Skip to main content

Browse the archive

https://github.com/dereneaton/ipyrad
22 March 2024, 03:55:05 UTC
sort by:
Revision Author Date Message Commit Date
f3f1a9a Isaac Overcast 04 March 2020, 15:53:19 UTC "Updating ipyrad/__init__.py to version - 0.9.44 04 March 2020, 15:53:19 UTC
58511a4 Isaac Overcast 04 March 2020, 15:52:55 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 04 March 2020, 15:52:55 UTC
4c3759f Isaac Overcast 04 March 2020, 15:52:49 UTC Fix the treemix output so it actually generates. Took WAYYYY longer than I thought it would. 04 March 2020, 15:52:49 UTC
f9136b5 Isaac Overcast 04 March 2020, 14:42:39 UTC Update faq.rst 04 March 2020, 14:42:39 UTC
a0c48a6 Isaac Overcast 04 March 2020, 14:40:22 UTC Update faq.rst 04 March 2020, 14:40:22 UTC
28c7760 Isaac Overcast 26 February 2020, 16:57:06 UTC "Updating ipyrad/__init__.py to version - 0.9.43 26 February 2020, 16:57:06 UTC
11e34c3 Isaac Overcast 26 February 2020, 16:35:19 UTC Fix off by 2 error in minsamp when using reference sequence 26 February 2020, 16:35:19 UTC
958b5d7 dereneaton 20 February 2020, 22:24:20 UTC window extacter working for denovo loci 20 February 2020, 22:24:20 UTC
7dd08eb Isaac Overcast 20 February 2020, 13:17:53 UTC cosmetic 20 February 2020, 13:17:53 UTC
5743bcd Isaac Overcast 20 February 2020, 13:06:24 UTC cosmetic 20 February 2020, 13:06:24 UTC
94790ca Isaac Overcast 20 February 2020, 11:04:15 UTC Cleaning up a TON of sphinx warnings from the docs and fixing a bunch of docs issues. 20 February 2020, 11:04:15 UTC
1652dfd Isaac Overcast 20 February 2020, 08:27:57 UTC fix oops in baba.py (import sys) 20 February 2020, 08:27:57 UTC
776916e Isaac Overcast 19 February 2020, 20:49:04 UTC "Updating ipyrad/__init__.py to version - 0.9.42 19 February 2020, 20:49:04 UTC
824e4f4 Isaac Overcast 19 February 2020, 20:23:14 UTC cosmetic 19 February 2020, 20:23:14 UTC
f17ce32 Isaac Overcast 19 February 2020, 19:57:08 UTC cosmetic 19 February 2020, 19:57:08 UTC
4118a7e Isaac Overcast 19 February 2020, 19:55:51 UTC Fix oops in step 6 which was leaving bad sample names hanging after alignment. 19 February 2020, 19:55:51 UTC
79d097f Isaac Overcast 18 February 2020, 22:15:35 UTC "Updating ipyrad/__init__.py to version - 0.9.41 18 February 2020, 22:15:35 UTC
6450927 Isaac Overcast 18 February 2020, 22:14:46 UTC Set s6.data.ncpus value when routing around hierarchical clustering for ref based assemblies. 18 February 2020, 22:14:46 UTC
3d263f6 dereneaton 18 February 2020, 16:06:00 UTC disable hierarchical clustering until further testing 18 February 2020, 16:06:00 UTC
cf2d064 dereneaton 18 February 2020, 15:55:42 UTC split samples evenly among cgroups for hierarch clust 18 February 2020, 15:55:42 UTC
decd0e3 dereneaton 17 February 2020, 19:40:43 UTC digest genomes uses qual score B instead of b 17 February 2020, 19:40:43 UTC
9d72986 Isaac Overcast 16 February 2020, 06:33:54 UTC "Updating ipyrad/__init__.py to version - 0.9.40 16 February 2020, 06:33:54 UTC
216e4ee Isaac Overcast 16 February 2020, 06:33:25 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 February 2020, 06:33:25 UTC
44cfa92 Isaac Overcast 16 February 2020, 06:33:14 UTC cosmetic 16 February 2020, 06:33:14 UTC
3e44567 dereneaton 16 February 2020, 00:55:27 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 February 2020, 00:55:27 UTC
00e3120 dereneaton 16 February 2020, 00:55:21 UTC cosmetic 16 February 2020, 00:55:21 UTC
99618b3 dereneaton 16 February 2020, 00:55:08 UTC cosmetic 16 February 2020, 00:55:08 UTC
b655034 dereneaton 15 February 2020, 23:20:25 UTC subsample loci func added 15 February 2020, 23:20:25 UTC
1449f8d dereneaton 15 February 2020, 23:19:17 UTC counts rm duplicates in denovo and works with step6 skipping alignment of loci w/ dups 15 February 2020, 23:19:17 UTC
a122119 dereneaton 15 February 2020, 23:18:34 UTC denovo paired aligned separately again 15 February 2020, 23:18:34 UTC
0018eb1 dereneaton 15 February 2020, 23:17:54 UTC cosmetic 15 February 2020, 23:17:54 UTC
06fdcb1 dereneaton 15 February 2020, 23:17:40 UTC fastq qmax error in merge denovo fixed 15 February 2020, 23:17:40 UTC
19bf530 Isaac Overcast 15 February 2020, 20:20:47 UTC "Updating ipyrad/__init__.py to version - 0.9.39 15 February 2020, 20:20:47 UTC
f419b14 Isaac Overcast 15 February 2020, 20:19:33 UTC Why can't i figure out how to comment out this plotting code right? wtf! 15 February 2020, 20:19:33 UTC
5d8c9ac Isaac Overcast 15 February 2020, 19:45:29 UTC "Updating ipyrad/__init__.py to version - 0.9.38 15 February 2020, 19:45:29 UTC
200058c Isaac Overcast 15 February 2020, 19:45:07 UTC commented out the import of the baba_plot plotting function and the baba.plot() method as these are broken rn, and also the plotting/baba_plotting routine tries to access toyplot in a way that breaks the conda build since toyplot isn't a strict requirement. We could fix this in the future, but i'm tring to get the bioconda package to build successfully rn. 15 February 2020, 19:45:07 UTC
1e80b19 Isaac Overcast 15 February 2020, 18:23:17 UTC "Updating ipyrad/__init__.py to version - 0.9.37 15 February 2020, 18:23:17 UTC
bffa40a Isaac Overcast 15 February 2020, 18:23:00 UTC fix import checking for baba_panel_plot.py 15 February 2020, 18:23:00 UTC
280f072 Isaac Overcast 15 February 2020, 18:06:07 UTC "Updating ipyrad/__init__.py to version - 0.9.36 15 February 2020, 18:06:07 UTC
1c18864 Isaac Overcast 15 February 2020, 18:05:39 UTC Handle external imports in the baba module in the same way as the other analysis tools to fix the broken bioconda build. 15 February 2020, 18:05:39 UTC
61f4ef5 Isaac Overcast 13 February 2020, 08:33:09 UTC Add a pops file to the ipsimdata.tar.gz because it's always useful. 13 February 2020, 08:33:09 UTC
538f909 Isaac Overcast 12 February 2020, 21:44:24 UTC "Updating ipyrad/__init__.py to version - 0.9.35 12 February 2020, 21:44:24 UTC
3bfc5e3 Isaac Overcast 12 February 2020, 21:44:09 UTC "Updating ipyrad/__init__.py to version - 0.9.35 12 February 2020, 21:44:09 UTC
3d80bb9 Isaac Overcast 12 February 2020, 17:21:35 UTC Fix a bug in step 5 handling of RemoteError during indexing alleles. 12 February 2020, 17:21:35 UTC
25f1cfc Isaac Overcast 11 February 2020, 13:19:54 UTC cosmetic 11 February 2020, 13:19:54 UTC
4ca03d3 Isaac Overcast 09 February 2020, 19:54:30 UTC Report debug traceback for all crashes, not just API. This is essentially making the debug flag useless in v.0.9 09 February 2020, 19:54:30 UTC
03a1d26 Isaac Overcast 09 February 2020, 19:00:11 UTC "Updating ipyrad/__init__.py to version - 0.9.34 09 February 2020, 19:00:11 UTC
8cfc6be Isaac Overcast 09 February 2020, 18:58:38 UTC Roll back baba code to 0.7 version which doesn't use the current analysis format, but which still works. Saved ongoing baba code as baba.v0.9.py 09 February 2020, 18:58:38 UTC
f6fdb55 Isaac Overcast 06 February 2020, 17:50:08 UTC "Updating ipyrad/__init__.py to version - 0.9.33 06 February 2020, 17:50:08 UTC
fe531be Isaac Overcast 06 February 2020, 17:49:49 UTC Fix major oops in consens_se which failed step 5 every time. Bad! 06 February 2020, 17:49:49 UTC
ec03ba7 Isaac Overcast 06 February 2020, 10:11:32 UTC In step 6 use the sample.files.consens info, rather than data.dirs to allow for merging assemblies after step 5 where data.dirs is invalid/empty. 06 February 2020, 10:11:32 UTC
822ae39 Isaac Overcast 06 February 2020, 09:03:57 UTC cosmetic 06 February 2020, 09:03:57 UTC
08bfde8 Isaac Overcast 04 February 2020, 08:37:54 UTC "Updating ipyrad/__init__.py to version - 0.9.32 04 February 2020, 08:37:54 UTC
8148218 Isaac Overcast 03 February 2020, 09:09:40 UTC cosmetic 03 February 2020, 09:09:40 UTC
a53379c Isaac Overcast 03 February 2020, 08:56:30 UTC #392 allow scaffold names to be int 03 February 2020, 08:56:30 UTC
df4603d Isaac Overcast 02 February 2020, 20:56:06 UTC Add sensible error handling if only a few samples fail step 5. 02 February 2020, 20:56:06 UTC
1a30855 Isaac Overcast 02 February 2020, 18:20:42 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 02 February 2020, 18:20:42 UTC
1fed7ea Isaac Overcast 02 February 2020, 18:20:40 UTC add docs to clustmap_across 02 February 2020, 18:20:40 UTC
fd59b96 dereneaton 30 January 2020, 19:19:23 UTC fix for name re-ordering in window-extracter with multiple regions selected 30 January 2020, 19:19:23 UTC
3d7aba2 eaton-lab 30 January 2020, 17:54:31 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 30 January 2020, 17:54:31 UTC
5e78018 eaton-lab 30 January 2020, 17:54:28 UTC added comments 30 January 2020, 17:54:28 UTC
be415a5 eaton-lab 30 January 2020, 17:54:15 UTC added comments 30 January 2020, 17:54:15 UTC
4dcdf82 eaton-lab 30 January 2020, 17:53:58 UTC cosmetic 30 January 2020, 17:53:58 UTC
05b4879 eaton-lab 30 January 2020, 17:53:38 UTC added sys 30 January 2020, 17:53:38 UTC
1031c9b Isaac Overcast 30 January 2020, 17:10:51 UTC Actually handle failed samples in step 2. 30 January 2020, 17:10:51 UTC
e531fb1 eaton-lab 28 January 2020, 18:39:19 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 28 January 2020, 18:39:19 UTC
d234e73 eaton-lab 28 January 2020, 18:38:13 UTC fix for new h5py warning 28 January 2020, 18:38:13 UTC
2204fb2 eaton-lab 28 January 2020, 18:37:59 UTC fix for new sklearn warning 28 January 2020, 18:37:59 UTC
a81456c Isaac Overcast 19 January 2020, 23:34:34 UTC "Updating ipyrad/__init__.py to version - 0.9.31 19 January 2020, 23:34:34 UTC
e70b70d isaacovercast 19 January 2020, 23:32:50 UTC Fix error in bucky (progressbar hell). 19 January 2020, 23:32:50 UTC
f6a3ed3 isaacovercast 18 January 2020, 18:09:09 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 18 January 2020, 18:09:09 UTC
c1a983e isaacovercast 18 January 2020, 18:09:05 UTC Add error handling in a couple cases if run() hasn't been called, e.g. before draw, and also add the pcs() function as a convenience. 18 January 2020, 18:09:05 UTC
7b38aff Isaac Overcast 17 January 2020, 12:44:21 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 17 January 2020, 12:44:21 UTC
041050d Isaac Overcast 17 January 2020, 12:44:12 UTC Removed support for legacy argument format from bpp.py and updated the docs. 17 January 2020, 12:44:12 UTC
82aea63 isaacovercast 16 January 2020, 18:52:17 UTC Allow PCA() to import data as vcf. 16 January 2020, 18:52:17 UTC
b657e5f Isaac Overcast 16 January 2020, 16:56:35 UTC Add support for importing VCF into PCA 16 January 2020, 16:56:35 UTC
9b70b09 Isaac Overcast 16 January 2020, 15:31:28 UTC "Updating ipyrad/__init__.py to version - 0.9.30 16 January 2020, 15:31:28 UTC
5f6ba00 Isaac Overcast 16 January 2020, 15:30:48 UTC Fix whoops with bucky progressbars 16 January 2020, 15:30:48 UTC
ad5d1f6 Isaac Overcast 15 January 2020, 09:33:31 UTC "Updating ipyrad/__init__.py to version - 0.9.29 15 January 2020, 09:33:31 UTC
6f062ef Isaac Overcast 15 January 2020, 09:33:11 UTC Fix bucky progressbar calls. 15 January 2020, 09:33:11 UTC
59e9ca5 Isaac Overcast 15 January 2020, 09:07:04 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 15 January 2020, 09:07:04 UTC
26efacc Isaac Overcast 15 January 2020, 09:06:58 UTC Fixed progressbar calls in bucky.py 15 January 2020, 09:06:58 UTC
e0198c7 Isaac Overcast 14 January 2020, 12:49:14 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 14 January 2020, 12:49:14 UTC
eef08f7 Isaac Overcast 14 January 2020, 12:49:06 UTC Conda install instructions were wrong. 14 January 2020, 12:49:06 UTC
a1153c0 Isaac Overcast 14 January 2020, 10:34:24 UTC cosmetic 14 January 2020, 10:34:24 UTC
8089b77 Isaac Overcast 13 January 2020, 08:43:44 UTC add future print import to fasttree.py 13 January 2020, 08:43:44 UTC
1d4749d Isaac Overcast 12 January 2020, 18:48:53 UTC Add releasenotes to the TOC 12 January 2020, 18:48:53 UTC
853b798 Isaac Overcast 12 January 2020, 18:46:45 UTC cosmetic 12 January 2020, 18:46:45 UTC
8fcf950 Isaac Overcast 12 January 2020, 18:42:30 UTC "Updating ipyrad/__init__.py to version - 0.9.28 12 January 2020, 18:42:30 UTC
af9db3a Isaac Overcast 12 January 2020, 18:42:08 UTC Fix versioner.py to actually record releasenotes 12 January 2020, 18:42:08 UTC
d89fb35 Isaac Overcast 12 January 2020, 18:40:03 UTC Fix releasenotes in versioner script 12 January 2020, 18:40:03 UTC
ca251da Isaac Overcast 12 January 2020, 18:30:40 UTC Fix releasenotes 12 January 2020, 18:30:40 UTC
ea9bc83 Isaac Overcast 12 January 2020, 18:27:38 UTC "Updating ipyrad/__init__.py to version - 0.9.27 12 January 2020, 18:27:38 UTC
ac038da Isaac Overcast 12 January 2020, 18:13:46 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 12 January 2020, 18:13:46 UTC
904421d Isaac Overcast 12 January 2020, 18:13:37 UTC Add all the old commit info that has been blanked since the switch to v.0.9 12 January 2020, 18:13:37 UTC
bb2deb9 Isaac Overcast 11 January 2020, 16:45:18 UTC Update index.rst 11 January 2020, 16:45:18 UTC
843d501 Isaac Overcast 11 January 2020, 16:44:03 UTC Update README.rst 11 January 2020, 16:44:03 UTC
6865d60 Isaac Overcast 11 January 2020, 16:43:03 UTC Update README.rst 11 January 2020, 16:43:03 UTC
49753b5 Isaac Overcast 09 January 2020, 15:38:23 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 09 January 2020, 15:38:23 UTC
4d2d65a Isaac Overcast 09 January 2020, 15:37:56 UTC Tweek install directions to support new no change /home/isaac/miniconda3/condabin/conda no change /home/isaac/miniconda3/bin/conda no change /home/isaac/miniconda3/bin/conda-env no change /home/isaac/miniconda3/bin/activate no change /home/isaac/miniconda3/bin/deactivate no change /home/isaac/miniconda3/etc/profile.d/conda.sh no change /home/isaac/miniconda3/etc/fish/conf.d/conda.fish no change /home/isaac/miniconda3/shell/condabin/Conda.psm1 no change /home/isaac/miniconda3/shell/condabin/conda-hook.ps1 no change /home/isaac/miniconda3/lib/python3.7/site-packages/xontrib/conda.xsh no change /home/isaac/miniconda3/etc/profile.d/conda.csh no change /home/isaac/.bashrc No action taken. process 09 January 2020, 15:37:56 UTC
back to top