Update matchms dependencies

[BioGeek]

Update matchms dependencies to match those in the pyproject.toml of the project

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[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces updates to the meta.yaml file for the matchms package. The version number is incremented from 0.27.0 to 0.27.1, and the build number changes from 0 to 1. The Python version requirement has been adjusted from >=3.8,<3.12 to >=3.9,<3.13. Additionally, several dependencies have been updated with specific version constraints. The deprecated package now requires a minimum version of 1.2.14, while lxml, matplotlib-base, networkx, numba, numpy, pyyaml, rdkit, requests, scipy, tqdm, pillow, and pandas have all been updated to reflect new version requirements or exclusions. Notably, the pillow package now explicitly excludes version 9.4.0. There are no changes to the test imports or the about section of the package.

Possibly related PRs

• Update PhyloAcc recipe #51090: The changes in the meta.yaml file for the PhyloAcc package include updates to the build number and Python version compatibility, which are similar in nature to the updates made in the matchms package's meta.yaml.
• Update tbtamr dependencies #51140: The tbtamr package's meta.yaml updates include changes to the Python version requirement, which aligns with the modifications made in the matchms package's meta.yaml.
• Update assembly_finder recipe #51449: The assembly_finder package's meta.yaml updates include changes to the Python version requirement and dependency updates, similar to the changes made in the matchms package's meta.yaml.

Suggested labels

new version

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 63b1db5 and f3c7ece.

📒 Files selected for processing (1)

• recipes/matchms/meta.yaml (2 hunks)

🧰 Additional context used

🔇 Additional comments (9)

recipes/matchms/meta.yaml (9)

13-13: LGTM: Build number increment is correct.

Incrementing the build number from 0 to 1 is appropriate when updating dependencies without changing the package version. This change follows conda packaging best practices.

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25-30: LGTM: Dependency updates look good.

The updates to dependency versions (deprecated, lxml, matplotlib-base, networkx, numba, numpy) appear to be in line with the PR objectives. These changes likely reflect the latest compatible versions.

To ensure these updates don't introduce compatibility issues, consider running the package's test suite with these new dependency versions.

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33-33: LGTM: Python version consistency achieved.

The update to python >=3.9,<3.13 in the run section now matches the host section, resolving the inconsistency noted in the previous review. This change ensures compatibility between the build and runtime environments.

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34-37: LGTM: Further dependency updates look good.

The updates to dependency versions (pyyaml, rdkit, requests, scipy) continue to align with the PR objectives. These changes likely reflect the latest compatible versions for the package.

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39-39: LGTM: tqdm version update is appropriate.

Specifying a minimum version for tqdm (>=4.65.0) is a good practice. This ensures compatibility with the latest features or bug fixes in the tqdm package.

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40-40: Please clarify the pillow version constraint.

The pillow dependency has been changed from =9.5 to !=9.4.0. While excluding a specific version can be valid, it's unclear why this particular version (9.4.0) is being excluded. Could you provide more context on this change?

Is there a known issue with pillow 9.4.0 that necessitates this exclusion? If so, consider adding a comment in the meta.yaml file explaining the reason for this constraint.

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41-41: LGTM: pandas version update is appropriate.

Specifying a minimum version for pandas (>=2.0.3) is a good practice. This ensures compatibility with the latest features or bug fixes in the pandas package.

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Line range hint 1-70: Summary of review for recipes/matchms/meta.yaml

The changes in this file largely meet the PR objectives of updating dependencies for the matchms package. Key points:

1. The build number has been correctly incremented.
2. Python version requirements have been updated and are now consistent between host and run sections.
3. Most dependency updates look good and align with the goal of using the latest compatible versions.
4. The change to the pillow dependency requires clarification.

Overall, the changes improve the package's compatibility with newer dependency versions. Once the pillow dependency change is clarified, this update should be ready for merging.

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22-22: Verify Python version consistency.

The update to python >=3.9,<3.13 in the host section is good. However, please ensure this change is consistent with the Python version specified in the run section (line 33) to address the previous review comment about version inconsistency.

Run the following script to check for consistency:

✅ Verification successful

Python version requirement is now consistent between host and run sections.
The update to python >=3.9,<3.13 ensures both sections are aligned, addressing the previous inconsistency.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check Python version requirements in recipes/matchms/meta.yaml
rg -i 'python\s*(:|version|=|>=|<=|<|>)' recipes/matchms/meta.yaml

Length of output: 118

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[coderabbitai]

Actionable comments posted: 2

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 496918d and 63b1db5.

📒 Files selected for processing (1)

• recipes/matchms/meta.yaml (2 hunks)

🧰 Additional context used

🔇 Additional comments (5)

recipes/matchms/meta.yaml (5)

13-13: LGTM: Build number increment is correct.

Incrementing the build number from 0 to 1 is appropriate when making changes to the package without changing the version. This change follows conda-forge best practices.

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25-25: Verify specific version requirement for 'deprecated' package.

The deprecated package now requires a minimum version of 1.2.14. Please confirm that this specific version requirement aligns with the upstream project's needs and doesn't introduce any compatibility issues.

---

30-30: Verify numpy version range expansion.

The numpy package requirement has been changed from <1.25 to >1.22,<1.27. This expands the range of supported numpy versions. Please confirm that this change is intentional and doesn't introduce any compatibility issues with other dependencies or the package itself.

---

40-40: Clarify pillow version requirement change.

The pillow package requirement has changed from =9.5 to !=9.4.0. This change removes the strict version requirement and only excludes version 9.4.0. Please provide clarification on:

1. The reason for excluding specifically version 9.4.0.
2. Why the strict version requirement (=9.5) was removed.
3. Whether this change aligns with the upstream project's requirements.

---

25-41: Verify alignment of dependency updates with upstream project.

Several dependencies have been updated with specific version constraints. Please ensure that these changes align with the requirements specified in the upstream project's pyproject.toml or setup.py file.

To verify the dependency versions in the upstream project, you can run:

#!/bin/bash
# Check dependency versions in pyproject.toml or setup.py
rg -i 'dependencies|install_requires' pyproject.toml setup.py

[BioGeek]

@BiocondaBot please add label

[BioGeek]

Also pinging @hechth and @maximskorik for review.