Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

V0.2 #293

Merged
merged 28 commits into from
Jul 8, 2024
Merged

V0.2 #293

merged 28 commits into from
Jul 8, 2024

Conversation

thomashopf
Copy link
Contributor

Will progressively update with new features to prepare v0.2 release

aaronkollasch and others added 28 commits March 16, 2023 11:04
@aaronkollasch
Support a3m format in existing alignment protocol
d472e4b
@thomashopf
Prepare tests for new version, update readme and setup
7192161
@thomashopf
Keep as is due to github security restrictions
b4fc441
@thomashopf
Fix numpy dtype deprecation, fixes #291
e136240
@thomashopf
fix deprecation in pandas df equality checking in tests
7863312
@thomashopf
Merge pull request #286 from aaronkollasch/a3m-support
7eab82c 
Support a3m format in existing alignment protocol
@thomashopf
pin yaml due to upcoming API change
a880fea
@thomashopf
Fix alignment identifier memory usage, add header splitting, fixes #289
5cd4033
@thomashopf
Correct wrong exception raise, fixes #199
2324ed6
@thomashopf
better handler around occasional plmc segfaults, fixes #292
9d34d5e
@thomashopf
Numpy deprecation fix, closes #248
5b3b3f0
bump to python3.10
b9951e4 
bump to python3.11
update GH actions
add yml files
55ccdf5
build
5a50ab9
add build
686ca3c
@thomashopf
Fix PDB chain retrieval regression by pandas/numpy updates
b4eb674
@thomashopf
Merge pull request #301 from zachcp/v0.2-patch
8fbf92d 
V0.2 patch
@thomashopf
Replace MMTF with bCIF
c2a766d
@thomashopf
Make model handling consistent to previous class
cde87ae
@thomashopf
Replace pd.append with pd.concat
2872d3d
@thomashopf
fix overlapping secondary structure elements
4778267
@thomashopf
fix numpy warning (#306)
cccc1ca
@thomashopf
fix scikit-learn warning, cf. #306
05c6423
@thomashopf
better backward compatibility for chain extraction
6567251
@thomashopf
fix charge handling
7e2c0bb
@thomashopf
fix charge handling pt2
58aa2c0
@thomashopf
fix alt_loc
9bfa113
@thomashopf
fix yet another pandas deprecation
476700b
@thomashopf
Copy link
Contributor Author

Fixes:

  • MMTF phaseout by RCSB, now loading bCIF structures instead
  • Many small regressions that have accumulated over the years. Should now install cleanly with up-to-date versions of numpy and pandas. Packages that depend on specific versions are pinned in setup.py

@thomashopf thomashopf merged commit 374d4c5 into develop Jul 8, 2024
4 checks passed
@thomashopf thomashopf deleted the v0.2 branch July 8, 2024 11:36
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@thomashopf @aaronkollasch