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Author SHA1 Message Date
Olamide Isreal
8dd0ef8d6a Configure propka pipeline for WES/k8s execution
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- Update container reference to harbor.cluster.omic.ai/omic/propka:latest
- Add k8s profile to nextflow.config matching reference tool pattern
- Update params.json with s3://omic/eureka/propka/ paths
- Add stageInMode 'copy' to process definition
- Set params defaults to null for WES compatibility
 2026-03-24 21:03:07 +01:00
Olamide Israel
1c6d9582d0 Add Nextflow pipeline for PROPKA with Docker configuration
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2025-03-14 10:46:31 -07:00
Thomas Holder
27e0ad2f8d Merge pull request #187 from speleo3/remove-unused 
Remove unused code
 2024-02-19 08:39:07 +01:00
Thomas Holder
25ed65eed9 More static typing 2024-02-02 19:49:51 +01:00
Thomas Holder
c8d93f6f01 Remove unused arguments, replace mutable defaults 
Closes https://github.com/jensengroup/propka/issues/53
Closes https://github.com/jensengroup/propka/issues/56
 2024-02-02 19:49:51 +01:00
Thomas Holder
9ea6d8815d Remove some unused code 
- Remove all code which was previously marked with
  `NotImplementedError("unused")`.
- Remove unsued command line arguments
 2024-02-02 19:49:51 +01:00
Thomas Holder
6ee0df8e6d Merge pull request #186 from speleo3/windows-ci 
Add Windows CI
 2024-01-21 17:01:30 +01:00
Thomas Holder
725c4186b5 CI: Add Windows 2024-01-21 11:54:31 +01:00
Thomas Holder
c9a05509f9 CI: Update "uses" versions 2024-01-21 10:49:32 +01:00
Nathan Baker
b45e57298d Merge pull request #185 from jensengroup/nathan/184 
Update Sphinx package versions.
 2024-01-16 06:25:42 -08:00
Nathan Baker
1ba71af5e1 Update Sphinx package versions. 
Fixes #184.
 2024-01-15 19:52:01 -08:00
Nathan Baker
94142ffc04 Merge pull request #183 from jensengroup/nathan/168 
Version 3.5.1 release candidate
 2024-01-01 18:13:12 -08:00
Nathan Baker
c9f3fc6e68 Fix typo in RST file. 2023-12-31 17:19:05 -08:00
Nathan Baker
01152d7db8 Add sphinx_sitemap requirement. 2023-12-31 08:59:26 -08:00
Nathan Baker
0035cad1d1 Pinning doc version numbers. 2023-12-31 08:57:02 -08:00
Nathan Baker
fd17693ed8 Add Sphinx requirements.txt 2023-12-31 08:52:33 -08:00
Nathan Baker
edd118d716 Add readthedocs config file. 2023-12-31 08:49:00 -08:00
Nathan Baker
6c1d5e2552 Update ChangeLog 2023-12-31 08:44:05 -08:00
Nathan Baker
af0fd55bcb Merge pull request #182 from jensengroup/nathan/181 
Fix problem with ZIP paths on Windows.
 2023-12-30 19:08:33 -08:00
Nathan Baker
8659f0372e Clean up POSIX path conversion. 
Replace `str.join` with `Path.as_posix`.
 2023-12-30 15:25:46 -08:00
Nathan Baker
a757325efb Fix problem with ZIP paths on Windows. 
Fixes #181.
 2023-12-29 08:26:02 -08:00
Thomas Holder
5a00d059b2 Merge pull request #177 from speleo3/mypy-2 
More static typing
 2023-12-19 10:51:58 +01:00
Thomas Holder
abd3d05910 Add py.typed 2023-12-16 09:35:35 +01:00
Thomas Holder
1d50cf4b0b Typing: Atom members 2023-12-16 09:35:35 +01:00
Thomas Holder
0aafca7f73 Typing: Options 2023-12-16 09:35:35 +01:00
Thomas Holder
723609cc33 Deprecate Vector operator overloads 2023-12-16 09:35:35 +01:00
Thomas Holder
57ad5d8384 Typing: Parameters, vector_algebra 
- Parameters typing
- vector_algebra tests and refactoring
- Various pyright typing improvements
 2023-12-16 09:35:35 +01:00
Thomas Holder
4106726483 Raise NotImplementedError from unused functions 2023-12-16 09:13:23 +01:00
Thomas Holder
9d4b59c825 Remove unused MultiVector 2023-12-16 09:10:40 +01:00
Thomas Holder
83c17217f9 Merge pull request #176 from speleo3/replace-pkg_resources 
Refactor deprecated pkg_resources usage
 2023-12-10 22:34:47 +01:00
Thomas Holder
50f62c61fb Refactor deprecated pkg_resources usage 
- Locate resources relative to `__file__`
- Support egg/zip with `open_file_for_reading`
 2023-12-10 11:59:21 +01:00
Thomas Holder
a62e2a4dae Merge pull request #172 from speleo3/mypy 
Add type annotations and mypy CI job
 2023-11-03 12:46:28 +01:00
Thomas Holder
57d7c6721b Add type annotations and mypy CI job 2023-10-26 11:46:54 +02:00
Thomas Holder
ee89e36f58 Merge pull request #171 from speleo3/versioneer-0.29 
Update versioneer to version 0.29
 2023-10-21 09:57:05 +02:00
Thomas Holder
a03d903acc Add Python 3.12 to CI 2023-10-21 09:32:06 +02:00
Thomas Holder
1c8885d400 Update versioneer to version 0.29 
Installed versioneer 0.29 with Python 3.12 and ran

```
versioneer install
```
 2023-10-21 09:20:54 +02:00
Nathan Baker
8ba1692e42 Merge pull request #170 from speleo3/test-issue-140 
Add test for issue #140
 2023-10-20 19:13:17 -07:00
Thomas Holder
54d76ec145 Add test for issue #140 2023-10-20 23:22:17 +02:00
Maohua Yang
33158d1172 Add more element valence (#169) 
* Add valence electrons for all elements
* fix: add unknown element valence to 4
* fix: group None bug
 2023-10-20 23:20:51 +02:00
Nathan Baker
d1d3b37b82 Merge pull request #167 from speleo3/top_up_from_atoms 
Improve MolecularContainer.top_up_conformations
 2023-09-17 08:18:26 -07:00
Thomas Holder
7d78acac6e Improve MolecularContainer.top_up_conformations 
Top up from all conformations, not just first.

Fixes https://github.com/jensengroup/propka/issues/147
 2023-09-17 15:30:29 +02:00
Nathan Baker
fd7b155171 Merge pull request #159 from jensengroup/nathan/153 
Release candidate for 3.5.0.
 2023-02-13 19:53:08 -08:00
Nathan Baker
af1b08dcbb Release candidate for 3.5.0. 
Fixes #153.

Once tagged as v3.5.0 (after commit to master), the version should
automatically update via versioneer.
 2023-02-12 20:49:59 -08:00
Nathan Baker
3155badf33 Merge pull request #158 from jensengroup/nathan/155 
Add past changes to ChangeLog.
 2023-02-05 14:16:26 -08:00
Nathan Baker
c74e7cda66 Clarify change in log. 
Fixes a863426e63 (r1096640761)
 2023-02-05 14:13:28 -08:00
Nathan Baker
0de6387b69 Clarify change in log. 
Fixes a863426e63 (r1096641709)
 2023-02-05 14:12:16 -08:00
Nathan Baker
a863426e63 Add past changes to ChangeLog. 
Fixes #155.
 2023-02-04 19:21:08 -08:00
Nathan Baker
430b631c9d Merge pull request #156 from jensengroup/nathan/154 
Update Python support.
 2023-02-04 18:47:55 -08:00
Nathan Baker
72c4950683 Remove Python 3.6 and 3.7 from more files. 2023-01-29 15:07:51 -08:00
Nathan Baker
74b8425234 Remove Python 3.7 support. 
Make corresponding changes to other files (including a few that I
missed before).
 2023-01-29 14:58:57 -08:00