././@PaxHeader 0000000 0000000 0000000 00000000033 00000000000 010211 x ustar 00 27 mtime=1768809958.253436
pycorrfit-1.3.1/ 0000755 0001751 0001751 00000000000 15133362746 013215 5 ustar 00runner runner ././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1768809958.2224307
pycorrfit-1.3.1/.github/ 0000755 0001751 0001751 00000000000 15133362746 014555 5 ustar 00runner runner ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/.github/FUNDING.yml 0000644 0001751 0001751 00000000053 15133362741 016363 0 ustar 00runner runner github: paulmueller
liberapay: paulmueller
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1768809958.2234309
pycorrfit-1.3.1/.github/workflows/ 0000755 0001751 0001751 00000000000 15133362746 016612 5 ustar 00runner runner ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/.github/workflows/check.yml 0000644 0001751 0001751 00000007072 15133362741 020413 0 ustar 00runner runner name: Checks
on:
push:
branches:
- main
pull_request:
branches:
- main
jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
matrix:
python-version: ['3.11']
os: [macos-latest, ubuntu-latest, windows-latest]
env:
# Display must be available globally for linux to know where xvfb is
DISPLAY: :0
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.python-version }}
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 \
libegl-mesa0 \
libgl1-mesa-dri
# start xvfb in the background
sudo /usr/bin/Xvfb $DISPLAY -screen 0 1280x1024x24 &
- name: Install dependencies
run: |
# prerequisites
python -m pip install --upgrade pip wheel
python -m pip install coverage flake8 pytest
python -m pip install -r tests/requirements.txt
# install dependencies
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@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
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/.github/workflows/deploy_github.yml 0000644 0001751 0001751 00000004016 15133362741 022167 0 ustar 00runner runner name: Deploy to GitHub Releases
on:
push:
tags:
- '*'
jobs:
build:
name: Create Release
runs-on: ${{ matrix.os }}
strategy:
matrix:
python-version: ['3.11']
os: [macos-latest, windows-latest]
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v3
with:
python-version: "3.11"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install setuptools wheel twine
pip install -e .
- name: Build app for Mac
if: runner.os == 'macOS'
working-directory: ./build-recipes
run: |
bash ./macos_build_app.sh PyCorrFit $(python -m pycorrfit --version)
- name: Build app for Win
if: runner.os == 'windows'
working-directory: ./build-recipes
run: |
pip install -r win_build_requirements.txt
pyinstaller -y --log-level=WARN win_BMicro.spec
.\dist\PyCorrFit\PyCorrFit.exe --version
python win_make_iss.py
iscc /Q win_bmicro.iss
- name: Release macOS assets
if: runner.os == 'macOS'
uses: softprops/action-gh-release@v1
with:
name: PyCorrFit ${{ github.ref_name }}
draft: true
prerelease: false
body: |

files: |
./build-recipes/dist/PyCorrFit_${{ github.ref_name }}_macosx.dmg
./build-recipes/dist/PyCorrFit_${{ github.ref_name }}_macosx.pkg
- name: Release windows assets
if: runner.os == 'windows'
uses: softprops/action-gh-release@v1
with:
name: BMicro ${{ github.ref_name }}
draft: true
prerelease: false
body: |

files: |
./build-recipes/Output/PyCorrFit_${{ github.ref_name }}_win_64bit_setup.exe
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/.github/workflows/deploy_pypi.yml 0000644 0001751 0001751 00000001642 15133362741 021670 0 ustar 00runner runner name: Release to PyPI
on:
push:
tags:
- '*'
jobs:
build_sdist:
name: Build source distribution
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@main
with:
fetch-depth: 0
- name: Build sdist
run: pipx run build --sdist
- name: publish
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
run: |
pipx install twine
twine upload --skip-existing dist/*
build_wheels:
name: Build wheel
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@main
with:
fetch-depth: 0
- name: Build sdist
run: pipx run build --wheel
- name: publish
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_PWD }}
run: |
pipx install twine
twine upload --skip-existing dist/*
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/.gitignore 0000644 0001751 0001751 00000001234 15133362741 015200 0 ustar 00runner runner *.py[cod]
_version_save.py
# C extensions
*.so
# Packages
*.egg
*.egg-info
dist
build
eggs
parts
bin
var
sdist
develop-eggs
.installed.cfg
lib
lib64
# Installer logs
pip-log.txt
# Unit test / coverage reports
.coverage
.tox
nosetests.xml
# Translations
*.mo
# Mr Developer
.mr.developer.cfg
.project
.pydevproject
# Latex
*.ps
*.aux
*.glo
*.idx
*.log
*.toc
*.ist
*.acn
*.acr
*.alg
*.bbl
*.blg
*.dvi
*.glg
*.gls
*.ilg
*.ind
*.lof
*.lot
*.maf
*.mtc
*.mtc1
*.out
*.synctex.gz
*.pdf
*.bak
# ~
*.py~
*.md~
*.yml~
*.sh~
*.spec~
*.c
*.txt~
# test data
tests/data
.cache
__pycache__
.eggs
.env
.pytest_cache
htmlcov
docs/_build
# pycharm
.idea
_version.py
*.swp
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/.readthedocs.yml 0000644 0001751 0001751 00000000425 15133362741 016277 0 ustar 00runner runner version: 2
formats:
- pdf
build:
os: ubuntu-22.04
tools:
python: "3.11"
jobs:
post_checkout:
- git fetch --unshallow || true
sphinx:
configuration: docs/conf.py
python:
install:
- requirements: docs/requirements.txt
- method: pip
path: .
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/CHANGELOG 0000644 0001751 0001751 00000040066 15133362741 014430 0 ustar 00runner runner 1.3.1
- maintenance release
1.3.0
- fix: import error (#208)
- enh: add support for PicoQuant ptu file format (#84)
- enh: deprecate cython (#204)
- tests: set up tox for all supported python version
- tests: add placeholder ruff/ty/codespell configuration for gradual improvements
- setup: drop support for Python <3.11 (due to ptufile)
- setup: fix building docs
1.2.1
- fix: compatibility with newer versions of scipy (#211)
1.2.0
- enh: add support for PicoQuant cor file format
- ref: code cleanup
- setup: modernize build pipeline
- tests: remove deprecated pytest-runner
- setup: require Python 3.10
1.1.8
- docs: fix typo in legacy PDF (#195)
1.1.7
- docs: add sponsor links to contribute section
- docs: add gallery with all images in docs/gallery
1.1.6
- fix: improve support for Confocor FCS file format
(see discussion in #37)
- ref: make pathlib.Path a standard in readfiles
- code cleanup
- drop support for Python<3.6
1.1.5
- docs: fix build with recent version of latex (#191)
1.1.4
- maintenance release
1.1.3
- maintenance release
1.1.2
- ci: Automated release to PyPI with appveyor and travis-ci
- fix: support lmfit >= 0.9.11
1.1.1
- Fix plotting error with LaTeX (thanks @toubol) (#179)
- Update documentation
1.1.0
- BREAKING CHANGE: Move to Python3 (thanks @toubol) (#173)
- GUI:
- Add option in Preferences to automatically close tools after usage
- Add keyboard shortcuts (thanks @toubol)
- Fix entry point for GUI (#172)
- Refactor several asserts into raises
1.0.1
- Improved support for ALV ".ASC" file format (#169)
- NumPy 0.13 support for ".ptu" file reader
- Code cleanup:
- Fetch latest available version from GitHub releases
- New dependency for "simplejson" Python package
- Move appveyor recipe to separate folder
1.0.0
- New confocal fitting models T+T+2D and T+T+3D
- Fix regression: .sin files could not be opened (#167)
0.9.9
- Remove admin-requirement during install (Windows)
- Support newer correlator.com .sin file format (experimental, #135)
- Add smart progress dialog for fitting (#155)
- Statistics: check "filename/title" by default (#151)
- Documentation: fix bad LaTeX commands (#163)
0.9.8
- Bugfixes:
- Indexing error when saving sessions (#154)
- Page number truncated in csv export (#159)
- Export of csv files used incorrect normalization (#153)
- Normalization parameter was not displayed in the 'Info' tool
0.9.7
- Second triplet time is now larger than first triplet time
by default
- Remove a hack that causes a run through all pages
e.g. when an average is created
- Bugfixes:
- Opening sessions with user-defined models
- Saving sessions with comments containing non-ASCII characters
- Windows build: Graphical plot export was misconfigured
(added matplotlibrc patch in .spec file)
0.9.6
- Bugfixes:
- Fixed minor wx sizer problems for the tools
- Fixed 'AttributeError' in page.py if no weights are present
- New confocal fitting models (#111):
- 3D+3D, 2D+2D, 3D+2D; no triplet
- T+T+2D+2D, T+T+3D+2D; double triplet
- T+3D+3D+3D, T+3D+3D+2D (#40, #59)
- Under the hood:
- Separation of core and GUI modules
- Include tests in distributions for PyPI
- Improve automated testing on Windows and Mac OS
- More constraint options for fitting
0.9.5
- Bugfixes
- Closing the batch control window causes segfault bug (#142)
- Closing page causes error when batch control is active (#143)
- Plot normalization causes "Save Session" to fail (#144)
- Plot normalization not loaded from session (#145)
0.9.4
- Batch control allows to select individual parameters (#108)
- Allow to exclude pages from batch fitting (#107)
- Bugfixes:
- Fix 'ValueError' in parameter display
- Possibly fixed error with 'yaml.safe_dump'
on Mac OSx 10.8.5
- Make sure background is lower than signal (#137)
0.9.3
- Fitting: migrate to lmfit
- This introduces a new dependency for building PyCorrFit.
(e.g. in Debian, the package "python-lmfit" is required)
- Improved fitting behavior at parameter boundaries
- Removed "Polak-Ribiere" fitting algorithm
- Added "Sequential Linear Squares Programming" algorithm
- Heuristic fit (#109):
- Detect parameters that are stuck during fitting
- Fit each curve five times or less and check
whether the fit converges.
- If two diffusion time parameter exist in a model, always
make sure that one parameter is the larger one. This
feature can currently not be disabled (#110).
- Allow infinity ("inf" and "-inf") parameters for models
and boundaries.
- New model: confocal T+T+3D+3D
- Bugfixes:
- Sessions saved with 64bit Windows were not opened (#136)
- Old sessions and "KeyError: 'chi2'"
- Old session file extension was not recognized (#106)
0.9.2
- Bugfixes:
- "Slider Simulation"/"Parm Range" broken (#133)
- Computation of average intensity did not work
correctly for unequally spaced traces
- Update .pt3 reader to version 8399ff7401
- Import traces of .pt3 files (experimental, #118)
Warning: Absolute values for intensity might be wrong
0.9.1
- Tool 'Overlay curves': improve UI (#117)
- Tool 'Statistics view': improve UI (#113)
- Tool 'Trace view': display countrate (#121)
- Bugfixes:
- Unicode errors in statistics tool (#131)
- Load session errors with empty pages
0.9.0
- Improve parameter display (#52, #114)
- Display Chi2 on each page (#115)
- The displayed Chi2-value for non-weighted fits is now
normalized to the expected values of the fit. The
documentation has been updated accordingly.
- Add "All files" option in save dialogs (#97)
- Improved plot export dialog (#99)
0.8.9
- Improved support for "ALV-7004" files (#104)
- Increase resolution for image export
- Load weights from PyCorrFit csv files
- Tool 'Overlay Curves': show cropped correlation curves
- Tool 'Trace view': increase size of window (#93)
- Tool 'Global fitting': remove forced, joint weights
- Session comment dialog: more intuitive behavior (#116)
- Improve plot export (#95)
- Bugfixes:
- Weighted fits at borders of fit interval were
computed incorrectly due to integer division
- Fitting algorithms did not work (#94)
- Creating averages did not work (#123)
- ASCII errors in statistics tool (#112)
- Under the hood:
- Introduce new classes: Correlation, Fit, Trace
- Code cleanup and rewrite to support planned features
- In some cases support older versions of NumPy
0.8.8
- Improved support for "ALV-7004" files
- If you install the GUI with pip, you now need to include
the 'GUI' requirement: 'pip install pycorrfit[GUI]'.
The GUI depends on matplotlib and wxPython which is not
required for scripting with the pycorrfit module.
- Bugfix: missing version string on SuSe linux (#101)
- Under the hood:
- Python entry point script replaces "bin/" script
- Windows build system hosted by appveyor.com
- MacOS X build system hosted by travis-ci.org
- New builds use wxPython3 (#85)
- Unicode support without 'reload(sys)'
- Error messages are more verbose
0.8.7
- Removed unused fitting parameter d_eva from model 6022 and
secured backwards compatibility.
- Improved support for ALV700X (#92)
- Bugfix: Corrected false display of Unicode characters on Windows
- Under the hood:
- Code cleanup with pyflakes
- Repo cleanup (#98)
0.8.6
- Bugfix: Opening .fcs files with only one AC curve works now
- Zip files with measurements may now contain subfolders
- Improved pt3-file support from
https://github.com/dwaithe/FCS_point_correlator (#89)
0.8.5
- Fixed bug that made it impossible to load data (#88)
- Exceptions are now handled by wxPython
- Under the hood:
- Pythonic repository structure
- Relative imports
- Windows build machine is now Windows 7
- Removed strict dependency on matplotlib
0.8.4
- Support for PicoQuant data file format
Many thanks to Dominic Waithe (@dwaithe)
- Improved compatibility with Zeiss .fcs file format
- PyCorrFit is now dependent on Cython
- The module 'openfile' is now available from within Python
- Installer for Windows
0.8.3
- New .pcfs (PyCorrFit Session) file format (#60)
- Additional fitting algorithms: Nelder-Mead, BFGS, Powell, Polak-Ribiere (#71)
- Improvements
- Massive speed-up when working with large data sets (#77)
- Plot export: legend position and displayed parameters (#54)
- Average tool: traces may now start at time points != 0
- Statistics tool: display on smaller screens
- ALV data files: updated parser to identify curve types and segment traces
- Zeiss ConfoCor3 data files: some files could not be opened due to dummy AC curves
- Models: default parameters were changed to prevent unstable fits
- Software: notification dialogs for missing modules or other software
- Bugfixes
- User could accidently clear a session (#65)
- wxPython plotting problem on MacOSx (#64)
- Statistics view: some parameters were duplicated (#76)
- Caught zero-division warnings (models with triplet component)
- Corrected x-axis scaling of statistics view and trace view
0.8.2
- The documentation has been thoroughly reworked
- The user is now warned if he does not have a TeX distribution installed
- Improvements:
- Complete support for installing PyCorrFit with virtualenv and pip
(This is documented in the wiki)
- Statistics tool now displays average and SD (#43)
- Bugfix: TeX did not work on Ubuntu due to missing imports
0.8.1
- Thanks to Alex Mestiashvili for providing initial setup.py files
and for debianizing PyCorrFit (@mestia)
- Thanks to Thomas Weidemann for his contributions to the documentation (@weidemann)
- Bugfixes
- Some ConfoCor files were not imported
- The cpp was not calculated correctly in case of background correction (#45)
- Enabled averaging of single pages (#58)
- Background correction for cross-correlation data is now computed (#46)
- Improvements of the user interface
- The menus have been reordered (#47, #50)
- The fitting panel has been optimized (#49)
- the slider simulation got a reset button (#51)
- The Help menu contains documentation and wiki (#56)
- Model functions that are somehow redundant have been removed from the menu,
but are still supported
- The model doc strings were fully converted to Unicode
- Several text messages were modified for better coherence
- The background correction tool is more intuitive
- Statistics panel improvements (#43)
- Run information is included in the Data set title
- The page counter starts at "1" instead of "0" (#44)
- New handling of background correction (#46, #53)
0.8.0
- Filename/title of each tab now shows up in the notebook (#39)
- Statistics tool can plot parameters and page selection with the Overlay
tool is possible (#31)
0.7.9
- Support for Mac OSx
- Enhancements:
- Export file format (.csv) layout improved
- Model function info text in UTF-8
- Improved waring message when opening sessions from future versions
- New feature lets user set the range for the fitting parameters
- Bugfixes:
- Cleaned minor tracebacks and exceptions created by the frontend
- Mac version now works as expected, but .app bundling failed
- Latex plotting features now support more characters such as "[]{}^"
0.7.8
- Enhancements:
- Averages can now be calculated from user-selected pages
- Pages selected in the Overlay tool are now automatically set
for computation of average and for global fitting
- Source pages are now displayed in average title
- Graph normalization with particle numbers is now possible
- Bugfixes:
- Errors during fitting with weights equal to zero
- Overlay tool displayed last curve after all pages have been removed
- Global fit did not work with weights
- Session saving now uses 20 digits accuracy
- CSV export is now using tab-delimited data for easier Excel-import
- Added version checking for session management
0.7.7
- Fixed: Tools windows could not be closed (or moved on MS Windows)
- Fixed: .csv export failed in some cases where no weights were used
- Enhancement: The user is now asked before a page is closed
- Enhancement: Tool "Page Info" and in exported .csv files, variables and
values are now separated by a tab stop instead of a "="
- Fixed: Opening a session with an empty page failed in some cases
- Fixed: Tool "Statistics" missed to output the column "filename/title"
if that key value is empty - replaced empty strings with "NoName"
- Enhancement: Tool "Overlay" now asks the user to check kept curves
instead of showing the curves to be removed
- Enhancement: Tool "Overlay" now has a "Cancel" button
0.7.6
- Improved handling
- Tools are now sorted according to a standard work-flow
- Renamed "Curve selection" to "Overlay tool" - this is more intuitive
- Tools will now stay open or may be opened when there are no open pages (#25)
- Filenames and runs are now displayed on each page (also added filename/title tag) (#23)
- Notebook: moved close button to each tab to prevent accidental closing of tabs
- Improved tool "Statistics" (#21)
- Fixed the case where "useless" data was produced - instead we write "NaN" data,
removed warning message accordingly
- Row-wise ordering according to page numbers (#22)
- Column-wise ordering is now more intuitive
(Fitted parameters with errors first)
- Some columns are now checked by default
- PyCorrFit remembers checked parameters for a page (not saved in session)
- Improved tool "Overlay" (#23)
- New feature: Overlay shows run number of each file (upon import),
the run (or index) of an experimental file is unique to PyCorrFit
- Upon import, filenames and runs are displayed
- In a session, the filename/title is displayed
- Web address of PyCorrFit changed
from "fcstools.dyndns.org/pycorrfit" to "pycorrfit.craban.de"
- Minor bugfixes: Batch control, Global fitting, import dialog
0.7.5
- Added model functions to documentation.
- Weights from fitting are now exported in .csv files.
- Rework of info panel for fitting
- Cleared unintuitive behavior of session saving:
The fitting parameters were read from the frontend. This could have
led to saving false fit meta data.
- During fitting, units are now displayed as "human readable" (#17).
- Slider simulation now also uses human readable units (#17).
- Secured support for Ubuntu 12.10 and 13.04
- Fixed: new line (\n) characters for LaTeX plotting on Windows
0.7.4
- New tool: Colorful curve selection
- Import data: Curve selection possible
- Average: Crop average according to current page.
- Fixed: Page now displays Chi-squared of global fit.
- Fixed: Chi-squared and parameters of global fitting are now stored in sessions.
0.7.3
- Issue closed. External weights from averages saved in session (#11).
- Solved minor bugs
- Added estimation of errors of fit (Issue #12/#14)
- Fixed: Some .fcs files containing averages were not imported.
0.7.2
- Bugfix: Issue #10; we now have a goodness of the fit, if weighted
fitting is performed
- Bugfix: Weights for fitting not properly calculated (sqrt(std)).
- Bugfix: Batch control IndexError with Info window opened
- Tool Statistics: Sort values according to page numbers
- Tool global: Added weighted fitting
- Residuals: According to weighted fitting, weighted residuals are plotted
- Average: Variances from averaging can be used for weighted fitting
0.7.1
- Feature: Added Python shell
- Bugfix: Saving image was not performed using WXAgg
- Bugfix: Notebook pages were drag'n'dropable
- Update function now works in its own thread
- Code cleanup: documentation of model functions
- Added program icon
0.7.0
- File import dialog was enhanced (#4, #5 - subsequently #7, #8):
- Now there is only one "load data" dialog in the file menu
- The model function is chosen for each type of data that is
to be imported (AC, CC, etc.)
- Bugfix: Channel selection window causes crash on file import (#1).
- Bugfix: Hidden feature changes fixed parameters during fitting (#2).
- Feature: Convert TIR model function parameters lambda and NA to sigma (#3).
- Code cleanup: Opening data files is now handled internally differently.
0.6.9
- Initital GitHub commit
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/CONTRIBUTING.md 0000644 0001751 0001751 00000000142 15133362741 015436 0 ustar 00runner runner # Quickstart
```
uv build
```
Running tests:
```
uv tool install tox --with tox-uv
uvx tox
```
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/LICENSE 0000644 0001751 0001751 00000036607 15133362741 014231 0 ustar 00runner runner Copyright (C) 2011-2012 Paul Müller
PyCorrFit is free software; you can redistribute it and/or modify
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././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/MANIFEST.in 0000644 0001751 0001751 00000000530 15133362741 014744 0 ustar 00runner runner include CHANGELOG
include LICENSE
include README.rst
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 LICENSE README
prune docs/_build
exclude docs/_version_save.py
././@PaxHeader 0000000 0000000 0000000 00000000033 00000000000 010211 x ustar 00 27 mtime=1768809958.252436
pycorrfit-1.3.1/PKG-INFO 0000644 0001751 0001751 00000005061 15133362746 014314 0 ustar 00runner runner Metadata-Version: 2.4
Name: pycorrfit
Version: 1.3.1
Summary: Scientific tool for fitting correlation curves on a logarithmic plot.
Author: Thomas Bischof
Author-email: Paul Müller
License-Expression: GPL-2.0-only
Project-URL: repository, https://github.com/FCS-analysis/PyCorrFit
Keywords: fluorescence correlation spectroscopy (FCS)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Intended Audience :: Science/Research
Requires-Python: <4,>=3.11
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: lmfit>=0.9.2
Requires-Dist: numpy>=1.14.2
Requires-Dist: pyyaml>=3.12
Requires-Dist: scipy>=1.0.1
Requires-Dist: ptufile>=2025.12.12
Requires-Dist: looseversion>=1.3.0
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: urllib3; extra == "test"
Requires-Dist: ruff; extra == "test"
Requires-Dist: ty; extra == "test"
Requires-Dist: codespell; extra == "test"
Provides-Extra: gui
Requires-Dist: matplotlib>=2.2.2; extra == "gui"
Requires-Dist: sympy>=1.1.1; extra == "gui"
Requires-Dist: simplejson; extra == "gui"
Requires-Dist: wxPython>=4.0.1; extra == "gui"
Dynamic: license-file
|PyCorrFit|
===========
|PyPI Version| |Build Status| |Build Status Win| |Coverage Status| |Docs Status|
Documentation
-------------
The documentation of PyCorrFit is available at https://pycorrfit.readthedocs.org.
Problems
--------
If you find a bug or need help with a specific topic, do not hesitate to ask a question
at the `issues page `__.
.. |PyCorrFit| image:: https://raw.github.com/FCS-analysis/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png
.. |PyPI Version| image:: https://img.shields.io/pypi/v/PyCorrFit.svg
:target: https://pypi.python.org/pypi/pycorrfit
.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/FCS-analysis/PyCorrFit/check.yml
:target: https://github.com/FCS-analysis/PyCorrFit/actions/workflows/check.yml
.. |Build Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/PyCorrFit/master.svg?label=build_win
:target: https://ci.appveyor.com/project/paulmueller/pycorrfit
.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/FCS-analysis/PyCorrFit/master.svg
:target: https://codecov.io/gh/FCS-analysis/PyCorrFit
.. |Docs Status| image:: https://readthedocs.org/projects/pycorrfit/badge/?version=latest
:target: https://readthedocs.org/projects/pycorrfit/builds/
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/README.rst 0000644 0001751 0001751 00000002477 15133362741 014711 0 ustar 00runner runner |PyCorrFit|
===========
|PyPI Version| |Build Status| |Build Status Win| |Coverage Status| |Docs Status|
Documentation
-------------
The documentation of PyCorrFit is available at https://pycorrfit.readthedocs.org.
Problems
--------
If you find a bug or need help with a specific topic, do not hesitate to ask a question
at the `issues page `__.
.. |PyCorrFit| image:: https://raw.github.com/FCS-analysis/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png
.. |PyPI Version| image:: https://img.shields.io/pypi/v/PyCorrFit.svg
:target: https://pypi.python.org/pypi/pycorrfit
.. |Build Status| image:: https://img.shields.io/github/actions/workflow/status/FCS-analysis/PyCorrFit/check.yml
:target: https://github.com/FCS-analysis/PyCorrFit/actions/workflows/check.yml
.. |Build Status Win| image:: https://img.shields.io/appveyor/ci/paulmueller/PyCorrFit/master.svg?label=build_win
:target: https://ci.appveyor.com/project/paulmueller/pycorrfit
.. |Coverage Status| image:: https://img.shields.io/codecov/c/github/FCS-analysis/PyCorrFit/master.svg
:target: https://codecov.io/gh/FCS-analysis/PyCorrFit
.. |Docs Status| image:: https://readthedocs.org/projects/pycorrfit/badge/?version=latest
:target: https://readthedocs.org/projects/pycorrfit/builds/
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/appveyor.yml 0000644 0001751 0001751 00000007201 15133362741 015600 0 ustar 00runner runner # Changes in online interface:
# - Set build schedule to "0 3 * * *" for nightly builds.
#skip_commits:
# # Do not build on commits. Only nightly builds (web interface)
# author: /.*/
# Do not use shallow_clone, because coveralls needs a git repository
#shallow_clone: true
# Use large clone depth so that a tag is included for versioning
clone_depth: 256
notifications:
- provider: Email
on_build_success: false
on_build_failure: false
on_build_status_changed: false
environment:
PYPI_USR: ci_fcs
PYPI_PWD:
secure: EKcG8PgUSje7gsGc7AT7+Hk7c5MRH8nVgqIA9JvBV0oW0uU5FlxGjw5S+dUk1X1D
matrix:
- PYTHON: "C:\\Miniconda36-x64"
PYTHON_VERSION: "3.10"
PYTHON_ARCH: "64"
cache:
# data files for testing
- tests\data
init:
- "ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH%"
install:
# Install InnoSetup and add to path
# Copied from
# https://github.com/Phonations/Joker/blob/master/appveyor.yml
- appveyor-retry choco install -y InnoSetup
# Determine platform
- '%PYTHON%/python -c "import platform; print(platform.uname())"'
- '%PYTHON%/python -c "import sys; print(sys.version)"'
# Prepend newly installed Python to the PATH of this build (this cannot be
# done from inside the powershell script as it would require to restart
# the parent CMD process).
- "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
# Check that we have the expected version and architecture for Python
- "python --version"
# Install package-specific libraries
# CONDA installs
# Pinned versions are defined in .appveyor\pinned
- xcopy .appveyor\pinned %PYTHON%\conda-meta\ /Y
- "appveyor-retry conda install --yes --quiet matplotlib numpy pip scipy wxpython"
# PIP installs
# Install the build dependencies of the project.
- "pip install cython wheel"
# Install package-specific libraries
- "pip install simplejson sympy"
- "pip install lmfit==0.9.2"
# Install pyinstaller (includes dependency for pywin32)
- "pip install pyinstaller==3.3.1"
# Run develop (installs yet missing packages and runs cython)
- "pip install -e ."
# Show the installed packages
- "pip freeze"
build: off
test_script:
- 'python -c "import pycorrfit; print(pycorrfit.__version__)"'
- "pip install coverage"
- "pip install codecov"
- "coverage run --source=pycorrfit -m pytest tests"
- "coverage report -m"
- "codecov || exit 0"
after_test:
# If tests are successful, create a whl package for the project.
- "appveyor-retry pip install twine wheel"
- "python setup.py bdist_wheel"
- "python setup.py sdist"
- ps: "ls dist"
# Setup PyPI credentials
- cmd: "echo [pypi] > %USERPROFILE%\\.pypirc"
- cmd: "echo username: %PYPI_USR% >> %USERPROFILE%\\.pypirc"
- cmd: "echo password: %PYPI_PWD% >> %USERPROFILE%\\.pypirc"
# Run pyinstaller
# This will create the "win7_innosetup.iss" file
- "pyinstaller -y --log-level=WARN build-recipes\\win_PyCorrFit_win7.spec"
# Create InnoSetup installers
# Set InnoSetup path here, because Cython complained about it.
- set PATH=%PATH%;"C:\\Program Files (x86)\\Inno Setup 5"
- iscc /Q win7_innosetup.iss
artifacts:
# Archive the generated wheel package in the ci.appveyor.com build report.
- path: dist\*
# InnoSetup files
- path: Output\*
on_success:
- cmd: "if [%APPVEYOR_REPO_TAG%]==[true] twine upload --skip-existing dist\\*.whl"
- cmd: "if [%APPVEYOR_REPO_TAG%]==[true] twine upload --skip-existing dist\\*.tar.gz"
deploy:
provider: GitHub
auth_token:
secure: u94ePbzUmuyh5jZU+1xvST73Ueuxepu86/XQsGx/15AnSd4NhQHKE1UXIe1vBIwf
artifact: /.*\.exe/
draft: true
prerelease: true
on:
appveyor_repo_tag: true # deploy on tag push only
././@PaxHeader 0000000 0000000 0000000 00000000034 00000000000 010212 x ustar 00 28 mtime=1768809958.2254312
pycorrfit-1.3.1/build-recipes/ 0000755 0001751 0001751 00000000000 15133362746 015744 5 ustar 00runner runner ././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/build-recipes/linux_build-wheels.sh 0000755 0001751 0001751 00000000734 15133362741 022105 0 ustar 00runner runner #!/bin/bash
set -e -x
cd /io
for PYBIN in /opt/python/cp${TRAVIS_PYTHON_VERSION//./}*/bin/; do
# Install
"${PYBIN}/pip" install -e .
"${PYBIN}/python" setup.py build_ext --inplace --force
# Test
"${PYBIN}/python" setup.py test
# Wheels
"${PYBIN}/pip" wheel /io/ -w wheelhouse/ --no-deps
rm -rf .eggs
done
# Bundle external shared libraries into the wheels
for whl in /io/wheelhouse/*.whl; do
auditwheel repair "$whl" -w /io/dist/
done
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/build-recipes/linux_dist.sh 0000755 0001751 0001751 00000000663 15133362741 020465 0 ustar 00runner runner #!/bin/bash
# Call this script from the parent directory
# This will produce wheels using docker
set -e
# remove all .pyc files to prevent error:
# - import file mismatch / unique basename
find . | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
docker pull $DOCKER_IMAGE
mkdir -p dist
docker run -e TRAVIS_PYTHON_VERSION --rm -v `pwd`:/io $DOCKER_IMAGE $PRE_CMD /io/.travis/linux_build-wheels.sh
python setup.py sdist
ls -l dist/
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/build-recipes/linux_install.sh 0000755 0001751 0001751 00000001441 15133362741 021163 0 ustar 00runner runner #!/bin/bash
set -e
#deactivate
sudo apt-get update -qq
# Fixes the error:
# - ImportError: No module named _tkinter, please install the python-tk package
sudo apt-get install -qq python3-pip python3-tk virtualenv
# requirements for building wxPython4 on Ubuntu 17.10
# see https://github.com/wxWidgets/Phoenix/blob/master/README.rst
#sudo apt-get install -qq libgtk2.0 libgtk2.0-dev libwebkitgtk-dev dpkg-dev build-essential python3.6-dev libjpeg-dev libtiff-dev libsdl1.2-dev libnotify-dev freeglut3 freeglut3-dev libsm-dev libgtk-3-dev libwebkit2gtk-4.0-dev libxtst-dev libgstreamer-plugins-base1.0-dev
# use separate virtual environment
#virtualenv --system-site-packages -p python ~/env
#source ~/env/bin/activate
#pip install --upgrade pip
#pip install cython matplotlib lmfit numpy scipy sympy
././@PaxHeader 0000000 0000000 0000000 00000000026 00000000000 010213 x ustar 00 22 mtime=1768809953.0
pycorrfit-1.3.1/build-recipes/osx_PyCorrFit.icns 0000644 0001751 0001751 00000341515 15133362741 021400 0 ustar 00runner runner icns Mis32 /Ύ>C׆.1
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