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.

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

Bump biopython from 1.84 to 1.85 in /pipeline/seq_retrieval #489

Merged

Conversation

dependabot[bot]
Copy link
Contributor

@dependabot dependabot bot commented on behalf of github Jan 27, 2025

Bumps biopython from 1.84 to 1.85.

Changelog

Sourced from biopython's changelog.

15 January 2025: Biopython 1.85

This release of Biopython supports Python 3.9, 3.10, 3.11, 3.12 and 3.13. It has also been tested on PyPy3.9 v7.3.13. Python 3.9 is approaching end of life, our support for it is now deprecated.

Some optimisation work was done for Bio.SeqIO including avoiding nested iterators, and speeding up both FASTA and FASTQ parsing.

Bio.motifs now supports reading PFM from Cys2His2 Zinc Finger Proteins PWM Predictor and reading motifs in pfm-four-columns format will set motif name to "" instead of None, when no motif name was found.

Tests that use assertAlmostEqual calls now use places parameter with enough presision when comparing very small numbers in scientific notation.

Bio.motifs now supports reverse complementing RNA motifs and correctly generating degenerate consensus sequences for RNA motifs.

Bio.motifs.minimal now supports parsing RNA motifs and parsing motifs for which not all statistics are provided (e.g. missing E-values or nsites).

Bio.motifs.clusterbuster now supports parsing GAP and WEIGHT parameters and can optionally write Cluster Buster motif files with floats instead of integers, by specifying the precision=<int> parameter when writing: e.g. motifs.write(motifs, "clusterbuster", precision=2)

Additionally, a number of small bugs and typos have been fixed with additions to the test suite and type annotations.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

  • Alan Medlar
  • Carlos Peña
  • Gert Hulselmans
  • Peter Cock
  • Michiel de Hoon
Commits

Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.


Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

  • @dependabot rebase will rebase this PR
  • @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
  • @dependabot merge will merge this PR after your CI passes on it
  • @dependabot squash and merge will squash and merge this PR after your CI passes on it
  • @dependabot cancel merge will cancel a previously requested merge and block automerging
  • @dependabot reopen will reopen this PR if it is closed
  • @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
  • @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
  • @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
  • @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
  • @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jan 27, 2025
Copy link

The validation workflow automatically applied the below dependency lock file updates.
A bundle with all dependency lock files is available here as artifact called deps_lock_files_bundle.

shared_aws/py_package/tests/requirements.txt
diff --git a/shared_aws/py_package/tests/requirements.txt b/shared_aws/py_package/tests/requirements.txt
index 2dfcac8..8bf3714 100644
--- a/shared_aws/py_package/tests/requirements.txt
+++ b/shared_aws/py_package/tests/requirements.txt
@@ -44,9 +44,9 @@ botocore==1.36.7 \
     # via
     #   boto3
     #   s3transfer
-botocore-stubs==1.36.6 \
-    --hash=sha256:e4b35ed9557e15d6ba0cb110bffe89f5ed6a8a202e7cf4c9a67667e7e4a7790c \
-    --hash=sha256:f47c30036a5e3c842ef7347aeb2067a952959a7b9c32c7dc0ed27040a231350d
+botocore-stubs==1.36.7 \
+    --hash=sha256:51c51da5379d3e4c4cb7e3dbe8451f572ecbfe6a5ced3a76a6b958941ef72409 \
+    --hash=sha256:77052e3a86a3f77383c638db63379652bafac3a2b310954392e0cfb3dacd3dad
     # via boto3-stubs
 cattrs==24.1.2 \
     --hash=sha256:67c7495b760168d931a10233f979b28dc04daf853b30752246f4f8471c6d68d0 \

@dependabot dependabot bot force-pushed the dependabot/pip/pipeline/seq_retrieval/biopython-1.85 branch from a94b40f to ca65db1 Compare January 28, 2025 14:57
Copy link

Automatic dependency lock file updates enabled, but no updates found. No (additional) dependency updates will be made when merging this PR.

@mluypaert
Copy link
Member

@dependabot rebase

Bumps [biopython](https://github.com/biopython/biopython) from 1.84 to 1.85.
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

---
updated-dependencies:
- dependency-name: biopython
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot force-pushed the dependabot/pip/pipeline/seq_retrieval/biopython-1.85 branch from ca65db1 to 8b1d677 Compare January 28, 2025 16:11
Copy link

Automatic dependency lock file updates enabled, but no updates found. No (additional) dependency updates will be made when merging this PR.

@mluypaert mluypaert merged commit b608fff into main Jan 28, 2025
32 checks passed
@mluypaert mluypaert deleted the dependabot/pip/pipeline/seq_retrieval/biopython-1.85 branch January 28, 2025 16:19
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
dependencies Pull requests that update a dependency file python Pull requests that update Python code
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant