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Add ptu support and pyproject.toml, deprecate cython (#213)
A user requested the ability to load ptu (t2) files from a PicoQuant PicoHarp. The test suite covers HydraHarp (t2, t3) and PicoHarp (t2) but the code should be as general as the underlying ptufile package. In the process of setting this up I debugged a bit and made a few changes: * rewrite fib4.pyx as fib4.py, which deprecates cython * bump minimum Python version to 3.11 to support ptufile * migrated from setup.py to pyproject.toml (tested on Linux) * set up tox.ini for running the test suite * set up ruff, ty, and codespell placeholders for gradual linting (remove the exclusions as desired) * fix some stray numpy bugs (np.float_ deprecation) * remove distutils due to deprecation in Python 3.12 * do version generation through setuptools_scm * ensure the test suite fully passes for all versions supported * ensure the CI check stage works up through testing Deprecating cython There was only one function that required cython. I have replaced it with a pure numpy implementation that seems to perform equivalently and gets the same results for both random and test data. In tests/test_file_format.py:test_pt3_basic the behavior is the same as before (expected 2037 is actually 2037.5) but I have no insight as to why that happened in the first place. The correlation data (last two lines of that test) pass on my machine though. So all I can say is that no observable behavior has changed for loading pt3 or running dividAndConquer, not that the trace value is actually correct.
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‎.github/workflows/check.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.10']
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python-version: ['3.11']
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os: [macos-latest, ubuntu-latest, windows-latest]
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env:
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# Display must be available globally for linux to know where xvfb is
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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# building on macos results in a long run due to having to build the font cache
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- name: Cache Matplotlib font cache
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uses: actions/cache@v3
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with:
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path: ~/.cache/matplotlib
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key: ${{ runner.os }}-matplotlib-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-matplotlib-
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- name: Setup xvfb (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 libegl1-mesa
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sudo apt-get install -y \
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xvfb \
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libxkbcommon-x11-0 \
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libxcb-icccm4 \
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libxcb-image0 \
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libxcb-keysyms1 \
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libxcb-randr0 \
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libxcb-render-util0 \
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libxcb-xinerama0 \
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libxcb-xinput0 \
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libxcb-xfixes0 \
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libegl1 \
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libegl-mesa0 \
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libgl1-mesa-dri
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# start xvfb in the background
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sudo /usr/bin/Xvfb $DISPLAY -screen 0 1280x1024x24 &
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- name: Install dependencies
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pip install -e .
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# show installed packages
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pip freeze
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# - name: Install large dependencies (Linux)
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# if: runner.os == 'Linux'
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# run: |
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# pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-24.04 wxPython
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# pip install .[GUI]
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# - name: Install large dependencies (macOS)
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# if: runner.os == 'macOS'
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# run: |
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# pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-24.04 wxPython
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# pip install --prefer-binary matplotlib
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# pip install .[GUI]
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# - name: Install large dependencies (Windows)
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# if: runner.os == 'windows'
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# run: |
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# pip install .[GUI]
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- name: Test
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run: |
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coverage run --source=pycorrfit -m pytest tests
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3
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- name: Create app and check if it runs (macOS)
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if: runner.os == 'macOS'
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working-directory: ./build-recipes
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run: |
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bash ./macos_build_app.sh PyCorrFit $(python -m pycorrfit --version)
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- name: Upload build artifacts
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if: (runner.os == 'macOS')
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uses: actions/upload-artifact@v3
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with:
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name: PyCorrFit_macosx
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path: |
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./build-recipes/dist/*.dmg
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- name: Create app and check if it runs (Win)
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if: runner.os == 'windows'
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working-directory: ./build-recipes
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run: |
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pip install -r win_build_requirements.txt
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pyinstaller -y --log-level=WARN win_PyCorrFit.spec
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.\dist\PyCorrFit\PyCorrFit.exe --version
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python win_make_iss.py
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iscc /Q win_bmicro.iss
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- name: Upload build artifacts
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if: (runner.os == 'windows')
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uses: actions/upload-artifact@v3
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with:
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name: PyCorrFit
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path: |
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./build-recipes/Output/*.exe
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# - name: Create app and check if it runs (macOS)
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# if: runner.os == 'macOS'
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# working-directory: ./build-recipes
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# run: |
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# bash ./macos_build_app.sh PyCorrFit $(python -m pycorrfit --version)
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# - name: Upload build artifacts
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# if: (runner.os == 'macOS')
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# uses: actions/upload-artifact@v4
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# with:
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# name: PyCorrFit_macosx
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# path: |
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# ./build-recipes/dist/*.dmg
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# - name: Create app and check if it runs (Win)
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# if: runner.os == 'windows'
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# working-directory: ./build-recipes
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# run: |
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# pip install -r win_build_requirements.txt
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# pyinstaller -y --log-level=WARN win_PyCorrFit.spec
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# .\dist\PyCorrFit\PyCorrFit.exe --version
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# python win_make_iss.py
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# iscc /Q win_bmicro.iss
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# - name: Upload build artifacts
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# if: (runner.os == 'windows')
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# uses: actions/upload-artifact@v4
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# with:
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# name: PyCorrFit
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# path: |
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# ./build-recipes/Output/*.exe

‎.github/workflows/deploy_github.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.10']
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python-version: ['3.11']
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os: [macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: "3.10"
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python-version: "3.11"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip

‎.github/workflows/deploy_pypi.yml‎

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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python-version: ['3.10']
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python-version: ['3.11']
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os: [macos-latest, windows-latest]
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steps:
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- uses: actions/checkout@v3

‎.gitignore‎

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tests/data
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.cache
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__pycache__
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.eggs
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.env
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# pycharm
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.idea
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_version.py
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*.swp

‎CHANGELOG‎

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[unreleased]
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- enh: add support for PicoQuant ptu file format
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- setup: drop support for Python <3.11 (due to ptufile)
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- tests: set up tox for all supported python version
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- tests: add placeholder ruff/ty/codespell configuration for gradual improvements
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- enh: deprecate cython
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1.2.1
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- fix: compatibility with newer versions of scipy (#211)
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1.2.0

‎CONTRIBUTING.md‎

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# Quickstart
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```
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uv build
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```
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Running tests:
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```
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uv tool install tox --with tox-uv
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uvx tox
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```

‎MANIFEST.in‎

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recursive-include doc *.tex *.bib *.pdf *.md *.png *.svg
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recursive-include docs *.py *.md *.txt *.rst *.bib *.gif *.jpg *.png
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recursive-include tests *.py *.md
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recursive-include pycorrfit LICENCE README
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recursive-include pycorrfit LICENSE README
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prune docs/_build
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exclude docs/_version_save.py

‎build-recipes/win_build_requirements.txt‎

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pyinstaller

‎pycorrfit/__init__.py‎

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PyCorrFit is a tool to fit fluorescence correlation spectroscopy
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data on a logarithmic scale.
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"""
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from . import meta
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from . import models
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from . import openfile
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from . import readfiles
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from importlib.metadata import PackageNotFoundError, version
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from . import meta, models, openfile, readfiles
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from .correlation import Correlation
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from .fit import Fit
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from .trace import Trace
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from ._version import version as __version__
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__author__ = u"Paul Müller"
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try:
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__version__ = version("pycorrfit")
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except PackageNotFoundError:
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# package is not installed
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__version__ = "unknown"
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__author__ = "Paul Müller"
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__license__ = "GPL v2"
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__all__ = ["meta", "models", "openfile", "readfiles", "Fit", "Trace", "Correlation"]

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