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Bump pyslim from 1.1.0 to 1.1.1 in /requirements/CI#1813

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Bump pyslim from 1.1.0 to 1.1.1 in /requirements/CI#1813
dependabot[bot] wants to merge 1 commit intomainfrom
dependabot/pip/requirements/CI/pyslim-1.1.1

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@dependabot dependabot bot commented on behalf of github Mar 9, 2026

Bumps pyslim from 1.1.0 to 1.1.1.

Release notes

Sourced from pyslim's releases.

Maintenance release

  • Improved performance on remove_vacant (#393)
  • Require Python >= 3.11
Changelog

Sourced from pyslim's changelog.


[1.1.2] - 2026-XX-XX


In development


[1.1.1] - 2026-03-06


Maintenance release.

  • Improved performance on remove_vacant (:issue:393)
  • Require Python >= 3.11

[1.1.0] - 2025-08-16


Major update release to support the release of SLiM v5.0. The main update here is support for multiple chromosomes, which entailed a change to the node table metadata that records "vacancy" for chromosomes not diploid in a given individual. Changes are minimal if you're simulating a single, diploid chromosome; for more information see https://tskit.dev/pyslim/docs/latest/previous_versions.html

Breaking changes:

  • SLiM tree sequence file version number has changed to 0.9.

  • This is a change in SLiM, really, but top-level SLiM metadata now requires a "this_chromosome" entry.

  • Similarly, node metadata no longer has genome_type or is_null; instead they have is_vacant, and the chromosome type is in top-level metadata, under metadata['SLiM']['this_chromosome'].

  • pyslim.slim_metadata_schemas["node"] has an appropriate metadata schema for a single-chromosome simulation (not a breaking change), but users wishing to set up a multi-chromosome simulation should use instead pyslim.slim_node_metadata_schema (which has the appropriate value in ["properties"]["is_vacant"]["length"]) (:user:petrelharp, :pr:367).

  • Previously, pyslim.annotate would leave existing node and individual metadata, even if this metadata came from a different schema. This could silently create garbage metadata. Now, annotate removes any existing metadata, and warns if this occurs (:user:petrelharp, :pr:390).

... (truncated)

Commits
  • e8e39fc Tidy up requirements in pyproject
  • 6854f2d Update changelog pre-release
  • d6a572e remove redundant python version
  • a6486cb Pin shared workflows to v15, set uv to 0.10.0
  • 07476c8 Update dev docs
  • b694797 Skip another failing windows test
  • 367dbc1 Make the windows test skip broader
  • 7b0ddd3 Really skip on windows
  • e178167 Use only-group
  • 617ca73 Pin workflows at v14
  • Additional commits viewable in compare view

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Bumps [pyslim](https://github.com/tskit-dev/pyslim) from 1.1.0 to 1.1.1.
- [Release notes](https://github.com/tskit-dev/pyslim/releases)
- [Changelog](https://github.com/tskit-dev/pyslim/blob/main/CHANGELOG.rst)
- [Commits](tskit-dev/pyslim@1.1.0...1.1.1)

---
updated-dependencies:
- dependency-name: pyslim
  dependency-version: 1.1.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Mar 9, 2026
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codecov bot commented Mar 9, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.81%. Comparing base (e23d255) to head (9307290).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1813   +/-   ##
=======================================
  Coverage   99.81%   99.81%           
=======================================
  Files         142      142           
  Lines        4873     4873           
  Branches      472      472           
=======================================
  Hits         4864     4864           
  Misses          6        6           
  Partials        3        3           

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