New upstream version 1.1.1+dfsg (2dfb3b2e) · Commits · Debian Med / pycorrfit

CHANGELOG

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		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

		No newline at end of file

ChangeLog.txt

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MANIFEST.in

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		include ChangeLog.txt
		include CHANGELOG
		include LICENSE
		include README.rst
		recursive-include examples *.txt
		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 .py LICENCE README .pyx
		recursive-include pycorrfit LICENCE README
		prune docs/_build
		exclude docs/_version_save.py

README.rst

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		@@ -3,35 +3,11 @@

		\|PyPI Version\| \|Build Status Win\| \|Build Status Travis\| \|Coverage Status\|

		A graphical fitting tool for fluorescence correlation spectroscopy (FCS) that comes with support for several file formats, can be applied to a large variety of problems, and attempts to be as user-friendly as possible. Some of the features are

		- Averaging of curves
		- Background correction
		- Batch processing
		- Overlay tool to identify outliers
		- Fast simulation of model parameter behavior
		- Session management
		- User-defined model functions
		- High quality plot export using LaTeX (bitmap or vector graphics)


		Getting started
		===============

		Installation
		------------
		Installers for PyCorrFit are available at the `release page <https://github.com/FCS-analysis/PyCorrFit/releases>`__.

		Documentation
		-------------
		A detailed documentation including an explanation of the graphical user interface and available model
		functions is available as a `PDF file <https://github.com/FCS-analysis/PyCorrFit/wiki/PyCorrFit_doc.pdf>`__.
		The documentation of PyCorrFit is available at https://pycorrfit.readthedocs.org.

		Wiki
		----
		If you are interested in a specific topic or wish to contribute with your own HowTo, have a look at the
		`PyCorrFit wiki <https://github.com/FCS-analysis/PyCorrFit/wiki/>`__. There you will also find information
		on `how to write your own model functions <https://github.com/FCS-analysis/PyCorrFit/wiki/Writing-model-functions>`__.

		Problems
		--------
		@@ -39,56 +15,6 @@ If you find a bug or need help with a specific topic, do not hesitate to ask a q
		at the `issues page <https://github.com/FCS-analysis/PyCorrFit/wiki/Creating-a-new-issue>`__.


		Advanced usage
		--------------
		If you have Python installed you can install PyCorrFit, including its scripting functionalities, from the Python package index:

		::

		pip install pycorrfit[GUI]

		More information is available in the `PyCorrFit wiki <https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source>`__.


		Information for developers
		==========================

		Running from source
		-------------------
		The easiest way to run PyCorrFit from source is to use
		`Anaconda <http://continuum.io/downloads>`__. PyCorrFit requires wxPython which is not
		available at the Python package index. Make sure you install a unicode version of wxPython.
		Detailed installation instructions are `here <https://github.com/FCS-analysis/PyCorrFit/wiki/Running-from-source>`__.


		Contributing
		------------
		The main branch for developing PyCorrFit is develop. Small changes that do not
		break anything can be submitted to this branch.
		If you want to do big changes, please (fork ShapeOut and) create a separate branch,
		e.g. ``my_new_feature_dev``, and create a pull-request to develop once you are done making
		your changes.
		Please make sure to also update the
		`changelog <https://github.com/FCS-analysis/PyCorrFit/blob/develop/ChangeLog.txt>`__.

		Tests
		-----
		PyCorrFit is tested using pytest. If you have the time, please write test
		methods for your code and put them in the ``tests`` directory. You may
		run the tests manually by issuing:

		::

		python setup.py test


		Windows test binaries
		---------------------
		After each commit to the PyCorrFit repository, a binary installer is created
		by `Appveyor <https://ci.appveyor.com/project/paulmueller/PyCorrFit>`__. Click
		on a build and navigate to ``ARTIFACTS`` (upper right corner right under
		the running time of the build). From there you can download the Windows installer of the commit.


		.. \|PyCorrFit\| image:: https://raw.github.com/FCS-analysis/PyCorrFit/master/doc/Images/PyCorrFit_logo_dark.png
		.. \|PyPI Version\| image:: http://img.shields.io/pypi/v/PyCorrFit.svg

docs/README.md

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		PyCorrFit documentation
		=======================
		This is the new sphinx-based documentation of PyCorrFit which will replace
		the LaTeX-based documentation eventually.


		To install the requirements for building the documentation, run

		pip install -r requirements.txt

		To compile the documentation, run

		sphinx-build . _build


		Notes
		=====
		To view the sphinx inventory of PyCorrFit, run

		python -m sphinx.ext.intersphinx 'http://pycorrfit.readthedocs.io/en/latest/objects.inv'