https://github.com/yaml2sbml-dev/yaml2sbml

sort by:
Revision Author Date Message Commit Date
43ef3cb correct data release notes 30 July 2021, 11:38:30 UTC
ee5655f Update release_notes.rst 30 July 2021, 11:37:53 UTC
fce2329 Merge pull request #137 from yaml2sbml-dev/prepare_v025 version 0.2.5 30 July 2021, 11:37:15 UTC
507e98a prepare new version 30 July 2021, 10:36:15 UTC
4ad4c8c Fix remove unit assignments (#136) * remove units * remove units from SBML tests Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 29 July 2021, 21:55:33 UTC
01b9100 avoid unit checks (#135) 29 July 2021, 16:46:15 UTC
773f4c5 fix typo in example notebook 08 June 2021, 12:26:16 UTC
a4d88a2 Merge pull request #134 from yaml2sbml-dev/develop v024 (#133) 28 May 2021, 22:01:54 UTC
139300c Prepare v024 (#133) * add citation * increase version number * add PR number to releasenotes * Update README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 28 May 2021, 15:46:34 UTC
07864fb Merge pull request #131 from yaml2sbml-dev/develop Version 0.2.3 25 May 2021, 11:54:29 UTC
514d19f Prepare v023 (#130) * add releasenotes * update version 25 May 2021, 11:15:40 UTC
c82485a Adress comments regarding the software in the JOSS reviewing process (#128) * comments reviewer 1 * delete links in Jupiter notebook delete links, as they are not displayed correctly online on GitHub... * Change relative to absolute GH link The relative link to the file is not displayed correctly on GitHub -> change to absolute link on GitHub page... * Update INSTALL.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update doc/examples/Format_Features/Format_Features.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update doc/examples/Format_Features/Format_Features.ipynb Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * Update INSTALL.rst Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 24 May 2021, 20:12:55 UTC
6f42ee5 Merge pull request #122 from yaml2sbml-dev/develop Version 0.2.2 21 March 2021, 22:32:50 UTC
d680fdc Fix tests (#123) * fix tests * Update tests/test_yaml2sbml.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * Update tests/test_yaml2sbml.py Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> 21 March 2021, 19:12:06 UTC
7a9cba2 fix ubuntu latest 19 March 2021, 18:03:52 UTC
8f594a8 Merge branch 'develop' of https://github.com/yaml2sbml-dev/yaml2sbml into develop 19 March 2021, 15:58:20 UTC
29d99b4 Prepare v022 (#121) * add missing release notes (#111) (#112) * add missing release notes * minor changes * version ++1 * minor typos in docs * add release notes * Update doc/release_notes.rst Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> * add commit numbers to release notes Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> 19 March 2021, 15:11:51 UTC
3c268ee Merge branch 'main' into develop 19 March 2021, 12:46:50 UTC
2e8c5b4 Unfix AMICI version, fix notebooks (#113) * unfix AMICI * fix notebooks Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> 16 March 2021, 22:02:42 UTC
9923197 Fix pydocstyle was not called; update swig (#120) * update swig * add pydocstyle, min versions of flake8 * fix pydocstyle 12 March 2021, 13:45:53 UTC
bed9158 Feature check sbml success (#118) * fix notebooks * add tests if SBML parts were created succesfully * change to libsbml.LIBSBML_OPERATION_SUCCESS * fix yanniks remarks * try fixing hdf5 * try without hdf5 * try ubuntu 18.04 * try ubuntu-latest again * simplify build * test cache * make build windows-compatible Co-authored-by: dilpath <dilan.private+github@outlook.com> Co-authored-by: yannikschaelte <yannik.schaelte@gmail.com> 11 March 2021, 22:04:50 UTC
1c1d234 fix notebooks (#117) 07 March 2021, 21:31:13 UTC
fa62bc2 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 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
8f3bd49 add missing release notes (#111) (#112) * add missing release notes * minor changes 22 February 2021, 15:43:36 UTC
c4bbf43 add missing release notes (#111) * add missing release notes * minor changes 22 February 2021, 15:41:14 UTC
cd32853 fix logo 22 February 2021, 15:20:53 UTC
ee788e5 Merge pull request #110 from yaml2sbml-dev/develop New release 22 February 2021, 15:14:19 UTC
b1a6b50 add Dilans review remarks 22 February 2021, 15:04:50 UTC
01b72d9 version 0.2.1 (#97) Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 19 February 2021, 17:07:34 UTC
8c2634a 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 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 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 Fix link to format documentation on README (#103) 14 February 2021, 13:53:11 UTC
52d574b 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 Update issue templates (#96) Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com> 12 February 2021, 12:24:48 UTC
3b08415 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 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 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 Fix Sorensen and Lotka-Volterra model editor notebooks (#91) 05 February 2021, 12:24:29 UTC
64211f9 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 Fix logo link and README typos (#85) 04 February 2021, 11:40:52 UTC
3befa77 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 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 Merge pull request #80 from yaml2sbml-dev/fixes_ys add gha deploy script 03 February 2021, 22:00:35 UTC
b02d053 Merge branch 'develop' into fixes_ys 03 February 2021, 21:56:54 UTC
1e615fe Merge pull request #79 from yaml2sbml-dev/feature_long_description add long descrition 03 February 2021, 21:55:31 UTC
cf2a2b2 Update setup.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 03 February 2021, 21:33:09 UTC
6e0597e Update setup.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 03 February 2021, 21:32:58 UTC
3ddc0b9 add gha deploy script 03 February 2021, 18:22:01 UTC
cd5324d add long descrition 03 February 2021, 17:22:51 UTC
9563a47 Merge pull request #71 from yaml2sbml-dev/add_sphinx_docs Add sphinx docs 03 February 2021, 17:03:40 UTC
d549fd9 Merge branch 'develop' into add_sphinx_docs 03 February 2021, 16:58:22 UTC
492c08d Merge pull request #76 from yaml2sbml-dev/fix_pypi minor fixes for pypi deployment 03 February 2021, 15:51:41 UTC
f827958 undo deleted example files 03 February 2021, 15:49:05 UTC
4e5df50 minor fixes for pypi deployment 03 February 2021, 14:29:23 UTC
a8abacb Merge pull request #75 from yaml2sbml-dev/develop Version 0.2.0 03 February 2021, 10:53:02 UTC
3f5c1f7 add release notes 03 February 2021, 10:48:07 UTC
a75fcdb docs: Add authors to sphinx docs 02 February 2021, 23:10:35 UTC
fd36c44 chore: Update docs requirements.txt 02 February 2021, 23:04:28 UTC
b62b87d docs: Merge install into index 02 February 2021, 22:55:53 UTC
d60c3a5 chore: Remove leftover README from doc/examples 02 February 2021, 22:55:24 UTC
732a01a docs: Add short description of the package to index 02 February 2021, 22:53:27 UTC
15ca6a9 docs: Add example notebooks to sphinx 02 February 2021, 22:53:16 UTC
4333a5d chore: Remove examples folder from docs 02 February 2021, 22:45:51 UTC
2b03b33 docs: Update rtd documentation 31 January 2021, 15:11:53 UTC
69a797b Add Python 3.6 and 3.9 to CI (#70) 30 January 2021, 22:07:11 UTC
94f935b undo direct commit 30 January 2021, 19:34:09 UTC
bb72ca5 add python versions to ci 30 January 2021, 19:24:21 UTC
ad3bf5f Merge pull request #68 from yaml2sbml-dev/feature_example_FSP Finish up examples 30 January 2021, 00:17:22 UTC
c29e959 Merge branch 'feature_example_FSP' of https://github.com/yaml2sbml-dev/yaml2sbml into feature_example_FSP 29 January 2021, 23:22:35 UTC
4ac0641 add references 29 January 2021, 23:22:14 UTC
fed9bc1 Merge pull request #57 from yaml2sbml-dev/feature_version add __version__ closes #56 29 January 2021, 23:12:40 UTC
46855d9 adress codacy 29 January 2021, 16:56:27 UTC
3aa1d60 codacy 29 January 2021, 16:40:10 UTC
f1272c5 codacy 29 January 2021, 16:30:18 UTC
c6a943c codacy 29 January 2021, 16:16:04 UTC
44713fb Update doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb 28 January 2021, 22:50:21 UTC
2c345ae Update doc/examples/README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 28 January 2021, 21:58:28 UTC
d89b24a 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 Update doc/examples/README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 28 January 2021, 21:57:47 UTC
50f017c Update doc/examples/README.md Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 28 January 2021, 21:57:41 UTC
5470707 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 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 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 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 change to version 0.2.0 28 January 2021, 17:00:14 UTC
56ede88 refactor Examples, add FSP example 28 January 2021, 16:43:10 UTC
7e803b1 restructure Lotka Volterra Examples 28 January 2021, 16:41:27 UTC
3e4c789 fix hardcoded directory 28 January 2021, 16:05:21 UTC
402e3ae 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 Merge Dilans suggestions 25 January 2021, 15:33:06 UTC
e8ef262 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 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 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 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 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 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 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 Update yaml2sbml/YamlModel.py Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> 25 January 2021, 15:31:14 UTC
back to top