CHANGELOG

THIS CHANGELOG FILE CONTANS PRE-SVN CHANGELOGS AND SUMMARIES OF POST-SVN CHANGELOGS.
FROM 0.8.4 ONWARD, DETAILED CHANGELOGS ARE AVAILABLE ON THE HOOKE SUBVERSION REPOSITORY.

0.8.4
(2008-x-x)
    PLUGINS:
    macro.py:
        hooke does not crash if it doesn't have permissions to create the folder
	fixed overwriting of export for curves with the same name and different numerical extension
	fixed macrodir (out of try-catch)
	cleaned debug output in execmacro
    DRIVERS:
	alternative version of picoforce driver
    INPUT
	merged (partially) libinput (so far in hooke_cli)
    OUTLET	
	merged liboutlet


0.8.3
(2008-04-16)
    PLUGINS:
    generalvclamp.py:
        fixed autopeak header 
        fixed autopeak slope (now unwanted slope values are discarded)

0.8.2
(2008-04-10)
    PLUGINS:
    flatfilts.py:
        convfilt does not crash if a file is not a curve
    generalvclamp.py:
        autopeak now saves curve data correctly
        autopeak now generates a dummy note (so that copylog/notelog is aware you measured the curve)

0.8.1
(2008-04-07)
    PLUGINS:
    generalvclamp.py:
        fixed DeprecationWarning in flatten
    flatfilts.py
        convfilt now working
        

0.8.0:
(2008-04-04)
    hooke.py:
        sanity check of CLI plugins to avoid function overloading at startup
    hooke_cli.py ; libhooke.py:
        now playlists keep the index (when you reload the playlist, it starts from the
            last observed curve)
        updated plot to use _send_plot()
        hooke.conf accepts lists as arguments for variables in <display>
        txt, export now have consistent argument order (thanks to A.G.Casado for pointing me that)
        txt crashes no more if no filename is given (thanks to A.G.Casado for pointing me that)
    libhookecurve.py:
        added add_set() , remove_set() methods to make life easier for plugin writers
    procplots.py:
        plotmanip_correct() works with new picoforce.py deflection output (see)
    PLUGINS:
    fit.py:
        updated wlc to use _send_plot()
        wlc noauto now keeps the contact point
        wlc reclick to click again the contact point
        temperature now set in hooke.conf
    generalvclamp.py:
        implemented slope (thanks to Marco Brucale)
        implemented autopeak
    flatfilts.py:
        convfilt,peaks use flattened curve
    macro.py:
        (new) added macro plugin (thanks to Alberto Gomez Casado)
    DRIVERS:
    picoforce.py:
        fixed trigger bug! (thanks to Alberto Gomez Casado)
        better deflection output (separated extension,retraction)

0.7.5:
(2008-03-27)
    hooke_cli.py:
        removed outdated size command
    PLUGINS:
    generalvclamp.py:
        implemented flatten
    DRIVERS:
    added tutorialdriver.py driver
    csvdriver.py:
        fixed (forgot close_all() method)

0.7.4:
(2008-03-19)
    added csvdriver driver
    hooke_cli.py:
        fixed plot manipulators handling (now it's safe to comment a
              plot manipulator on hooke.conf)
    PLUGINS:
    fit.py:
        fixed possible crash when clicking two times the same point on wlc

0.7.3:
(2008-01-10)
    hooke_cli.py:
        fixed crash on copylog
    PLUGINS:
        massanalysis.py:
            Initial release
        tutorial.py:
            Tutorial plugin, initial release

0.7.2.1:
(2007-11-30)
    PLUGINS:
        flatfilt.py:
            fixed crash on Windows

0.7.2:
(2007-11-29)
    hooke.py:
        new configuration variable hookedir
    hooke_cli.py:
        copylog now checks if the destination is a real directory
        fixed crashes in set
    PLUGINS:
        generalvclamp.py:
            fixed a crash in forcebase when picking two times the same point
        flatfilt.py:
            fixed crash due to convfilt.conf impossible to load
            initial implementation of the blind window for convfilt
            initial data set maps (NOT FINISHED)

0.7.1:
(2007-11-26)
    PLUGINS:
        flatfilts.py:
            fixed possible crash in convfilt
            implemented configuration file convfilt.conf
            convfilt defaults are now 5 peaks 5 times more the noise absdev
            implemented convconf
            implemented setconf
        libpeakspot.py:
            fixed:now it really uses noise_absdev

0.7.0:
(2007-11-15)
    hooke_cli.py:
        implemented _send_plot() helper API function
    PLUGINS:
        generalvclamp.py:
            fixed forcebase to work with subtplot
        flatfilts.py:
            implemented convfilt!
            added libpeakspot.py (helping library for convolution filter)

0.6.5:
(2007-11-06)
    hooke_cli.py, hooke.py:
        plateau and contact (unmaintained) deleted and scheduled for re-release in generalvramp
        implemented _measure_N_points()
    PLUGINS:
    generalvclamp.py:
        implemented forcebase
    fit.py:
        wlc now accepts and uses temperature as an argument
        wlc has been cleaned and uses new APIs

0.6.4:
(2007-10-23)
    hooke_cli.py, libhooke.py:
        implemented support for defining order of plotmanip methods in hooke.conf
    hooke_cli.py:
        implemented delta
        implemented point
        attempted fix to bug 0033 (notelog crashing Hooke when using Unicode characters)
    PLUGINS:
    generalvramp.py:
        began to move velocity ramp force spectroscopy-specific things in separate plugin
    procplots.py:
        added detriggerize; "set detrigger" 0/1 disables/enables it.
    DRIVERS:
    picoforce.py:
        removed detriggerize() from driver

0.6.3:
(2007-10-02)
    hooke_cli.py:
        rewritten txt command, now working
    DRIVERS:
    picoforce.py:
        implemented detriggerize() to bypass the Picoforce trigger bug
    PLUGINS:
    superimpose.py:
        implemented plotavgimpose

0.6.2:
(2007-09-27)
    hooke_cli.py:
        fixed error handling in notelog
        smarter handling of directory names in genlist
        unexpected error handling in do_plot() 
    hooke.py:
        implemented GetDisplayedPlot event and handlers
    PLUGINS:
    fit.py:
        fixed (bug 0029) about replotting of wlc on a subtplot curve
        multiple fitting displayed (to refine...)

0.6.1:
(2007-08-06)
    libhooke.py , hooke.py:
        initial support for workdir configuration variable
    libhooke.py:
        fixed Driver() etc. semantics for gracefully handling unrecognized plots
    hooke_cli.py:
        fixed export namehandling
        fixed plot error handling
    PLUGINS:
    flatfilts.py:
        fixed memory leak
    generalclamp.py:
        fixed step command

0.6.0 "Anko":
(2007-07-25)
    hooke.py:
        initial plugin support for the gui
        wlc fitting now 100% plugin
        measure_points replaces measure_couple etc. and provides much better extensibility
    hooke_cli.py:
	curves are sorted at beginning
    PLUGINS:
    procplots.py:
        fft now allows for user selection of curve segment; select the plot; etc.
    fit.py:
        added gui section of plugin, now completely independent
        fixed bug of wlc output
    superimpose.py:
        new plugin for superimposition of curve segments (still in development)
    generalclamp.py:
        all clamp commands now in a single plugin
        implemented step

0.5.4:
(2007-06-15)
    procplots.py:
        fixed fft crash with Numpy 1.0.1
    hooke.py:
        fixed crashes if plot.scatter[] was empty
        fixed management of multiple plots (bug #0025)
    hooke_cli.py
        fixed zpiezo error in measurement
    hemingclamp.py, picoforce.py:
        implemented close_all() method in drivers to avoid too many open files error
    flatfilts.py:
        fixed memory leak
0.5.3:
(2007-06-06)
    wlc.py, hooke.py:
        fixing and cleaning fit code: now the fit is part of a PlotObject and 100% coded in wlc.py
        plotting of the wlc.py clicked points also begin to be part of a PlotObject
        management of 'scatter' style property of plots
    hooke_cli.py
        fixed measuring error in defl, zpiezo
    flatfilts.py:
        slightly optimized has_features() routine
    procplots.py:
        fixed derivplot for every number of vectors
        fixed possible crash of subtplot if applied on a file with != 2 plots
        added fft command
    libhookecurve.py:
        fixed xaxis, yaxis for non-default plots: now defined from PlotObject
        PlotObject now defines a styles[] vector
0.5.2:
(2007-05-21)
    versioning a bit cleaned
    fixed bug in hemingclamp.py preventing filename to appear
    fixed wxversion problem for 2.8
    fixed too many open files bug (bug 0024)
    added index command
0.5.1:
(2007-05-09)
    using wxversion to choose from multiple wx versions
    fixed old dependencies remaining
0.5.0 "Ingyo":
(2007-05-03)
    general code updating and rewriting due to plugin support/better plot management
    hooke.py:
        initial plugin architecture for the command line.
        initial plugin architecture for file drivers
        initial plugin architecture for processing plots
        export can now export both top and bottom plot (not together)
    hooke_cli.py:
        wlc fitting moved to fit.py plugin
        flatfilt moved to flatfilts.py plugin
        subtplot, derivplot moved to procplots.py plugin
        double plot temporarily fixed for previous commands
        export can now export both top and bottom plot (not together)

0.4.1:
(2007-02-13)
    hooke_cli.py:
        double plot now default for clamp experiments
    libhooke.py:
        fixed bug that prevented flatfilt to work
        (maybe) fixed memory leak in flatfilt
    
0.4.0 "Hanzei":
(2007-02-08)
    general code updating and rewriting due to double plot/force clamp supports
    hooke.py:
        initial dummy menu sketch
    hooke.py, hooke_cli.py:
        first general support in code for double plot: 
        - derivplot now in separate plot
        - implemented show and close commands
        - all functions should be double plot-aware
        - clicking a point is double plot-aware
    libhooke.py, hooke_cli.py:
        general code cleanup: vectors_to_plot(), subtract_plot(), find_contact_point() and derivplot routines are now methods of class HookeCurve
    hooke_cli.py:
        implemented quit (alias of exit)
        implemented version
    libhooke.py, hooke.py, hooke_cli.py:
        initial support for force clamp experiments:
        - hemingclamp driver supported
        - "experiment" flag describes what kind of experiment is a curve
        - time, zpiezo, defl commands implemented
    libhemingclamp.py:
        inital release.

0.3.1:
    hooke.py:
        fixed stupid bug in plateau
        fixed bug in derivplot and subtplot not taking into account xaxes/yaxes variables
0.3.0:
    from now on, all changelog is stored in CHANGELOG
    hooke.py, libhooke.py, hooke_cli.py:
        fixed plot and flatfilt crash when processing corrupt files
        flatfilt output now more verbose
        implemented system (execute an external OS command)
        implemented copylog (copies annotated curves to a given directory) (todo 0033)
        initial txt implementation (exports the current curve as a text file) (todo 0023)
        fixed exit behaviour (bug 0013)
        xaxes and yaxes variables now control visualization of plot (todo 0018)
        new (better) contact point algorithm + workaround for the picoforce trigger bug
0.2.2 :
    hooke.py, hooke_cli.py, libhooke.py:
        support for fixed persistent length in WLC
0.2.1 :
    hooke.py , libhooke.py:
        fixed 'wlc noauto' bug (0012) preventing correct contact point to be used
0.2.0 : 
    hooke_cli.py:
        implemented getlist (alias of genlist)
        implemented contact (to plot the contact point)
        fixed bug 0001 (Hooke crashes when opening a non-pf file)
        fixed bug 0008  (Hooke crashes when generating a playlist with malformed namefiles/nonexistent files)
        now the plot is refreshed after a "set" command (todo 0014)
        wlc fit can use the (new) automatic contact point detection (old behaviour is preserved with "noauto" option)
    hooke.py:
        fixed versioning printing
        complete refactoring of contact point routines
        wlc fit adapted to use the (new) automatic contact point detection
        wlc fit code a bit cleaned; parts moved to libhooke.py
    libhooke.py:
        new contact point algorithm (new algorithm)
        wlc fit now uses a fancier domain (from contact point to a bit more than last point); initial chunk preparation section moved from hooke.py
    

OLDER CHANGELOGS:

hooke.py:
0.1.1   : 
    From now on, all changelog is stored in hooke.py
    hooke_cli.py:
        corrected bug 0010 (addtolist bug), alerts when hitting start/end of playlist
2006_09_15_devel=0.1.0: initial WLC fit support. We hit 0.1 milestone :D
2006_08_28_devel: refactoring of plot interaction
2006_06_14_devel: fixed libhooke calls
2006_06_08_devel: initial automatic contact point finding
2006_05_30_devel: configuration file support

hooke_cli.py:
0.1.1 : from now on, all changelog is in hooke.py
2006_09_15_devel: implemented wlc; 0.1.0 milestone.
2006_08_28_devel: refactoring of plot interaction
2006_07_23_devel: implemented note; implemented flatfilt; implemented notelog; exit now warns if playlist/notes 
                  have not been saved.
2006_07_18_devel: implemented subtplot; bug 0007 ("cd" crashing) fixed
2006_06_16_devel: moved math helper functions in libhooke.py
2006_06_14_devel: fixed "jump" output; fixed "exit" (now it works!); fixed off-by-one bug in deflection-correction
2006_06_08_devel: fixed "loadlist" output;
2006_05_30_devel: initial configuration file support; added "set" command; initial deflection-correction support; added "ls" command as an alias of "dir"
2006_05_23_devel: rewriting of playlist-handling code due to major rewrite of hooke_playlist.py

libhooke.py
0.1.1   : from now on, all changelog is in hooke.py
2006_09_15_devel : initial WLC support
2006_09_14_devel : initial support for Hemingway velocity clamp files, minor refactorings
2006_07_22_devel : implemented math function has_features
2006_06_16_devel : math functions moved here
2006_06_08_devel : hooke_playlist.py becomes libhooke.py
2006_05_30_devel : support for deflection in HookeCurve
2006_05_29_devel : Initial configuration file support
2006_05_23_devel : Major rewrite. Fixed bug 0002