| 106ed78 | dparks1134 | 31 October 2022, 13:52:47 UTC | Support gzipped protein files as input (thanks to alienzj for the PR) | 31 October 2022, 13:52:47 UTC |
| 753a315 | Donovan Parks | 31 October 2022, 13:47:50 UTC | Merge pull request #354 from alienzj/support_compressed_protein Support gzipped proteins as input | 31 October 2022, 13:47:50 UTC |
| 8f76830 | alienzj | 26 October 2022, 09:35:05 UTC | Support gziped proteins as input | 26 October 2022, 09:35:05 UTC |
| 8b42a8c | dparks1134 | 03 August 2022, 22:28:24 UTC | Bumped version number. | 03 August 2022, 22:28:24 UTC |
| ab52bfe | Donovan Parks | 03 August 2022, 22:19:42 UTC | Merge pull request #333 from misialq/issue-272 Rename private class methods | 03 August 2022, 22:19:42 UTC |
| 7478d15 | Donovan Parks | 03 August 2022, 22:19:24 UTC | Merge branch 'master' into issue-272 | 03 August 2022, 22:19:24 UTC |
| 1343a1c | Donovan Parks | 30 April 2022, 17:44:24 UTC | Modified how bin IDs are identified to improve output tables | 30 April 2022, 17:44:24 UTC |
| 29916b6 | Michal Ziemski | 28 April 2022, 12:10:09 UTC | Rename private class methods | 28 April 2022, 12:10:09 UTC |
| d74bb68 | Donovan Parks | 21 April 2022, 22:40:24 UTC | Merge branch 'master' of https://github.com/Ecogenomics/CheckM | 21 April 2022, 22:40:24 UTC |
| f4b4182 | Donovan Parks | 21 April 2022, 22:40:01 UTC | Fixed bug with missing bCalledGenes flag that was impacting a number of commands. | 21 April 2022, 22:40:01 UTC |
| f45269f | Donovan Parks | 21 April 2022, 22:39:12 UTC | Merge pull request #331 from alienzj/fix_binFiles_bugs Thanks! | 21 April 2022, 22:39:12 UTC |
| ec7d32c | alienzj | 21 April 2022, 04:09:42 UTC | avoid UnboundLocalError | 21 April 2022, 04:09:42 UTC |
| 40720cc | Donovan Parks | 14 April 2022, 19:41:34 UTC | fixed support for gzip input FASTA files | 14 April 2022, 19:41:34 UTC |
| da43034 | Donovan Parks | 10 April 2022, 14:52:17 UTC | - accepted PRs allowing bins to be specified via an input table, fixing import error with prettytable, and enhancing identification of bins via their extension | 10 April 2022, 14:52:17 UTC |
| 3638c2d | Donovan Parks | 10 April 2022, 14:25:03 UTC | Merge pull request #322 from jjacobson95/patch-1 Fix prettytable. | 10 April 2022, 14:25:03 UTC |
| 674e470 | Donovan Parks | 10 April 2022, 14:12:58 UTC | Merge pull request #329 from alienzj/support_table_input Support table as input for checkm bins | 10 April 2022, 14:12:58 UTC |
| 70edb32 | alienzj | 10 April 2022, 02:50:21 UTC | fix API useage | 10 April 2022, 02:50:21 UTC |
| 4b05075 | alienzj | 10 April 2022, 02:39:31 UTC | Support table as input for checkm bins | 10 April 2022, 02:39:31 UTC |
| 2c27394 | Donovan Parks | 09 April 2022, 03:47:43 UTC | Allow CheckM data path to be set through the environmental variable CHECKM_DATA_PATH | 09 April 2022, 03:47:43 UTC |
| 9209dff | Donovan Parks | 09 April 2022, 01:27:17 UTC | added maxibor's PR to allow path to DATA_CONFIG file to be set | 09 April 2022, 01:27:17 UTC |
| 0cf55fc | Donovan Parks | 02 March 2022, 18:18:25 UTC | Merge pull request #326 from maxibor/master Allow user to specify path to `DATA_CONFIG` file, for use with Singularity containers | 02 March 2022, 18:18:25 UTC |
| b45059e | maxibor | 01 March 2022, 15:21:38 UTC | change setRoot argument order | 01 March 2022, 15:21:38 UTC |
| 1cfdf2e | maxibor | 01 March 2022, 15:06:01 UTC | configFile can also be specified by user | 01 March 2022, 15:06:01 UTC |
| 0483d9c | Jeremy Jacobson | 22 January 2022, 23:02:42 UTC | Fix prettytable. Current 'checkm profile' command does not work due to prettytable error. This small change fixes it. | 22 January 2022, 23:02:42 UTC |
| e79d420 | dparks1134 | 11 May 2021, 14:33:15 UTC | Merge branch 'master' of github.com:Ecogenomics/CheckM | 11 May 2021, 14:33:15 UTC |
| d25ba8d | dparks1134 | 11 May 2021, 14:32:04 UTC | Fix to coding density calculation which was off by 1 base per sequence. | 11 May 2021, 14:32:04 UTC |
| 56c228c | Donovan Parks | 10 August 2020, 14:10:27 UTC | Update README.md | 10 August 2020, 14:10:27 UTC |
| 1a8d128 | dparks1134 | 10 August 2020, 13:50:25 UTC | Added customer_marker_sets directory and marker set for CPR (Patescibacteria) genomes by Adarsh Singh | 10 August 2020, 13:50:25 UTC |
| 2a0766e | dparks1134 | 09 July 2020, 15:07:46 UTC | Minor bug fixes to handle invalid GFF files produced by Prodigal, and compatibility with Matplotlib changes | 09 July 2020, 15:07:46 UTC |
| b08edd7 | dparks1134 | 04 May 2020, 18:43:35 UTC | Changed `normed` to `density` in Matplotlib hist plots. | 04 May 2020, 18:43:35 UTC |
| 6438d9a | Donovan Parks | 04 May 2020, 18:07:56 UTC | Merge pull request #255 from bernt-matthias/topic/name_parsers name all subparsers | 04 May 2020, 18:07:56 UTC |
| c845107 | Matthias Bernt | 18 April 2020, 15:03:17 UTC | name all subparsers should not hurt, but help a lot when generating tools for Galaxy | 18 April 2020, 15:30:24 UTC |
| 3eac958 | dparks1134 | 22 December 2019, 16:04:46 UTC | Minor bug fixes to setting up reference data. | 22 December 2019, 16:04:46 UTC |
| 91eef2f | dparks1134 | 04 December 2019, 17:23:54 UTC | Updated version number. | 04 December 2019, 17:23:54 UTC |
| 0c403c4 | Donovan Parks | 04 December 2019, 17:20:37 UTC | Merge pull request #238 from sjaenick/master python3 fixes from sjaenick | 04 December 2019, 17:20:37 UTC |
| 760df5b | Sebastian Jaenicke | 04 December 2019, 16:16:44 UTC | unzip .egg during install | 04 December 2019, 16:16:44 UTC |
| 044c500 | Sebastian Jaenicke | 04 December 2019, 15:50:28 UTC | python3 fixes | 04 December 2019, 15:50:28 UTC |
| c69f3bf | Donovan Parks | 01 December 2019, 17:25:35 UTC | Update README.md | 01 December 2019, 17:25:35 UTC |
| 89606da | Donovan Parks | 01 December 2019, 17:25:04 UTC | Update README.md | 01 December 2019, 17:25:04 UTC |
| a1ca35b | Donovan Parks | 01 December 2019, 17:24:41 UTC | Update README.md | 01 December 2019, 17:24:41 UTC |
| 2350dea | Donovan Parks | 01 December 2019, 17:21:18 UTC | Update README.md | 01 December 2019, 17:21:18 UTC |
| 6dd81f6 | Donovan Parks | 01 December 2019, 17:17:54 UTC | Merge pull request #237 from Ecogenomics/python3_dev Migration to Python 3 | 01 December 2019, 17:17:54 UTC |
| 6a262dc | Donovan Parks | 01 December 2019, 17:13:00 UTC | Merge branch 'master' into python3_dev | 01 December 2019, 17:13:00 UTC |
| 3a7d5c4 | Donovan Parks | 07 November 2019, 22:38:18 UTC | Update setup.py | 07 November 2019, 22:38:18 UTC |
| e2dd856 | Donovan Parks | 07 November 2019, 18:12:29 UTC | Update README.md | 07 November 2019, 18:12:29 UTC |
| 3eecdee | Donovan Parks | 07 November 2019, 18:11:52 UTC | Update README.md | 07 November 2019, 18:11:52 UTC |
| ae03a87 | Donovan Parks | 07 November 2019, 18:10:44 UTC | Update README.md | 07 November 2019, 18:10:44 UTC |
| f5e88eb | Donovan Parks | 07 November 2019, 18:10:13 UTC | Update README.md | 07 November 2019, 18:10:13 UTC |
| 7424ca1 | dparks1134 | 05 November 2019, 22:38:57 UTC | Ensured error code of 1 returned for all errors. | 05 November 2019, 22:38:57 UTC |
| 05de071 | Donovan Parks | 31 October 2019, 16:29:11 UTC | Update README.md | 31 October 2019, 16:29:11 UTC |
| a091207 | dparks1134 | 31 October 2019, 16:19:09 UTC | Validation of CheckM Python 3 port. Removed some methods to simplify code base. Fixed a few minor bugs. | 31 October 2019, 16:19:09 UTC |
| 680dca4 | Donovan Parks | 31 October 2019, 16:18:11 UTC | Update README.md | 31 October 2019, 16:18:11 UTC |
| 19c968a | Donovan Parks | 31 October 2019, 16:17:03 UTC | Update README.md | 31 October 2019, 16:17:03 UTC |
| 2b7cd55 | Donovan Parks | 31 October 2019, 16:16:40 UTC | Update README.md | 31 October 2019, 16:16:40 UTC |
| c0a7be1 | Donovan Parks | 31 October 2019, 16:14:22 UTC | Update README.md | 31 October 2019, 16:14:22 UTC |
| 1973b65 | Donovan Parks | 31 October 2019, 16:14:02 UTC | Update README.md | 31 October 2019, 16:14:02 UTC |
| b776257 | Donovan Parks | 31 October 2019, 01:02:00 UTC | Update README.md | 31 October 2019, 01:02:00 UTC |
| 4d0df75 | Donovan Parks | 31 October 2019, 01:01:37 UTC | Update README.md | 31 October 2019, 01:01:37 UTC |
| 6097bfb | Donovan Parks | 31 October 2019, 01:00:58 UTC | Update README.md | 31 October 2019, 01:00:58 UTC |
| 3d68725 | dparks1134 | 30 October 2019, 18:29:19 UTC | Fixed conflicts in setup.py | 30 October 2019, 18:29:19 UTC |
| dbab27b | dparks1134 | 30 October 2019, 18:28:11 UTC | Merge branch 'master' of https://github.com/Ecogenomics/CheckM into python3_dev Conflicts: checkm/DATA_CONFIG checkm/checkmData.py checkm/defaultValues.py checkm/main.py checkm/plot/codingDensityPlots.py checkm/test/test_ecoli.py setup.py | 30 October 2019, 18:28:11 UTC |
| 22b9dd8 | dparks1134 | 11 August 2019, 18:05:14 UTC | - fix to CLI of bin_qa_plot (thanks to Finesim97 for PR) | 11 August 2019, 18:05:14 UTC |
| 4c631ec | Donovan Parks | 11 August 2019, 18:01:36 UTC | Merge pull request #218 from Finesim97/patch-1 Fixed binQAPlot: Results are stored in the results_dir | 11 August 2019, 18:01:36 UTC |
| 2000b15 | Finesim97 | 11 August 2019, 14:48:44 UTC | Results are stored in the results_dir | 11 August 2019, 14:48:44 UTC |
| 1a93438 | dparks1134 | 10 August 2019, 15:14:00 UTC | fixed bug with CLI of plotting methods introduced in 1.0.16 | 10 August 2019, 15:14:00 UTC |
| 64cab7f | dparks1134 | 08 August 2019, 20:58:32 UTC | - made ~/.checkm the default directory for CheckM reference data - "checkm data setRoot <directory>" is no longer interactive and the directory must be given on the command line | 08 August 2019, 20:58:32 UTC |
| 1cda8cf | dparks1134 | 08 August 2019, 19:00:54 UTC | - fixed CheckM data setRoot command to work from command line (thanks to cbt for PR) - added logging to files - improved reporting of CheckM results to include timestamp - removed "--force-overwrite" option and now allow output directories to already exist | 08 August 2019, 19:00:54 UTC |
| 3799630 | Donovan Parks | 01 August 2019, 13:46:08 UTC | Merge pull request #213 from ctb/fix/checkm_setRoot Fix checkm data setRoot command to work from command line. | 01 August 2019, 13:46:08 UTC |
| 5362658 | C. Titus Brown | 01 August 2019, 11:36:24 UTC | somewhat hacky fix to problem that checkm data setRoot doesn't work properly from the command line | 01 August 2019, 11:36:24 UTC |
| 39f7a83 | Donovan Parks | 21 July 2019, 22:33:34 UTC | Merge pull request #206 from asafpr/python3_dev Python3 dev | 21 July 2019, 22:33:34 UTC |
| 0f65cab | Asaf Peer | 05 July 2019, 15:32:24 UTC | passed test | 05 July 2019, 15:32:24 UTC |
| 5d8ea59 | Asaf Peer | 05 July 2019, 15:01:07 UTC | lineage_wf works | 05 July 2019, 15:01:07 UTC |
| 54d87b3 | Donovan Parks | 15 January 2019, 23:20:11 UTC | Create CONTRIBUTING | 15 January 2019, 23:20:11 UTC |
| be31dcd | Donovan Parks | 15 January 2019, 23:17:12 UTC | Update README.md | 15 January 2019, 23:17:12 UTC |
| 4c7be0e | dparks1134 | 15 January 2019, 23:12:35 UTC | Fixed bug with E. coli test case. | 15 January 2019, 23:12:35 UTC |
| e91c625 | dparks1134 | 08 January 2019, 17:13:30 UTC | Development branch; primarily for accepting PRs and porting to Python 3 | 08 January 2019, 17:13:30 UTC |
| f9ad7a4 | dparks1134 | 07 January 2019, 20:04:48 UTC | Failed commands now exit with error code 1. Added "--force-overwrite" option to tree command. | 07 January 2019, 20:04:48 UTC |
| b5b04ee | dparks1134 | 14 September 2018, 15:08:36 UTC | Fix to properly remove temporary files. | 14 September 2018, 15:08:36 UTC |
| 0a94da0 | dparks1134 | 14 September 2018, 15:00:59 UTC | Merge branch 'master' of github.com:Ecogenomics/CheckM | 14 September 2018, 15:00:59 UTC |
| 0227029 | dparks1134 | 14 September 2018, 14:59:42 UTC | Fixed issue with missing bVerbose parameter causing CheckM to fail on some systems. | 14 September 2018, 14:59:42 UTC |
| e0473ec | Donovan Parks | 16 February 2018, 18:14:23 UTC | Update README.md | 16 February 2018, 18:14:23 UTC |
| 0398260 | dparks1134 | 16 February 2018, 18:13:35 UTC | Added LICENSE. | 16 February 2018, 18:13:35 UTC |
| 8902888 | dparks1134 | 03 January 2018, 02:55:12 UTC | Fixed lineage_wf CLI bug causing crash due to missing coverage_file argument | 03 January 2018, 02:55:12 UTC |
| ee3a41d | dparks1134 | 22 December 2017, 17:23:02 UTC | CheckM v1.0.10. Updated version number for upload to pypi. | 22 December 2017, 17:23:02 UTC |
| d8ad828 | dparks1134 | 22 December 2017, 17:12:42 UTC | Merge branch 'master' of github.com:Ecogenomics/CheckM | 22 December 2017, 17:12:42 UTC |
| 2c6acca | dparks1134 | 22 December 2017, 17:12:03 UTC | CheckM v1.0.9. Minor bug fixes and interface improvements. | 22 December 2017, 17:12:03 UTC |
| cc3688d | Donovan Parks | 11 December 2017, 18:37:01 UTC | Update README.md | 11 December 2017, 18:37:01 UTC |
| 98ce6ac | Donovan Parks | 11 December 2017, 18:36:42 UTC | Update README.md | 11 December 2017, 18:36:42 UTC |
| c37d303 | dparks1134 | 11 December 2017, 18:35:02 UTC | Change README to markdown format. | 11 December 2017, 18:35:02 UTC |
| 03b1524 | Donovan Parks | 11 December 2017, 18:34:04 UTC | Update README.txt | 11 December 2017, 18:34:04 UTC |
| 412e7f0 | dparks1134 | 11 December 2017, 18:24:40 UTC | Removed ScreamingBackpack as a dependency and modifeid CheckM to mever removes user files | 11 December 2017, 18:24:40 UTC |
| 24d0876 | dparks1134 | 09 November 2017, 18:53:11 UTC | Fix for the lineage_wf command that was causing an invalid marker set to be selected in rare cases when using the reduced_tree flag. | 09 November 2017, 18:53:11 UTC |
| 82cb6d9 | dparks1134 | 02 September 2016, 19:31:24 UTC | Fixed incorrect reporting of number of marker genes/sets for taxonomic-specific marker sets. | 02 September 2016, 19:31:24 UTC |
| 3af2772 | dparks1134 | 23 May 2016, 16:48:02 UTC | Merge branch 'master' of github.com:Ecogenomics/CheckM | 23 May 2016, 16:48:02 UTC |
| dfb249f | dparks1134 | 23 May 2016, 16:46:14 UTC | Better handling of bins with no sequences. | 23 May 2016, 16:46:14 UTC |
| 719f85e | Donovan Parks | 20 May 2016, 00:36:21 UTC | Update README.txt | 20 May 2016, 00:36:21 UTC |
| 7ff0ea7 | Donovan Parks | 20 May 2016, 00:35:53 UTC | Update README.txt | 20 May 2016, 00:35:53 UTC |
| cdeb8e2 | dparks1134 | 24 April 2016, 23:28:09 UTC | updated data config file | 24 April 2016, 23:28:09 UTC |
| 69aebb7 | dparks1134 | 23 April 2016, 22:01:20 UTC | Minor bug fixes to 'test' and 'data setRoot' commands. | 23 April 2016, 22:01:20 UTC |
| 496765e | dparks1134 | 10 November 2015, 23:46:27 UTC | Fixed bug with "test" command missing --pplacer_threads argument. | 10 November 2015, 23:46:27 UTC |
