| d46fa78 | Carsten Fortmann-Grote | 24 September 2020, 06:23:19 UTC | Merge pull request #30 from mpievolbio-scicomp/develop JOSS Badge | 24 September 2020, 06:23:19 UTC |
| 0b4ea23 | Carsten Fortmann-Grote | 24 September 2020, 06:22:25 UTC | Adding JOSS paper badge to README. | 24 September 2020, 06:22:25 UTC |
| 300130c | Carsten Fortmann-Grote | 23 September 2020, 09:51:31 UTC | Merge pull request #29 from mpievolbio-scicomp/develop Addressing EIC comments | 23 September 2020, 09:51:31 UTC |
| c494f1f | Carsten Fortmann-Grote | 23 September 2020, 09:49:48 UTC | Adding statement of need to readme (Addressing EIC @comments in https://github.com/openjournals/joss-reviews/issues/2436#issuecomment-695065949) | 23 September 2020, 09:49:48 UTC |
| 2eb8a65 | Carsten Fortmann-Grote | 23 September 2020, 08:35:40 UTC | Addressing EIC @comments in https://github.com/openjournals/joss-reviews/issues/2436#issuecomment-695065949 | 23 September 2020, 08:35:40 UTC |
| c8a5bc2 | Carsten Fortmann-Grote | 18 September 2020, 08:47:52 UTC | Merge pull request #28 from mpievolbio-scicomp/develop Proof corrections. | 18 September 2020, 08:47:52 UTC |
| 0550559 | Carsten Fortmann-Grote | 18 September 2020, 08:41:38 UTC | Merge branch 'proof_corrections' into develop | 18 September 2020, 08:41:38 UTC |
| 76729b4 | Carsten Fortmann-Grote | 18 September 2020, 08:41:21 UTC | Proof corrections. | 18 September 2020, 08:41:21 UTC |
| 133abce | Carsten Fortmann-Grote | 18 September 2020, 08:10:18 UTC | Merge branch 'master' into develop | 18 September 2020, 08:10:18 UTC |
| bd75302 | Carsten Fortmann-Grote | 18 September 2020, 08:08:23 UTC | Add Jacob's middle name initial | 18 September 2020, 08:08:23 UTC |
| 3ff3df7 | Carsten Fortmann-Grote | 18 September 2020, 08:07:48 UTC | Add Jacob's middle name initial | 18 September 2020, 08:07:48 UTC |
| a612ec1 | Carsten Fortmann-Grote | 17 September 2020, 08:44:53 UTC | Update setup.py Bump version to 2.0.1 | 17 September 2020, 08:44:53 UTC |
| 10ec005 | Carsten Fortmann-Grote | 17 September 2020, 08:44:23 UTC | Update codemeta.json Bump version to 2.0.1 | 17 September 2020, 08:44:23 UTC |
| dcd2932 | Carsten Fortmann-Grote | 16 September 2020, 15:32:18 UTC | Merge pull request #26 from pdebuyl/fix_md_syntax fix md syntax | 16 September 2020, 15:32:18 UTC |
| ab98d9c | Pierre de Buyl | 16 September 2020, 14:07:54 UTC | fix md syntax | 16 September 2020, 14:07:54 UTC |
| 305492d | Carsten Fortmann-Grote | 31 August 2020, 10:57:17 UTC | Delete response_to_referees.md | 31 August 2020, 10:57:17 UTC |
| 7220c89 | Carsten Fortmann-Grote | 31 August 2020, 10:49:36 UTC | Merge pull request #25 from mpievolbio-scicomp/develop develop | 31 August 2020, 10:49:36 UTC |
| f6bb7f4 | Carsten Fortmann-Grote | 31 August 2020, 10:31:01 UTC | Last fixes | 31 August 2020, 10:31:01 UTC |
| bd47526 | Carsten Fortmann-Grote | 28 August 2020, 14:45:20 UTC | Arne's comments on paper.md. | 28 August 2020, 14:45:20 UTC |
| e05b3f8 | Carsten Fortmann-Grote | 28 August 2020, 14:41:49 UTC | Removed unneeded rename from installation instructions. | 28 August 2020, 14:41:49 UTC |
| 1687f88 | Carsten Fortmann-Grote | 20 August 2020, 11:38:47 UTC | fixing linebreak. | 20 August 2020, 11:38:47 UTC |
| b6443f5 | Carsten Fortmann-Grote | 20 August 2020, 11:37:29 UTC | Merge branch 'master' into develop | 20 August 2020, 11:37:29 UTC |
| 38c16fc | Carsten Fortmann-Grote | 20 August 2020, 10:37:09 UTC | Added draft referee response. | 20 August 2020, 10:37:09 UTC |
| 61fc2c2 | Carsten Fortmann-Grote | 20 August 2020, 10:36:17 UTC | Merge branch 'master' into develop | 20 August 2020, 10:36:17 UTC |
| 4be7668 | Carsten Fortmann-Grote | 20 August 2020, 10:35:16 UTC | Merge pull request #24 from mpievolbio-scicomp/restart_doc Restart from dump and sampling positions. | 20 August 2020, 10:35:16 UTC |
| 95a30d4 | Carsten Fortmann-Grote | 20 August 2020, 10:01:28 UTC | Moving discussion of future directions to Summary. | 20 August 2020, 10:17:47 UTC |
| 4581588 | Carsten Fortmann-Grote | 20 August 2020, 09:32:22 UTC | Clarified multiregion sampling in paper. | 20 August 2020, 09:32:22 UTC |
| e36e374 | Carsten Fortmann-Grote | 20 August 2020, 08:35:32 UTC | Adding sampling_position to parameter table. | 20 August 2020, 08:35:32 UTC |
| df2fade | Carsten Fortmann-Grote | 20 August 2020, 08:29:06 UTC | Adding short instructions for parameter use. | 20 August 2020, 08:29:06 UTC |
| 839c23a | Carsten Fortmann-Grote | 19 August 2020, 14:39:03 UTC | Update doc and params.py. Fix to main() to pick up new parameter 'sampling_positions' | 19 August 2020, 14:39:03 UTC |
| fe2ceb9 | Carsten Fortmann-Grote | 19 August 2020, 13:59:00 UTC | Merge branch 'sampling_positions' into restart_doc | 19 August 2020, 13:59:00 UTC |
| cb8e293 | Carsten Fortmann-Grote | 19 August 2020, 13:58:46 UTC | Fixing remaining tests. | 19 August 2020, 13:58:46 UTC |
| 7e32183 | Carsten Fortmann-Grote | 19 August 2020, 13:52:57 UTC | Implemented sample position user interface. This disturbed the sequence of random numbers, hence had to make new reference data. | 19 August 2020, 13:52:57 UTC |
| 24d97c0 | Carsten Fortmann-Grote | 19 August 2020, 10:31:32 UTC | Log beneficial events. Notebook updated." | 19 August 2020, 10:31:32 UTC |
| ed20551 | Carsten Fortmann-Grote | 19 August 2020, 09:25:49 UTC | Cleanup conditional statements and logic. | 19 August 2020, 09:25:49 UTC |
| 02e2112 | Carsten Fortmann-Grote | 19 August 2020, 09:09:09 UTC | Revert "Use numpy.random everywhere, remove Lib.random" This reverts commit 0d9d131140a1aa05a471a22b41bd826395c209b3. | 19 August 2020, 09:09:09 UTC |
| 0d9d131 | Carsten Fortmann-Grote | 19 August 2020, 08:55:09 UTC | Use numpy.random everywhere, remove Lib.random | 19 August 2020, 08:55:09 UTC |
| 6f0486d | Carsten Fortmann-Grote | 17 August 2020, 08:00:54 UTC | Adding notebook to study the effect of adv_* parameters. | 17 August 2020, 08:00:54 UTC |
| cb1e319 | Carsten Fortmann-Grote | 14 August 2020, 07:03:16 UTC | Add notebook to study effect of adv. parameters. | 14 August 2020, 07:03:16 UTC |
| 6299180 | Carsten Fortmann-Grote | 13 August 2020, 15:34:22 UTC | Do not render graphs. | 13 August 2020, 15:34:22 UTC |
| dad82f9 | Carsten Fortmann-Grote | 13 August 2020, 15:22:50 UTC | Set loglevel to debug for mutation info. | 13 August 2020, 15:22:50 UTC |
| 09b36b9 | Carsten Fortmann-Grote | 13 August 2020, 15:20:29 UTC | Set loglevel to info. | 13 August 2020, 15:20:29 UTC |
| fbd0d4c | Carsten Fortmann-Grote | 13 August 2020, 15:16:20 UTC | Update notebook. | 13 August 2020, 15:16:20 UTC |
| 93e47a0 | Carsten Fortmann-Grote | 13 August 2020, 15:15:51 UTC | Implement and document restart from dump. | 13 August 2020, 15:15:51 UTC |
| 8c1f7d5 | Luka Opasic | 12 August 2020, 08:03:28 UTC | addressing minor comments from review #11 | 12 August 2020, 08:03:28 UTC |
| e940122 | Carsten Fortmann-Grote | 11 August 2020, 13:01:03 UTC | Revert "Set graphic size." This reverts commit 453e29e75cbfdb3c1d5942b00262935716742662. | 11 August 2020, 13:01:03 UTC |
| 453e29e | Carsten Fortmann-Grote | 11 August 2020, 12:57:27 UTC | Set graphic size. | 11 August 2020, 12:57:27 UTC |
| 5187dee | Carsten Fortmann-Grote | 11 August 2020, 12:33:29 UTC | Adding a comment on future directions. | 11 August 2020, 12:33:29 UTC |
| 70422f7 | Carsten Fortmann-Grote | 11 August 2020, 10:07:26 UTC | Adding proper caption to figure. | 11 August 2020, 10:07:26 UTC |
| 39d2f35 | Carsten Fortmann-Grote | 11 August 2020, 09:51:32 UTC | Adding mutation profile heatmap. | 11 August 2020, 09:51:32 UTC |
| 6a58828 | Carsten Fortmann-Grote | 11 August 2020, 08:40:52 UTC | Fixing table linebreaks. | 11 August 2020, 08:40:52 UTC |
| 29aa12e | Carsten Fortmann-Grote | 11 August 2020, 07:59:31 UTC | Some fixes and typos in doc and paper. Removed tutorial-like code and file listings from the paper as demanded by @pdebuyl in https://github.com/openjournals/joss-reviews/issues/2436#issuecomment-667910281. | 11 August 2020, 07:59:31 UTC |
| 8d4f8c6 | Carsten Fortmann-Grote | 10 August 2020, 15:59:53 UTC | Merge pull request #23 from mpievolbio-scicomp/develop Develop | 10 August 2020, 15:59:53 UTC |
| 1f0f222 | Carsten Fortmann-Grote | 10 August 2020, 15:47:03 UTC | Merge pull request #22 from mpievolbio-scicomp/tests++ Merge more tests. | 10 August 2020, 15:47:03 UTC |
| 5e22473 | Carsten Fortmann-Grote | 10 August 2020, 15:24:18 UTC | ensure images are found. | 10 August 2020, 15:24:18 UTC |
| afb00e0 | Carsten Fortmann-Grote | 10 August 2020, 15:20:41 UTC | Replace histograms by correct versions. | 10 August 2020, 15:20:41 UTC |
| 5dabd20 | Carsten Fortmann-Grote | 10 August 2020, 15:15:07 UTC | More cosmetic fixes. | 10 August 2020, 15:15:07 UTC |
| 9d3b4e8 | Carsten Fortmann-Grote | 10 August 2020, 15:12:15 UTC | Attempt to render citations as hyperlinks. | 10 August 2020, 15:12:15 UTC |
| 7f42e9d | Carsten Fortmann-Grote | 10 August 2020, 15:10:46 UTC | Attempt to render citations as hyperlinks. | 10 August 2020, 15:10:46 UTC |
| 16c2d5c | Carsten Fortmann-Grote | 10 August 2020, 15:08:53 UTC | Attempt to render citations as hyperlinks. | 10 August 2020, 15:08:53 UTC |
| f42f366 | Carsten Fortmann-Grote | 10 August 2020, 15:05:52 UTC | Fixing references. | 10 August 2020, 15:05:52 UTC |
| 811276d | Carsten Fortmann-Grote | 10 August 2020, 14:41:05 UTC | Small fix. | 10 August 2020, 14:41:05 UTC |
| 5e54e5a | Carsten Fortmann-Grote | 10 August 2020, 14:39:02 UTC | Fix typo. | 10 August 2020, 14:39:02 UTC |
| 3a693d0 | Carsten Fortmann-Grote | 10 August 2020, 14:18:23 UTC | Remove comment. | 10 August 2020, 14:18:23 UTC |
| 1b15a78 | Carsten Fortmann-Grote | 10 August 2020, 14:18:01 UTC | Update notebook to reflect fixes and changes in the code. | 10 August 2020, 14:18:01 UTC |
| e77deb2 | Carsten Fortmann-Grote | 10 August 2020, 14:17:37 UTC | Format parameter names. | 10 August 2020, 14:17:37 UTC |
| dea1333 | Carsten Fortmann-Grote | 10 August 2020, 13:11:44 UTC | Make sure log is also written to the log file in /log/casim.log. | 10 August 2020, 13:16:09 UTC |
| 6c8b664 | Carsten Fortmann-Grote | 10 August 2020, 13:11:44 UTC | Make sure log is also written to the log file in /log/casim.log. | 10 August 2020, 13:11:44 UTC |
| c687d55 | Carsten Fortmann-Grote | 10 August 2020, 12:02:15 UTC | Testing all parameters are correctly set when starting from params.py. | 10 August 2020, 12:02:15 UTC |
| 2c31dda | Carsten Fortmann-Grote | 10 August 2020, 11:59:42 UTC | Testing all parameters are correctly set when starting from params.py. | 10 August 2020, 11:59:42 UTC |
| d175ecd | Carsten Fortmann-Grote | 10 August 2020, 08:49:52 UTC | Merge branch 'master' into develop | 10 August 2020, 08:49:52 UTC |
| 873db41 | Carsten Fortmann-Grote | 10 August 2020, 08:46:07 UTC | Merge branch 'luka_review' | 10 August 2020, 08:46:07 UTC |
| f992ce4 | Carsten Fortmann-Grote | 10 August 2020, 08:22:51 UTC | Merge pull request #15 from mpievolbio-scicomp/doc_examples Examples doc | 10 August 2020, 08:22:51 UTC |
| c96f261 | Carsten Fortmann-Grote | 10 August 2020, 07:52:41 UTC | Parameter rename was not applied in tests. | 10 August 2020, 07:52:41 UTC |
| 482e4d7 | Carsten Fortmann-Grote | 10 August 2020, 07:45:08 UTC | Cosmetic fixes. | 10 August 2020, 07:49:03 UTC |
| 55adbb3 | Carsten Fortmann-Grote | 07 August 2020, 13:27:49 UTC | Merge branch 'master' into doc_examples | 07 August 2020, 13:27:49 UTC |
| f046b6d | Carsten Fortmann-Grote | 07 August 2020, 13:06:17 UTC | Merge pull request #21 from mpievolbio-scicomp/parameter_names parameter names | 07 August 2020, 13:06:17 UTC |
| 9e2be3e | Carsten Fortmann-Grote | 07 August 2020, 13:03:42 UTC | Improve wording, fix some bugs (parameters not taken over.) | 07 August 2020, 13:03:42 UTC |
| cf77ab4 | Carsten Fortmann-Grote | 07 August 2020, 12:26:36 UTC | Change adv_mutation_interval to adv_mutation_wait_time. | 07 August 2020, 12:26:36 UTC |
| 626097d | Luka Opasic | 07 August 2020, 09:35:28 UTC | description of the example | 07 August 2020, 09:35:28 UTC |
| 4a39b4d | Luka Opasic | 07 August 2020, 09:17:33 UTC | changes in manuscript to address reviewers comments. Better explanation of key parameters. expansion of introduction. correction of grammatical errors | 07 August 2020, 09:17:33 UTC |
| d6a38d9 | Carsten Fortmann-Grote | 06 August 2020, 12:01:14 UTC | Merge pull request #19 from mpievolbio-scicomp/parameter_names Harmonized parameter names across code, tests, doc, paper. Add valid … | 06 August 2020, 12:01:14 UTC |
| b452789 | Carsten Fortmann-Grote | 06 August 2020, 11:41:51 UTC | Harmonized parameter names across code, tests, doc, paper. Add valid ranges in doc. | 06 August 2020, 11:41:51 UTC |
| e4161ff | Carsten Fortmann-Grote | 06 August 2020, 10:05:10 UTC | Mention that cancer sim is provided as the 'casim' module. (see review comments #16.) | 06 August 2020, 10:05:38 UTC |
| 3760a0e | Carsten Fortmann-Grote | 06 August 2020, 08:41:19 UTC | Documentation of output data. | 06 August 2020, 08:41:19 UTC |
| 4fb51ca | Carsten Fortmann-Grote | 29 July 2020, 10:29:09 UTC | Adding output documentation to CancerSimulator.run() | 29 July 2020, 10:29:09 UTC |
| 1e1ee09 | Carsten Fortmann-Grote | 28 July 2020, 11:51:30 UTC | Providing more info on output files in README and notebook. | 28 July 2020, 11:51:30 UTC |
| 61220b7 | Carsten Fortmann-Grote | 28 July 2020, 11:23:07 UTC | Small amendment and documenting output in notebook. | 28 July 2020, 11:23:07 UTC |
| 1f6d263 | Carsten Fortmann-Grote | 28 July 2020, 09:25:21 UTC | Improve example documentation. | 28 July 2020, 09:25:21 UTC |
| f95e938 | Carsten Fortmann-Grote | 27 July 2020, 15:21:22 UTC | Merge pull request #14 from mpievolbio-scicomp/mutation_probability Parameter rename | 27 July 2020, 15:21:22 UTC |
| 54b8868 | Carsten Fortmann-Grote | 27 July 2020, 15:12:23 UTC | Fixing tests after refactoring the CLI as suggested by reviewers in #6. | 27 July 2020, 15:12:23 UTC |
| d6de508 | Carsten Fortmann-Grote | 27 July 2020, 12:59:47 UTC | Harmonized parameter names. | 27 July 2020, 12:59:47 UTC |
| c1d6158 | Carsten Fortmann-Grote | 27 July 2020, 12:10:50 UTC | Merge pull request #13 from mpievolbio-scicomp/fix_pip Fix pip | 27 July 2020, 12:10:50 UTC |
| fa6cc18 | Carsten Fortmann-Grote | 27 July 2020, 11:54:35 UTC | Merge pull request #12 from mpievolbio-scicomp/community_support Added community guidelines. | 27 July 2020, 11:54:35 UTC |
| d77927b | Carsten Fortmann-Grote | 27 July 2020, 11:50:42 UTC | Adding cwd to requirements. Fixes gh issue #5. | 27 July 2020, 11:50:42 UTC |
| 9904e76 | Carsten Fortmann-Grote | 27 July 2020, 11:40:42 UTC | Adding cwd to environment. Fixes gh issue #5. | 27 July 2020, 11:40:42 UTC |
| 46e9fc6 | Carsten Fortmann-Grote | 27 July 2020, 10:04:39 UTC | Added community guidelines in response to gh issue #7. | 27 July 2020, 10:04:39 UTC |
| 24b7b4b | Carsten Fortmann-Grote | 15 June 2020, 07:35:52 UTC | Create LICENSE | 15 June 2020, 07:35:52 UTC |
| efad147 | Carsten Fortmann-Grote | 17 March 2020, 15:07:44 UTC | Tagged version 1.0.0 | 17 March 2020, 15:07:44 UTC |
| 4db7a8c | Carsten Fortmann-Grote | 17 March 2020, 15:03:51 UTC | fix for binder to run the installation. | 17 March 2020, 15:03:51 UTC |
