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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
f4d48ab dereneaton 18 August 2016, 22:26:27 UTC "Updating ipyrad/__init__.py to version - 0.3.31 18 August 2016, 22:26:27 UTC
68d4293 dereneaton 18 August 2016, 21:41:51 UTC better print message for MPI nodes 18 August 2016, 21:41:51 UTC
2e95c3f dereneaton 18 August 2016, 21:41:33 UTC cleaning up globals for cleaner code 18 August 2016, 21:41:33 UTC
6e4c54b dereneaton 18 August 2016, 21:34:07 UTC test script for CI, and more descriptive force printout 18 August 2016, 21:34:07 UTC
7235799 dereneaton 18 August 2016, 21:02:16 UTC cosmetic cleanup 18 August 2016, 21:02:16 UTC
1250cc1 dereneaton 18 August 2016, 20:56:14 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 18 August 2016, 20:56:14 UTC
e87168b dereneaton 18 August 2016, 20:55:57 UTC big cleanup to ipcluster call from Assembly, and cleaner code by externalizing global exceptions. 18 August 2016, 20:55:57 UTC
5e09bac dereneaton 18 August 2016, 20:55:13 UTC removed unused import 18 August 2016, 20:55:13 UTC
8660d0b dereneaton 18 August 2016, 20:54:58 UTC more flexible importing 18 August 2016, 20:54:58 UTC
a7eab16 dereneaton 18 August 2016, 20:54:32 UTC cleaned up some exception messages 18 August 2016, 20:54:32 UTC
767cac4 dereneaton 18 August 2016, 20:54:04 UTC modified tetrad ipcluster init to work the same as ipyrad's 18 August 2016, 20:54:04 UTC
c1757af dereneaton 18 August 2016, 20:53:42 UTC modified parallelism in tetrad 18 August 2016, 20:53:42 UTC
376afa3 dereneaton 18 August 2016, 20:15:11 UTC generalized ipcluster setup 18 August 2016, 20:15:11 UTC
2337b5a dereneaton 18 August 2016, 20:14:32 UTC much simplified ipcluster calls setup, more generalized to allow API more flexibility 18 August 2016, 20:14:32 UTC
61e5b4f isaacovercast 18 August 2016, 18:08:02 UTC "Updating ipyrad/__init__.py to version - 0.3.30 18 August 2016, 18:08:02 UTC
610cce9 isaacovercast 18 August 2016, 18:07:20 UTC Fixed very stupid error that was not accurately tracking max_fragment_length. 18 August 2016, 18:07:20 UTC
457e929 dereneaton 18 August 2016, 01:39:28 UTC changed svd4tet to tetrad 18 August 2016, 01:39:28 UTC
75b0d87 dereneaton 18 August 2016, 01:38:43 UTC changed name of svd4tet to tetrad 18 August 2016, 01:38:43 UTC
45df0ba dereneaton 18 August 2016, 01:38:04 UTC changed name of svd4tet to tetrad 18 August 2016, 01:38:04 UTC
58642af isaacovercast 18 August 2016, 01:06:23 UTC Better error handling on malformed params file. Allows blank lines in params (prevents that gotcha). 18 August 2016, 01:06:23 UTC
0a3b5c6 isaacovercast 18 August 2016, 00:20:47 UTC Cosmetic changes to step 7 interaction if samples are missing from db 18 August 2016, 00:20:47 UTC
9c47a55 isaacovercast 18 August 2016, 00:13:58 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 18 August 2016, 00:13:58 UTC
3bf4487 isaacovercast 18 August 2016, 00:13:54 UTC Changed behavior of step 7 to allow writing output for all samples that are ready. Allows the user to choose whether to continue or quit. 18 August 2016, 00:13:54 UTC
ddc77c5 deren 17 August 2016, 23:10:52 UTC prettier print func at splash 17 August 2016, 23:10:52 UTC
ad93854 deren 17 August 2016, 23:10:36 UTC prettier splash 17 August 2016, 23:10:36 UTC
d29ac62 deren 17 August 2016, 22:21:37 UTC testing hpc mpi setups 17 August 2016, 22:21:37 UTC
9ae0e0d deren 17 August 2016, 22:21:16 UTC created new format for ipyparallel wrapper function that is much more efficient and clean. Also prints [cores]:hostname 17 August 2016, 22:21:16 UTC
309b66d deren 17 August 2016, 22:20:27 UTC edited splash length, added newclient arg to run 17 August 2016, 22:20:27 UTC
261840d deren 17 August 2016, 20:09:27 UTC testing MPI on HPC multiple nodes 17 August 2016, 20:09:27 UTC
f15bb72 deren 17 August 2016, 20:06:07 UTC testing MPI on HPC multiple nodes 17 August 2016, 20:06:07 UTC
5ce2a6b deren 17 August 2016, 19:56:17 UTC testing MPI on HPC multiple nodes 17 August 2016, 19:56:17 UTC
c25fd22 deren 17 August 2016, 19:52:20 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 17 August 2016, 19:52:20 UTC
c540af3 deren 17 August 2016, 19:52:12 UTC testing MPI on HPC multiple nodes 17 August 2016, 19:52:12 UTC
4ada6f4 deren 17 August 2016, 19:51:55 UTC testing MPI on HPC multiple nodes 17 August 2016, 19:51:55 UTC
b397ed0 deren 17 August 2016, 19:51:34 UTC updating docs parameters 17 August 2016, 19:51:34 UTC
bc11772 isaacovercast 16 August 2016, 21:06:34 UTC "Updating ipyrad/__init__.py to version - 0.3.29 16 August 2016, 21:06:34 UTC
dda8e6a isaacovercast 16 August 2016, 21:06:13 UTC Temp debug code in jointestimate for tracking a bug 16 August 2016, 21:06:13 UTC
d1338e4 dereneaton 16 August 2016, 18:11:12 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 16 August 2016, 18:11:12 UTC
3b6405c dereneaton 16 August 2016, 18:10:45 UTC updating cookbook in progress 16 August 2016, 18:10:45 UTC
1b9e686 isaacovercast 16 August 2016, 14:24:48 UTC Step 5 - Fixed info message for printing sample names not in proper state. Cosmetic but confusing. 16 August 2016, 14:24:48 UTC
c1c66d4 isaacovercast 13 August 2016, 23:51:55 UTC "Updating ipyrad/__init__.py to version - 0.3.28 13 August 2016, 23:51:55 UTC
aff3248 isaacovercast 13 August 2016, 23:46:35 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 13 August 2016, 23:46:35 UTC
7488334 iovercast 13 August 2016, 23:43:03 UTC Added statically linked binaries for all linux progs. Updated version for bedtools and samtools. Updated vsearch but did not change symlink (ipyrad will still use 1.10) 13 August 2016, 23:43:03 UTC
a8a6abb isaacovercast 13 August 2016, 19:10:21 UTC Bugfix that threw a divide by zero error if no samples were actually ready for step 5 13 August 2016, 19:10:21 UTC
1ff80f8 isaacovercast 13 August 2016, 18:47:44 UTC "Updating ipyrad/__init__.py to version - 0.3.27 13 August 2016, 18:47:44 UTC
668fb17 isaacovercast 13 August 2016, 18:47:20 UTC Fixed a race condition where sometimes last_sample gets cleaned up before the current sample finishes, caused a KeyError. Very intermittent and annoying, but should work now 13 August 2016, 18:47:20 UTC
74a5243 deren 11 August 2016, 20:55:54 UTC "Updating ipyrad/__init__.py to version - 0.3.26 11 August 2016, 20:55:54 UTC
78f2bf2 deren 11 August 2016, 20:43:01 UTC fix merge conflict 11 August 2016, 20:43:01 UTC
5b8c3da deren 11 August 2016, 20:42:05 UTC removed future changes to demultiplex, fixed 1M array size error 11 August 2016, 20:42:05 UTC
6853ca1 deren 11 August 2016, 20:41:35 UTC added notes todo 11 August 2016, 20:41:35 UTC
65e6cb6 deren 11 August 2016, 20:41:14 UTC removed unnecessary imports 11 August 2016, 20:41:14 UTC
7b80dbf deren 11 August 2016, 20:15:54 UTC cosmetic changes 11 August 2016, 20:15:54 UTC
13307a9 dereneaton 31 July 2016, 22:47:01 UTC removed backticks from printouts 31 July 2016, 22:47:01 UTC
7a0a102 dereneaton 31 July 2016, 22:46:49 UTC removed backticks from printouts 31 July 2016, 22:46:49 UTC
5ab585d dereneaton 31 July 2016, 22:46:16 UTC removed unnecessary '\' from list of args 31 July 2016, 22:46:16 UTC
8541230 dereneaton 31 July 2016, 22:45:47 UTC code cleanup for svd4tet 31 July 2016, 22:45:47 UTC
fd11ab2 dereneaton 31 July 2016, 22:45:12 UTC update to some error messages in svd4tet 31 July 2016, 22:45:12 UTC
9163759 dereneaton 31 July 2016, 22:44:48 UTC slight modification to -n printout 31 July 2016, 22:44:48 UTC
51a8207 dereneaton 31 July 2016, 22:44:23 UTC updated analysis docs 31 July 2016, 22:44:23 UTC
a32382b deren 26 July 2016, 22:55:22 UTC minor docs edits 26 July 2016, 22:55:22 UTC
5ab524a deren 26 July 2016, 17:57:33 UTC updated releasenotes 26 July 2016, 17:57:33 UTC
bb62a60 deren 26 July 2016, 17:52:10 UTC "Updating ipyrad/__init__.py to version - 0.3.25 26 July 2016, 17:52:10 UTC
9a0083e deren 26 July 2016, 17:51:27 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 26 July 2016, 17:51:27 UTC
48b670a deren 26 July 2016, 17:51:18 UTC better error message if sample names in barcodes file have spaces in them 26 July 2016, 17:51:18 UTC
361ebc7 deren 26 July 2016, 17:50:41 UTC VCF now writes chr ('chromosomes' or 'RAD loci') as ints, since vcftools and other software hate strings apparently 26 July 2016, 17:50:41 UTC
225f214 deren 26 July 2016, 17:49:42 UTC fix for concatenating multiple fastq files in step2 26 July 2016, 17:49:42 UTC
c32d4bb deren 26 July 2016, 17:49:09 UTC fix for cluster stats output bug 26 July 2016, 17:49:09 UTC
2e93a3a isaacovercast 26 July 2016, 09:03:43 UTC "Updating ipyrad/__init__.py to version - 0.3.24 26 July 2016, 09:03:43 UTC
116ef84 isaacovercast 26 July 2016, 09:02:36 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 26 July 2016, 09:02:36 UTC
42742a9 isaacovercast 26 July 2016, 09:02:21 UTC added nbconvert as a run dependency for the conda build 26 July 2016, 09:02:21 UTC
1f8572a deren 25 July 2016, 21:54:42 UTC "Updating ipyrad/__init__.py to version - 0.3.23 25 July 2016, 21:54:42 UTC
bb9a65c deren 25 July 2016, 21:49:53 UTC cosmetic code cleanup 25 July 2016, 21:49:53 UTC
bfb6f37 deren 25 July 2016, 21:49:32 UTC svd4tet load func improved 25 July 2016, 21:49:32 UTC
a422e5a deren 24 July 2016, 00:25:17 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 24 July 2016, 00:25:17 UTC
c5f207f deren 24 July 2016, 00:24:42 UTC fixed bug with floating point numbers on weights. More speed improvements with fancy matrix tricks. 24 July 2016, 00:24:42 UTC
b1c1cab deren 24 July 2016, 00:23:54 UTC added force support to svd4tet 24 July 2016, 00:23:54 UTC
565e369 Deren Eaton 23 July 2016, 23:32:00 UTC update releasenotes 23 July 2016, 23:32:00 UTC
344271d deren 23 July 2016, 00:42:57 UTC added stats storage to svd4tet 23 July 2016, 00:42:57 UTC
029e207 deren 21 July 2016, 00:39:28 UTC loci bootstrap sampling implemented in svd4tet 21 July 2016, 00:39:28 UTC
f1037cf dereneaton 20 July 2016, 15:06:47 UTC init_seqarray rearrangement for speed improvement to svd4tet 20 July 2016, 15:06:47 UTC
5338a6c dereneaton 19 July 2016, 18:25:22 UTC removed svd and dstat storage attributes from Assembly Class 19 July 2016, 18:25:22 UTC
47d2194 dereneaton 19 July 2016, 18:24:44 UTC added a plink map output file format for snps locations 19 July 2016, 18:24:44 UTC
b8eed20 dereneaton 19 July 2016, 17:54:29 UTC further minimized depth storage in JSON file. Only saved here for a quick summary plot. Full info is in the catg file if needed. Reduces bloat of JSON. 19 July 2016, 17:54:29 UTC
1fc7451 dereneaton 19 July 2016, 17:53:37 UTC huge rewrite of svd4tet with Quartet Class Object. Much more concise code 19 July 2016, 17:53:37 UTC
2f54d1f dereneaton 19 July 2016, 17:53:06 UTC big rearrangement to svd4tet CLI commands 19 July 2016, 17:53:06 UTC
cbe4e22 dereneaton 19 July 2016, 17:52:00 UTC code cleanup 19 July 2016, 17:52:00 UTC
57fc85a dereneaton 19 July 2016, 16:37:33 UTC "Updating ipyrad/__init__.py to version - 0.3.22 19 July 2016, 16:37:33 UTC
1f4cfbd dereneaton 18 July 2016, 23:16:54 UTC "Updating ipyrad/__init__.py to version - 0.3.22 18 July 2016, 23:16:54 UTC
2217699 dereneaton 18 July 2016, 22:40:09 UTC only store cluster depth histogram info for bins with data. Removes hugely unnecessary bloat to the JSON file. 18 July 2016, 22:40:09 UTC
24e43d8 deren 16 July 2016, 00:53:47 UTC fixed open closure 16 July 2016, 00:53:47 UTC
fa2f394 deren 16 July 2016, 00:51:31 UTC massive speed improvement to svd4tet funcs with numba jit compiled C code 16 July 2016, 00:51:31 UTC
f23ecdc deren 16 July 2016, 00:50:40 UTC added cores arg to svd4tet 16 July 2016, 00:50:40 UTC
9d295c2 deren 15 July 2016, 02:04:32 UTC "Updating ipyrad/__init__.py to version - 0.3.21 15 July 2016, 02:04:32 UTC
361c57f deren 15 July 2016, 02:03:57 UTC new defaults - lower maxSNPs and higher max_shared_Hs 15 July 2016, 02:03:57 UTC
2570a8d deren 15 July 2016, 02:03:10 UTC massive reworking with numba code for filtering. About 100X speed up. 15 July 2016, 02:03:10 UTC
99e980c deren 15 July 2016, 02:02:42 UTC reworking numba code in svd4tet for speed 15 July 2016, 02:02:42 UTC
fd08eb5 deren 15 July 2016, 02:02:20 UTC added debugger to svd4tet 15 July 2016, 02:02:20 UTC
d9da5d7 deren 13 July 2016, 22:32:33 UTC numba compiling some funcs, and view superseqs as ints instead of strings gives big speedups 13 July 2016, 22:32:33 UTC
de9cb39 deren 13 July 2016, 20:44:45 UTC Merge branch 'master' of https://github.com/dereneaton/ipyrad 13 July 2016, 20:44:45 UTC
4b41d0f dereneaton 13 July 2016, 20:42:04 UTC fix to statcounter in demultiplex stats 13 July 2016, 20:42:04 UTC
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