-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Matt Olm
committed
Sep 21, 2017
1 parent
7494811
commit 3743be7
Showing
1 changed file
with
174 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,174 @@ | ||
| # Change Log | ||
| All notable changes to this project will be documented in this file. | ||
|
|
||
| The format is based on [Keep a Changelog](http://keepachangelog.com/) | ||
| and this project (attempts to) adhere to [Semantic Versioning](http://semver.org/). | ||
|
|
||
| ## [1.2.0] - 2017-19-11 | ||
| ### fixed | ||
| - Scoring with regards to strain heterogeneity modified | ||
|
|
||
| ## [1.1.3] - 2017-09-11 | ||
| ### fixed | ||
| - N50 calculation is now correct | ||
|
|
||
| ## [1.1.2] - 2017-08-25 | ||
| ### Changed | ||
| - fixed proper pip sklean-learn (thanks Ben Woodcroft) | ||
| - added the blank folder test_backend/ so that the test suite will work | ||
|
|
||
| ## [1.1.1] - 2017-07-26 | ||
| ### Changed | ||
| - added links to ISME publication in readme and documentation | ||
|
|
||
| ## [1.1.0] - 2017-07-20 | ||
| ### Added | ||
| - genome input for bonus | ||
| - option to to the 'percent' method for determining taxonomy | ||
| - testing for taxonomy | ||
| - Tdb now includes the columns "best_hit" and "full_tax" (for both methods of determining taxonomy) | ||
|
|
||
| ## [1.0.0] - 2017-07-14 | ||
| ### Added | ||
| - bonus --check_dependencies now exists | ||
| - gANI now gives a message when it fails | ||
|
|
||
| ### Fixed | ||
| - pytest is now automatically installed with pip | ||
| - the logger now does ' '.join(args) when printing the args to run dRep | ||
| - documentation now correctly says "ANIcalculator" | ||
| - makes sure ANIcalculator and checkM work when loading them (even if you can find them in the system path) | ||
|
|
||
| ## [0.5.7] - 2017-04-26 | ||
| ### Fixed | ||
| - having the user add their own Chdb now works | ||
| - in bonus, changed an erroneous > to >= when calling centrifuge | ||
| - changed the way the test_suite compares dataframes | ||
|
|
||
| ## [0.5.6] - 2017-04-23 | ||
| ### Fixed | ||
| - nc option now works with gANI (controller makes it a float) | ||
| - test_backend is now a thing automatically | ||
|
|
||
| ## [0.5.5] - 2017-04-09 | ||
| ### Fixed | ||
| - coverage values at the threshold are now accepted (< instead of <=) | ||
| - setup now automatically installs scikit-bio (needed for MDS plot) | ||
|
|
||
| ### Changed | ||
| - the loop in which genome lengths are calculated in d_cluster is changed to | ||
| prevent errors when running large numbers of genomes | ||
|
|
||
| ## [0.5.4] - 2017-03-28 | ||
| ### Changed | ||
| - default coverage method is now larger (tests are updated to reflect this) | ||
|
|
||
| ### Fixed | ||
| - gANI now properly computes the coverage using the "larger" method | ||
| - gANI can now tell when it's not installed | ||
|
|
||
| ## [0.5.3] - 2017-03-28 | ||
| ### Changed | ||
| - documentation about dependencies changed; versions added as well | ||
| - changed the way ani averaging is done; substantial speed increase when working with very large secondary clusters | ||
| - added the dRep version to the log file | ||
|
|
||
| ## [0.5.2] - 2017-03-24 | ||
| ### Fixed | ||
| - prodigal now properly threads for gANI | ||
|
|
||
| ## [0.5.1] - 2017-03-17 | ||
| ### Fixed | ||
| - Plot 3 (MDS) now prints onto a square grid | ||
| - Testing suite now launches all tests automatically | ||
|
|
||
| ## [0.5.0] - 2017-03-16 | ||
| ### Added | ||
| - The final analyze plot can now be made! | ||
|
|
||
| ### Fixed | ||
| - pyenv message | ||
| - log typos | ||
|
|
||
| ## [0.4.0] - 2017-03-10 | ||
| ### Fixed | ||
| - prodigal now multithreads the correct amount | ||
| - compare_wf double-printing issue | ||
| - --SkipMash now works | ||
|
|
||
| ### Changed | ||
| - default checkM method is now lineage_wf in dereplicate_wf, filter, and choose | ||
| - pyenv now reverences non-anaconda in the documentation and error messages | ||
| - default min length in now 50,000 | ||
|
|
||
| ### Added | ||
| - more thorough testing (though still not nearly enough) | ||
| - log now contains the exact command run | ||
|
|
||
| ## [0.3.8] - 2017-03-06 | ||
| ### Fixed | ||
| - Mash sketch size argument actually works now | ||
|
|
||
| ## [0.3.7] | ||
| ### Fixed | ||
| - Fixed analyze to produce non-ugly plots | ||
|
|
||
| ## [0.3.6] | ||
| ### Added | ||
| - Can now change the method of calculating coverage with ANIn | ||
| - Added TODO | ||
|
|
||
| ## [0.3.5] | ||
| ### Fixed | ||
| - Bug that caused the program to crash when looking for Mash | ||
| - Lots of typos (in documentation and program help) | ||
|
|
||
| ## [0.3.4] | ||
| ### Changed | ||
| - Fixed some typos in documentation | ||
| - Added bioRxiv link in documentation | ||
|
|
||
| ### Fixed | ||
| - Edited matplotlib to make text that can be edited by illustrator | ||
|
|
||
| ## [0.3.3] | ||
| ### Fixed | ||
| - Small bug in telling the user when checkM/prodigal is not in system path | ||
| - Small bug preventing SkipSecondary from working | ||
|
|
||
| ### Added | ||
| - Test for SkipSecondary | ||
|
|
||
| ## [0.3.2] | ||
| ### Fixed | ||
| - Time estimates now take into account threading | ||
| - Fixed the "choose" operation erroneously taking the "adjust" arguments as well | ||
| - Removed the 'mauve' option as a secondary algorithm | ||
| - Fixed a lot of erroneous logging | ||
|
|
||
| ### Changed | ||
| - Removed a bunch of commented-out methods | ||
|
|
||
| ## [0.3.1] | ||
| ### Changed | ||
| - READme updated | ||
|
|
||
| ### Added | ||
| - Documentation | ||
|
|
||
| ### Fixed | ||
| - A bug where '-h' wasn't working properly | ||
| - Some messages in cluster that should be going to log | ||
|
|
||
| ## [0.3.0] - 2017-01-30 | ||
| ### Added | ||
| - Basic functional testing | ||
| - This here Changelog | ||
| - Probably a lot of other stuff that I don't remember (due to the previous lack of Changelog) | ||
|
|
||
| ### Changed | ||
| - Moved the argument parsing to a "controller" class | ||
| - The backend of the way the log runs. It's better now | ||
|
|
||
| ## [0.1.0] - 2017-01-15 | ||
| - This is the name of the release generated before implementation of a changelog. The development version number for this release was 0.2.3 |