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  • bf7728d976 Add k8s executor and storage config to nextflow.config main Olamide Isreal 2026-03-24 21:08:54 +01:00
  • 8dd0ef8d6a Configure propka pipeline for WES/k8s execution Olamide Isreal 2026-03-24 21:03:07 +01:00
  • 1c6d9582d0 Add Nextflow pipeline for PROPKA with Docker configuration Olamide Israel 2025-03-14 10:46:31 -07:00
  • 27e0ad2f8d Merge pull request #187 from speleo3/remove-unused Thomas Holder 2024-02-19 08:39:07 +01:00
  • 25ed65eed9 More static typing Thomas Holder 2024-01-21 09:23:10 +01:00
  • c8d93f6f01 Remove unused arguments, replace mutable defaults Thomas Holder 2023-12-21 22:42:51 +01:00
  • 9ea6d8815d Remove some unused code Thomas Holder 2023-12-21 22:24:29 +01:00
  • 6ee0df8e6d Merge pull request #186 from speleo3/windows-ci Thomas Holder 2024-01-21 17:01:30 +01:00
  • 725c4186b5 CI: Add Windows Thomas Holder 2024-01-21 09:38:29 +01:00
  • c9a05509f9 CI: Update "uses" versions Thomas Holder 2024-01-21 10:48:47 +01:00
  • b45e57298d Merge pull request #185 from jensengroup/nathan/184 Nathan Baker 2024-01-16 06:25:42 -08:00
  • 1ba71af5e1 Update Sphinx package versions. Nathan Baker 2024-01-15 19:52:01 -08:00
  • 94142ffc04 Merge pull request #183 from jensengroup/nathan/168 Nathan Baker 2024-01-01 18:13:12 -08:00
  • c9f3fc6e68 Fix typo in RST file. Nathan Baker 2023-12-31 17:19:05 -08:00
  • 01152d7db8 Add sphinx_sitemap requirement. Nathan Baker 2023-12-31 08:59:26 -08:00
  • 0035cad1d1 Pinning doc version numbers. Nathan Baker 2023-12-31 08:57:02 -08:00
  • fd17693ed8 Add Sphinx requirements.txt Nathan Baker 2023-12-31 08:52:33 -08:00
  • edd118d716 Add readthedocs config file. Nathan Baker 2023-12-31 08:49:00 -08:00
  • 6c1d5e2552 Update ChangeLog Nathan Baker 2023-12-31 08:44:05 -08:00
  • af0fd55bcb Merge pull request #182 from jensengroup/nathan/181 Nathan Baker 2023-12-30 19:08:33 -08:00
  • 8659f0372e Clean up POSIX path conversion. Nathan Baker 2023-12-30 15:25:46 -08:00
  • a757325efb Fix problem with ZIP paths on Windows. Nathan Baker 2023-12-29 08:26:02 -08:00
  • 5a00d059b2 Merge pull request #177 from speleo3/mypy-2 Thomas Holder 2023-12-19 10:51:58 +01:00
  • abd3d05910 Add py.typed Thomas Holder 2023-12-13 15:49:40 +01:00
  • 1d50cf4b0b Typing: Atom members Thomas Holder 2023-12-13 19:53:16 +01:00
  • 0aafca7f73 Typing: Options Thomas Holder 2023-12-13 15:18:39 +01:00
  • 723609cc33 Deprecate Vector operator overloads Thomas Holder 2023-12-13 08:12:42 +01:00
  • 57ad5d8384 Typing: Parameters, vector_algebra Thomas Holder 2023-12-12 20:41:17 +01:00
  • 4106726483 Raise NotImplementedError from unused functions Thomas Holder 2023-12-12 20:39:59 +01:00
  • 9d4b59c825 Remove unused MultiVector Thomas Holder 2023-12-14 08:47:13 +01:00
  • 83c17217f9 Merge pull request #176 from speleo3/replace-pkg_resources Thomas Holder 2023-12-10 22:34:47 +01:00
  • 50f62c61fb Refactor deprecated pkg_resources usage Thomas Holder 2023-12-10 11:59:21 +01:00
  • a62e2a4dae Merge pull request #172 from speleo3/mypy Thomas Holder 2023-11-03 12:46:28 +01:00
  • 57d7c6721b Add type annotations and mypy CI job Thomas Holder 2023-09-21 20:32:23 +02:00
  • ee89e36f58 Merge pull request #171 from speleo3/versioneer-0.29 Thomas Holder 2023-10-21 09:57:05 +02:00
  • a03d903acc Add Python 3.12 to CI Thomas Holder 2023-10-21 09:32:06 +02:00
  • 1c8885d400 Update versioneer to version 0.29 Thomas Holder 2023-10-21 09:17:52 +02:00
  • 8ba1692e42 Merge pull request #170 from speleo3/test-issue-140 Nathan Baker 2023-10-20 19:13:17 -07:00
  • 54d76ec145 Add test for issue #140 Thomas Holder 2023-09-24 16:49:37 +02:00
  • 33158d1172 Add more element valence (#169) Maohua Yang 2023-10-21 05:20:51 +08:00
  • d1d3b37b82 Merge pull request #167 from speleo3/top_up_from_atoms Nathan Baker 2023-09-17 08:18:26 -07:00
  • 7d78acac6e Improve MolecularContainer.top_up_conformations Thomas Holder 2023-09-17 15:19:25 +02:00
  • fd7b155171 Merge pull request #159 from jensengroup/nathan/153 Nathan Baker 2023-02-13 19:53:08 -08:00
  • af1b08dcbb Release candidate for 3.5.0. Nathan Baker 2023-02-12 20:49:59 -08:00
  • 3155badf33 Merge pull request #158 from jensengroup/nathan/155 Nathan Baker 2023-02-05 14:16:26 -08:00
  • c74e7cda66 Clarify change in log. Nathan Baker 2023-02-05 14:13:28 -08:00
  • 0de6387b69 Clarify change in log. Nathan Baker 2023-02-05 14:12:16 -08:00
  • a863426e63 Add past changes to ChangeLog. Nathan Baker 2023-02-04 19:21:08 -08:00
  • 430b631c9d Merge pull request #156 from jensengroup/nathan/154 Nathan Baker 2023-02-04 18:47:55 -08:00
  • 72c4950683 Remove Python 3.6 and 3.7 from more files. Nathan Baker 2023-01-29 15:07:51 -08:00
  • 74b8425234 Remove Python 3.7 support. Nathan Baker 2023-01-29 14:58:57 -08:00
  • 967e8e7912 Convert Python version numbers to strings. Nathan Baker 2023-01-29 14:53:12 -08:00
  • 0a0602761b Update Python support. Nathan Baker 2023-01-29 14:45:54 -08:00
  • 01bf46ce74 Merge pull request #150 from IAlibay/py311 Nathan Baker 2022-11-09 18:58:07 -08:00
  • 3e897b792f Update python-package.yml Irfan Alibay 2022-11-09 18:34:23 +00:00
  • f6f3c51c1c Update CI and docs for Python up to py311 IAlibay 2022-11-09 14:16:59 +00:00
  • 8acfb4fe1b Merge pull request #148 from speleo3/fix-get_pi Nathan Baker 2022-08-08 19:52:36 -07:00
  • 80c7bf07cd Refactor MolecularContainer.get_pi Thomas Holder 2022-08-08 21:21:45 +02:00
  • 6388e0c4ee Test pI (isoelectric point) result Thomas Holder 2022-08-08 21:18:30 +02:00
  • ab80128c45 Merge pull request #141 from latrocinia/master Nathan Baker 2022-03-02 20:16:20 -08:00
  • b920f5aeec Add unit test for protonate.py Gydo van Zundert 2022-03-02 15:45:11 -05:00
  • f49eaedefb protonate.py: Rename Vanadium element from Va to V Gydo van Zundert 2022-02-24 11:47:08 -05:00
  • beddb0ac87 Merge pull request #124 from danny305/master Nathan Baker 2021-11-22 15:09:47 -08:00
  • 17197831de Merge pull request #133 from speleo3/open_file_for_reading_context_manager Darren Curtis 2021-11-01 11:19:34 -07:00
  • ed087b02c7 Return context manager from open_file_for_reading Thomas Holder 2021-10-31 18:36:38 +01:00
  • c37f54b93c refactored Decimal/round order of operation. Danny Diaz 2021-03-06 11:02:41 -06:00
  • 38aab010dc Addressed bug CLI parameters for the -g and -w options did not output to .pka file Danny Diaz 2021-02-17 20:39:29 -08:00
  • 68007f065c Merge pull request #121 from jensengroup/nathan/docs Nathan Baker 2020-12-18 19:24:20 -08:00
  • a22fd506be Remove numbering from Sphinx documentation. Nathan Baker 2020-12-17 16:00:00 -08:00
  • c443b218a8 Merge pull request #120 from jensengroup/nathan/changelog Nathan Baker 2020-12-16 19:35:32 -08:00
  • 52e3649e27 Address comments on change log. Nathan Baker 2020-12-15 20:10:40 -08:00
  • d87afb3df5 Document changes associated with older releases. Nathan Baker 2020-12-13 16:49:26 -08:00
  • d1df3844fe Fix incorrect restructured text. Nathan Baker 2020-12-13 16:46:27 -08:00
  • 2f10ecdd1f Merge pull request #114 from jensengroup/issue-17 Nathan Baker 2020-12-13 10:45:27 -08:00
  • 82879cdda5 Add a changelog Thomas Holder 2020-12-09 12:39:03 +01:00
  • 578b57694f propka3 --version prints version Thomas Holder 2020-12-06 20:36:58 +01:00
  • f028562026 Missing N or O in AMD Group: Keep going Thomas Holder 2020-12-07 09:26:53 +01:00
  • 3937cb1467 Merge pull request #112 from jensengroup/fix-105 Thomas Holder 2020-12-06 17:40:49 +01:00
  • 8f8aa29be4 Fix propka --display-coupled-residues Thomas Holder 2020-12-06 17:22:30 +01:00
  • 31b41c32df Merge pull request #110 from jensengroup/fix-97-speedup-box-bonding Thomas Holder 2020-12-03 10:19:01 +01:00
  • c78345c75c Refactor box bonding Thomas Holder 2020-12-02 08:52:59 +01:00
  • cc8514e3dc Fix BondMaker.put_atom_in_box Thomas Holder 2020-12-02 08:15:59 +01:00
  • 45aa08a79c Merge pull request #109 from jensengroup/nathan/logging Nathan Baker 2020-12-01 11:55:26 -08:00
  • e081bd53b3 Add line breaks to error message. Nathan Baker 2020-12-01 06:40:44 -08:00
  • de020599d3 Raise error for ligand pKa errors. Nathan Baker 2020-11-30 15:21:47 -08:00
  • c281623078 Change logging message to error. Nathan Baker 2020-11-30 15:17:18 -08:00
  • fda4fe577b Merge branch 'master' into nathan/logging Nathan Baker 2020-11-29 16:14:43 -08:00
  • 9350799be1 Remove logging abstraction to facilitate debugging and reduce bloat. Nathan Baker 2020-11-29 16:09:45 -08:00
  • f3bbd807ae Merge pull request #100 from IAlibay/rm-propkainput Nathan Baker 2020-11-29 15:41:28 -08:00
  • 3ca674776f Remove unused attributes IAlibay 2020-11-18 18:15:42 +00:00
  • 67039aabc0 Merge pull request #102 from IAlibay/python3.9 Nathan Baker 2020-11-18 09:32:51 -08:00
  • b164c1db1a Adds python3.9 to CI IAlibay 2020-11-18 01:27:41 +00:00
  • 196a2c6a1f remove unused command IAlibay 2020-11-18 01:13:59 +00:00
  • 012865e9e9 fix argparse typo IAlibay 2020-11-18 00:53:07 +00:00
  • da7999832d Remove unused initialized_atom_group IAlibay 2020-11-18 00:51:46 +00:00
  • d6ebd48473 missed conf container code IAlibay 2020-11-18 00:31:15 +00:00
  • 239c8183c9 Initial removal of PROPKA input IAlibay 2020-11-17 23:31:24 +00:00
  • 9dfd87a0eb Fix handling of multi-model PDB without MODEL 1 Thomas Holder 2020-11-10 19:05:19 +01:00
  • 810750cdd7 Fix pI reporting in last line of .pka file Thomas Holder 2020-07-21 13:05:41 +02:00
  • 552dd133e6 Report correct version in .pka file header Thomas Holder 2020-07-21 13:45:18 +02:00