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

Refactoring & new web app #5

Merged
merged 34 commits into from
Aug 22, 2024
Merged

Refactoring & new web app #5

Changes from 1 commit
Commits
Show all changes
34 commits
Select commit Hold shift + click to select a range
0c31846
KAN-83 fix metagenomics bug
aromberg Mar 4, 2024
2213879
fix code format
aromberg Mar 4, 2024
68f526f
KAN-19 add basic documentation
aromberg Mar 4, 2024
1ad6ec9
KAN-19 update documentation
aromberg Mar 4, 2024
5dcb8f4
KAN-109 ensure Jellyfish is installed
aromberg Mar 4, 2024
9732d15
KAN-118 add exception handling for entrez literature search
aromberg Mar 5, 2024
744d6f6
KAN-79 add meaningful error when attempting to train a genus with no …
aromberg Mar 5, 2024
7b18b20
KAN-79 fix literature search
aromberg Mar 5, 2024
3492992
KAN-112 fix browser loading
aromberg Mar 6, 2024
d155f12
update gitignore
aromberg Jun 12, 2024
0e3d22e
major refactor to use COBS as the main underlying data structure
aromberg Jun 12, 2024
0d11b1e
add sparse sampling
aromberg Jun 12, 2024
ba42338
update dependencies
aromberg Jun 12, 2024
54f2c6f
update dependencies
aromberg Jun 12, 2024
87a932e
update model downloads
aromberg Jun 12, 2024
7ea5a8c
fix pyproject.toml
aromberg Jun 12, 2024
badf5ba
fix svm model fit test
aromberg Jun 12, 2024
119c908
load complete index into RAM before calculating hits
aromberg Jun 13, 2024
67fbe08
fix error when collecting metadata
aromberg Aug 12, 2024
3b4c000
refactor web app
aromberg Aug 12, 2024
6669cd2
remove Flask
aromberg Aug 12, 2024
d6554c4
update dependencies
aromberg Aug 12, 2024
2523b79
fix linting errors
aromberg Aug 17, 2024
b561e8f
add pylint workflow
aromberg Aug 17, 2024
3ea8409
update readme
aromberg Aug 17, 2024
862b4e3
update readme
aromberg Aug 17, 2024
76b8b18
update docs
aromberg Aug 17, 2024
32c9755
remove xspect web files
aromberg Aug 18, 2024
111855e
refactor extraction
aromberg Aug 18, 2024
78bad47
calculate results on a by-sequence basis and output them to a dedicat…
aromberg Aug 19, 2024
e50dbe8
add dynamic pipelines & result objects
aromberg Aug 22, 2024
9acbb51
bump version
aromberg Aug 22, 2024
51fdad4
add PyPi workflow
aromberg Aug 22, 2024
569ec9d
fix ci
aromberg Aug 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
bump version
  • Loading branch information
@aromberg
aromberg committed Aug 22, 2024
commit 9acbb513b6e794145ccba9279a906ac528d1e9d9
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[project]
name = "XspecT"
version = "0.1.3"
version = "0.2.0"
description = "Tool to monitor and characterize pathogens using Bloom filters."
readme = {file = "README.md", content-type = "text/markdown"}
license = {file = "LICENSE"}
Expand Down