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https://github.com/dereneaton/ipyrad
22 May 2024, 15:02:59 UTC
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Revision Author Date Message Commit Date
28143f2 Isaac Overcast 24 March 2020, 16:14:43 UTC "Updating ipyrad/__init__.py to version - 0.9.46 24 March 2020, 16:14:43 UTC
b65829a Isaac Overcast 24 March 2020, 16:11:07 UTC Fix pd.as_matrix() call which is deprecated. 24 March 2020, 16:11:07 UTC
d258e2d Isaac Overcast 16 March 2020, 19:10:51 UTC Force pca.draw() to honor the length of the color list if it is sufficiently long to color all samples in the imap, or at least use the length of the color list to set the value of the variable. 16 March 2020, 19:10:51 UTC
1bdb8f2 Isaac Overcast 12 March 2020, 15:31:50 UTC Fix oops in baba.py for importing msprime. Pushed it to Sim.__init__, since if you want to do baba, and don't care about sims, then you shouldn't have to install msprime. 12 March 2020, 15:31:50 UTC
52b1253 dereneaton 09 March 2020, 15:05:28 UTC h5py warning fix 09 March 2020, 15:05:28 UTC
3f30d92 dereneaton 09 March 2020, 15:05:15 UTC use _pnames to use filtered names in run() 09 March 2020, 15:05:15 UTC
b7eccb1 Isaac Overcast 08 March 2020, 14:03:01 UTC "Updating ipyrad/__init__.py to version - 0.9.45 08 March 2020, 14:03:01 UTC
4a20ebd Isaac Overcast 08 March 2020, 14:00:26 UTC Allow more flexibility in sorted fastqs directory (DO NOT DELETE if it points to projectdir + _fastqs) 08 March 2020, 14:00:26 UTC
6ac3b17 dereneaton 05 March 2020, 21:51:08 UTC window extracter fix for multiple loci w/ reduce 05 March 2020, 21:51:08 UTC
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
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