Skip to content

[WIP] v2.0.0 release #123

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
Draft
nicodr97 wants to merge 577 commits into
base: trimAl
Choose a base branch
from
Draft

[WIP] v2.0.0 release #123

nicodr97 wants to merge 577 commits into from

Conversation

@nicodr97
Copy link
Collaborator

@nicodr97 nicodr97 commented Nov 14, 2025

No description provided.

Victor Fernandez and others added 30 commits April 12, 2019 11:11
Merge remote-tracking branch 'origin/ngs' into trimAl
1330fce
Updated AUTHORS to reflect current maintainer and updated affiliations
399d205
@scapella
Merge branch 'trimAl' of https://github.com/Vicfero/trimal into Vicfe…
f4e9922 
…ro-trimAl
@scapella
Merge branch 'Vicfero-trimAl' into 2.0_RC
e718e73
@scapella
Fixed the minimum cmake version required to compile trimAl
fb0eb74 
Fixed some legacy code introduced during the massive push request
@scapella
Internal benchmarking is now deactivated by default.
3c5b178 
When active, this feaure signficantly slows down the time performance.
@scapella
Merge pull request #50 from scapella/trimAl
0eab54b 
Improved variable names for a better code readibility
Updated Authors and Build values. Also updated the Usage section on m…
dde3983 
…ain page of the documentation
Address feedback #51 (review)
0c02094
Solved an issue where additive gap stats were added for each gap stat…
3d33da6 
… requested (sgc|sgt)
@scapella
Merge pull request #51 from Vicfero/2.0_RC
a96bded 
Updated hard-coded values and documentation source.
Fixed a bug detected while computing the general gaps statistics.
@scapella
Include the tag "RC" as version. This is still a release candidate
0698fc1
@danieledler
Fix print correct input type in readAl
f8bed4f 
Datatype 'unknown' printed as 'amino-acids_degenerate_codes'
@althonos
Add function to count the number of occurences of a character in a st…
b4646ee 
…ring
@althonos
Add method to get the length of a single sequence in Alignment
b7ce24d
@althonos
Avoid building new string when computing a sequence length in `Cleane…
365b839 
…r` and `Alignment`
@althonos
Use memchr to improve performance of utils::countCharacter
eb52430
@nicodr97
Correct functions descriptions
cfc6c47
@nicodr97
Merge pull request #73 from althonos/count-character
04181d8 
Improve performance of sequence length computation
@althonos
Rewrite alignment identity into a statistic managed by `statistics::M…
423bfef 
…anager`
@althonos
Move overlap computation into a dedicated statistic class
5f6df54
@althonos
Avoid recomputing overlap vector in calculateSpuriousVector
e640ba1
@althonos
Add method to calculate spurious vector directly from Manager
916ef8f
@althonos
Fix call to calculateSpuriousVec in cleanSpuriousSeq
821fd7e
@althonos
Fix comment for Overlap::overlaps attribute
13b54f1
@althonos
Revert back to original implementations in Overlap statistics
ad4d093
@nicodr97
Merge pull request #72 from althonos/identity-statistics
6da1fa0 
Move identity and overlap computation into dedicated `statistics` classes
@althonos
Add utility methods to similarityMatrix
98074c4
@althonos
Declare some methods as virtual to support overloading from SIMD va…
95c18e5 
…riants
@althonos
Add generic SIMD template with concrete SSE2 implementation
9945a48
nicodr97 and others added 29 commits February 23, 2024 09:35
@nicodr97
Test only x86_64
1698868
@nicodr97
Fix gap threshold in strict method calculations
9469eb3
@nicodr97
Update README.md
464aef6
@nicodr97
Update README.md
3226f92
@nicodr97
Add command to download cpu_features submodule
4ca7510
@althonos
Remove outdated comment lines from parser code
f6892a9
@nicodr97
Merge pull request #97 from althonos/stream-load
3b3018c 
Refactor the parsers for better compatibility and memory usage
@nicodr97
Ignore known different test MSAs
dd51f64
@nicodr97
Add aarch64 to build workflow
11ed3c2
@nicodr97
Remove debugging log
fc59219
@nicodr97
Make script alpine shell compatible
15a9817
@nicodr97
Add armv7 architecture and refactor build workflow
47ebee4
@nicodr97
Add os matrix to test best arm simulator
93c83c6
@nicodr97
Avoid repeated jobs
7b23d4c
@nicodr97
Add missing conditions
12556cc
@nicodr97
Add missing flag to arm compilations
9e65ff7
@nicodr97
Use alpine for arm arch
cb69033
@nicodr97
Fix armv7 compilation parameters
eb09557
@nicodr97
Add explanation for binaries and warning message
d89ffc3
@nicodr97
Add automated2 method
008fb5b
@nicodr97
Add test_msas folder to gitignore
c83182b
@nicodr97
Add automated2 trimmed MSAs
8d6e082
@scapella
Merge pull request #59 from danieledler/2.0_RC
6629fe2 
Fix print correct input type in readAl
@althonos
Fix missing stdint.h includes necessary for uint32_t typedef
af4a50b
@althonos
Fix uninitialized values and division-by-zero in `Cleaner::getCutPoin…
e975b27 
…tClusters`
@althonos
Fix uninitialized local min/max accumulators in `Cleaner::getCutPoint…
a867405 
…Clusters`
@scapella
Merge pull request #117 from althonos/fix-clusters
87207c3 
Fix `-clusters` options from the CLI
@althonos
Fix for loop brackets and average counter initializer in `Cleaner::…
d65a19d 
…getCutPointClusters`
@nicodr97
Merge pull request #118 from althonos/2.0_RC
447ea91 
Fix `for` loop brackets and average counter initializer in `Cleaner::getCutPointClusters`
@sonarqubecloud
Copy link

sonarqubecloud bot commented Nov 14, 2025

Quality Gate Failed Quality Gate failed

Failed conditions
89 Security Hotspots
4.8% Duplication on New Code (required ≤ 3%)
E Reliability Rating on New Code (required ≥ A)

See analysis details on SonarQube Cloud

Catch issues before they fail your Quality Gate with our IDE extension SonarQube for IDE

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.

5 participants

@nicodr97 @scapella @danieledler @althonos