| 75d1630 | Padraig Gleeson | 16 December 2021, 14:09:58 UTC | Merge pull request #119 from NeuralEnsemble/development NeuroML 2.2 release | 16 December 2021, 14:09:58 UTC |
| ef4da12 | Padraig Gleeson | 16 December 2021, 12:18:24 UTC | Remove travis badge | 16 December 2021, 12:18:24 UTC |
| 8c333d3 | Ankur Sinha | 02 December 2021, 18:21:49 UTC | Merge pull request #120 from NeuralEnsemble/feat/py2-pin-numexpr chore(py27): pin numexpr | 02 December 2021, 18:21:49 UTC |
| 74239ec | Ankur Sinha (Ankur Sinha Gmail) | 02 December 2021, 18:17:13 UTC | chore(py27): pin numexpr | 02 December 2021, 18:17:13 UTC |
| 04a359a | Ankur Sinha | 26 November 2021, 14:46:09 UTC | Merge pull request #118 from NeuralEnsemble/fix/py2-stringio Fix/py2 stringio | 26 November 2021, 14:46:09 UTC |
| fcdcd56 | Ankur Sinha (Ankur Sinha Gmail) | 26 November 2021, 14:29:03 UTC | fix: correctly fix py2/3 StringIO error In python 2, we must use `from StringIO import StringIO` for strings. This is not the same as `from io import StringIO` in Python2 (or in Python3). The former handles strings, the latter handles unicode. For Py2, since we're not prefixing all strings with `u""` to make them unicode, we need to use the first one. So, different `StringIO` classes need to be imported for Python2 and Python3. The same `from io import StringIO` cannot be shared. - https://docs.python.org/2.7/library/stringio.html?highlight=stringio#StringIO.StringIO - https://docs.python.org/2.7/library/io.html?highlight=io%20stringio#io.StringIO | 26 November 2021, 14:35:08 UTC |
| fb74540 | Ankur Sinha (Ankur Sinha Gmail) | 26 November 2021, 13:40:25 UTC | Revert "fix: py2 build" This reverts commit aa025c608a678697d14acaca1cf8d7ed0a0a7fd6. | 26 November 2021, 13:40:25 UTC |
| 914cb2c | Padraig Gleeson | 24 November 2021, 11:18:30 UTC | To v0.3.1 | 24 November 2021, 11:18:30 UTC |
| 61f6e17 | Padraig Gleeson | 24 November 2021, 11:01:23 UTC | Merge pull request #110 from NeuralEnsemble/feat/dev-new-generateds Regenerate genrateDS with Python3, add CI to test generation, drop json serialisation (doesn't work with lxml), add generic `add` method | 24 November 2021, 11:01:23 UTC |
| aa025c6 | Ankur Sinha (Ankur Sinha Gmail) | 22 November 2021, 13:18:36 UTC | fix: py2 build Use BytesIO for py2, but StringIO for py3. I'm not entirely sure why this is needed here. It isn't necessarily an issue in nml.py---it could be in the loaders where we're not being too careful about py2/py3. The versions of pytables in use are also different because pytables dropped support for py2 in 3.6.x. | 22 November 2021, 13:18:36 UTC |
| bbe4cb6 | Ankur Sinha (Ankur Sinha Gmail) | 19 November 2021, 11:15:15 UTC | chore: use latest available generateds | 19 November 2021, 11:15:15 UTC |
| e5ada98 | Ankur Sinha (Ankur Sinha Gmail) | 19 November 2021, 10:53:18 UTC | test: only use assertRegex/assertNotRegex on Python3+ assertRegex was added in 3.1 assertNotRegex was added in 3.2 | 19 November 2021, 10:53:18 UTC |
| 39c1437 | Ankur Sinha (Ankur Sinha Gmail) | 19 November 2021, 10:43:06 UTC | test: only use assertWarns check on Python3 It was added in Python 3.2 and is not present in Python 2.7. Reference: https://docs.python.org/3.10/library/unittest.html#unittest.TestCase.assertWarns | 19 November 2021, 10:43:06 UTC |
| 3da2d83 | Ankur Sinha (Ankur Sinha Gmail) | 19 November 2021, 10:32:58 UTC | chore: regenerate nml.py | 19 November 2021, 10:32:58 UTC |
| a97d808 | Ankur Sinha (Ankur Sinha Gmail) | 19 November 2021, 10:32:41 UTC | chore: sync XSD | 19 November 2021, 10:32:41 UTC |
| aaad763 | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 18:50:22 UTC | chore: do not lint build folder | 18 November 2021, 18:50:22 UTC |
| 99e0ae7 | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 18:29:04 UTC | Merge branch 'development' into feat/dev-new-generateds | 18 November 2021, 18:29:04 UTC |
| c047804 | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 18:21:43 UTC | chore: regenerate nml.py | 18 November 2021, 18:21:43 UTC |
| f3fc7f9 | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 18:21:35 UTC | chore: sync XSD | 18 November 2021, 18:21:35 UTC |
| cc673e1 | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 10:46:17 UTC | docs: add note about autogeneration of nml.py documentation | 18 November 2021, 10:46:17 UTC |
| 3b7306a | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 10:45:59 UTC | chore: regenerate nml.py | 18 November 2021, 10:45:59 UTC |
| 353d1c9 | Ankur Sinha (Ankur Sinha Gmail) | 18 November 2021, 10:45:52 UTC | chore: sync XSD | 18 November 2021, 10:45:52 UTC |
| 891cbeb | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 17:25:57 UTC | docs: change class doc format | 17 November 2021, 17:25:57 UTC |
| bb53446 | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 17:25:10 UTC | docs: show base classes | 17 November 2021, 17:25:10 UTC |
| 6b09503 | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 17:22:07 UTC | chore: regenerate nml.py | 17 November 2021, 17:22:07 UTC |
| 492d59f | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 17:21:51 UTC | chore: sync XSD | 17 November 2021, 17:21:51 UTC |
| 7080720 | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 15:11:56 UTC | chore: regenerate nml.py | 17 November 2021, 15:11:56 UTC |
| 26864c7 | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 15:11:21 UTC | chore: sync XSD | 17 November 2021, 15:11:21 UTC |
| 71c209c | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 14:29:11 UTC | chore: regenerate nml.py | 17 November 2021, 14:29:11 UTC |
| e655b5e | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 14:27:14 UTC | chore: sync XSD | 17 November 2021, 14:27:14 UTC |
| ebe354f | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 11:12:55 UTC | Merge branch 'feat/generic-add-method' into feat/dev-new-generateds | 17 November 2021, 11:12:55 UTC |
| 36ef5c7 | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 11:11:46 UTC | chore: regenerate nml.py to include documentation | 17 November 2021, 11:11:46 UTC |
| 7984589 | Ankur Sinha (Ankur Sinha Gmail) | 17 November 2021, 11:07:52 UTC | chore: update to documented XSD file File from https://github.com/NeuroML/NeuroML2/pull/172 | 17 November 2021, 11:07:52 UTC |
| 5afb7af | Ankur Sinha | 17 November 2021, 11:04:05 UTC | Merge pull request #115 from NeuralEnsemble/feat/generic-add-method feat: add method to add child/children elements to objects | 17 November 2021, 11:04:05 UTC |
| b9acf1f | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:35:32 UTC | docs: update changelog | 08 November 2021, 21:35:32 UTC |
| 815737b | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:29:59 UTC | refactor: add deprecation warning to `append_to_element` utility method | 08 November 2021, 21:29:59 UTC |
| 1092bf9 | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:24:32 UTC | chore: reformat with black | 08 November 2021, 21:24:32 UTC |
| 0b56d56 | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:23:03 UTC | chore(nml.py): regenerate | 08 November 2021, 21:23:03 UTC |
| 2dcbbd2 | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:22:29 UTC | test(xml_parser): user pytest.parameterize to run on different files Also a few other clean ups. | 08 November 2021, 21:22:29 UTC |
| 38a160b | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:21:42 UTC | test(nml.py): add test for containers objects | 08 November 2021, 21:21:42 UTC |
| 2dcd2a7 | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:21:22 UTC | chore: update comment | 08 November 2021, 21:21:22 UTC |
| dad20c2 | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:15:48 UTC | test(nml.py): update assertion to check for a warning | 08 November 2021, 21:15:48 UTC |
| 93f7328 | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:14:58 UTC | feat(helper_methods): update `append` to use new `add` method | 08 November 2021, 21:14:58 UTC |
| 564927b | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:11:47 UTC | fix(helper_methods): use shallow copy We want a copy of the object to add other inherited member_data_types_ to. If we use `=`, we get a reference to `self.member_data_types_` object and end up modifying it, which we do not want to do. Not only does that change the nml.py representation, it also means that all the "expanded" lists of `member_data_types_` is held in memory for every neuroml object which greatly increases the memory foot print of models. So, calculate the complete list of member_data_types_ when required and then forget about it, which will allow memory to be garbage collected and freed up. | 08 November 2021, 21:11:47 UTC |
| f6e167b | Ankur Sinha (Ankur Sinha Gmail) | 08 November 2021, 21:10:10 UTC | improvement(helper_methods): convert exception to warning Attempting to readd an object is harmless, so make this a warning. Also fixes the comparison to not use `is` because it doesn't only compare the reference, it also compares the value. | 08 November 2021, 21:10:10 UTC |
| 5e4fb35 | Ankur Sinha (Ankur Sinha Gmail) | 05 November 2021, 14:58:30 UTC | test: add test for get_members | 05 November 2021, 14:58:30 UTC |
| 675736b | Ankur Sinha (Ankur Sinha Gmail) | 05 November 2021, 14:58:21 UTC | chore: regenerate nml.py | 05 November 2021, 14:58:21 UTC |
| 174513a | Ankur Sinha (Ankur Sinha Gmail) | 05 November 2021, 14:58:02 UTC | feat: collect inherited members also | 05 November 2021, 14:58:02 UTC |
| 58cccfa | Ankur Sinha (Ankur Sinha Gmail) | 29 October 2021, 14:17:52 UTC | meh: squash | 29 October 2021, 14:17:52 UTC |
| 8837155 | Ankur Sinha (Ankur Sinha Gmail) | 29 October 2021, 14:17:43 UTC | chore: make mypy ignore nml.py | 29 October 2021, 14:17:43 UTC |
| 69d10f8 | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 17:20:43 UTC | chore: regenerate nml.py | 26 October 2021, 17:20:43 UTC |
| 886b82d | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 17:20:32 UTC | feat: improve output string | 26 October 2021, 17:20:32 UTC |
| 29f6902 | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 16:57:01 UTC | test: update method call | 26 October 2021, 16:57:01 UTC |
| 3fe4bcb | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 16:51:26 UTC | chore: regenerate nml.py | 26 October 2021, 16:51:26 UTC |
| 88ef5d3 | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 16:39:34 UTC | feat: make add show current obj information without any arguments So users can primarily just use `add()`. | 26 October 2021, 16:39:34 UTC |
| 8454b15 | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 16:38:04 UTC | feat: improve output from info method | 26 October 2021, 16:38:04 UTC |
| e923143 | Ankur Sinha (Ankur Sinha Gmail) | 26 October 2021, 16:37:48 UTC | feat: update name of helper function | 26 October 2021, 16:37:48 UTC |
| 6c4ed0d | Ankur Sinha | 18 October 2021, 16:55:53 UTC | Merge pull request #116 from NeuralEnsemble/fix/flake-ignore-nml ci: ignore nml.py for flake | 18 October 2021, 16:55:53 UTC |
| e2b565c | Ankur Sinha (Ankur Sinha Gmail) | 18 October 2021, 16:42:09 UTC | ci: also ignore build dir | 18 October 2021, 16:42:09 UTC |
| cf96416 | Ankur Sinha (Ankur Sinha Gmail) | 18 October 2021, 16:37:55 UTC | ci: ignore nml.py for flake | 18 October 2021, 16:37:55 UTC |
| 656c45b | Padraig Gleeson | 18 October 2021, 15:59:15 UTC | To v0.2.58 Some more files in black | 18 October 2021, 15:59:15 UTC |
| daf3762 | Ankur Sinha (Ankur Sinha Gmail) | 14 October 2021, 14:52:43 UTC | feat: add gitter chat badge | 14 October 2021, 14:52:43 UTC |
| 62a7cc4 | Ankur Sinha (Ankur Sinha Gmail) | 13 October 2021, 14:36:28 UTC | test(nml.py): add basic tests for new helper functions - get_member_info - add | 13 October 2021, 14:36:28 UTC |
| 1394d12 | Ankur Sinha (Ankur Sinha Gmail) | 13 October 2021, 14:36:17 UTC | chore: regenerate nml.py | 13 October 2021, 14:36:17 UTC |
| 99a9517 | Ankur Sinha (Ankur Sinha Gmail) | 13 October 2021, 14:35:55 UTC | feat: tweak member_info method to also return the string This will be useful for testing purposes. | 13 October 2021, 14:35:55 UTC |
| 06329f0 | Ankur Sinha (Ankur Sinha Gmail) | 13 October 2021, 12:48:38 UTC | chore: reformat Exception strings | 13 October 2021, 12:48:38 UTC |
| 6ab810c | Ankur Sinha (Ankur Sinha Gmail) | 13 October 2021, 12:36:21 UTC | chore: regenerate nml.py | 13 October 2021, 12:45:45 UTC |
| e300042 | Ankur Sinha (Ankur Sinha Gmail) | 13 October 2021, 12:32:11 UTC | feat: add method to add child/children elements to objects - also adds a corresponding method to get some information about them The function is added to `BaseWithoutId` and so should be inherited by everything. The `add` method: - gets the list of the members defined by generateDS for each each class - checks the type of the object being added to the types of the members to find the right member to add to. If a member with the type cannot be found, an Exception is raised. - if a member is found, it can either be a child member (can only have one value) or a children member (can have multiple values in a list). - For child members a check is made to see if a value is already set. If not, the value is set to the given object. - For children members, a check is made to see if the object has already been added. If not, the object is added. - If either test fails, an Exception is raised (since one does not need to re-add objects to update their value) - A `force` option allows overwriting and readdition, but is set to `False` by default. So, example usage would be of this type: ``` cell = neuroml.Cell(id="acell") biprop = neuroml.BiophysicalProperties(id="biprop") cell.add(biprop) # success cell.add(biprop) # will throw an Exception unless `force=True` cell.add("a string") # will throw an Exception since no member has a type "str" ``` Note: we have a few ComponentTypes which don't inherit from anywhere, and we need to check if these are correctly defined in the XSD file (Location is an example). | 13 October 2021, 12:36:49 UTC |
| 11c2539 | Ankur Sinha | 13 October 2021, 09:14:52 UTC | Merge pull request #114 from NeuralEnsemble/fix/neuroml-113 Raise TypeError if file loaded is not a NeuroML file | 13 October 2021, 09:14:52 UTC |
| f201ac9 | Ankur Sinha (Ankur Sinha Gmail) | 11 October 2021, 17:32:56 UTC | feat: improve error message | 11 October 2021, 17:32:56 UTC |
| b7aea15 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 18:11:14 UTC | feat: add test for loader reading a non-NeuroML file | 08 October 2021, 18:11:14 UTC |
| 5cf468e | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 18:10:29 UTC | fix: raise TypeError if file read is not a neuroml file Fixes #113 | 08 October 2021, 18:10:29 UTC |
| ac95271 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 16:36:30 UTC | feat: make CI fail if generateDS is not found | 08 October 2021, 16:36:30 UTC |
| 3959a89 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 16:06:27 UTC | fix: remove exit statements | 08 October 2021, 16:06:27 UTC |
| c880d49 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 16:04:10 UTC | chore: correct black command check | 08 October 2021, 16:04:10 UTC |
| e30413a | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 16:04:00 UTC | fix: correct python version extraction | 08 October 2021, 16:04:00 UTC |
| cd87061 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:57:45 UTC | fix: use correct test function for regex check | 08 October 2021, 15:57:45 UTC |
| dea3b49 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:51:38 UTC | fix: tweak regenerate script for py2.7 The version of generateDS we use for Python 2.7 has a slightly different way of taking in the helper method file. It does not require the `.py` suffix. | 08 October 2021, 15:51:51 UTC |
| d3d6644 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:44:46 UTC | chore: correct version markers in requirements-dev | 08 October 2021, 15:44:46 UTC |
| dd7303d | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:41:27 UTC | chore: pin generateds to latest known working version for Py2 | 08 October 2021, 15:41:27 UTC |
| 9a671cf | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:36:54 UTC | fix: correct nml.py regeneration in ci | 08 October 2021, 15:36:54 UTC |
| 44c00c2 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:32:50 UTC | feat!: drop json serialisation lxml.etree._Element objects cannot be pickled. See #111 for more information. Fixes #111 BREAKING CHANGE: drops json serialisation | 08 October 2021, 15:34:25 UTC |
| 4a9a5e3 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:13:31 UTC | chore: regenerated nml.py | 08 October 2021, 15:13:31 UTC |
| 4a7cfe9 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:12:57 UTC | refactor: improve nml.py generator script | 08 October 2021, 15:12:57 UTC |
| 39f9f00 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 15:11:33 UTC | fix: correct file mode for py3 | 08 October 2021, 15:11:33 UTC |
| 33a520c | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 11:43:34 UTC | chore: limit black to py3 | 08 October 2021, 11:43:34 UTC |
| 3c338f3 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 11:04:00 UTC | Merge branch 'feat/add-nmlpy-tests' into feat/dev-new-generateds | 08 October 2021, 11:04:00 UTC |
| 4c547b2 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 11:01:40 UTC | Merge branch 'development' into feat/dev-new-generateds | 08 October 2021, 11:01:40 UTC |
| 21abc16 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 10:58:30 UTC | chore: tweak generateds command | 08 October 2021, 10:58:30 UTC |
| 50ee7d0 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 10:57:13 UTC | chore(nml.py): add conditional imports for py2/3 | 08 October 2021, 10:57:13 UTC |
| 1bd1d1b | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 10:00:20 UTC | chore: update readme for regenerating nml.py | 08 October 2021, 10:00:20 UTC |
| e2ce455 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 09:59:20 UTC | ci(nml.py): add an action to regenerate nml.py and run all tests This ensures we regularly check that nml.py is correctly generated. | 08 October 2021, 09:59:20 UTC |
| f3ecc6c | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 09:57:45 UTC | chore: add generateDS version constraints also add black to dev requirements | 08 October 2021, 09:57:45 UTC |
| 000eab5 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 09:43:42 UTC | chore: add section for 0.2.57 in changelog (and reformat) | 08 October 2021, 09:43:42 UTC |
| cafdb8f | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 09:43:26 UTC | chore: add python 3.10 in setup.py (and reformat with black) | 08 October 2021, 09:43:26 UTC |
| c9d6c0e | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 09:34:12 UTC | chore: add numpy to dev to allow pytables wheels to build | 08 October 2021, 09:34:12 UTC |
| 13d1882 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 09:23:44 UTC | chore: reorder requirements Cython must be installed before pip tries to build pytables. Also moves flake and pytest to requirements-dev. | 08 October 2021, 09:23:44 UTC |
| a408744 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 08:51:42 UTC | chore: use latest git snapshot for tables for python >= 3.10 The last release they made does not work with Python 3.10. Fixes are in the GitHub repo but pending a new release. | 08 October 2021, 08:51:42 UTC |
| 33e1e81 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 08:35:53 UTC | chore: add wheel to dev requirements | 08 October 2021, 08:35:53 UTC |
| f28eda7 | Ankur Sinha (Ankur Sinha Gmail) | 08 October 2021, 08:34:50 UTC | ci: install liblzo2-dev for pytables The docs say it's optional, but the pytables build failure seems to indicate it's required. | 08 October 2021, 08:34:50 UTC |
