fix: remove unecessary deps

[fgvieira]

QC

• I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• test.py was updated to call any added or updated example rules in a Snakefile
• input: and output: file paths in the rules can be chosen arbitrarily
• wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• the meta.yaml contains a link to the documentation of the respective tool or command under url:
• conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• Chores
  • Removed explicit Python version pins from multiple GATK3 environments.
  • Removed samtools from Paladin index and prepare environments.
  • Removed numpy, pandas and polars from the datavzrd environment.
  • Updated Conda tooling metadata to 25.9.0 and reduced explicit third‑party package pins in several manifests.

[coderabbitai]

📝 Walkthrough

Walkthrough

Removed explicit Python (python=3.14.0) pins from several GATK3 environment files, removed samtools from Paladin environments, deleted numpy/pandas/polars from the datavzrd environment, and pruned many entries and updated conda metadata in multiple pinned environment manifests.

Changes

Cohort / File(s)	Summary
GATK3 Python dependency removals bio/gatk3/baserecalibrator/environment.yaml, bio/gatk3/indelrealigner/environment.yaml, bio/gatk3/printreads/environment.yaml, bio/gatk3/realignertargetcreator/environment.yaml	Removed explicit python =3.14.0 pin from dependencies in each GATK3 environment YAML.
Paladin samtools removal bio/paladin/index/environment.yaml, bio/paladin/prepare/environment.yaml	Deleted samtools from Paladin environment YAML dependencies.
Paladin pinned environment cleanup bio/paladin/index/environment.linux-64.pin.txt, bio/paladin/prepare/environment.linux-64.pin.txt	Updated created-by conda metadata (24.9.2 → 25.9.0) and removed several explicit pinned artifacts (bzip2, libdeflate, liblzma, htslib, samtools, etc.) from the Linux-64 pin manifests.
DataVzrd dependency removals utils/datavzrd/environment.yaml	Removed numpy, pandas, and polars from the datavzrd environment YAML dependencies.
DataVzrd pinned manifest pruning utils/datavzrd/environment.linux-64.pin.txt	Removed numerous platform-specific and Python/ecosystem pins (numpy, pandas, libgfortran variants, BLAS/LAPACK, tzdata, python-dateutil, polars, etc.) from the Linux-64 pin manifest.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

• Multiple environment YAMLs and pinned manifests changed; changes are repetitive but affect reproducibility and dependency matrices.
• Pay extra attention to:
  • Compatibility implications of removing Python pins in GATK3 wrappers.
  • Downstream consumers expecting samtools in Paladin environments.
  • Datavzrd removal of numpy/pandas/polars and the large pin pruning in environment.linux-64.pin.txt.

Possibly related PRs

• fix: fixed datavzrd environment pinning to include numpy, pandas and polars #3426 — also modifies utils/datavzrd environment pins and numpy/pandas/polars entries.
• perf: Update datavzrd wrapper #3635 — updates utils/datavzrd environment files and pinned manifests, closely related to the pin pruning here.
• perf: autobump bio/gatk3/printreads #3129 — touches bio/gatk3/printreads Python pinning; related to Python pin removal in GATK3 files.

Suggested labels

bio/gatk3/printreads

Suggested reviewers

• johanneskoester
• cmeesters

Pre-merge checks and finishing touches

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Description Check	⚠️ Warning	The PR description is largely incomplete despite following the template structure. The main descriptive section—where the author should explain what dependencies are being removed and why they are unnecessary—is entirely empty, with only the template placeholder comments visible. While the QC checklist is fully completed with all boxes checked, most of these items are not applicable to this PR about environment configuration changes (e.g., "test.py was updated," "input:/output: file paths can be chosen arbitrarily," "temporary files are stored appropriately," and "meta.yaml contains documentation links" are not relevant to removing environment dependencies). The description lacks substantive information about the rationale for removing these specific dependencies or any technical justification for the changes.	Add a meaningful description explaining which dependencies are being removed, why they are unnecessary, and any relevant context or testing performed. Also review the QC checklist to ensure only applicable items are marked as completed; several items in the list do not pertain to environment configuration changes. The description should provide enough detail that reviewers understand the motivation and scope of this dependency cleanup effort.
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (1 passed)

Check name	Status	Explanation
Title Check	✅ Passed	The title "fix: remove unecessary deps" follows the conventional commit style with "fix:" as the type prefix and provides a clear, concise description of the main change. The changeset demonstrates exactly what the title claims: removing dependencies across multiple environment files (Python 3.14.0 from gatk3 modules, samtools from paladin modules, and numpy/pandas/polars from datavzrd). Despite a minor typo ("unecessary" instead of "unnecessary"), the title is specific enough that a teammate reviewing the commit history would quickly understand the primary objective of this PR. The title accurately summarizes the changeset and relates directly to the actual modifications.

✨ Finishing touches

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• Create PR with unit tests
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📜 Recent review details

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 17ef091 and 9e694c0.

📒 Files selected for processing (1)

• utils/datavzrd/environment.linux-64.pin.txt (0 hunks)

💤 Files with no reviewable changes (1)

• utils/datavzrd/environment.linux-64.pin.txt

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• GitHub Check: testing
• GitHub Check: docs
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[johanneskoester]

@fxwiegand I think these were added intentionally weren't they?

[fgvieira]

The tests do not fail and, if they are needed by datavzrd, shouldn't they be added directly on the conda recipe?

[fxwiegand]

They were added because of this template rendering issue with YTE that complained about something with numpy I think. @johanneskoester is this solved now?

[johanneskoester]

I think they have to be present whenever the datavzrd config that is passed to the wrapper is a YTE template that contains numpy, pandas, or polars elements. Before we remove them, we should definitely extend the test case in this repo to also do that, maybe in a followup PR instead of changing it here?