| 8ed576f | Isaac Overcast | 17 December 2020, 11:46:05 UTC | "Updating ipyrad/__init__.py to version - 0.9.63 | 17 December 2020, 11:46:05 UTC |
| 1275de9 | Isaac Overcast | 17 December 2020, 11:45:45 UTC | Fix off-by-one error in nexus output | 17 December 2020, 11:45:45 UTC |
| 21d0770 | deren | 15 December 2020, 16:54:24 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 December 2020, 16:54:24 UTC |
| 036de34 | deren | 15 December 2020, 16:54:18 UTC | update struct testdocs | 15 December 2020, 16:54:18 UTC |
| a5f7c6c | Isaac Overcast | 07 December 2020, 16:18:03 UTC | cosmetic | 07 December 2020, 16:18:03 UTC |
| 8bd0f6f | Isaac Overcast | 07 December 2020, 16:06:26 UTC | Add Tajima's D denominator equation to the popgen analysis tool, because I coded it before and it's a nightmare. | 07 December 2020, 16:06:26 UTC |
| ac66878 | Isaac Overcast | 05 December 2020, 14:15:20 UTC | cosmetic | 05 December 2020, 14:15:20 UTC |
| 3819b60 | Deren | 03 December 2020, 06:01:58 UTC | use quiet in lex | 03 December 2020, 06:01:58 UTC |
| e483765 | Deren | 25 November 2020, 18:28:37 UTC | plot posteriors range limits removed | 25 November 2020, 18:28:37 UTC |
| 65957a3 | Deren | 25 November 2020, 18:28:00 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 25 November 2020, 18:28:00 UTC |
| a0a9040 | Isaac Overcast | 20 November 2020, 12:10:39 UTC | Actually fix pca cookbook | 20 November 2020, 12:10:39 UTC |
| 38ca596 | Isaac Overcast | 20 November 2020, 11:42:23 UTC | fix malformatted pca cookbook | 20 November 2020, 11:42:23 UTC |
| 41095b9 | Isaac Overcast | 11 November 2020, 18:22:08 UTC | cosmetic | 11 November 2020, 18:22:08 UTC |
| 31b052e | Deren | 09 November 2020, 18:46:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 09 November 2020, 18:46:38 UTC |
| 3c229b6 | Isaac Overcast | 03 November 2020, 15:30:23 UTC | "Updating ipyrad/__init__.py to version - 0.9.62 | 03 November 2020, 15:30:23 UTC |
| b013ff3 | Deren | 02 November 2020, 05:27:21 UTC | raxml w/ gamma rates | 02 November 2020, 05:27:21 UTC |
| 547d2e6 | Deren | 28 October 2020, 20:26:15 UTC | updating mb cookbook | 28 October 2020, 20:26:15 UTC |
| 1824c38 | Deren | 28 October 2020, 17:59:30 UTC | bpp transform parser bugfix | 28 October 2020, 17:59:30 UTC |
| 6168404 | Deren | 27 October 2020, 18:30:03 UTC | add bpp dev nb | 27 October 2020, 18:30:03 UTC |
| 76556d3 | Deren | 27 October 2020, 18:28:24 UTC | allow non-blocking calls again in bpp | 27 October 2020, 18:28:24 UTC |
| e00fcee | Deren | 27 October 2020, 16:49:18 UTC | bpp result split on delimiter | 27 October 2020, 16:49:18 UTC |
| 9c86022 | Deren | 21 October 2020, 19:34:47 UTC | allow empty node dist in bpp | 21 October 2020, 19:34:47 UTC |
| 2cea712 | Deren | 21 October 2020, 16:53:35 UTC | add option to extract as string/bytes | 21 October 2020, 16:53:35 UTC |
| ed70aae | Deren | 20 October 2020, 21:26:49 UTC | snps_extracter: report maf filter as unique filtered | 20 October 2020, 21:26:49 UTC |
| a4762ed | Deren | 18 October 2020, 20:02:12 UTC | snps extracter reports n unlinked snps | 18 October 2020, 20:02:12 UTC |
| 5f4b303 | Deren | 18 October 2020, 19:43:41 UTC | tmp dir for new cookbook docs | 18 October 2020, 19:43:41 UTC |
| ad9d09d | Deren | 18 October 2020, 04:11:24 UTC | allow maf filter in structure | 18 October 2020, 04:11:24 UTC |
| 93809eb | Deren | 18 October 2020, 04:11:10 UTC | node_dists check for tips in bpp plot | 18 October 2020, 04:11:10 UTC |
| 05a179b | Deren | 18 October 2020, 02:59:35 UTC | new plotting tools for bpp results | 18 October 2020, 02:59:35 UTC |
| 7b33767 | Deren | 18 October 2020, 02:59:10 UTC | added download util | 18 October 2020, 02:59:10 UTC |
| 999d034 | Deren | 18 October 2020, 02:58:40 UTC | add minmaf filter to snps_extracter, pca | 18 October 2020, 02:58:40 UTC |
| a90c21d | Deren | 15 October 2020, 17:24:00 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 October 2020, 17:24:00 UTC |
| c0067e1 | Deren | 15 October 2020, 17:23:58 UTC | additionall bpp summary tools | 15 October 2020, 17:23:58 UTC |
| 93ebe75 | Isaac Overcast | 15 October 2020, 14:42:43 UTC | cosmetic | 15 October 2020, 14:42:43 UTC |
| f9b2da3 | Isaac Overcast | 15 October 2020, 10:11:02 UTC | "Updating ipyrad/__init__.py to version - 0.9.61 | 15 October 2020, 10:11:02 UTC |
| ef9ee14 | Isaac Overcast | 15 October 2020, 10:10:14 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 15 October 2020, 10:10:14 UTC |
| 516ed3c | Isaac Overcast | 15 October 2020, 10:10:11 UTC | Fix nasty nasty bug in step 7 for issue #422 | 15 October 2020, 10:10:11 UTC |
| d607692 | Isaac Overcast | 13 October 2020, 08:49:24 UTC | "Updating ipyrad/__init__.py to version - 0.9.60 | 13 October 2020, 08:49:24 UTC |
| ecec2cb | Isaac Overcast | 13 October 2020, 08:49:05 UTC | Fix mapping minus reads bug step 3 | 13 October 2020, 08:49:05 UTC |
| 1e189ab | Isaac Overcast | 20 September 2020, 19:24:49 UTC | "Updating ipyrad/__init__.py to version - 0.9.59 | 20 September 2020, 19:24:49 UTC |
| c3f6b4a | Isaac Overcast | 20 September 2020, 19:24:21 UTC | In structure._call_structure() self is not in scope, so now we pass in the full path to the structure binary. | 20 September 2020, 19:24:21 UTC |
| 1d35b2e | Isaac Overcast | 10 September 2020, 16:05:52 UTC | "Updating ipyrad/__init__.py to version - 0.9.58 | 10 September 2020, 16:05:52 UTC |
| ce790fe | Isaac Overcast | 10 September 2020, 16:05:44 UTC | fix oops in window_extracter | 10 September 2020, 16:05:44 UTC |
| f0057d5 | Isaac Overcast | 10 September 2020, 16:02:40 UTC | Allow scaffold idxs to be int | 10 September 2020, 16:02:40 UTC |
| 5b22c8c | eaton-lab | 31 August 2020, 15:45:44 UTC | bugfix to skip scaffs with no hits even when end=None | 31 August 2020, 15:45:44 UTC |
| 3186f56 | eaton-lab | 31 August 2020, 15:33:42 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 31 August 2020, 15:33:42 UTC |
| b2e7e0a | eaton-lab | 31 August 2020, 15:33:29 UTC | end arg offset bugfix, may have affected size of windows in treeslider | 31 August 2020, 15:33:29 UTC |
| 4fad04b | Isaac Overcast | 31 August 2020, 07:55:06 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 31 August 2020, 07:55:06 UTC |
| 75b6fb9 | Isaac Overcast | 31 August 2020, 07:53:48 UTC | Add handler for malformed loci in baba.py | 31 August 2020, 07:53:48 UTC |
| 5edbbef | eaton-lab | 30 August 2020, 16:16:17 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 30 August 2020, 16:16:17 UTC |
| f81602d | eaton-lab | 30 August 2020, 16:16:15 UTC | fix to allow digest of single end RAD | 30 August 2020, 16:16:15 UTC |
| a12aa6d | Carlos Alonso Maya Lastra | 26 August 2020, 14:47:34 UTC | Changed astral annotation to default (#417) Changed current default (-t 1) to Astral default (-t 3) | 26 August 2020, 14:47:34 UTC |
| ff94022 | Isaac Overcast | 21 August 2020, 20:47:16 UTC | Update dependency documentation | 21 August 2020, 20:47:16 UTC |
| 3d6b653 | eaton-lab | 17 August 2020, 18:10:03 UTC | baba2 draw fix | 17 August 2020, 18:10:03 UTC |
| cad93e6 | eaton-lab | 17 August 2020, 16:42:31 UTC | return canvas in draw | 17 August 2020, 16:42:31 UTC |
| 4d5b467 | Isaac Overcast | 15 August 2020, 13:19:36 UTC | Fix an oops iff hackersonly.declone_PCR_duplicates && reference assembly | 15 August 2020, 13:19:36 UTC |
| 3585f93 | Deren Eaton | 12 August 2020, 16:02:36 UTC | Merge pull request #409 from camayal/master Changes in Drawing class | 12 August 2020, 16:02:36 UTC |
| b4962c0 | eaton-lab | 12 August 2020, 15:51:04 UTC | path fix for conda envs | 12 August 2020, 15:51:04 UTC |
| bed3259 | eaton-lab | 12 August 2020, 15:50:02 UTC | path fix for conda envs | 12 August 2020, 15:50:02 UTC |
| 93f9132 | eaton-lab | 10 August 2020, 22:37:39 UTC | update for py38 | 10 August 2020, 22:37:39 UTC |
| 7b4e282 | eaton-lab | 10 August 2020, 22:37:28 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 10 August 2020, 22:37:28 UTC |
| 8b08876 | Isaac Overcast | 10 August 2020, 18:11:06 UTC | Update faq.rst | 10 August 2020, 18:11:06 UTC |
| fbc23ab | eaton-lab | 10 August 2020, 16:47:17 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 10 August 2020, 16:47:17 UTC |
| 24cc1a1 | eaton-lab | 10 August 2020, 16:47:16 UTC | pca docs | 10 August 2020, 16:47:16 UTC |
| b669d18 | Isaac Overcast | 10 August 2020, 13:38:15 UTC | Change exit code for successful merging from 1 to 0. | 10 August 2020, 13:38:15 UTC |
| 1401998 | Isaac Overcast | 03 August 2020, 16:49:29 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 03 August 2020, 16:49:29 UTC |
| e515deb | Isaac Overcast | 03 August 2020, 16:49:21 UTC | Remove the png outfile from pca because it wants ghostscript package installed and apparently toytree doesn't have that as a dependency. Annoying. | 03 August 2020, 16:49:21 UTC |
| c14a62a | Isaac Overcast | 03 August 2020, 14:14:52 UTC | Update README.rst | 03 August 2020, 14:14:52 UTC |
| e39aa0a | Isaac Overcast | 02 August 2020, 12:48:10 UTC | Allow pca to write png as well. | 02 August 2020, 12:48:10 UTC |
| 8b9f535 | Isaac Overcast | 01 August 2020, 21:34:24 UTC | "Updating ipyrad/__init__.py to version - 0.9.57 | 01 August 2020, 21:34:24 UTC |
| 53dfd7d | Isaac Overcast | 01 August 2020, 21:11:52 UTC | Add functionality to pca to allow adding easy text titles to the plots with the param | 01 August 2020, 21:11:52 UTC |
| e6ed7d5 | Isaac Overcast | 01 August 2020, 14:54:26 UTC | Document writing pca figure to a file | 01 August 2020, 14:54:26 UTC |
| 4866826 | Isaac Overcast | 01 August 2020, 14:50:38 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 01 August 2020, 14:50:38 UTC |
| 37568d6 | Isaac Overcast | 01 August 2020, 14:50:30 UTC | Allow pca.draw() to write out pdf and svg | 01 August 2020, 14:50:30 UTC |
| c57da2a | eaton-lab | 23 July 2020, 15:35:02 UTC | force option to remove cftable in snaq | 23 July 2020, 15:35:02 UTC |
| b19df8a | eaton-lab | 22 July 2020, 19:38:48 UTC | fix ntaxa in phy header for lex | 22 July 2020, 19:38:48 UTC |
| fca497a | eaton-lab | 22 July 2020, 17:22:55 UTC | mb ipcoal doc up | 22 July 2020, 17:22:55 UTC |
| 3fdbc29 | eaton-lab | 22 July 2020, 16:18:03 UTC | get locus phy uppers | 22 July 2020, 16:18:03 UTC |
| a1bae65 | eaton-lab | 22 July 2020, 16:14:09 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 22 July 2020, 16:14:09 UTC |
| 3269559 | eaton-lab | 22 July 2020, 16:14:08 UTC | cosmetic | 22 July 2020, 16:14:08 UTC |
| 9a009b1 | eaton-lab | 22 July 2020, 16:13:45 UTC | changed default nboots in baba | 22 July 2020, 16:13:45 UTC |
| 9011ba6 | eaton-lab | 22 July 2020, 16:13:26 UTC | cosmetic | 22 July 2020, 16:13:26 UTC |
| fe14e05 | eaton-lab | 22 July 2020, 16:13:12 UTC | cosmetic | 22 July 2020, 16:13:12 UTC |
| d4d184b | Isaac Overcast | 20 July 2020, 08:34:19 UTC | cosmetic | 20 July 2020, 08:34:19 UTC |
| e72e6d6 | Isaac Overcast | 14 July 2020, 20:50:42 UTC | Set pandas max_colwidth=250 to allow for very long sample names. | 14 July 2020, 20:50:42 UTC |
| 3db851c | Isaac Overcast | 14 July 2020, 20:50:11 UTC | Fix oops in step 7 where trim_loci 3' R1 wasn't being used. | 14 July 2020, 20:50:11 UTC |
| 6ac32fd | Isaac Overcast | 14 July 2020, 17:25:09 UTC | Allow imap pops to be specified as np.ndarray in snps_extracter | 14 July 2020, 17:25:09 UTC |
| 5a35e9e | Isaac Overcast | 14 July 2020, 12:18:21 UTC | cosmetic | 14 July 2020, 12:18:21 UTC |
| 53b103d | deren | 14 July 2020, 01:52:32 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 14 July 2020, 01:52:32 UTC |
| 8e9c5f4 | deren | 14 July 2020, 01:52:31 UTC | cosmetic | 14 July 2020, 01:52:31 UTC |
| 82def2a | deren | 13 July 2020, 21:07:30 UTC | fix path snaq log | 13 July 2020, 21:07:30 UTC |
| c170935 | Isaac Overcast | 10 July 2020, 16:19:44 UTC | cosmetic | 10 July 2020, 16:19:44 UTC |
| 99062c4 | Isaac Overcast | 10 July 2020, 16:07:59 UTC | Fix branching oops | 10 July 2020, 16:07:59 UTC |
| 3e98108 | eaton-lab | 09 July 2020, 15:09:25 UTC | snaq working | 09 July 2020, 15:09:25 UTC |
| ea51c96 | eaton-lab | 09 July 2020, 15:06:15 UTC | snaq | 09 July 2020, 15:06:15 UTC |
| ce8c94f | deren | 09 July 2020, 15:05:39 UTC | network updated | 09 July 2020, 15:05:39 UTC |
| 39526cd | eaton-lab | 09 July 2020, 13:44:37 UTC | testing network analysis | 09 July 2020, 13:44:37 UTC |
| 1a55d25 | Carlos Alonso Maya Lastra | 08 July 2020, 16:24:59 UTC | Added fade option for blocks and tooltips Added: Fading function that change opacity of blocks when the test has a Z-score non-significant Z-score threshold variable Z-score vertical line in histograms panel Tooltips for some elements: names of samples in blocks, D-statistic, and Z-scores | 08 July 2020, 16:24:59 UTC |
| 49345ae | Carlos Alonso Maya Lastra | 07 July 2020, 16:22:41 UTC | Merge pull request #1 from camayal/camayal-baba2-work Changes in Drawing class | 07 July 2020, 16:22:41 UTC |
| cb8ca59 | Carlos Alonso Maya Lastra | 07 July 2020, 16:18:34 UTC | Changes in Drawing class Now prune and sort method are in Drawing class, not in Baba class. This allows make baba plots from csv tables with sort and prune functions. | 07 July 2020, 16:18:34 UTC |
