Pull requests and issues closed in the development cycle for emperor between 0.9.0 and 0.9.1.

Emperor 0.9.1

.. _github-stats:
Github stats
============

GitHub stats for 2013/05/14 - 2013/10/21 (tag: 0.9.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 4 authors contributed 220 commits.

* Antonio Gonzalez
* Jackson Chen
* Meg Pirrung
* Yoshiki Vázquez Baeza


We closed a total of 142 issues, 45 pull requests and 97 regular issues;
this is the full list (generated with the script 
:file:`github_stats.py from the matplotlib repository`):

Pull Requests (45):

* :ghpull:`200`: Release 0.9.1
* :ghpull:`198`: Documentation Additions
* :ghpull:`197`: [important] Change license of Emperor to BSD
* :ghpull:`196`: Enhancements to separator bar
* :ghpull:`182`: Fixes #155, #171, and #166
* :ghpull:`195`: Update the links for the examples
* :ghpull:`186`: Fixes #165 by displaying an info box if WebGL is not detected
* :ghpull:`190`: Adds data about the emperor installation to every visualization
* :ghpull:`188`: Fixes #185 by changing the Chrome link from Spanish to English
* :ghpull:`179`: Solves Issue 149
* :ghpull:`175`: Solves Issue 157 and Issue 42
* :ghpull:`174`: Add logos for the project
* :ghpull:`163`: Add color selector to biplot labels
* :ghpull:`152`: Changes for comparison plots
* :ghpull:`146`: Screenshot
* :ghpull:`142`: Update setup.py script
* :ghpull:`138`: Arrows to change the metadata in colors
* :ghpull:`116`: Add documentation in HTML format
* :ghpull:`139`: Add controllers to change the labels and line color
* :ghpull:`137`: Changing default color scheme to discrete
* :ghpull:`135`: Remove script usage examples
* :ghpull:`130`: Fixed view menu conflicts
* :ghpull:`127`: Fixes problem with parallel plots
* :ghpull:`126`: Change URLs to point to emperor.colorado.edu
* :ghpull:`123`: Add ability draw plot comparisons
* :ghpull:`125`: This should address issues 48 and 120
* :ghpull:`124`: Checking in Parallel Plots functionality
* :ghpull:`118`: Fixing issue 117
* :ghpull:`114`: This solves #102 and solves #2
* :ghpull:`111`: Add a new tab for scaling per category 
* :ghpull:`110`: Add opacity per category in visibility tab
* :ghpull:`108`: Fixes bug with transparency 
* :ghpull:`104`: Fixes Issue 84
* :ghpull:`100`: Add new identifying way for elements
* :ghpull:`101`: Add file with centralized licenses
* :ghpull:`98`: Order is preserved when concatenating headers
* :ghpull:`97`: Add option to sort categories alphabetically
* :ghpull:`86`: Code review
* :ghpull:`92`: Add remove_empty_rows to parse_otu_table
* :ghpull:`90`: Add verbose output for missing_samples
* :ghpull:`83`: 0.9.0-dev changes 
* :ghpull:`82`: 0.9.0 version change
* :ghpull:`81`: Fixes repeated link in README.md
* :ghpull:`79`: Add usage examples and description to README.md
* :ghpull:`76`: Issue 6  -- add_vectors functionality

Issues (97):

* :ghissue:`191`: --vectors_algorithm=VECTORS_ALGORITHM is missing
* :ghissue:`200`: Release 0.9.1
* :ghissue:`187`: How to save images? (add to tutorial)
* :ghissue:`198`: Documentation Additions
* :ghissue:`197`: [important] Change license of Emperor to BSD
* :ghissue:`25`: Default view-point should be PC1 vs PC2
* :ghissue:`196`: Enhancements to separator bar
* :ghissue:`182`: Fixes #155, #171, and #166
* :ghissue:`155`: Flip axes directions
* :ghissue:`166`: Install Documentation Error
* :ghissue:`171`: changing axes does not change labels
* :ghissue:`195`: Update the links for the examples
* :ghissue:`194`: keep only one selection menu for metadata?
* :ghissue:`186`: Fixes #165 by displaying an info box if WebGL is not detected
* :ghissue:`165`: Add check for WebGL 
* :ghissue:`190`: Adds data about the emperor installation to every visualization
* :ghissue:`148`: Add extra info to every emperor visualization file
* :ghissue:`188`: Fixes #185 by changing the Chrome link from Spanish to English
* :ghissue:`185`: The link to Google Chrome in the front page links to spanish version
* :ghissue:`149`: remove enter from the filter by key
* :ghissue:`179`: Solves Issue 149
* :ghissue:`42`: Fullscreen mode
* :ghissue:`157`: adjust the size of the figure area or right panel with mouse
* :ghissue:`175`: Solves Issue 157 and Issue 42
* :ghissue:`174`: Add logos for the project
* :ghissue:`163`: Add color selector to biplot labels
* :ghissue:`162`: can't display biplot taxa label in anything but white
* :ghissue:`143`: Add procrustes vector coloring selector
* :ghissue:`152`: Changes for comparison plots
* :ghissue:`121`: Scaling by percents explained with vectors is not working properly
* :ghissue:`144`: Add option to set a reference coordinate matrix
* :ghissue:`151`: Axes don't display right
* :ghissue:`22`: Generate publication quality legends for the plot being displayed.
* :ghissue:`156`: Allow user to specify svg export file name
* :ghissue:`154`: Screenshot command change from just P to ctrl key+p
* :ghissue:`35`: Make save as svg work
* :ghissue:`146`: Screenshot
* :ghissue:`142`: Update setup.py script
* :ghissue:`138`: Arrows to change the metadata in colors
* :ghissue:`131`: keyboard scrolling through metadata
* :ghissue:`116`: Add documentation in HTML format
* :ghissue:`107`: Setup user documentation
* :ghissue:`134`: axes' color change 
* :ghissue:`139`: Add controllers to change the labels and line color
* :ghissue:`136`: make "use discrete colors" the default
* :ghissue:`137`: Changing default color scheme to discrete
* :ghissue:`115`: New "view" tab
* :ghissue:`129`: Delete examples from repository
* :ghissue:`135`: Remove script usage examples
* :ghissue:`130`: Fixed view menu conflicts
* :ghissue:`122`: View menu
* :ghissue:`106`: Parallel Plots 
* :ghissue:`127`: Fixes problem with parallel plots
* :ghissue:`126`: Change URLs to point to emperor.colorado.edu
* :ghissue:`96`: Examples are not rendered correctly
* :ghissue:`103`: Add ability to plot procrustes analysis plots
* :ghissue:`123`: Add ability draw plot comparisons
* :ghissue:`125`: This should address issues 48 and 120
* :ghissue:`48`: We should be able to select different values for different groups in -x
* :ghissue:`120`: Axes tab doesn't mention custom axes
* :ghissue:`124`: Checking in Parallel Plots functionality
* :ghissue:`31`: Using emperor in Chrome will randomly crash your computer
* :ghissue:`118`: Fixing issue 117
* :ghissue:`117`: vectors and jackknifed plots  are broken 
* :ghissue:`2`: % explained hidden in y axis
* :ghissue:`102`: Add option to visualize other coordinate axes.
* :ghissue:`114`: This solves #102 and solves #2
* :ghissue:`105`: Sphere scaling by category 
* :ghissue:`111`: Add a new tab for scaling per category 
* :ghissue:`19`: Transparency on a per sample basis
* :ghissue:`110`: Add opacity per category in visibility tab
* :ghissue:`109`: jackknifed is broken.
* :ghissue:`108`: Fixes bug with transparency 
* :ghissue:`84`: Update THREE.js
* :ghissue:`104`: Fixes Issue 84
* :ghissue:`78`: make_3d_plots.py with continuous coloring and scientific notation (imported from qiime)
* :ghissue:`100`: Add new identifying way for elements
* :ghissue:`15`: Error in coloring due to non alphanumeric characters
* :ghissue:`99`: HTML IDs and special characters
* :ghissue:`101`: Add file with centralized licenses
* :ghissue:`85`: Create a file with proper license attributions
* :ghissue:`98`: Order is preserved when concatenating headers
* :ghissue:`93`: Changing order of fields in option -b is not reflected in the resulting combination
* :ghissue:`97`: Add option to sort categories alphabetically
* :ghissue:`91`: The metadata select box should be ordered alphabetically 
* :ghissue:`86`: Code review
* :ghissue:`92`: Add remove_empty_rows to parse_otu_table
* :ghissue:`73`: Empty rows in OTU table for biplots will produce warning
* :ghissue:`90`: Add verbose output for missing_samples
* :ghissue:`89`: if -v is used and there are discrepancies between the pcoa and the map file you should get a list of the missing samples
* :ghissue:`80`: all examples should be updated to the latest GUI
* :ghissue:`83`: 0.9.0-dev changes 
* :ghissue:`82`: 0.9.0 version change
* :ghissue:`81`: Fixes repeated link in README.md
* :ghissue:`8`: add:   --add_vectors=ADD_VECTORS
* :ghissue:`79`: Add usage examples and description to README.md
* :ghissue:`76`: Issue 6  -- add_vectors functionality