First commit with code and github workflows for unit tests and releasing

Author: felixchenier

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve. For feature requests, please go to the Discussions instead.
+title: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+
+**Traceback**
+If applicable, copy/paste the traceback here. The traceback is the complete error message, starting by the line `Traceback (most recent call last):` all the way to the end.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Python installation**
+Select: python.org, Anaconda, conda-forge, etc.
+
+**Operating system**
+ - OS: [e.g. macOS, Windows, Linux]
+ - Version [e.g. Big Sur, 10]
+
+**Additional context**
+Add any other context about the problem here.
+

.github/workflows/publish_package.yml

@@ -0,0 +1,30 @@
+name: Publish Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools wheel twine
+
+      - name: Build and publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.github/workflows/run_tests.yml

@@ -0,0 +1,53 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: run_tests
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+  
+jobs:
+  unittests:
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        
+    steps:
+    - uses: actions/checkout@v4
+    - name: Setup conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: anaconda-client-env
+    - name: Install dependencies
+      run: |
+        conda install -c conda-forge python=${{ matrix.python-version }} mamba pytest -y
+        mamba install -c conda-forge kineticstoolkit -y
+    - name: Test with pytest and crash on warnings (macos)
+      if: matrix.os == 'macos-latest'
+      run: |
+        export PYTHONPATH=":kineticstoolkit_extensions"
+        echo "Running tests with PYTHONPATH=$PYTHONPATH"
+        pytest tests -W error::RuntimeWarning
+    - name: Test with pytest and crash on warnings (linux)
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        export PYTHONPATH=":kineticstoolkit_extensions"
+        echo "Running tests with PYTHONPATH=$PYTHONPATH"
+        pytest tests -W error::RuntimeWarning
+    - name: Test with pytest and crash on warnings (windows)
+      if: matrix.os == 'windows-latest'
+      run: |
+        export PYTHONPATH=";kineticstoolkit_extensions"
+        echo "Running tests with PYTHONPATH=$PYTHONPATH"
+        pytest tests -W error::RuntimeWarning

README.md

@@ -3,9 +3,8 @@ Additional modules and development of new features for Kinetics Toolkit
 
 This repository will replace the different repositories used for the current extension system. It will also be distributed via pip and conda, like kineticstoolkit.
 
-It will contain features that are deemed too specific for Kinetics Toolkit, but still useful in some use cases. It will also contain new features in developement, before the features are integrated in the kineticstoolkit core. The main objective for this method is to:
+It will contain features that are deemed too specific for Kinetics Toolkit, but still useful in some use cases. It will also contain half-baked new features in development. The main objective for this method is to:
 
-- reach a stable 1.0 version for Kinetics Toolkit
-- continue developing new features with a clear separation between development/testing (here) and stable (core)
-- ease the installation of extensions, without adding unnecessary friction (i.e. maintaining multiple repositories)
-- adopt continuous integration practices for extensions as for kineticstoolkit (i.e. unit tests)
+- reach a stable 1.0 version for Kinetics Toolkit while continuing developing new features with a clear separation between misc/development/testing (kineticstoolkit_extensions) and stable (kineticstoolkit)
+- ease the installation of extensions, without adding unnecessary friction both for developers and users (i.e. maintaining multiple repositories)
+- adopt continuous integration practices (i.e. unit tests) for extensions, like for kineticstoolkit

data/n3d_sample_optotrak.n3d

@@ -0,0 +1 @@
+0.1.master

kineticstoolkit_extensions/VERSION

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Copyright 2020-2025 Félix Chénier
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Kinetics Toolkit Extensions."""
+__author__ = "Félix Chénier"
+__copyright__ = "Copyright (C) 2020-2025 Félix Chénier"
+__email__ = "[email protected]"
+__license__ = "Apache 2.0"
+
+import os
+
+import kineticstoolkit_extensions.n3d as n3d
+import kineticstoolkit_extensions.pushrimkinetics as pushrimkinetics
+
+
+def __dir__():
+    return ["n3d", "pushrimkinetics"]
+
+
+root_folder = os.path.dirname(os.path.dirname(__file__))

kineticstoolkit_extensions/__init__.py

@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Copyright 2022 Félix Chénier
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+"""
+Provide a short description of your extension.
+"""
+
+__author__ = "Félix Chénier"
+__copyright__ = "Copyright (C) 2022 Félix Chénier"
+__email__ = "[email protected]"
+__license__ = "Apache 2.0"
+
+
+from kineticstoolkit import TimeSeries
+import struct
+import numpy as np
+from typing import Sequence
+
+
+def read_n3d(filename: str, labels: Sequence[str] = []) -> TimeSeries:
+    """
+    Read markers from an NDI N3D file.
+
+    The markers positions are returned in a TimeSeries where each marker
+    corresponds to a data key. Each marker position is expressed in this form:
+
+    array([[x0, y0, z0, 1.], [x1, y1, z1, 1.], [x2, y2, z2, 1.], ...])
+
+    Parameters
+    ----------
+    filename : str
+        Path of the N3D file.
+    labels : list of str (optional)
+        Marker names
+
+    Returns
+    -------
+    TimeSeries
+
+    """
+    with open(filename, "rb") as fid:
+        _ = fid.read(1)  # 32
+        n_markers = struct.unpack("h", fid.read(2))[0]
+        n_data_per_marker = struct.unpack("h", fid.read(2))[0]
+        n_columns = n_markers * n_data_per_marker
+
+        n_frames = struct.unpack("i", fid.read(4))[0]
+
+        collection_frame_frequency = struct.unpack("f", fid.read(4))[0]
+        user_comments = struct.unpack("60s", fid.read(60))[0]
+        system_comments = struct.unpack("60s", fid.read(60))[0]
+        file_description = struct.unpack("30s", fid.read(30))[0]
+        cutoff_filter_frequency = struct.unpack("h", fid.read(2))[0]
+        time_of_collection = struct.unpack("8s", fid.read(8))[0]
+        _ = fid.read(2)
+        date_of_collection = struct.unpack("8s", fid.read(8))[0]
+        extended_header = struct.unpack("73s", fid.read(73))[0]
+
+        # Read the rest and put it in an array
+        ndi_array = np.ones((n_frames, n_columns)) * np.NaN
+
+        for i_frame in range(n_frames):
+            for i_column in range(n_columns):
+                data = struct.unpack("f", fid.read(4))[0]
+                if data < -1e25:  # technically, it is -3.697314e+28
+                    data = np.NaN
+                ndi_array[i_frame, i_column] = data
+
+        # Conversion from mm to meters
+        ndi_array /= 1000
+
+        # Transformation to a TimeSeries
+        ts = TimeSeries(
+            time=np.linspace(
+                0, n_frames / collection_frame_frequency, n_frames
+            )
+        )
+
+        for i_marker in range(n_markers):
+            if labels != []:
+                label = labels[i_marker]
+            else:
+                label = f"Marker{i_marker}"
+
+            ts.data[label] = np.block(
+                [
+                    [
+                        ndi_array[:, 3 * i_marker : 3 * i_marker + 3],
+                        np.ones((n_frames, 1)),
+                    ]
+                ]
+            )
+            ts = ts.add_data_info(label, "Unit", "m")
+
+    return ts
+
+
+"""
+The section below is optional. If you put code examples in your docstring,
+then running this file will test that your examples give the correct results.
+Please check https://docs.python.org/3/library/doctest.html for details.
+"""
+if __name__ == "__main__":  # pragma: no cover
+    import doctest
+
+    doctest.testmod(optionflags=doctest.NORMALIZE_WHITESPACE)