perf: update tools in conda environments #132
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WalkthroughSeveral environment YAML files were updated to specify newer versions of key dependencies, including Python, pandas, pysam, dnaio, picard, rtg-tools, bcftools, samtools, vembrane, scipy, scikit-learn, and statsmodels. No changes were made to channels or the structure of the environment files. Changes
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Actionable comments posted: 0
🧹 Nitpick comments (4)
workflow/envs/rtg-tools.yaml (1)
6-6: Add trailing newline for YAMLlint compliance
YAMLlint reports "no new line character at the end of file". Please add a blank line at EOF to satisfy the linter.--- a/workflow/envs/rtg-tools.yaml +++ b/workflow/envs/rtg-tools.yaml @@ dependencies: - - rtg-tools =3.13 + - rtg-tools =3.13 +# newline at end of file🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/vembrane.yaml (1)
6-6: Add trailing newline for YAMLlint compliance
This file is missing a newline at EOF. Adding a blank line will resolve the linter error.--- a/workflow/envs/vembrane.yaml +++ b/workflow/envs/vembrane.yaml @@ dependencies: - - bcftools =1.22 + - bcftools =1.22 +# newline at end of file🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/stats.yaml (1)
9-9: Add trailing newline for YAMLlint compliance
The missing newline at EOF triggers a lint error. Please append a blank line at the end of the file.--- a/workflow/envs/stats.yaml +++ b/workflow/envs/stats.yaml @@ -8,3 +8,5 @@ dependencies: - - statsmodels =0.14.4 + - statsmodels =0.14.4 +# newline at end of file🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/pysam.yaml (1)
9-9: Add newline at end of file
YAML files should end with a newline to satisfy formatting tools and avoid linter errors.🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (6)
workflow/envs/picard.yaml(1 hunks)workflow/envs/pysam.yaml(1 hunks)workflow/envs/rtg-tools.yaml(1 hunks)workflow/envs/stats.yaml(1 hunks)workflow/envs/tools.yaml(1 hunks)workflow/envs/vembrane.yaml(1 hunks)
🧰 Additional context used
🪛 YAMLlint (1.37.1)
workflow/envs/rtg-tools.yaml
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/stats.yaml
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/vembrane.yaml
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/pysam.yaml
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
🔇 Additional comments (6)
workflow/envs/picard.yaml (1)
5-5: Version bump for picard
Upgradingpicardfrom 3.1 to 3.4.0 aligns with the coordinated environment updates in this PR.workflow/envs/tools.yaml (1)
6-7: bcftools & samtools version bump
Bothbcftoolsandsamtoolshave been correctly bumped from 1.20 to 1.22, matching the upgrade in related environment files.workflow/envs/rtg-tools.yaml (1)
6-6: Upgrade rtg-tools to v3.13
The version update from 3.12.1 to 3.13 is consistent with the PR objectives and other tool upgrades.🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/vembrane.yaml (1)
5-6: Upgrade vembrane & bcftools versions
Updatedvembraneto 2.0.0 and alignedbcftoolsto 1.22, consistent with the rest of the workflow environments.🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 6-6: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/stats.yaml (1)
5-9: Update statistical package versions
All dependencies—pandas,python,scipy,scikit-learn, andstatsmodels—are correctly bumped to their new versions, ensuring compatibility and currency.🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
workflow/envs/pysam.yaml (1)
6-9:❓ Verification inconclusive
Verify compatibility of updated dependencies
Upgrading Python from 3.9 to 3.13.3 (and bumps for pysam, pandas, dnaio) may introduce breaking changes. Ensure downstream code and CI pipelines build and pass tests with these versions.Run the following to confirm the environment can be created and dependencies import successfully:
🏁 Script executed:
#!/bin/bash # Validate pysam environment build conda env create -f workflow/envs/pysam.yaml --name test-pysam-env --dry-run # Build and test imports conda env create -f workflow/envs/pysam.yaml --name test-pysam-env -y source activate test-pysam-env python - << 'EOF' import pysam, pandas, dnaio print("pysam:", pysam.__version__, "pandas:", pandas.__version__, "dnaio:", dnaio.__version__) EOFLength of output: 611
Verify compatibility of updated Python and dependencies
The sandbox cannot validate conda environments. Please run the following locally to ensure no breaking changes:
- Create the environment:
conda env create -f workflow/envs/pysam.yaml --name test-pysam-env- Activate and test imports:
conda activate test-pysam-env python - << 'EOF' import pysam, pandas, dnaio print("pysam:", pysam.__version__, "pandas:", pandas.__version__, "dnaio:", dnaio.__version__) EOF- Verify that downstream code and CI pipelines build and pass tests under Python 3.13.3 with pysam 0.23.3, pandas 2.3.0, and dnaio 1.2.3.
🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
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Actionable comments posted: 0
🧹 Nitpick comments (1)
workflow/envs/pysam.yaml (1)
9-9: Add newline at end of file.
The file currently lacks a trailing newline, which can trigger YAML lint errors.🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
workflow/envs/pysam.yaml(1 hunks)
🧰 Additional context used
🪛 YAMLlint (1.37.1)
workflow/envs/pysam.yaml
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Testing
🔇 Additional comments (1)
workflow/envs/pysam.yaml (1)
6-9:❓ Verification inconclusive
Verify dependency compatibility and test environment build.
Upgrading to Python 3.11, pysam 0.23.3, pandas 2.3.0, and dnaio 1.2.3 can introduce solver conflicts or unsupported builds. Please run a dry-run conda environment build to confirm no resolution errors:
🏁 Script executed:
#!/bin/bash # Dry-run install to catch solver conflicts conda env create --name test-pysam --file workflow/envs/pysam.yaml --dry-runLength of output: 174
Verify dependency compatibility and test environment build locally
Conda isn’t available in this environment, so automatic verification couldn’t run. Please execute the following on a machine with conda installed to confirm there are no solver conflicts:conda env create --name test-pysam --file workflow/envs/pysam.yaml --dry-run🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 9-9: no new line character at the end of file
(new-line-at-end-of-file)
famosab
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Actionable comments posted: 0
🧹 Nitpick comments (1)
workflow/envs/pysam.yaml (1)
10-10: Fix missing newline and trailing whitespace at EOF.YAMLLint flags a missing end-of-file newline and trailing spaces on the blank line. Apply this diff to remove the whitespace and add a final newline:
--- a/workflow/envs/pysam.yaml +++ b/workflow/envs/pysam.yaml @@ -9,1 +9,2 - - dnaio =1.2 + - dnaio =1.2 +🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 10-10: no new line character at the end of file
(new-line-at-end-of-file)
[error] 10-10: trailing spaces
(trailing-spaces)
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
workflow/envs/pysam.yaml(1 hunks)
🧰 Additional context used
🪛 YAMLlint (1.37.1)
workflow/envs/pysam.yaml
[error] 10-10: no new line character at the end of file
(new-line-at-end-of-file)
[error] 10-10: trailing spaces
(trailing-spaces)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Testing
🔇 Additional comments (1)
workflow/envs/pysam.yaml (1)
6-9: Confirm compatibility of upgraded dependencies.The bump to Python 3.11, pysam 0.23.3, and pandas 2.3.0 is significant—please ensure the downstream workflow and any custom scripts have been tested against Python 3.11 and that pysam/pandas APIs haven’t introduced breaking changes. Also verify that dnaio 1.2 remains compatible with the new Python and pandas versions.
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