initial commit

.github/workflows/build.yml

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+name: Test CLI App Packaging
+
+on: [push]
+
+jobs:
+  test-packaging:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install hatch
+      run: pip install hatch
+
+    - name: Build project
+      run: hatch build
+
+    - name: Install uv
+      run: pip install uv
+
+    - name: Create uv venv
+      run: | 
+        uv venv
+        . .venv/bin/activate
+
+    - name: Install package using uv
+      run: |
+        uv pip install dist/*.tar.gz
+
+    - name: Run dont fret serve
+      run: |
+        timeout 10s dont-fret serve || exit_code=$?
+        if [ $exit_code -eq 124 ]; then
+          echo "ran for 10 seconds without error"
+          exit 0
+        else
+          echo "failed or exited too quickly"
+          exit 1
+        fi

.github/workflows/lint.yml

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+name: Ruff
+on: [push, pull_request]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

.github/workflows/pin_requirements.yml

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+name: Generate Requirements Files
+
+on:
+  workflow_dispatch:
+
+jobs:
+  generate-requirements:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+        python-version: ["3.9", "3.10"]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install pip-tools
+        run: pip install pip-tools
+
+      - name: Generate requirements file
+        run: pip-compile --extra web --output-file requirements-${{ matrix.os }}-${{ matrix.python-version }}.txt pyproject.toml
+
+      - name: Upload requirements file
+        uses: actions/upload-artifact@v3
+        with:
+          name: requirements
+          path: requirements-${{ matrix.os }}-${{ matrix.python-version }}.txt

.github/workflows/pypi_main.yml

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+name: PyPi distribute main release
+on: [release]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install Hatch
+      run: pip install hatch
+    - name: Build
+      run: hatch build
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/pypi_test.yml

@@ -0,0 +1,26 @@
+name: PyPi distribute test push
+on: [push]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install Hatch
+      run: pip install hatch
+    - name: Build
+      run: hatch build
+    - name: Publish distribution 📦 to Test PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository-url: https://test.pypi.org/legacy/

.github/workflows/pytest.yml

@@ -0,0 +1,46 @@
+name: Testing
+on: [push]
+
+jobs:
+  test:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ "ubuntu-latest", "macos-latest" , "windows-latest"]
+        python-version: ["3.9", "3.10" ]
+    defaults:
+      run:
+        shell: bash
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Download test file windows
+        if: runner.os == 'Windows'
+        run: |
+            C:\\msys64\\usr\\bin\\wget.exe "https://filedn.eu/loRXwzWCNnU4XoFPGbllt1y/datafile_1.ptu" -O tests/test_data/input/ds1/datafile_1.ptu
+      - name: Download test file other platforms
+        if: runner.os != 'Windows'
+        run: |
+          wget "https://filedn.eu/loRXwzWCNnU4XoFPGbllt1y/datafile_1.ptu" -O tests/test_data/input/ds1/datafile_1.ptu
+
+      - name: Set up python ${{ matrix.python-version }}
+        id: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+          cache-dependency-path: requirements/requirements-${{ matrix.os }}-${{ matrix.python-version }}.txt
+
+      - name: Install pinned requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements/requirements-${{ matrix.os }}-${{ matrix.python-version }}.txt --prefer-binary
+
+      - name: Install test requirements
+        run: pip install .[test]
+
+      - name: Run tests
+        run: |
+          pytest tests/

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.venv*/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# PyCharm IDE
+.idea/
+
+# Generated conda requirements file
+_req-*.txt
+
+
+# project specific directories
+_archive/
+dev/
+server_user_id.txt
+_version.py
+
+# local testing datasets
+tests/test_data/input/ds1
+tests/test_data/input/ds2
+tests/test_data/input/ds3
+tests/test_data/input/ds4
+tests/test_data/input/ds5

.vscode/settings.json

@@ -0,0 +1,11 @@
+{
+    "python.analysis.typeCheckingMode": "basic",
+    "python.analysis.diagnosticSeverityOverrides": {
+        "reportPrivateImportUsage":"none" 
+      },
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

CITE.txt

@@ -0,0 +1,17 @@
+
+https://pypi.org/project/fastkde/
+FastKDE:
+    O’Brien, T. A., Kashinath, K., Cavanaugh, N. R., Collins, W. D. & O’Brien, J. P. A fast and objective multidimensional kernel density estimation method: fastKDE. Comput. Stat. Data Anal. 101, 148–160 (2016).
+
+    O’Brien, T. A., Collins, W. D., Rauscher, S. A. & Ringler, T. D. Reducing the computational cost of the ECF using a nuFFT: A fast and objective probability density estimation method. Comput. Stat. Data Anal. 79, 222–234 (2014).
+
+phconvert:
+https://github.com/Photon-HDF5/phconvert
+citation?
+
+photon-hdf5:
+https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4805879/
+
+burst search:
+"Data registration and selective single-molecule analysis using multi-parameter fluorescence detection"
+DOI: 10.1016/S0168-1656(00)00412-0

LICENSE

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+MIT License
+
+Copyright (c) 2024 Jochem Smit
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.