileName(
+            self, "Save dataset to", str(savefilename), filter="zarr files (*.zarr);;all files (*)"
+        )
 
         if len(savefilename):
             file_exists = os.path.exists(savefilename)
@@ -1422,10 +1456,16 @@ class PSV(MainWindow):
         self._add_keyed_menuitem(view_video, "Change other fly", self.change_other_fly, "Z")
         self._add_keyed_menuitem(view_video, "Swap flies", self.swap_flies, "X")
         view_video.addSeparator()
-        self._add_keyed_menuitem(view_video, "Move poses", partial(self.toggle, "move_poses"), "B", checkable=True, checked=self.move_poses)
+        self._add_keyed_menuitem(
+            view_video, "Move poses", partial(self.toggle, "move_poses"), "B", checkable=True, checked=self.move_poses
+        )
         view_video.addSeparator()
-        self._add_keyed_menuitem(view_video, "Show fly position", partial(self.toggle, "show_dot"), "O", checkable=True, checked=self.show_dot)
-        self._add_keyed_menuitem(view_video, "Show poses", partial(self.toggle, "show_poses"), "P", checkable=True, checked=self.show_poses)
+        self._add_keyed_menuitem(
+            view_video, "Show fly position", partial(self.toggle, "show_dot"), "O", checkable=True, checked=self.show_dot
+        )
+        self._add_keyed_menuitem(
+            view_video, "Show poses", partial(self.toggle, "show_poses"), "P", checkable=True, checked=self.show_poses
+        )
 
         view_audio = self.bar.addMenu("Audio")
         self._add_keyed_menuitem(view_audio, "Play waveform through speakers", self.play_audio, "E")
@@ -1449,7 +1489,9 @@ class PSV(MainWindow):
         self._add_keyed_menuitem(view_audio, "Select previous channel", self.set_next_channel, "Up")
         self._add_keyed_menuitem(view_audio, "Select next channel", self.set_prev_channel, "Down")
         view_audio.addSeparator()
-        self._add_keyed_menuitem(view_audio, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec)
+        self._add_keyed_menuitem(
+            view_audio, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec
+        )
         self._add_keyed_menuitem(view_audio, "Increase frequency resolution", self.inc_freq_res, "R")
         self._add_keyed_menuitem(view_audio, "Increase temporal resolution", self.dec_freq_res, "T")
         view_audio.addSeparator()
@@ -1503,20 +1545,34 @@ class PSV(MainWindow):
         self._add_keyed_menuitem(view_annotations, "Generate proposal by envelope thresholding", self.threshold, "I")
         self._add_keyed_menuitem(view_annotations, "Adjust thresholding mode", self.set_envelope_computation)
         view_annotations.addSeparator()
-        self._add_keyed_menuitem(view_annotations, "Approve proposals for active song type in view", self.approve_active_proposals, "G")
-        self._add_keyed_menuitem(view_annotations, "Approve proposals for all song types in view", self.approve_all_proposals, "H")
+        self._add_keyed_menuitem(
+            view_annotations, "Approve proposals for active song type in view", self.approve_active_proposals, "G"
+        )
+        self._add_keyed_menuitem(
+            view_annotations, "Approve proposals for all song types in view", self.approve_all_proposals, "H"
+        )
 
         view_view = self.bar.addMenu("View")
         self._add_keyed_menuitem(view_view, "Video, waveform, and spectrogram display parameters", self.set_spec_freq)
         view_view.addSeparator()
         # TODO? only show these if tracks and/or video
-        self._add_keyed_menuitem(view_view, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec)
-        self._add_keyed_menuitem(view_view, "Show waveform", partial(self.toggle, "show_trace"), None, checkable=True, checked=self.show_trace)
-        self._add_keyed_menuitem(view_view, "Show ethogram", partial(self.toggle, "show_annot"), None, checkable=True, checked=self.show_annot)
+        self._add_keyed_menuitem(
+            view_view, "Show spectrogram", partial(self.toggle, "show_spec"), None, checkable=True, checked=self.show_spec
+        )
+        self._add_keyed_menuitem(
+            view_view, "Show waveform", partial(self.toggle, "show_trace"), None, checkable=True, checked=self.show_trace
+        )
+        self._add_keyed_menuitem(
+            view_view, "Show ethogram", partial(self.toggle, "show_annot"), None, checkable=True, checked=self.show_annot
+        )
         if "pose_positions_allo" in self.ds:
-            self._add_keyed_menuitem(view_view, "Show tracks", partial(self.toggle, "show_tracks"), None, checkable=True, checked=self.show_tracks)
+            self._add_keyed_menuitem(
+                view_view, "Show tracks", partial(self.toggle, "show_tracks"), None, checkable=True, checked=self.show_tracks
+            )
         if self.vr is not None:
-            self._add_keyed_menuitem(view_view, "Show movie", partial(self.toggle, "show_movie"), None, checkable=True, checked=self.show_movie)
+            self._add_keyed_menuitem(
+                view_view, "Show movie", partial(self.toggle, "show_movie"), None, checkable=True, checked=self.show_movie
+            )
 
         self.hl = QtWidgets.QHBoxLayout()
 
@@ -1887,7 +1943,9 @@ class PSV(MainWindow):
 
     def delete_current_events(self, qt_keycode):
         if self.current_event_index is not None:
-            deleted_events = self.event_times.delete_range(self.current_event_name, self.time0 / self.fs_song, self.time1 / self.fs_song)
+            deleted_events = self.event_times.delete_range(
+                self.current_event_name, self.time0 / self.fs_song, self.time1 / self.fs_song
+            )
             nb_deleted_events = len(deleted_events)
             if nb_deleted_events:
                 logger.info(f"   Deleted {nb_deleted_events} annotation(s) of type {self.current_event_name}.")
@@ -1909,7 +1967,9 @@ class PSV(MainWindow):
     def threshold(self, qt_keycode):
         if self.STOP and self.current_event_name is not None:
             if self.event_times.categories[self.current_event_name] == "event":
-                indexes = peakutils.indexes(self.envelope, thres=self.slice_view.threshold, min_dist=self.thres_min_dist * self.fs_song, thres_abs=True)
+                indexes = peakutils.indexes(
+                    self.envelope, thres=self.slice_view.threshold, min_dist=self.thres_min_dist * self.fs_song, thres_abs=True
+                )
                 # add events to current song type
                 for t in self.x[indexes]:
                     self.event_times.add_time(self.current_event_name, t)
@@ -2061,7 +2121,9 @@ class PSV(MainWindow):
         dialog.exec_()
 
     def set_envelope_computation(self, qt_keycode):
-        dialog = YamlDialog(yaml_file=package_dir + "/gui/forms/envelope_computation.yaml", title="Set options for envelope computation")
+        dialog = YamlDialog(
+            yaml_file=package_dir + "/gui/forms/envelope_computation.yaml", title="Set options for envelope computation"
+        )
 
         dialog.form["thres_min_dist"] = self.thres_min_dist
         dialog.form["thres_env_std"] = self.thres_env_std
@@ -2139,7 +2201,9 @@ class PSV(MainWindow):
                 i1 = int(self.time1 / self.fs_ratio)
 
                 self.x_tracks = self.ds.time.data[i0:i1]
-                self.y_tracks = self.ds.pose_positions_allo.data[i0:i1, self.focal_fly, self.track_sel_names, self.track_sel_coords]
+                self.y_tracks = self.ds.pose_positions_allo.data[
+                    i0:i1, self.focal_fly, self.track_sel_names, self.track_sel_coords
+                ]
                 self.tracks_view.update_trace()
                 self.tracks_view.show()
             else:
@@ -2186,9 +2250,13 @@ class PSV(MainWindow):
             if self.event_times.categories[event_name] == "segment":
                 for onset, offset in zip(events_in_view[:, 0], events_in_view[:, 1]):
                     if self.show_trace:
-                        self.slice_view.add_segment(onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text)
+                        self.slice_view.add_segment(
+                            onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text
+                        )
                     if self.show_tracks:
-                        self.tracks_view.add_segment(onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text)
+                        self.tracks_view.add_segment(
+                            onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text
+                        )
                     if self.show_annot:
                         self.annot_view.add_segment(
                             onset,
@@ -2200,7 +2268,9 @@ class PSV(MainWindow):
                             text=segment_text,
                         )
                     if self.show_spec:
-                        self.spec_view.add_segment(onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text)
+                        self.spec_view.add_segment(
+                            onset, offset, event_index, brush=event_brush, pen=event_pen, movable=movable, text=segment_text
+                        )
             elif self.event_times.categories[event_name] == "event":
                 if self.show_trace:
                     self.slice_view.add_event(events_in_view[:, 0], event_index, event_pen, movable=movable, text=segment_text)
@@ -2233,7 +2303,9 @@ class PSV(MainWindow):
 
         new_region = region.getRegion()
         self.event_times.move_time(event_name_to_move, region.bounds, new_region)
-        logger.info(f"  Moved {event_name_to_move} from t=[{region.bounds[0]:1.4f}:{region.bounds[1]:1.4f}] to [{new_region[0]:1.4f}:{new_region[1]:1.4f}] seconds.")
+        logger.info(
+            f"  Moved {event_name_to_move} from t=[{region.bounds[0]:1.4f}:{region.bounds[1]:1.4f}] to [{new_region[0]:1.4f}:{new_region[1]:1.4f}] seconds."
+        )
 
         # FIXME for moving annotations in ethogram - fails in pyside6
         if self.annot_view.mousePoint is not None:
@@ -2305,7 +2377,10 @@ class PSV(MainWindow):
                 fly_pos = self.ds.pose_positions_allo.data[self.index_other, :, self.pose_center_index, :]
                 fly_pos = np.array(fly_pos)  # in case this is a dask.array
                 if self.crop:  # transform fly pos to coordinates of the cropped box
-                    box_center = self.ds.pose_positions_allo.data[self.index_other, self.focal_fly, self.pose_center_index] + self.box_size / 2
+                    box_center = (
+                        self.ds.pose_positions_allo.data[self.index_other, self.focal_fly, self.pose_center_index]
+                        + self.box_size / 2
+                    )
                     box_center = np.array(box_center)  # in case this is a dask.array
                     fly_pos = fly_pos - box_center
                 fly_dist = np.sum((fly_pos - np.array([mouseY, mouseX])) ** 2, axis=-1)
@@ -2345,7 +2420,9 @@ class PSV(MainWindow):
                 if self.event_times.categories[self.current_event_name] == "event":
                     logger.info(f"  Changed event at {changed_time[0]:1.4f} from {old_name} to {new_name}.")
                 else:
-                    logger.info(f"  Changed segment at {changed_time[0]:1.4f}:{changed_time[1]:1.4f} from {old_name} to {new_name}.")
+                    logger.info(
+                        f"  Changed segment at {changed_time[0]:1.4f}:{changed_time[1]:1.4f} from {old_name} to {new_name}."
+                    )
                 self.update_xy()
         elif mouseButton == QtCore.Qt.MouseButton.LeftButton:  # add event
             if self.current_event_index is not None:
@@ -2365,12 +2442,16 @@ class PSV(MainWindow):
                             stop_seconds=mouseT,
                             channel=self.current_channel_index,
                         )
-                        logger.info(f"  Added {self.current_event_name} on channel {self.current_channel_index} at t=[{self.sinet0:1.4f}:{mouseT:1.4f}] seconds.")
+                        logger.info(
+                            f"  Added {self.current_event_name} on channel {self.current_channel_index} at t=[{self.sinet0:1.4f}:{mouseT:1.4f}] seconds."
+                        )
                         self.sinet0 = None
                 if self.event_times.categories[self.current_event_name] == "event":
                     self.sinet0 = None
                     self.event_times.add_time(self.current_event_name, start_seconds=mouseT, channel=self.current_channel_index)
-                    logger.info(f"  Added {self.current_event_name} on channel {self.current_channel_index} at t={mouseT:1.4f} seconds.")
+                    logger.info(
+                        f"  Added {self.current_event_name} on channel {self.current_channel_index} at t={mouseT:1.4f} seconds."
+                    )
                 self.update_xy()
             else:
                 self.sinet0 = None
@@ -2462,7 +2543,7 @@ class PSV(MainWindow):
                 )
                 self.event_times.delete_range(name, t0, t1, strict=False)
                 if len(within_range_times):
-                    logger.info(f"   {len(within_range_times)} events of {name} to {name[:-len(proposal_suffix)]}")
+                    logger.info(f"   {len(within_range_times)} events of {name} to {name[: -len(proposal_suffix)]}")
         # update event selector in case the event did not exist yet
         self.nb_eventtypes = len(self.event_times)
         self.eventtype_colors = utils.make_colors(self.nb_eventtypes)

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/src/xarray_behave/io/movieparams.py

@@ -1,6 +1,4 @@
-"""Load parameters for DLP movies
-
-"""
+"""Load parameters for DLP movies"""
 
 import numpy as np
 import pandas as pd

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/tests/test_annot.py

@@ -56,9 +56,7 @@ def test_from_ds(test_data):
         ],
     )
     names.attrs["allowed_names"] = list(set(names.data))
-    times = xr.DataArray(
-        name="event_times", data=times, dims=["index", "event_time"], coords={"event_time": ["start_seconds", "stop_seconds"]}
-    )
+    times = xr.DataArray(name="event_times", data=times, dims=["index", "event_time"], coords={"event_time": ["start_seconds", "stop_seconds"]})
     names, times
     ds = xr.Dataset({da.name: da for da in [names, times]})
     ds.attrs["pulse"] = "event"

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/tests/test_imports.py

@@ -1,6 +1,3 @@
-import pytest
-
-
 def test_imports():
     import xarray_behave as xb
     import xarray_behave.event_utils

{xarray_behave-0.37.2 → xarray_behave-0.37.4}/tests/test_io.py

@@ -1,10 +1,8 @@
-import pytest
-
 import numpy as np
 import xarray as xr
 import pandas as pd
 from xarray_behave import io
 
+
 def test_call():
     io
-

xarray_behave-0.37.2/.github/workflows/publish.yaml

@@ -1,55 +0,0 @@
-name: Publish to Anaconda.org
-
-on:
-  release:
-    types:
-      - published
-  workflow_dispatch:
-    inputs:
-      logLevel:
-        description: 'Log level'
-        required: true
-        default: 'warning'
-      tags:
-        description: 'manual run'
-
-jobs:
-  publish:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: False
-      matrix:
-        python-version: ['3.10', '3.11', '3.12']
-        os: [ubuntu-latest, windows-latest, macOS-14]
-    defaults:  # https://github.com/marketplace/actions/setup-miniconda#use-a-default-shell
-      run:
-        shell: bash -l {0}
-    steps:
-    - uses: actions/checkout@v4
-    - name: Setup miniconda # https://github.com/marketplace/actions/setup-miniconda
-      uses: conda-incubator/setup-miniconda@v3
-      with:
-        auto-update-conda: true
-        channels: conda-forge,ncb
-        python-version: 3.12
-        auto-activate-base: false
-        activate-environment: anaconda-client-env
-        environment-file: build_env.yml
-        condarc-file: condarc.yml
-    - name: Build
-      run: |
-        mkdir ./build
-        conda build conda/xarray-behave --no-test --no-anaconda-upload --python ${{ matrix.python-version }} --output-folder ./build
-    - name: Test
-      run: |
-        conda deactivate
-        conda create -n xb_test python=${{ matrix.python-version }} xarray-behave -c ./build -c local -c conda-forge -c ncb -y
-        conda activate xb_test
-        python -c "import xarray_behave; print(xarray_behave.__version__)"
-        python -c "import xarray_behave.gui.app"
-        # xb --help  
-    - name: Upload
-      run: |
-        conda build conda/xarray-behave --no-test --python ${{ matrix.python-version }} --output-folder ./build --user ncb --token ${{ secrets.ANACONDA_TOKEN }}
-      env:
-        ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}

xarray_behave-0.37.2/README.md

@@ -1,9 +0,0 @@
-# xarray-behave
-
-Install a working conda installation (see [here](https://docs.conda.io/en/latest/miniconda.html)). 
-
-```shell
-conda create -c conda-forge -c ncb -n xb python=3.12 xarray-behave
-```
-
-See `demo.ipynb` for usage examples.

xarray_behave-0.37.2/build_env.yml

@@ -1,9 +0,0 @@
-name: anaconda-client-env
-channels:
-  - conda-forge
-dependencies:
-  - conda
-  - anaconda-client
-  - conda-build
-  - pip
-  - git

xarray_behave-0.37.2/conda/xarray-behave/bld.bat

@@ -1,10 +0,0 @@
-# We need to turn pip index back on because Anaconda turns
-# it off for some reason.
-set PIP_NO_INDEX=False
-set PIP_NO_DEPENDENCIES=False
-set PIP_IGNORE_INSTALLED=False
-
-"%PYTHON%" -m pip install simpleaudio -vv --no-dependencies
-"%PYTHON%" -m pip install pkgutil_resolve_name -vv --no-dependencies
-"%PYTHON%" -m pip install xarray-behave[gui] -vv --no-dependencies
-if errorlevel 1 exit 1

xarray_behave-0.37.2/conda/xarray-behave/build.sh

@@ -1,11 +0,0 @@
-# We need to turn pip index back on because Anaconda turns
-# it off for some reason.
-export PIP_NO_INDEX=False
-export PIP_NO_DEPENDENCIES=False
-export PIP_IGNORE_INSTALLED=False
-
-if [[ "$OSTYPE" == "darwin"* ]]; then
-  $PYTHON -m pip install simpleaudio -vv --no-dependencies
-fi
-$PYTHON -m pip install pkgutil_resolve_name -vv --no-dependencies
-$PYTHON -m pip install xarray-behave[gui] -vv --no-dependencies

xarray_behave-0.37.2/conda/xarray-behave/meta.yaml

@@ -1,58 +0,0 @@
-{% set data = load_setup_py_data(setup_file='../../setup.py', from_recipe_dir=True) %}
-{% set name = data.get('name') %}
-{% set version = data.get('version') %}
-
-package:
-  name: "{{ name }}"
-  version: "{{ version }}"
-
-source:
-  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-
-build:
-  number: 0
-
-requirements:
-  host:
-    - python {{ python }}
-    - pip
-  run:
-    - python {{ python }}
-    - defopt=6.3
-    - rich
-    - flammkuchen
-    - h5py
-    - pyyaml
-    - zarr
-    - numba
-    - xarray
-    - dask
-    - librosa>0.8
-    - pysoundfile
-    - python-sounddevice
-    - matplotlib
-    - colorcet
-    - pandas
-    - scipy>=1.9
-    - scikit-image
-    - scikit-learn
-    - peakutils
-    - pyside6
-    - pyqtgraph>0.12
-    - qtpy
-    - superqt
-    - ffmpeg
-    - pyvideoreader
-
-about:
-  home: "http://github.com/janclemenslab/xarray-behave"
-  license: MIT
-  license_family: MIT
-  license_file:
-  summary: "xarray behave"
-  doc_url: "https://janclemenslab.org/xarray-behave"
-  dev_url: "http://github.com/janclemenslab/xarray-behave"
-
-extra:
-  recipe-maintainers:
-    - postpop

xarray_behave-0.37.2/condarc.yml

@@ -1,9 +0,0 @@
-anaconda_upload: yes
-always_yes: yes
-changeps1: no
-channel_priority: flexible 
-channels:
-- conda-forge
-- ncb
-conda-build:
-   pkg_format: 2

xarray_behave-0.37.2/pyproject.toml

@@ -1,38 +0,0 @@
-[build-system]
-requires = ["flit_core >=3.2"]
-build-backend = "flit_core.buildapi"
-
-[project]
-name = "xarray-behave"
-authors = [
-       {name = "Jan Clemens", email = "clemensjan@googlemail.com"},
-]
-classifiers = ["License :: OSI Approved :: Apache Software License"]
-dynamic = ["version", "description"]
-requires-python = ">3.9"
-dependencies = ['defopt==6.3', 'rich',
-                'flammkuchen', 'h5py', 'pyyaml', 'zarr', 'dask', 'pandas', 'xarray',
-                'scikit-image', 'peakutils', 'numba', 'numpy', 'scipy>1.9',
-                'sounddevice', 'soundfile', 'librosa>0.8',
-                'opencv-python-headless', 'pyvideoreader',
-                'PySide6-Essentials', 'pyqtgraph>0.12.2', 'qtpy', 'superqt', 'colorcet'
-                ]
-
-readme = "README.md"
-
-[project.urls]
-source = "https://github.com/janclemenslab/xarray-behave"
-documentation = "https://janclemenslab.org/das/"
-
-[tool.flit.module]
-name = "xarray_behave"
-
-[tool.pytest.ini_options]
-minversion = "6.0"
-testpaths = ["tests",]
-
-[tool.ruff]
-extend-select = ["C4", "NPY", "PD", "TCH"]
-ignore = ["E501"]
-show-fixes = true
-line-length = 196