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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
651c872 deren 16 February 2016, 05:45:19 UTC "Updating ipyrad/__init__.py to version - 0.1.47 16 February 2016, 05:45:19 UTC
b787587 deren 16 February 2016, 05:44:12 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 February 2016, 05:44:12 UTC
fde4960 deren 16 February 2016, 05:44:06 UTC fix to debugger and to launch for api 16 February 2016, 05:44:06 UTC
f542453 isaacovercast 15 February 2016, 23:53:08 UTC Fixed change to ipyrad.bins.* 15 February 2016, 23:53:08 UTC
30d090e deren 13 February 2016, 21:46:59 UTC "Updating ipyrad/__init__.py to version - 0.1.46 13 February 2016, 21:46:59 UTC
6685575 deren 13 February 2016, 21:46:43 UTC hack around __loglevel__ setter for __init__ 13 February 2016, 21:46:43 UTC
3c818d0 deren 13 February 2016, 21:42:41 UTC "Updating ipyrad/__init__.py to version - 0.1.45 13 February 2016, 21:42:41 UTC
388c015 deren 13 February 2016, 21:42:29 UTC fix to 0.1.44 bugs 13 February 2016, 21:42:29 UTC
299face deren 13 February 2016, 21:30:21 UTC "Updating ipyrad/__init__.py to version - 0.1.44 13 February 2016, 21:30:21 UTC
941e946 deren 13 February 2016, 21:30:08 UTC created custom JSON encoder class to conserve tuples and ascii 13 February 2016, 21:30:08 UTC
c9d8bea deren 13 February 2016, 21:29:37 UTC API access 13 February 2016, 21:29:37 UTC
752b603 deren 13 February 2016, 21:29:22 UTC fix to remove error on duplicates, and chunking code 13 February 2016, 21:29:22 UTC
89ae295 deren 13 February 2016, 21:28:55 UTC code cleanup 13 February 2016, 21:28:55 UTC
451ce88 deren 13 February 2016, 20:44:23 UTC fixed debugger for new setup 13 February 2016, 20:44:23 UTC
860d485 deren 13 February 2016, 17:06:04 UTC ensure Objdicts are loaded as Objdicts 13 February 2016, 17:06:04 UTC
df18c45 deren 13 February 2016, 17:05:33 UTC need to ensure names are ascii not unicode for hdf5 attributes. JSON loading pulls in unicode 13 February 2016, 17:05:33 UTC
cd1358f deren 13 February 2016, 03:19:53 UTC "Updating ipyrad/__init__.py to version - 0.1.43 13 February 2016, 03:19:53 UTC
f7af39f deren 13 February 2016, 03:19:22 UTC merge params file naming 13 February 2016, 03:19:22 UTC
79a8c6a deren 13 February 2016, 03:17:51 UTC json saving and loading 13 February 2016, 03:17:51 UTC
9ca92ee deren 13 February 2016, 03:17:23 UTC prettier printing 13 February 2016, 03:17:23 UTC
ccd0f26 deren 13 February 2016, 03:17:05 UTC bins placement 13 February 2016, 03:17:05 UTC
1e155ea deren 13 February 2016, 03:16:37 UTC bins are now ip.bins. not part of assembly 13 February 2016, 03:16:37 UTC
38d3025 deren 13 February 2016, 03:15:58 UTC params-name.txt naming. load from assembly or json 13 February 2016, 03:15:58 UTC
92aa9db deren 13 February 2016, 03:15:01 UTC debug file resets eventually. load_json and save_json added 13 February 2016, 03:15:01 UTC
ef6f75d isaacovercast 13 February 2016, 02:40:34 UTC Fixed new params.txt file creation to reflect the params-watever.txt format. 13 February 2016, 02:40:34 UTC
ccb12a0 isaacovercast 13 February 2016, 02:23:29 UTC Fixed getassembly so it accurately tests for current assemblies before creating a new one. Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py 13 February 2016, 02:23:29 UTC
e1f5d24 isaacovercast 13 February 2016, 02:21:26 UTC Fixed CLI so it properly tests for existing assemblies and requests the -f flag if necessary 13 February 2016, 02:21:26 UTC
2682729 deren 12 February 2016, 01:26:03 UTC "Updating ipyrad/__init__.py to version - 0.1.42 12 February 2016, 01:26:03 UTC
707bf25 deren 12 February 2016, 01:25:53 UTC resolve merge conflict 12 February 2016, 01:25:53 UTC
e77e421 deren 12 February 2016, 01:18:54 UTC doubles count of merged reads 12 February 2016, 01:18:54 UTC
b7b4a9c deren 12 February 2016, 01:18:39 UTC merge pairs parallelized and with suffix 12 February 2016, 01:18:39 UTC
642b151 isaacovercast 12 February 2016, 01:18:05 UTC CLI branching works now 12 February 2016, 01:18:05 UTC
441c743 deren 12 February 2016, 01:18:00 UTC rigorous testing and improvements to clustering of pairgbs 12 February 2016, 01:18:00 UTC
79ca81e deren 12 February 2016, 01:17:27 UTC simple cleanup 12 February 2016, 01:17:27 UTC
ce1db7c deren 12 February 2016, 01:15:50 UTC simplification of logger 12 February 2016, 01:15:50 UTC
b21be9f isaacovercast 12 February 2016, 01:08:13 UTC Refactored preview_truncate_fq so now it actually works for all steps 1,2&3 added a third parameter that defaults to using 10% of the passed in file. Updated demult, rawed, and clust_wi in accordance. Also added try/except around shutil.rmtree calls to protect against the stupid nfs bug i was seeing. 12 February 2016, 01:08:13 UTC
e277fc1 deren 12 February 2016, 00:13:04 UTC need to build tests still, but getting closer.. 12 February 2016, 00:13:04 UTC
be4d379 deren 11 February 2016, 23:09:57 UTC upgrade vsearch. Read merging now parallelized 11 February 2016, 23:09:57 UTC
2563349 isaacovercast 11 February 2016, 22:02:23 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 February 2016, 22:02:23 UTC
a6fb904 deren 11 February 2016, 19:06:53 UTC "Updating ipyrad/__init__.py to version - 0.1.41 11 February 2016, 19:06:53 UTC
34d4c5b deren 11 February 2016, 19:06:22 UTC removed old vsearch 11 February 2016, 19:06:22 UTC
8f835dd deren 11 February 2016, 19:04:51 UTC upgrade vsearch to v.1.9.10. 11 February 2016, 19:04:51 UTC
8d23f91 deren 11 February 2016, 18:42:12 UTC some prettier printing for cli and for Errors. Better handling of edit_cutsites tuple 11 February 2016, 18:42:12 UTC
5597606 deren 11 February 2016, 18:41:40 UTC get sample file names for truncate from sample.name not sample.files.fastqs since fastqs are not necessarily in projdir/name_fastqs/ when step1 links_fastqs instead of demultiplexing 11 February 2016, 18:41:40 UTC
2753fb5 deren 11 February 2016, 18:40:29 UTC chdir into proj dir when creating new assembly, but stay in cur dir if just loading and load it from the full path to projdir/name 11 February 2016, 18:40:29 UTC
4a221b2 isaacovercast 11 February 2016, 18:17:50 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 11 February 2016, 18:17:50 UTC
cf75eba isaacovercast 11 February 2016, 18:17:37 UTC Error handling in assembly, and mostly done on -b for CLI 11 February 2016, 18:17:37 UTC
0c2b76f deren 11 February 2016, 17:50:17 UTC "Updating ipyrad/__init__.py to version - 0.1.40 11 February 2016, 17:50:17 UTC
507bca5 deren 11 February 2016, 17:49:58 UTC not in curdir, so don't collapse curdir path. print full path to assembly object 11 February 2016, 17:49:58 UTC
e8ecfe8 deren 11 February 2016, 17:49:31 UTC bug fix for too many open files, was loading multiple ip clients 11 February 2016, 17:49:31 UTC
6b786d0 deren 11 February 2016, 17:49:00 UTC correct orientation for unmerged pairs 11 February 2016, 17:49:00 UTC
5e68f2a deren 11 February 2016, 17:48:41 UTC loads assembly object from project_dir 11 February 2016, 17:48:41 UTC
16091d2 deren 11 February 2016, 17:19:27 UTC step2 does not do link_fastqs, but instead raises warning that step1 should be run 11 February 2016, 17:19:27 UTC
290a917 deren 11 February 2016, 17:19:02 UTC correct orientation of non-merged pairs 11 February 2016, 17:19:02 UTC
ecadfae deren 11 February 2016, 17:18:20 UTC -n flag takes a name argument 11 February 2016, 17:18:20 UTC
1fde58e deren 11 February 2016, 15:52:28 UTC merge fix 11 February 2016, 15:52:28 UTC
b49a125 isaacovercast 11 February 2016, 02:26:09 UTC oops. bad syntax fixed in cluster_within. 11 February 2016, 02:26:09 UTC
6df9bfe isaacovercast 11 February 2016, 02:23:16 UTC Cosmetic merge fixes to documentation/print statements Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py 11 February 2016, 02:23:16 UTC
e372b4e isaacovercast 11 February 2016, 02:17:14 UTC 2/3 done with -b branching for cli 11 February 2016, 02:17:14 UTC
cb8432b isaacovercast 11 February 2016, 02:16:00 UTC Fixed #108 (handle all-indel reverse gbs reads) 11 February 2016, 02:16:00 UTC
9bebc62 deren 11 February 2016, 02:00:13 UTC "Updating ipyrad/__init__.py to version - 0.1.39 11 February 2016, 02:00:13 UTC
943f3a8 deren 11 February 2016, 01:59:39 UTC never need to launch during load. Old idea. 11 February 2016, 01:59:39 UTC
2492d42 deren 11 February 2016, 01:59:11 UTC faster connection to known number of cores. Cleaner interface to data._ipcluster dict. 11 February 2016, 01:59:11 UTC
562878d deren 11 February 2016, 01:58:38 UTC new launch command. Better handling for bad params args. Empty defaults for paths params. 11 February 2016, 01:58:38 UTC
a17e3af deren 11 February 2016, 01:57:53 UTC IPyradWarningExit acts like sys.exit 11 February 2016, 01:57:53 UTC
9a2d839 deren 11 February 2016, 01:57:30 UTC better handling for finding input files 11 February 2016, 01:57:30 UTC
554ef1d deren 11 February 2016, 01:56:58 UTC no longer launch during load. ipcluster args are in a dict attribute of data. 11 February 2016, 01:56:58 UTC
5c6176d Isaac 09 February 2016, 22:50:50 UTC Fixed call to stats() to output all samples instead of just a subset. 09 February 2016, 22:50:50 UTC
dadc19a deren 09 February 2016, 00:17:33 UTC cosmetic 09 February 2016, 00:17:33 UTC
deb41c8 deren 08 February 2016, 16:13:17 UTC "Updating ipyrad/__init__.py to version - 0.1.38 08 February 2016, 16:13:17 UTC
b324e2c deren 08 February 2016, 16:10:12 UTC cosmetic 08 February 2016, 16:10:12 UTC
ebdd2ea deren 08 February 2016, 16:09:47 UTC s6 and s7 stats are assembly properties, not Sample properties 08 February 2016, 16:09:47 UTC
e51a013 deren 08 February 2016, 16:09:19 UTC can do MPI across nodes easy now with -ip flag 08 February 2016, 16:09:19 UTC
a56f42e deren 08 February 2016, 16:08:40 UTC cleaner launch for ipyparallel 5 08 February 2016, 16:08:40 UTC
a3a62cf deren 08 February 2016, 16:07:36 UTC writes stats and saves DFs to Assembly 08 February 2016, 16:07:36 UTC
ee6eb83 deren 08 February 2016, 16:07:01 UTC commented out all numba for faster start for now 08 February 2016, 16:07:01 UTC
fc7cc51 deren 08 February 2016, 16:06:45 UTC cosmetic 08 February 2016, 16:06:45 UTC
50fbe87 deren 08 February 2016, 16:06:30 UTC cleanup to prints from main 08 February 2016, 16:06:30 UTC
8d390fa deren 05 February 2016, 07:09:55 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 05 February 2016, 07:09:55 UTC
0529868 deren 05 February 2016, 07:09:50 UTC cosmetic fixes, and no auto add of * to sorted path 05 February 2016, 07:09:50 UTC
567e25a isaacovercast 05 February 2016, 02:34:13 UTC added numba to meta.yaml 05 February 2016, 02:34:13 UTC
999f537 isaacovercast 03 February 2016, 16:11:00 UTC Adding debug code 03 February 2016, 16:11:00 UTC
b795524 isaacovercast 31 January 2016, 00:01:16 UTC Error in ipyrad -n, can't use blank assembly names for tmp assembly anymore. 31 January 2016, 00:01:16 UTC
4895aa3 isaacovercast 30 January 2016, 23:47:24 UTC Fixed conda recipe so it acually works. 30 January 2016, 23:47:24 UTC
22dc93e isaacovercast 29 January 2016, 00:58:46 UTC "Updating ipyrad/__init__.py to version - 0.1.37 29 January 2016, 00:58:46 UTC
f1add56 isaacovercast 29 January 2016, 00:57:40 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/__main__.py ipyrad/core/assembly.py 29 January 2016, 00:57:40 UTC
7007f41 isaacovercast 29 January 2016, 00:54:27 UTC set_params on assembly name now errors out with a helpful message. Assembly name is SET at creation time, and is "unmodifiable". This is through both the CLI and the API, so the behavior is consistent. Also added some error checking at Assembly.__init__, basically making sure the passed in name doesn't have spaces or special characters. 29 January 2016, 00:54:27 UTC
d29090e deren 28 January 2016, 17:43:36 UTC "Updating ipyrad/__init__.py to version - 0.1.36 28 January 2016, 17:43:36 UTC
a2f04c0 deren 28 January 2016, 17:43:20 UTC pure cosmetic 28 January 2016, 17:43:20 UTC
511e88d deren 28 January 2016, 17:42:56 UTC 'prefix' was not defined'. some cleanup 28 January 2016, 17:42:56 UTC
f459706 deren 28 January 2016, 17:42:25 UTC added an ip.__interactive__ attribute to know if you are in the CLI or not 28 January 2016, 17:42:25 UTC
9dcec38 isaacovercast 28 January 2016, 06:11:57 UTC Fixing step1 preview not cleaning up preview files. in fact i fixed all preview mode file fsck not cleaning up. 28 January 2016, 06:11:57 UTC
a12105c isaacovercast 28 January 2016, 05:17:08 UTC "Updating ipyrad/__init__.py to version - 0.1.35 28 January 2016, 05:17:08 UTC
df4a7cd isaacovercast 28 January 2016, 05:14:10 UTC Huge refactor of paramsdict. Changed working_directory to project_dir, and also added a paramsdict[0]="assembly_name". 28 January 2016, 05:14:10 UTC
adda989 isaacovercast 27 January 2016, 17:53:31 UTC Disable keyboard interrupt during cluster init. 27 January 2016, 17:53:31 UTC
c58ad47 isaacovercast 27 January 2016, 02:09:40 UTC Fixed merge conflict, added more informative output to an except call Merge branch 'master' of https://github.com/dereneaton/ipyrad Conflicts: ipyrad/assemble/refmap.py 27 January 2016, 02:09:40 UTC
7d1467e isaacovercast 27 January 2016, 02:08:56 UTC Some cleanup, some debugging code. 27 January 2016, 02:08:56 UTC
a74d8c2 deren 27 January 2016, 02:04:37 UTC "Updating ipyrad/__init__.py to version - 0.1.34 27 January 2016, 02:04:37 UTC
caccae3 deren 27 January 2016, 02:04:10 UTC fix to pipe call from system bedtools to [...]bin/bedtools 27 January 2016, 02:04:10 UTC
b5feed0 isaacovercast 27 January 2016, 01:37:16 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 27 January 2016, 01:37:16 UTC
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