| 86b3e78 | Arnaud Belcour | 21 April 2020, 13:17:10 UTC | Try to fix metacom test. | 21 April 2020, 13:17:10 UTC |
| 811eada | cfrioux | 21 April 2020, 13:12:07 UTC | py3.8 not supported because of padmet dependencies | 21 April 2020, 13:12:07 UTC |
| dc90cf5 | Arnaud Belcour | 21 April 2020, 13:01:05 UTC | Try to fix issue with conda and readthedocs. | 21 April 2020, 13:01:05 UTC |
| 4e9f9e5 | cfrioux | 21 April 2020, 12:57:21 UTC | update biopython dependency for padmet in tests | 21 April 2020, 12:57:21 UTC |
| a69c9ed | cfrioux | 21 April 2020, 12:45:03 UTC | fix doc requirements, add one file for github actions, fix github action test | 21 April 2020, 12:45:03 UTC |
| a872486 | cfrioux | 21 April 2020, 12:28:48 UTC | github action test metacom py 3.6 to 3.8 | 21 April 2020, 12:28:48 UTC |
| 7e0a516 | cfrioux | 21 April 2020, 12:24:11 UTC | update doc, readme, complete requirements | 21 April 2020, 12:24:11 UTC |
| d949dd2 | Clémence Frioux | 21 April 2020, 09:40:25 UTC | Create pythonpublish.yml | 21 April 2020, 09:40:25 UTC |
| c655e33 | cfrioux | 07 April 2020, 06:58:38 UTC | update doc | 07 April 2020, 06:58:38 UTC |
| 3b4379a | cfrioux | 30 March 2020, 06:57:19 UTC | fix loggers and output writting for addedvalue | 30 March 2020, 06:57:19 UTC |
| c349f8f | cfrioux | 30 March 2020, 06:35:54 UTC | create a json file with addedvalue | 30 March 2020, 06:35:54 UTC |
| 6256fc1 | Arnaud Belcour | 23 March 2020, 17:15:00 UTC | Add better traceback for iscope. | 23 March 2020, 17:15:00 UTC |
| e84bdf9 | cfrioux | 23 March 2020, 15:03:21 UTC | beautify json, add link to mpwt doc in tuto | 23 March 2020, 15:03:21 UTC |
| de27bed | Arnaud Belcour | 11 March 2020, 10:54:38 UTC | Remove try and except hiding error messages. | 11 March 2020, 10:54:38 UTC |
| c9c4339 | cfrioux | 06 March 2020, 08:47:26 UTC | relocate file handler creation vs outdir creation | 06 March 2020, 08:47:26 UTC |
| e10c555 | cfrioux | 06 March 2020, 08:22:52 UTC | clean imports and fix typos | 06 March 2020, 08:22:52 UTC |
| 9c32aee | cfrioux | 05 March 2020, 19:49:14 UTC | create file logger in addition to stream stdout | 05 March 2020, 19:49:14 UTC |
| 042a06f | Arnaud Belcour | 04 March 2020, 14:05:02 UTC | Fix metacom tutorial in doc. | 04 March 2020, 14:05:02 UTC |
| 382d493 | Arnaud Belcour | 04 March 2020, 13:29:46 UTC | Fix test after removing -c to addedvalue/mincom/iscope/cscope. | 04 March 2020, 13:29:46 UTC |
| 88518f2 | Arnaud Belcour | 04 March 2020, 13:22:56 UTC | Add metacom to m2m doc. | 04 March 2020, 13:22:56 UTC |
| fa841a3 | Arnaud Belcour | 04 March 2020, 11:02:11 UTC | Add new command metacom. | 04 March 2020, 11:02:11 UTC |
| 6212e5b | Arnaud Belcour | 02 March 2020, 10:58:06 UTC | Create targets.sbml from addedvalue in workflow. | 02 March 2020, 10:58:06 UTC |
| 6cd42b8 | Arnaud Belcour | 28 February 2020, 12:54:57 UTC | Add recon -p to doc. | 28 February 2020, 12:54:57 UTC |
| 66a8785 | Arnaud Belcour | 14 February 2020, 16:25:18 UTC | Add tests for missing padmet/sbml after recon. | 14 February 2020, 16:25:18 UTC |
| d3e6d40 | Arnaud Belcour | 14 February 2020, 14:43:30 UTC | Fix issue introduced in previous commit. If there is no log_error.txt file the log will return an error. | 14 February 2020, 14:43:30 UTC |
| 6a491f5 | Arnaud Belcour | 12 February 2020, 16:34:50 UTC | Fix an issue when there is no reactions in metabolic network. Add log for mpwt and padmet creation. Fix the behaviour of m2m clean. Use the taxon_file.tsv if it is in the genomes folder. | 12 February 2020, 16:34:50 UTC |
| c3fd248 | Arnaud Belcour | 09 January 2020, 15:55:39 UTC | Move to 1.1.6. | 09 January 2020, 15:55:39 UTC |
| 30877ca | Arnaud Belcour | 09 January 2020, 15:48:46 UTC | Fix typos and add arguments from mpwt version 0.5.3. | 09 January 2020, 15:48:46 UTC |
| 2cb9557 | Arnaud Belcour | 07 January 2020, 16:16:39 UTC | Fix typos. | 07 January 2020, 16:16:39 UTC |
| 3e3b176 | Arnaud Belcour | 06 January 2020, 15:46:32 UTC | Add how to mount ptools-local folder for Singularity container. | 06 January 2020, 15:46:32 UTC |
| 32bb89f | Arnaud Belcour | 19 November 2019, 16:15:41 UTC | Move to 1.1.5. | 19 November 2019, 16:15:41 UTC |
| eb7ba8c | Arnaud Belcour | 19 November 2019, 13:24:26 UTC | Add graphviz to Travis dependencies. | 19 November 2019, 13:24:26 UTC |
| 768dceb | Arnaud Belcour | 19 November 2019, 13:19:38 UTC | Add powergrasp to Travis. | 19 November 2019, 13:19:38 UTC |
| 9ca2d78 | Arnaud Belcour | 19 November 2019, 12:58:57 UTC | Add compatibility with padmet 0.4. | 19 November 2019, 12:58:57 UTC |
| 02d92cc | Arnaud Belcour | 29 October 2019, 09:54:52 UTC | Move to 1.1.4. | 29 October 2019, 09:54:52 UTC |
| f156025 | Arnaud Belcour | 28 October 2019, 16:46:02 UTC | Fix issue with malformated seeds SBML. | 28 October 2019, 16:46:02 UTC |
| c7d55a0 | Arnaud Belcour | 28 October 2019, 10:42:43 UTC | Move to 1.1.3. | 28 October 2019, 10:42:43 UTC |
| f0bc717 | cfrioux | 24 October 2019, 15:31:36 UTC | do no try to create sbml file if no added value | 24 October 2019, 15:31:36 UTC |
| d189e05 | Arnaud Belcour | 23 October 2019, 12:34:24 UTC | Update readme with release notes. Add comment to check_oog_jar_file. | 23 October 2019, 12:34:24 UTC |
| 36c46ca | Arnaud Belcour | 22 October 2019, 14:03:36 UTC | Add check for Oog.jar. Add config file for powergrasp. | 22 October 2019, 14:03:36 UTC |
| 644caca | Arnaud Belcour | 21 October 2019, 12:45:40 UTC | Update Readme. Fix issue with miscoto stats file. | 21 October 2019, 12:45:40 UTC |
| 1f1070b | Arnaud Belcour | 21 October 2019, 08:56:11 UTC | Add labels to recipes. | 21 October 2019, 08:56:11 UTC |
| be52713 | Arnaud Belcour | 18 October 2019, 16:53:08 UTC | Move to 1.1.2. | 18 October 2019, 16:53:08 UTC |
| 8b23ed8 | Arnaud Belcour | 18 October 2019, 16:49:29 UTC | Fix issue in recon with mean and sd with one organism. | 18 October 2019, 16:49:29 UTC |
| 5aaa5bd | Arnaud Belcour | 18 October 2019, 16:02:44 UTC | Add missing dependency to travis. | 18 October 2019, 16:02:44 UTC |
| 8144b01 | Arnaud Belcour | 18 October 2019, 15:54:04 UTC | Add test for m2m_analysis (enum and graph). | 18 October 2019, 15:54:04 UTC |
| e19aab0 | Arnaud Belcour | 18 October 2019, 15:20:54 UTC | Add article seeds. | 18 October 2019, 15:20:54 UTC |
| e5b94dc | Arnaud Belcour | 18 October 2019, 14:00:36 UTC | Test sbml conversion. | 18 October 2019, 14:00:36 UTC |
| ee8bc2c | Arnaud Belcour | 18 October 2019, 13:14:46 UTC | Update readthedocs according to change in recipes. | 18 October 2019, 13:14:46 UTC |
| a5decf1 | Arnaud Belcour | 18 October 2019, 13:00:53 UTC | Update recipes (Songularity, Docker) with m2m_analysis. Update requirements. | 18 October 2019, 13:00:53 UTC |
| 139f3b1 | Clémence Frioux | 18 October 2019, 07:52:03 UTC | relax requirement constraints for padmet-utils, miscoto and menetools | 18 October 2019, 07:52:03 UTC |
| 1815422 | Arnaud Belcour | 17 October 2019, 15:07:10 UTC | Move to version 1.1.1. | 17 October 2019, 15:07:10 UTC |
| 2606693 | Arnaud Belcour | 17 October 2019, 13:29:18 UTC | Fix m2m_analysis readthedocs. Add log to m2m_analysis. Fix numerous issues with m2m_analysis. Add keystone species to m2m log. | 17 October 2019, 13:29:18 UTC |
| 1392498 | Arnaud Belcour | 16 October 2019, 16:25:16 UTC | Merge pull request #6 from AuReMe/m2m_analysis Add m2m_analysis | 16 October 2019, 16:25:16 UTC |
| aa58776 | Arnaud Belcour | 16 October 2019, 15:58:23 UTC | Add m2m_analysis in readthedocs. Remove lp intermediate files. Fix issue with phylum species. Move to version 1.1.0. | 16 October 2019, 15:58:23 UTC |
| 30aa3e2 | Arnaud Belcour | 16 October 2019, 09:39:12 UTC | Add comments in m2m_analysis. | 16 October 2019, 09:39:12 UTC |
| 86d8a56 | Arnaud Belcour | 16 October 2019, 09:07:56 UTC | Update Readme and requirements. | 16 October 2019, 09:07:56 UTC |
| 996f65c | Arnaud Belcour | 15 October 2019, 09:48:39 UTC | Update to_json miscoto function name. | 15 October 2019, 09:48:39 UTC |
| b1d24d6 | Arnaud Belcour | 14 October 2019, 07:49:23 UTC | Fix issue with mincom results. | 14 October 2019, 07:49:23 UTC |
| 26086d6 | Arnaud Belcour | 10 October 2019, 15:34:29 UTC | Fix indentation in m2m_analysis. | 10 October 2019, 15:34:29 UTC |
| 86bc247 | Arnaud Belcour | 09 October 2019, 14:57:15 UTC | Fix stats_analysis, graph_analysis and powergraph_analysis. | 09 October 2019, 14:57:15 UTC |
| aeb297f | Arnaud Belcour | 09 October 2019, 12:10:25 UTC | Fix stats_analysis. | 09 October 2019, 12:10:25 UTC |
| 3b0d6e8 | Arnaud Belcour | 09 October 2019, 11:40:05 UTC | Update m2m_analysis according to new main. | 09 October 2019, 11:40:05 UTC |
| 63c7046 | Arnaud Belcour | 08 October 2019, 15:19:11 UTC | Rewrite m2m_analysis.py according to the new main. | 08 October 2019, 15:19:11 UTC |
| 6aec90e | Arnaud Belcour | 08 October 2019, 15:16:55 UTC | Add main for m2m_analysis. | 08 October 2019, 15:16:55 UTC |
| 3ba7312 | Arnaud Belcour | 07 October 2019, 15:53:01 UTC | Add stats on key species and symbionts. | 07 October 2019, 15:53:01 UTC |
| 62b9258 | Arnaud Belcour | 02 October 2019, 15:14:40 UTC | Modify reactions with associated genes percentages. | 02 October 2019, 15:14:40 UTC |
| 305351d | Arnaud Belcour | 02 October 2019, 13:53:48 UTC | Add reactions associated with genes in sbml stats. | 02 October 2019, 13:53:48 UTC |
| c478a01 | Arnaud Belcour | 01 October 2019, 16:16:01 UTC | Add stats for GSMN. | 01 October 2019, 16:16:01 UTC |
| 7ba0e22 | Arnaud Belcour | 19 September 2019, 10:48:52 UTC | Update dependencies for m2m_analysis. | 19 September 2019, 10:48:52 UTC |
| 9087b7d | Arnaud Belcour | 16 September 2019, 16:59:18 UTC | Add draft for m2m_analysis. | 16 September 2019, 16:59:18 UTC |
| e5205e2 | Arnaud Belcour | 12 September 2019, 15:42:13 UTC | Fix the previous fix. | 12 September 2019, 15:42:13 UTC |
| 9652c14 | Arnaud Belcour | 12 September 2019, 15:37:31 UTC | Fix issue with m2m test. | 12 September 2019, 15:37:31 UTC |
| 6998868 | Arnaud Belcour | 02 September 2019, 09:10:59 UTC | Update doc with padmet files creation. | 02 September 2019, 09:10:59 UTC |
| 9a13d75 | Arnaud Belcour | 02 September 2019, 08:58:06 UTC | Add test for padmet creation. | 02 September 2019, 08:58:06 UTC |
| f4af68a | Arnaud Belcour | 01 September 2019, 19:33:33 UTC | Add argument to create padmet files. | 01 September 2019, 19:33:33 UTC |
| fc53068 | cfrioux | 01 September 2019, 15:15:27 UTC | add line breaks in asp instance for ease human reading if needed | 01 September 2019, 15:15:27 UTC |
| bd13350 | cfrioux | 31 August 2019, 17:15:45 UTC | update requirements w new msicoto version | 31 August 2019, 17:15:45 UTC |
| 2b5729d | Clémence Frioux | 31 August 2019, 16:17:04 UTC | Update requirements w newest version of Menetools | 31 August 2019, 16:17:04 UTC |
| f0aaa8e | cfrioux | 31 August 2019, 15:47:33 UTC | update version number | 31 August 2019, 15:47:33 UTC |
| b9a910d | cfrioux | 31 August 2019, 15:37:22 UTC | improved display of output and fixed pb with quotes for target sbml creation | 31 August 2019, 15:37:22 UTC |
| 91dd836 | cfrioux | 31 August 2019, 14:47:10 UTC | added small precisions to the logs | 31 August 2019, 14:47:10 UTC |
| c383720 | cfrioux | 31 August 2019, 14:29:09 UTC | print union and intersection of iscope | 31 August 2019, 14:29:09 UTC |
| 5be34a7 | Arnaud Belcour | 31 July 2019, 14:40:06 UTC | Add article data taxon_id.tsv. | 31 July 2019, 14:40:06 UTC |
| 3bdb5ec | Arnaud Belcour | 31 July 2019, 14:05:13 UTC | Fix typos in doc. | 31 July 2019, 14:05:13 UTC |
| d35f376 | Arnaud Belcour | 31 July 2019, 13:20:04 UTC | Update requirements.txt. | 31 July 2019, 13:20:04 UTC |
| 9ac64a7 | Arnaud Belcour | 31 July 2019, 13:11:43 UTC | Use workflow_data in tutorial instead of test data. | 31 July 2019, 13:11:43 UTC |
| dc47223 | Arnaud Belcour | 31 July 2019, 13:09:41 UTC | Recon test is now compatible with Pathway-Tools 23.0. | 31 July 2019, 13:09:41 UTC |
| ab7554d | Arnaud Belcour | 24 July 2019, 10:01:22 UTC | Fix copy of ptools-local folder in Singularity. | 24 July 2019, 10:01:22 UTC |
| c4b9c55 | Arnaud Belcour | 23 July 2019, 15:46:02 UTC | Remove OSX in Travis because compilation is too long. | 23 July 2019, 15:46:02 UTC |
| b44dbce | Arnaud Belcour | 23 July 2019, 15:43:29 UTC | Use Ubuntu 18.04 with Python 3.6 for Docker and Singularity (issue #5). | 23 July 2019, 15:43:29 UTC |
| 642fdd6 | Arnaud Belcour | 09 July 2019, 17:28:23 UTC | Try to fix python version used (Travis CI). | 09 July 2019, 17:28:23 UTC |
| 65479e8 | Arnaud Belcour | 09 July 2019, 17:21:38 UTC | Fix indent. | 09 July 2019, 17:21:38 UTC |
| 38fcc2c | Arnaud Belcour | 09 July 2019, 17:19:32 UTC | Try to fix travis.yml. | 09 July 2019, 17:19:32 UTC |
| f994b53 | Arnaud Belcour | 09 July 2019, 17:15:41 UTC | Try to fix Travis CI osx. | 09 July 2019, 17:15:41 UTC |
| b17f3ce | Arnaud Belcour | 09 July 2019, 14:28:45 UTC | Add osx to Travis CI. | 09 July 2019, 14:28:45 UTC |
| f8a04e4 | Arnaud Belcour | 06 June 2019, 15:11:21 UTC | Update Readme. | 06 June 2019, 15:11:21 UTC |
| 55fc792 | Arnaud Belcour | 06 June 2019, 13:58:52 UTC | Fix python3.6 in conda. | 06 June 2019, 13:58:52 UTC |
| 7fc8d89 | Arnaud Belcour | 06 June 2019, 13:46:46 UTC | In RTD environment, install package with pip. | 06 June 2019, 13:46:46 UTC |
| 5fe6008 | Arnaud Belcour | 06 June 2019, 13:39:37 UTC | Remove setup_py_install. | 06 June 2019, 13:39:37 UTC |
