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

v0.5.0-prerelease #43

Merged
merged 29 commits into from
Nov 3, 2023
Merged

v0.5.0-prerelease #43

merged 29 commits into from
Nov 3, 2023

Conversation

rhysnewell
Copy link
Owner

@rhysnewell rhysnewell commented Nov 3, 2023 •
edited
Loading

Fixes major issues related to #36, #42, #41, etc.

  • exposes flight error messages to user
  • second part of algorithm now runs in parallel
  • refine now runs in parallel
  • updated dependencies: tested in multiple conda installs. Versions should work.

closes #25 not viable, this version allows users to try and acces rust based umap but not recommended.

rhysnewell and others added 29 commits September 28, 2022 09:30
@rhysnewell
fix: indicatif dependency issue. cleanup warnings. v0.4.2
a3e0f28
@rhysnewell
update: master --> main
2371f03
@rhysnewell
fix: update build workflow and add docs workflow
4d33e8f
@rhysnewell
Update usage.md
8cb5985
@rhysnewell
Update README.md
5d784ad
rewriting rosella from scratch, hoping to abandon python completely
719b84b
feat: removing dependencies, lighten the load
a26bd48
feat: setting up embedding using annembed and hnsw
53ac9a1
fix: various bug fixes working initial version of UMAP and hdbscan bi…
fdda197 
…nning in rust
feat: better error messaging, debug mode writes bin stats
dcc1dba
@rhysnewell
testing verification
0692210
@rhysnewell
feat: iterative mutua k-nn graph filtering
960b8fe
@rhysnewell
feat: add silhouette score prototype
e1f096d
@rhysnewell
feat: integrate TNF table into main recovery pipeline. Subsetting emb…
85f983b 
…edding working
@rhysnewell
feat: intersecting graphs and reembedding clusters
f13c4af
@rhysnewell
feat: update rust based umap/hdbscan implementations
172c8ee
@rhysnewell
feat: added label propagation-esque algo for unbinned contigs and rel…
6bc42f5 
…ease script
@rhysnewell
feat: code refactoring and cluster connections using graphs
ab5d314
@rhysnewell
feat: add proportionality and CLR to kmer table
d12c045
@rhysnewell
fix: bug fix in coverage dist calculation
7f1f624
@rhysnewell
save commit for future reference, about to revert
17c49cc
@rhysnewell
staging for reversion
bb7ed2a
@rhysnewell
fix bin metric bug
83e936e
@rhysnewell
fix: now compatible with flight
77f3ec1
@rhysnewell
missed files
3d9fa85
@rhysnewell
ISS-36: add working refinery
bbdb47b
@rhysnewell
ISS-36: recover uses refinery as well for speed boost
f3e5726
@rhysnewell
feat(ISS-36): proper handling of refining. Dont put unbinned in refin…
ce64bf7 
…ery not worth
@rhysnewell
feat(ISS-36): update rosella.yml dependencies
bcfe383
@rhysnewell rhysnewell merged commit 3cf1b4b into dev Nov 3, 2023
@rhysnewell rhysnewell deleted the ISS-36 branch November 3, 2023 11:00
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.
1 participant
@rhysnewell