| 48ff99b | Jakob Vanhoefer | 07 March 2021, 16:53:47 UTC | fix notebooks | 07 March 2021, 16:53:47 UTC |
| fa62bc2 | Yannik Schälte | 07 March 2021, 11:59:56 UTC | Add MacOS+Windows tests; clean up .gitignore (#115) * .gitignore build folders * test macos * test windows * fix cache * fix typo * add all output files to .gitignore | 07 March 2021, 11:59:56 UTC |
| 0157684 | Yannik Schälte | 07 March 2021, 11:51:11 UTC | Add logo license; fixes #108 (#116) * add logo license; fixes #108 * add pypi badge * invert python versions for readability | 07 March 2021, 11:51:11 UTC |
| c4bbf43 | Jakob Vanhoefer | 22 February 2021, 15:41:14 UTC | add missing release notes (#111) * add missing release notes * minor changes | 22 February 2021, 15:41:14 UTC |
| cd32853 | Jakob Vanhoefer | 22 February 2021, 15:20:53 UTC | fix logo | 22 February 2021, 15:20:53 UTC |
| ee788e5 | Jakob Vanhoefer | 22 February 2021, 15:14:19 UTC | Merge pull request #110 from yaml2sbml-dev/develop New release | 22 February 2021, 15:14:19 UTC |
| b1a6b50 | Jakob Vanhoefer | 22 February 2021, 15:04:50 UTC | add Dilans review remarks | 22 February 2021, 15:04:50 UTC |
| 01b72d9 | Jakob Vanhoefer | 19 February 2021, 17:07:34 UTC | version 0.2.1 (#97) Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 19 February 2021, 17:07:34 UTC |
| 8c2634a | Jakob Vanhoefer | 19 February 2021, 16:55:49 UTC | fixes 98, fixes 101 (#105) * fix #101 * add model name suffix to PEtab tables * fix SBML string compares in tests * add observables_as_assignments keyword * fix new cli argument as flag * add documentation * delte reminder * fix review comments * fix imports * try to fix imports + flake8 * fix import, Yanniks suggestion * fix PEtab yaml creation Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> | 19 February 2021, 16:55:49 UTC |
| 545ea36 | Jakob Vanhoefer | 18 February 2021, 21:58:41 UTC | fix #99 fix #107 (#109) * fix #99 * fix notebook * Update doc/format_specification.rst Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update doc/format_specification.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update yaml2sbml/yaml_validation.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update yaml2sbml/yaml2sbml.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> | 18 February 2021, 21:58:41 UTC |
| e0cbcf9 | Marta Matos | 14 February 2021, 22:44:19 UTC | Add documentation badge to README and readthedocs (#104) * Add documentation badge to README * Add badge to index on readthedocs | 14 February 2021, 22:44:19 UTC |
| d1b33da | Marta Matos | 14 February 2021, 13:53:11 UTC | Fix link to format documentation on README (#103) | 14 February 2021, 13:53:11 UTC |
| 52d574b | Jakob Vanhoefer | 12 February 2021, 15:56:27 UTC | Fix codacy and coverage (#95) * fix pydocstyle * exclude examples README from codacy * add notebook tests to tox * test CLI within pytest * remove files created in tests * fix flake + remove CLI shell script (test now in test_CLI.py) * add review comments * fix flkae8 * remove assert for strin equality * add documentation in tox.ini * add Dilans comments * fix deleted letter | 12 February 2021, 15:56:27 UTC |
| eccdc56 | Jakob Vanhoefer | 12 February 2021, 12:24:48 UTC | Update issue templates (#96) Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> | 12 February 2021, 12:24:48 UTC |
| 3b08415 | Jakob Vanhoefer | 09 February 2021, 19:48:51 UTC | Rewrite README (#55) * adapt README * Fix docstring style * new README.md * finetuning * fix Table of contents * update README * add pip install * Add logo position * add basic syntax * pollish README * Update README.md Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update README.md Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * fix README and input signatures (_dir etc. ...) Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> | 09 February 2021, 19:48:51 UTC |
| 75f9b0d | Yannik Schälte | 08 February 2021, 23:02:15 UTC | add sphinx plugins; test docs build (#94) * add sphinx plugins; test docs build * annotate * restrict build to 3.9 * fix typo * install pandoc | 08 February 2021, 23:02:15 UTC |
| bdb17fb | Yannik Schälte | 05 February 2021, 16:02:56 UTC | Tox (#88) * test * reduce test load * fix typo * python>=3.7 * fix typo * fix typo * fix * fix flake8 * add tox * coverage xml * add notebook tests * remove run_flake8 * fix * add amici * improve docs * parallelize * remove parallelization * ignore coverage files * fix deps * set min py 36 * fix cache * add pypesto,notebook deps * add code docs * allow nbs to fail * extend docs * annotate tox.ini * disable * disable * fix * test * finalize * fix amici 0.11.10 * add todo | 05 February 2021, 16:02:56 UTC |
| 8a39fb3 | Dilan Pathirana | 05 February 2021, 12:24:29 UTC | Fix Sorensen and Lotka-Volterra model editor notebooks (#91) | 05 February 2021, 12:24:29 UTC |
| 64211f9 | Yannik Schälte | 05 February 2021, 11:40:33 UTC | Use setup.cfg file instead of setup.py (#87) * test * reduce test load * fix typo * python>=3.7 * fix typo * fix typo * fix * fix deps * set min py 36 | 05 February 2021, 11:40:33 UTC |
| 3c45897 | Dilan Pathirana | 04 February 2021, 11:40:52 UTC | Fix logo link and README typos (#85) | 04 February 2021, 11:40:52 UTC |
| 3befa77 | Yannik Schälte | 04 February 2021, 09:44:16 UTC | Extend and simplify docs; remove requirement files (#81) * various edits * test * test * test * test * minor fix * add contacts * fix badges * add link to badge * fix badges * add logo * Update README.md * add logo+version to docs * fix weird rescaling * change fix extension * fix file extension in README * rm .svg.png files * merge logo * fix contacts * multiple recipients in contacts * address reviewer comments Co-authored-by: Jakob Vanhoefer <jakob.vanhoefer@uni-bonn.de> | 04 February 2021, 09:44:16 UTC |
| f134631 | Yannik Schälte | 03 February 2021, 22:27:33 UTC | Add logo (#82) * add logo * Update README.md * change fix extension * fix file extension in README * rm .svg.png files Co-authored-by: Jakob Vanhoefer <jakob.vanhoefer@uni-bonn.de> | 03 February 2021, 22:27:33 UTC |
| ed2a3dc | Yannik Schälte | 03 February 2021, 22:00:35 UTC | Merge pull request #80 from yaml2sbml-dev/fixes_ys add gha deploy script | 03 February 2021, 22:00:35 UTC |
| b02d053 | Jakob Vanhoefer | 03 February 2021, 21:56:54 UTC | Merge branch 'develop' into fixes_ys | 03 February 2021, 21:56:54 UTC |
| 1e615fe | Jakob Vanhoefer | 03 February 2021, 21:55:31 UTC | Merge pull request #79 from yaml2sbml-dev/feature_long_description add long descrition | 03 February 2021, 21:55:31 UTC |
| cf2a2b2 | Jakob Vanhoefer | 03 February 2021, 21:33:09 UTC | Update setup.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 03 February 2021, 21:33:09 UTC |
| 6e0597e | Jakob Vanhoefer | 03 February 2021, 21:32:58 UTC | Update setup.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 03 February 2021, 21:32:58 UTC |
| 3ddc0b9 | yannikschaelte | 03 February 2021, 18:22:01 UTC | add gha deploy script | 03 February 2021, 18:22:01 UTC |
| cd5324d | Jakob Vanhoefer | 03 February 2021, 17:22:51 UTC | add long descrition | 03 February 2021, 17:22:51 UTC |
| 9563a47 | Jakob Vanhoefer | 03 February 2021, 17:03:40 UTC | Merge pull request #71 from yaml2sbml-dev/add_sphinx_docs Add sphinx docs | 03 February 2021, 17:03:40 UTC |
| d549fd9 | Jakob Vanhoefer | 03 February 2021, 16:58:22 UTC | Merge branch 'develop' into add_sphinx_docs | 03 February 2021, 16:58:22 UTC |
| 492c08d | Jakob Vanhoefer | 03 February 2021, 15:51:41 UTC | Merge pull request #76 from yaml2sbml-dev/fix_pypi minor fixes for pypi deployment | 03 February 2021, 15:51:41 UTC |
| f827958 | Jakob Vanhoefer | 03 February 2021, 15:49:05 UTC | undo deleted example files | 03 February 2021, 15:49:05 UTC |
| 4e5df50 | Jakob Vanhoefer | 03 February 2021, 14:29:23 UTC | minor fixes for pypi deployment | 03 February 2021, 14:29:23 UTC |
| a8abacb | Jakob Vanhoefer | 03 February 2021, 10:53:02 UTC | Merge pull request #75 from yaml2sbml-dev/develop Version 0.2.0 | 03 February 2021, 10:53:02 UTC |
| 3f5c1f7 | Jakob Vanhoefer | 03 February 2021, 10:48:07 UTC | add release notes | 03 February 2021, 10:48:07 UTC |
| a75fcdb | martamatos | 02 February 2021, 23:10:35 UTC | docs: Add authors to sphinx docs | 02 February 2021, 23:10:35 UTC |
| fd36c44 | martamatos | 02 February 2021, 23:04:28 UTC | chore: Update docs requirements.txt | 02 February 2021, 23:04:28 UTC |
| b62b87d | martamatos | 02 February 2021, 22:55:53 UTC | docs: Merge install into index | 02 February 2021, 22:55:53 UTC |
| d60c3a5 | martamatos | 02 February 2021, 22:55:24 UTC | chore: Remove leftover README from doc/examples | 02 February 2021, 22:55:24 UTC |
| 732a01a | martamatos | 02 February 2021, 22:53:27 UTC | docs: Add short description of the package to index | 02 February 2021, 22:53:27 UTC |
| 15ca6a9 | martamatos | 02 February 2021, 22:47:04 UTC | docs: Add example notebooks to sphinx | 02 February 2021, 22:53:16 UTC |
| 4333a5d | martamatos | 02 February 2021, 22:45:51 UTC | chore: Remove examples folder from docs | 02 February 2021, 22:45:51 UTC |
| 2b03b33 | martamatos | 31 January 2021, 15:11:53 UTC | docs: Update rtd documentation | 31 January 2021, 15:11:53 UTC |
| 69a797b | Dilan Pathirana | 30 January 2021, 22:07:11 UTC | Add Python 3.6 and 3.9 to CI (#70) | 30 January 2021, 22:07:11 UTC |
| 94f935b | dilpath | 30 January 2021, 19:34:09 UTC | undo direct commit | 30 January 2021, 19:34:09 UTC |
| bb72ca5 | dilpath | 30 January 2021, 19:24:21 UTC | add python versions to ci | 30 January 2021, 19:24:21 UTC |
| ad3bf5f | Jakob Vanhoefer | 30 January 2021, 00:17:22 UTC | Merge pull request #68 from yaml2sbml-dev/feature_example_FSP Finish up examples | 30 January 2021, 00:17:22 UTC |
| c29e959 | Jakob Vanhoefer | 29 January 2021, 23:22:35 UTC | Merge branch 'feature_example_FSP' of https://github.com/yaml2sbml-dev/yaml2sbml into feature_example_FSP | 29 January 2021, 23:22:35 UTC |
| 4ac0641 | Jakob Vanhoefer | 29 January 2021, 23:22:14 UTC | add references | 29 January 2021, 23:22:14 UTC |
| fed9bc1 | Jakob Vanhoefer | 29 January 2021, 23:12:40 UTC | Merge pull request #57 from yaml2sbml-dev/feature_version add __version__ closes #56 | 29 January 2021, 23:12:40 UTC |
| 46855d9 | Jakob Vanhoefer | 29 January 2021, 16:56:27 UTC | adress codacy | 29 January 2021, 16:56:27 UTC |
| 3aa1d60 | dilpath | 29 January 2021, 16:40:10 UTC | codacy | 29 January 2021, 16:40:10 UTC |
| f1272c5 | dilpath | 29 January 2021, 16:30:18 UTC | codacy | 29 January 2021, 16:30:18 UTC |
| c6a943c | dilpath | 29 January 2021, 16:16:04 UTC | codacy | 29 January 2021, 16:16:04 UTC |
| 44713fb | Dilan Pathirana | 28 January 2021, 22:50:21 UTC | Update doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb | 28 January 2021, 22:50:21 UTC |
| 2c345ae | Jakob Vanhoefer | 28 January 2021, 21:58:28 UTC | Update doc/examples/README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:58:28 UTC |
| d89b24a | Jakob Vanhoefer | 28 January 2021, 21:58:08 UTC | Update doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:58:08 UTC |
| ebae0ec | Jakob Vanhoefer | 28 January 2021, 21:57:47 UTC | Update doc/examples/README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:57:47 UTC |
| 50f017c | Jakob Vanhoefer | 28 January 2021, 21:57:41 UTC | Update doc/examples/README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:57:41 UTC |
| 5470707 | Jakob Vanhoefer | 28 January 2021, 21:57:03 UTC | Update doc/examples/Finite_State_Projection/utils.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:57:03 UTC |
| f468300 | Jakob Vanhoefer | 28 January 2021, 21:56:35 UTC | Update doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:56:35 UTC |
| cfbb0e7 | Jakob Vanhoefer | 28 January 2021, 21:56:24 UTC | Update doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:56:24 UTC |
| 03e4489 | Jakob Vanhoefer | 28 January 2021, 21:56:14 UTC | Update doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 28 January 2021, 21:56:14 UTC |
| 7e2096d | Jakob Vanhoefer | 28 January 2021, 17:00:14 UTC | change to version 0.2.0 | 28 January 2021, 17:00:14 UTC |
| 56ede88 | Jakob Vanhoefer | 28 January 2021, 16:43:10 UTC | refactor Examples, add FSP example | 28 January 2021, 16:43:10 UTC |
| 7e803b1 | Jakob Vanhoefer | 28 January 2021, 16:41:27 UTC | restructure Lotka Volterra Examples | 28 January 2021, 16:41:27 UTC |
| 3e4c789 | Jakob Vanhoefer | 28 January 2021, 16:05:21 UTC | fix hardcoded directory | 28 January 2021, 16:05:21 UTC |
| 402e3ae | Jakob Vanhoefer | 25 January 2021, 15:50:50 UTC | Merge pull request #64 from yaml2sbml-dev/feature_model_editor_example Feature model editor example closes #58 | 25 January 2021, 15:50:50 UTC |
| afd49c6 | Jakob Vanhoefer | 25 January 2021, 15:33:06 UTC | Merge Dilans suggestions | 25 January 2021, 15:33:06 UTC |
| e8ef262 | Jakob Vanhoefer | 25 January 2021, 15:32:38 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:32:38 UTC |
| 9b9a5ce | Jakob Vanhoefer | 25 January 2021, 15:32:31 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:32:31 UTC |
| 27f055d | Jakob Vanhoefer | 25 January 2021, 15:32:24 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:32:24 UTC |
| 777800c | Jakob Vanhoefer | 25 January 2021, 15:32:09 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:32:09 UTC |
| f0ae4a1 | Jakob Vanhoefer | 25 January 2021, 15:32:01 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:32:01 UTC |
| a215bb5 | Jakob Vanhoefer | 25 January 2021, 15:31:52 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:31:52 UTC |
| a8f946d | Jakob Vanhoefer | 25 January 2021, 15:31:45 UTC | Update doc/examples/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:31:45 UTC |
| b3bb218 | Jakob Vanhoefer | 25 January 2021, 15:31:14 UTC | Update yaml2sbml/YamlModel.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> | 25 January 2021, 15:31:14 UTC |
| d717cf8 | Jakob Vanhoefer | 25 January 2021, 11:41:01 UTC | over_write -> overwrite | 25 January 2021, 11:41:01 UTC |
| 2264e46 | Jakob Vanhoefer | 25 January 2021, 11:35:07 UTC | fix merge conflicts | 25 January 2021, 11:35:07 UTC |
| d7274bc | Dilan Pathirana | 22 January 2021, 21:36:44 UTC | Sorensen example (#63) Co-authored-by: Jakob Vanhoefer <jakob.vanhoefer@uni-bonn.de> | 22 January 2021, 21:36:44 UTC |
| c703ca7 | Jakob Vanhoefer | 22 January 2021, 17:11:09 UTC | change comment | 22 January 2021, 17:11:09 UTC |
| 2dc270a | Jakob Vanhoefer | 22 January 2021, 16:33:31 UTC | try version parsing as in pypesto | 22 January 2021, 16:33:31 UTC |
| d3e7727 | martamatos | 19 January 2021, 22:20:22 UTC | docs: Add sphinx docs, draft | 19 January 2021, 22:20:22 UTC |
| 79be234 | Jakob Vanhoefer | 18 January 2021, 22:10:18 UTC | add new example to example README | 18 January 2021, 22:10:18 UTC |
| aecc3d7 | Jakob Vanhoefer | 18 January 2021, 22:06:10 UTC | add Model Editor Examples notebook | 18 January 2021, 22:06:10 UTC |
| 5a2d831 | Jakob Vanhoefer | 18 January 2021, 22:02:03 UTC | fix load model with missing blcok, fixes#61 | 18 January 2021, 22:02:03 UTC |
| c93bc68 | Jakob Vanhoefer | 18 January 2021, 22:00:51 UTC | fix time | 18 January 2021, 22:00:51 UTC |
| 513b169 | Jakob Vanhoefer | 17 January 2021, 20:44:09 UTC | fix parsing version string | 17 January 2021, 20:44:09 UTC |
| 48756d7 | Jakob Vanhoefer | 17 January 2021, 15:52:29 UTC | add __version__ and automated reading in... | 17 January 2021, 15:52:29 UTC |
| 1afbc73 | Jakob Vanhoefer | 16 January 2021, 11:26:09 UTC | Merge pull request #48 from yaml2sbml-dev/feature_tests Improve tests (closes #18, #34) | 16 January 2021, 11:26:09 UTC |
| 7e5b69c | Jakob Vanhoefer | 16 January 2021, 10:45:36 UTC | redo install test deps | 16 January 2021, 10:45:36 UTC |
| 1ce985d | Jakob Vanhoefer | 16 January 2021, 10:41:09 UTC | fix Yanniks review | 16 January 2021, 10:41:09 UTC |
| 716e396 | Jakob Vanhoefer | 15 January 2021, 22:22:11 UTC | add nbmake installation | 15 January 2021, 22:22:11 UTC |
| fbaf841 | Jakob Vanhoefer | 15 January 2021, 22:19:38 UTC | add flake8 installation | 15 January 2021, 22:19:38 UTC |
| bf807f1 | Jakob Vanhoefer | 15 January 2021, 20:15:17 UTC | second try chmod | 15 January 2021, 20:15:17 UTC |
| d4eed11 | Jakob Vanhoefer | 15 January 2021, 20:08:27 UTC | change permission shell test scripts | 15 January 2021, 20:08:27 UTC |
| 9167a9c | Jakob Vanhoefer | 15 January 2021, 19:07:49 UTC | fix flake8 test command | 15 January 2021, 19:07:49 UTC |
| 1cb693d | Jakob Vanhoefer | 15 January 2021, 18:43:11 UTC | change to github workflows | 15 January 2021, 18:43:11 UTC |
| 9a23a00 | Jakob Vanhoefer | 15 January 2021, 18:04:00 UTC | Merge pull request #54 from yannikschaelte/master closes #53 Move tests to github actions; add optional amici dependency | 15 January 2021, 18:04:00 UTC |
