CHANGELOG

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