| 4aa45d1 | Isaac Overcast | 31 May 2023, 21:37:52 UTC | "Updating ipyrad/__init__.py to version - 0.9.92 | 31 May 2023, 21:37:52 UTC |
| 242a8c1 | Isaac Overcast | 31 May 2023, 21:37:41 UTC | analysis.popgen: Allow missing data without crashing | 31 May 2023, 21:37:41 UTC |
| 89f0a0b | Isaac Overcast | 29 May 2023, 19:10:19 UTC | cosmetic | 29 May 2023, 19:10:19 UTC |
| 8cabc48 | Isaac Overcast | 29 May 2023, 17:39:44 UTC | Fixed the popgen sumstats analysis tool and the cookbook | 29 May 2023, 17:39:44 UTC |
| ffd7e50 | Isaac Overcast | 27 May 2023, 15:12:43 UTC | "Updating ipyrad/__init__.py to version - 0.9.91 | 27 May 2023, 15:12:43 UTC |
| 3b39f7b | Isaac Overcast | 27 May 2023, 15:12:28 UTC | Fix numpy deprecation of np.int and np.bool | 27 May 2023, 15:12:28 UTC |
| a41737d | Isaac Overcast | 26 May 2023, 21:56:02 UTC | Update environment.yml | 26 May 2023, 21:56:02 UTC |
| f612e35 | Isaac Overcast | 26 May 2023, 21:48:11 UTC | Update README.rst | 26 May 2023, 21:48:11 UTC |
| 570c06e | Isaac Overcast | 26 May 2023, 21:47:42 UTC | Update README.rst | 26 May 2023, 21:47:42 UTC |
| 69e8bbb | Isaac Overcast | 26 May 2023, 21:46:19 UTC | README - Add binder badge | 26 May 2023, 21:46:19 UTC |
| a241817 | Isaac Overcast | 07 May 2023, 20:40:47 UTC | cosmetic | 07 May 2023, 20:40:47 UTC |
| 9db5a9b | Isaac Overcast | 04 April 2023, 13:15:50 UTC | Allow mrbayes.py to pass in the binary path | 04 April 2023, 13:15:50 UTC |
| eb83a89 | Isaac Overcast | 03 April 2023, 20:14:28 UTC | "Updating ipyrad/__init__.py to version - 0.9.90 | 03 April 2023, 20:14:28 UTC |
| 525eadd | Isaac Overcast | 03 April 2023, 20:14:06 UTC | Fixing a bunch of AttributeErrors on h5py attribute decode attempts | 03 April 2023, 20:14:06 UTC |
| dbb5ebc | Isaac Overcast | 03 April 2023, 20:09:55 UTC | Pin muscle < v5.0 in meta.yaml | 03 April 2023, 20:09:55 UTC |
| 9396588 | Isaac Overcast | 30 March 2023, 20:38:40 UTC | "Updating ipyrad/__init__.py to version - 0.9.89 | 30 March 2023, 20:38:40 UTC |
| 49ca401 | Isaac Overcast | 30 March 2023, 20:36:13 UTC | Fix for #502 | 30 March 2023, 20:36:13 UTC |
| dcb06d3 | Isaac Overcast | 25 March 2023, 15:11:14 UTC | Update install instructions to point to libmamba-solver | 25 March 2023, 15:11:14 UTC |
| d6c05f0 | Isaac Overcast | 12 March 2023, 15:48:54 UTC | "Updating ipyrad/__init__.py to version - 0.9.88 | 12 March 2023, 15:48:54 UTC |
| 12197ed | Isaac Overcast | 11 March 2023, 14:51:45 UTC | Update faq.rst | 11 March 2023, 14:51:45 UTC |
| 42ce7f8 | Isaac Overcast | 11 March 2023, 14:48:48 UTC | Update faq.rst | 11 March 2023, 14:48:48 UTC |
| ec5c844 | Isaac Overcast | 07 December 2022, 15:09:29 UTC | cosmetic | 07 December 2022, 15:09:29 UTC |
| 495ff5b | Carlos Alonso Maya Lastra | 07 December 2022, 15:08:20 UTC | Solving retro-compatibility in windows (#496) Looks good. | 07 December 2022, 15:08:20 UTC |
| 729608b | Isaac Overcast | 28 November 2022, 19:48:42 UTC | "Updating ipyrad/__init__.py to version - 0.9.87 | 28 November 2022, 19:48:42 UTC |
| 165b5c3 | Isaac Overcast | 28 November 2022, 19:48:27 UTC | Fix oops in clustmap.py #494 | 28 November 2022, 19:48:27 UTC |
| 4a0317f | Isaac Overcast | 18 November 2022, 23:02:43 UTC | "Updating ipyrad/__init__.py to version - 0.9.86 | 18 November 2022, 23:02:43 UTC |
| db6bbaa | Isaac Overcast | 18 November 2022, 22:58:05 UTC | step3: Filter by min MAPQ in samtools view #494 | 18 November 2022, 22:58:05 UTC |
| 5e8fc03 | Isaac Overcast | 02 November 2022, 15:05:13 UTC | Allow project_dir directories to create recursively | 02 November 2022, 15:05:13 UTC |
| 5804d99 | Isaac Overcast | 16 September 2022, 13:21:21 UTC | mod rtfd reqs.txt to unpin jinja2 version | 16 September 2022, 13:21:21 UTC |
| 1fafefa | Isaac Overcast | 16 September 2022, 13:09:47 UTC | cosmetic | 16 September 2022, 13:09:47 UTC |
| e745036 | Isaac Overcast | 16 September 2022, 12:52:19 UTC | Add rtfd yml file | 16 September 2022, 12:52:19 UTC |
| e73dd94 | Isaac Overcast | 15 September 2022, 23:26:43 UTC | "Updating ipyrad/__init__.py to version - 0.9.85 | 15 September 2022, 23:26:43 UTC |
| a59aa63 | Isaac Overcast | 15 September 2022, 23:24:16 UTC | Fix #493 - ValueError in step 6 if all R2s empty | 15 September 2022, 23:24:16 UTC |
| 52c4bb1 | Isaac Overcast | 25 August 2022, 20:57:23 UTC | Update 3-installation.rst | 25 August 2022, 20:57:23 UTC |
| c299327 | Isaac Overcast | 25 August 2022, 20:56:39 UTC | Update README.rst | 25 August 2022, 20:56:39 UTC |
| 4ed5204 | Isaac Overcast | 30 July 2022, 19:26:08 UTC | Update faq.rst Add reference to Pearman et al 2022 to the faq. | 30 July 2022, 19:26:08 UTC |
| 1bf17a9 | Isaac Overcast | 13 July 2022, 19:18:02 UTC | Handle call to decode() in case older version of h5py file. | 13 July 2022, 19:18:02 UTC |
| 8b03720 | Isaac Overcast | 20 April 2022, 12:41:46 UTC | cosmetic | 20 April 2022, 12:41:46 UTC |
| 666a555 | Isaac Overcast | 22 March 2022, 14:44:01 UTC | Clean up tempdir after step 5 | 22 March 2022, 14:44:01 UTC |
| 2181844 | Isaac Overcast | 20 March 2022, 19:38:37 UTC | Update faq.rst | 20 March 2022, 19:38:37 UTC |
| c9919f3 | Isaac Overcast | 05 February 2022, 22:15:26 UTC | "Updating ipyrad/__init__.py to version - 0.9.84 | 05 February 2022, 22:15:26 UTC |
| ac64f73 | Isaac Overcast | 05 February 2022, 22:00:48 UTC | fix pd 1.4.0 issue with setting options #475 | 05 February 2022, 22:00:48 UTC |
| 39bbe96 | Isaac Overcast | 02 February 2022, 00:41:49 UTC | "Updating ipyrad/__init__.py to version - 0.9.83 | 02 February 2022, 00:41:49 UTC |
| 9d98188 | Isaac Overcast | 02 February 2022, 00:41:11 UTC | ipyrad.core.sample Set dtype of stats pd.Series as object to silence a pd warning. | 02 February 2022, 00:41:11 UTC |
| 5e3cfe7 | Isaac Overcast | 02 February 2022, 00:34:15 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 02 February 2022, 00:34:15 UTC |
| 211ade7 | Isaac Overcast | 02 February 2022, 00:34:11 UTC | Test vsearch version to handle derep_fulllength deprecation #469 | 02 February 2022, 00:34:11 UTC |
| 3b9b988 | Tankred Ott | 24 January 2022, 16:45:02 UTC | structure error reporting (#471) Co-authored-by: TankredO <tankred.ott@ur.de> | 24 January 2022, 16:45:02 UTC |
| 8e34471 | Isaac Overcast | 21 January 2022, 14:01:48 UTC | "Updating ipyrad/__init__.py to version - 0.9.82 | 21 January 2022, 14:01:48 UTC |
| dcb534a | Isaac Overcast | 21 January 2022, 14:01:33 UTC | pin vsearch version <=2.19 #469 | 21 January 2022, 14:01:33 UTC |
| 3f99a4b | Isaac Overcast | 27 November 2021, 12:53:29 UTC | analysis.snps_extracter: allow passing in vcf file (assuming RADSeq data). | 27 November 2021, 12:53:29 UTC |
| 9a59482 | Isaac Overcast | 04 October 2021, 09:04:57 UTC | Add check for executable of structure binary | 04 October 2021, 09:04:57 UTC |
| ad33d81 | Tankred Ott | 06 September 2021, 07:48:43 UTC | kmeans imputation niters fix (#459) Co-authored-by: TankredO <ott.tankred@gmail.com> | 06 September 2021, 07:48:43 UTC |
| a199c4a | Isaac Overcast | 20 July 2021, 18:07:16 UTC | cookbook-bpp: Update tauprior to bpp 4.x inverse gamma standard | 20 July 2021, 18:07:16 UTC |
| 8e3fd41 | Isaac Overcast | 20 July 2021, 18:03:56 UTC | cookbook-bpp remove randomize_order flag from run() as this doesn't exist anymore | 20 July 2021, 18:03:56 UTC |
| 5e4ecdb | Isaac Overcast | 16 June 2021, 23:07:49 UTC | "Updating ipyrad/__init__.py to version - 0.9.81 | 16 June 2021, 23:07:49 UTC |
| f6c64f3 | Isaac Overcast | 16 June 2021, 23:07:27 UTC | Step5 add filter_max_alleles() function to honor the max_alleles_consens parameter. | 16 June 2021, 23:07:27 UTC |
| 6ad93ab | Isaac Overcast | 09 June 2021, 23:01:18 UTC | "Updating ipyrad/__init__.py to version - 0.9.80 | 09 June 2021, 23:01:18 UTC |
| cd0b402 | Isaac Overcast | 09 June 2021, 23:01:00 UTC | samtools defaults to using the flag to generate .csi index files, to allow for chrom size > 500Mb | 09 June 2021, 23:01:00 UTC |
| 1f88f52 | Isaac Overcast | 09 June 2021, 05:28:33 UTC | cosmetic | 09 June 2021, 05:28:33 UTC |
| 3c1129e | Isaac Overcast | 09 June 2021, 04:35:05 UTC | "Updating ipyrad/__init__.py to version - 0.9.79 | 09 June 2021, 04:35:05 UTC |
| 4815d6d | Isaac Overcast | 09 June 2021, 04:34:48 UTC | Step 2 - Do NOT take the complement for the p5 (R2) adapter sequence, otherwise the adapter trimming doesn't work. | 09 June 2021, 04:34:48 UTC |
| 9102152 | Isaac Overcast | 28 May 2021, 16:21:00 UTC | "Updating ipyrad/__init__.py to version - 0.9.78 | 28 May 2021, 16:21:00 UTC |
| 8a7db8d | Isaac Overcast | 28 May 2021, 16:20:17 UTC | #444: fix bytes to string comp oops | 28 May 2021, 16:20:17 UTC |
| 333779d | Isaac Overcast | 11 May 2021, 22:59:52 UTC | "Updating ipyrad/__init__.py to version - 0.9.77 | 11 May 2021, 22:59:52 UTC |
| 8a8216a | Isaac Overcast | 11 May 2021, 22:59:42 UTC | cosmetic | 11 May 2021, 22:59:42 UTC |
| 3398cc0 | Isaac Overcast | 11 May 2021, 22:57:34 UTC | "Updating ipyrad/__init__.py to version - 0.9.76 | 11 May 2021, 22:57:34 UTC |
| 0ee75ab | Isaac Overcast | 11 May 2021, 22:57:15 UTC | cosmetic | 11 May 2021, 22:57:15 UTC |
| fc6e9d4 | Isaac Overcast | 11 May 2021, 22:17:31 UTC | "Updating ipyrad/__init__.py to version - 0.9.75 | 11 May 2021, 22:17:31 UTC |
| 82782ca | Isaac Overcast | 08 May 2021, 23:57:05 UTC | "Updating ipyrad/__init__.py to version - 0.9.74 | 08 May 2021, 23:57:05 UTC |
| 980f41e | Isaac Overcast | 08 May 2021, 23:56:47 UTC | cosmetic | 08 May 2021, 23:56:47 UTC |
| 5a78cd0 | Isaac Overcast | 07 May 2021, 15:35:03 UTC | "Updating ipyrad/__init__.py to version - 0.9.73 | 07 May 2021, 15:35:03 UTC |
| fb87679 | Isaac Overcast | 07 May 2021, 15:34:45 UTC | cosmetic | 07 May 2021, 15:34:45 UTC |
| 2d4f63a | Isaac Overcast | 07 May 2021, 15:21:50 UTC | "Updating ipyrad/__init__.py to version - 0.9.72 | 07 May 2021, 15:21:50 UTC |
| b16f665 | Isaac Overcast | 07 May 2021, 15:21:36 UTC | cosmetic | 07 May 2021, 15:21:36 UTC |
| cfc70ee | Isaac Overcast | 07 May 2021, 15:17:31 UTC | Docs: add some assembly guidelines | 07 May 2021, 15:17:31 UTC |
| c9a8e6a | Isaac Overcast | 07 May 2021, 14:38:14 UTC | cosmetic | 07 May 2021, 14:38:14 UTC |
| 0f27083 | Isaac Overcast | 07 May 2021, 14:23:43 UTC | Docs: update sharing and popgen sumstats | 07 May 2021, 14:23:43 UTC |
| 4731e8f | Isaac Overcast | 05 May 2021, 15:06:54 UTC | Step1.FileLinker fix oops with trapping bz2 formatted input files. | 05 May 2021, 15:06:54 UTC |
| fd39d7c | Isaac Overcast | 16 April 2021, 14:39:56 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 16 April 2021, 14:39:56 UTC |
| 5eb3f27 | Isaac Overcast | 16 April 2021, 14:39:51 UTC | cosmetic | 16 April 2021, 14:39:51 UTC |
| 3b6dbea | Isaac Overcast | 15 April 2021, 19:50:41 UTC | "Updating ipyrad/__init__.py to version - 0.9.71 | 15 April 2021, 19:50:41 UTC |
| 65783d4 | Isaac Overcast | 15 April 2021, 18:31:06 UTC | demultiplex: Properly handle 3rad barcodes of different length | 15 April 2021, 18:31:06 UTC |
| 4456d08 | Isaac Overcast | 01 April 2021, 19:22:37 UTC | "Updating ipyrad/__init__.py to version - 0.9.70 | 01 April 2021, 19:22:37 UTC |
| 9ff02e3 | Isaac Overcast | 01 April 2021, 19:22:14 UTC | Merge branch 'master' of https://github.com/dereneaton/ipyrad | 01 April 2021, 19:22:14 UTC |
| 0c13134 | Isaac Overcast | 01 April 2021, 19:22:09 UTC | Allow snps_extractor to handle snps.hdf5 files with names not encoded as bytes | 01 April 2021, 19:22:09 UTC |
| ebe1c91 | Mike Renfro | 01 April 2021, 10:17:23 UTC | Fixing mismatch of #SBATCH and command parameters (#440) | 01 April 2021, 10:17:23 UTC |
| 8a566f1 | Isaac Overcast | 19 March 2021, 17:16:32 UTC | "Updating ipyrad/__init__.py to version - 0.9.69 | 19 March 2021, 17:16:32 UTC |
| c61e27a | Isaac Overcast | 19 March 2021, 17:16:02 UTC | ipa.structure: handle edge case with running more jobs with different K values | 19 March 2021, 17:16:02 UTC |
| 955de66 | Isaac Overcast | 23 February 2021, 11:04:23 UTC | "Updating ipyrad/__init__.py to version - 0.9.68 | 23 February 2021, 11:04:23 UTC |
| 8f45ab9 | Isaac Overcast | 23 February 2021, 11:04:00 UTC | Handle i7 demux to strip trailing newline from barcode | 23 February 2021, 11:04:00 UTC |
| e414641 | Isaac Overcast | 23 February 2021, 10:43:12 UTC | demultiplex.py: Allow very short input fq files. | 23 February 2021, 10:43:12 UTC |
| 1c0e095 | Isaac Overcast | 22 February 2021, 19:06:12 UTC | Fix project_dir inconsistency in merged assemblies. | 22 February 2021, 19:06:12 UTC |
| d314684 | Isaac Overcast | 22 February 2021, 17:26:31 UTC | Raise an error if setting a bad parameter in API mode #354 | 22 February 2021, 17:26:31 UTC |
| ce7d76c | Isaac Overcast | 21 February 2021, 10:40:14 UTC | "Updating ipyrad/__init__.py to version - 0.9.67 | 21 February 2021, 10:40:14 UTC |
| 86d0805 | Isaac Overcast | 21 February 2021, 10:37:53 UTC | Don't blank extra p3/p5 adapters in step2.check_adapters if filter_adapters != 3. | 21 February 2021, 10:37:53 UTC |
| 4c5bce4 | Isaac Overcast | 21 February 2021, 10:19:17 UTC | cosmetic | 21 February 2021, 10:19:17 UTC |
| 00c5b49 | Isaac Overcast | 18 February 2021, 11:09:29 UTC | "Updating ipyrad/__init__.py to version - 0.9.66 | 18 February 2021, 11:09:29 UTC |
| d9d8698 | Isaac Overcast | 11 February 2021, 21:33:50 UTC | cosmetic | 11 February 2021, 21:33:50 UTC |
| 1ae1075 | Isaac Overcast | 08 February 2021, 20:55:29 UTC | cosmetic | 08 February 2021, 20:55:29 UTC |
| 88697ea | Isaac Overcast | 03 February 2021, 10:02:03 UTC | analysis.popgen: _collect_results() function to compile and organize results from the engines. It's a little ugly. | 03 February 2021, 10:02:03 UTC |
