Add ptu support and pyproject.toml, deprecate cython

.github/workflows/check.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
         os: [macos-latest, ubuntu-latest, windows-latest]
     env:
       # Display must be available globally for linux to know where xvfb is
@@ -27,11 +27,32 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+    # building on macos results in a long run due to having to build the font cache
+    - name: Cache Matplotlib font cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache/matplotlib
+        key: ${{ runner.os }}-matplotlib-${{ hashFiles('pyproject.toml') }}
+        restore-keys: |
+          ${{ runner.os }}-matplotlib-
     - name: Setup xvfb (Linux)
       if: runner.os == 'Linux'
       run: |
         sudo apt-get update
-        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
+        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 \
+          libegl-mesa0 \
+          libgl1-mesa-dri
         # start xvfb in the background
         sudo /usr/bin/Xvfb $DISPLAY -screen 0 1280x1024x24 &
     - name: Install dependencies
@@ -44,37 +65,51 @@ jobs:
         pip install -e .
         # show installed packages
         pip freeze
+#    - name: Install large dependencies (Linux)
+#      if: runner.os == 'Linux'
+#      run: | 
+#        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-24.04 wxPython
+#        pip install .[GUI]
+#    - name: Install large dependencies (macOS)
+#      if: runner.os == 'macOS'
+#      run: | 
+#        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-24.04 wxPython
+#        pip install --prefer-binary matplotlib
+#        pip install .[GUI]
+#    - name: Install large dependencies (Windows)
+#      if: runner.os == 'windows'
+#      run: |
+#        pip install .[GUI]
     - name: Test
       run: |
         coverage run --source=pycorrfit -m pytest tests
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v3
-    - name: Create app and check if it runs (macOS)
-      if: runner.os == 'macOS'
-      working-directory: ./build-recipes
-      run: |
-        bash ./macos_build_app.sh PyCorrFit $(python -m pycorrfit --version)
-    - name: Upload build artifacts
-      if: (runner.os == 'macOS')
-      uses: actions/upload-artifact@v3
-      with:
-        name: PyCorrFit_macosx
-        path: |
-          ./build-recipes/dist/*.dmg
-
-    - name: Create app and check if it runs (Win)
-      if: runner.os == 'windows'
-      working-directory: ./build-recipes
-      run: |
-        pip install -r win_build_requirements.txt
-        pyinstaller -y --log-level=WARN win_PyCorrFit.spec
-        .\dist\PyCorrFit\PyCorrFit.exe --version
-        python win_make_iss.py
-        iscc /Q win_bmicro.iss
-    - name: Upload build artifacts
-      if: (runner.os == 'windows')
-      uses: actions/upload-artifact@v3
-      with:
-        name: PyCorrFit
-        path: |
-          ./build-recipes/Output/*.exe
+#    - name: Create app and check if it runs (macOS)
+#      if: runner.os == 'macOS'
+#      working-directory: ./build-recipes
+#      run: |
+#        bash ./macos_build_app.sh PyCorrFit $(python -m pycorrfit --version)
+#    - name: Upload build artifacts
+#      if: (runner.os == 'macOS')
+#      uses: actions/upload-artifact@v4
+#      with:
+#        name: PyCorrFit_macosx
+#        path: |
+#          ./build-recipes/dist/*.dmg
+#    - name: Create app and check if it runs (Win)
+#      if: runner.os == 'windows'
+#      working-directory: ./build-recipes
+#      run: |
+#        pip install -r win_build_requirements.txt
+#        pyinstaller -y --log-level=WARN win_PyCorrFit.spec
+#        .\dist\PyCorrFit\PyCorrFit.exe --version
+#        python win_make_iss.py
+#        iscc /Q win_bmicro.iss
+#    - name: Upload build artifacts
+#      if: (runner.os == 'windows')
+#      uses: actions/upload-artifact@v4
+#      with:
+#        name: PyCorrFit
+#        path: |
+#          ./build-recipes/Output/*.exe

.github/workflows/deploy_github.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
         os: [macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v3
@@ -20,7 +20,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: "3.11"
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/deploy_pypi.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
         os: [macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v3

.gitignore

@@ -77,6 +77,7 @@ nosetests.xml
 tests/data
 
 .cache
+__pycache__
 .eggs
 .env
 
@@ -86,3 +87,6 @@ docs/_build
 
 # pycharm
 .idea
+
+_version.py
+*.swp

CHANGELOG

@@ -1,3 +1,9 @@
+[unreleased]
+ - enh: add support for PicoQuant ptu file format
+ - setup: drop support for Python <3.11 (due to ptufile)
+ - tests: set up tox for all supported python version
+ - tests: add placeholder ruff/ty/codespell configuration for gradual improvements
+ - enh: deprecate cython
 1.2.1
  - fix: compatibility with newer versions of scipy (#211)
 1.2.0

CONTRIBUTING.md

@@ -0,0 +1,12 @@
+# Quickstart
+
+```
+uv build
+```
+
+Running tests:
+
+```
+uv tool install tox --with tox-uv
+uvx tox
+```

MANIFEST.in

@@ -5,6 +5,6 @@ recursive-include examples *.txt *.pcfs
 recursive-include doc *.tex *.bib *.pdf *.md *.png *.svg
 recursive-include docs *.py *.md *.txt *.rst *.bib *.gif *.jpg *.png
 recursive-include tests *.py *.md
-recursive-include pycorrfit LICENCE README
+recursive-include pycorrfit LICENSE README
 prune docs/_build
 exclude docs/_version_save.py

build-recipes/win_build_requirements.txt

@@ -0,0 +1 @@
+pyinstaller

pycorrfit/__init__.py

@@ -2,15 +2,21 @@
 PyCorrFit is a tool to fit fluorescence correlation spectroscopy
 data on a logarithmic scale.
 """
-from . import meta
-from . import models
-from . import openfile
-from . import readfiles
 
+from importlib.metadata import PackageNotFoundError, version
+
+from . import meta, models, openfile, readfiles
 from .correlation import Correlation
 from .fit import Fit
 from .trace import Trace
-from ._version import version as __version__
 
-__author__ = u"Paul Müller"
+try:
+    __version__ = version("pycorrfit")
+except PackageNotFoundError:
+    # package is not installed
+    __version__ = "unknown"
+
+
+__author__ = "Paul Müller"
 __license__ = "GPL v2"
+__all__ = ["meta", "models", "openfile", "readfiles", "Fit", "Trace", "Correlation"]