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Add mzpaf as requirement for mzSpecLib #52166

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121 changes: 121 additions & 0 deletions recipes/mzpaf/LICENSE
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@@ -0,0 +1,121 @@
Creative Commons Legal Code

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47 changes: 47 additions & 0 deletions recipes/mzpaf/meta.yaml
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{% set name = "mzpaf" %}
{% set version = "0.2.0a0" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/mzpaf-{{ version }}.tar.gz
sha256: dbabb1fe8234a5587b451407c44a3c6bb60e1cfbec48978952708b231b45f6d5

build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
run_exports:
- {{ pin_subpackage('mzpaf', max_pin="x") }}
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🛠️ Refactor suggestion

Consider stricter version pinning for alpha release

Using max_pin="x" allows minor version updates which might be too permissive for an alpha release where breaking changes are more likely.

-    - {{ pin_subpackage('mzpaf', max_pin="x") }}
+    - {{ pin_subpackage('mzpaf', max_pin="x.x.x") }}
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
run_exports:
- {{ pin_subpackage('mzpaf', max_pin="x") }}
run_exports:
- {{ pin_subpackage('mzpaf', max_pin="x.x.x") }}


requirements:
host:
- python
- pip
run:
- python
- pyteomics
Comment on lines +23 to +25
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🛠️ Refactor suggestion

Add version constraints for dependencies

Consider adding version constraints:

  1. Specify Python version compatibility range
  2. Add version bounds for pyteomics to ensure compatibility
  run:
-   - python
+   - python >=3.7
-   - pyteomics
+   - pyteomics >=4.0
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
run:
- python
- pyteomics
run:
- python >=3.7
- pyteomics >=4.0


test:
imports:
- mzpaf
commands:
- pip check
- python -c "import mzpaf; assert hasattr(mzpaf, '__version__')"
requires:
- pip

about:
home: https://github.com/HUPO-PSI/mzPAF
summary: HUPO-PSI Peptide peak annotation format
license: CC-BY-1.0
license_family: CC
license_file: LICENSE
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💡 Codebase verification

License information needs correction

The LICENSE file exists but there's a mismatch in the license specification. The recipe states CC-BY-1.0 but both the repository and the included LICENSE file use CC0-1.0 (Creative Commons Zero v1.0 Universal).

  • recipes/mzpaf/meta.yaml: Update license field from CC-BY-1.0 to CC0-1.0
  • recipes/mzpaf/meta.yaml: Update license_family from CC to Public-Domain
🔗 Analysis chain

Verify license file inclusion

Ensure the LICENSE file is included in the source distribution:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if LICENSE file exists in the source distribution
curl -sL "https://pypi.io/packages/source/m/mzpaf/mzpaf-0.2.0a0.tar.gz" | tar tz | grep -i license

Length of output: 280


Script:

#!/bin/bash
# Let's first check if the LICENSE file exists in the repository
fd -t f -i license

# Also check the content of meta.yaml to verify the license information
cat recipes/mzpaf/meta.yaml

Length of output: 9257


Script:

#!/bin/bash
# Let's check the content of the LICENSE file in the mzpaf recipe
cat recipes/mzpaf/LICENSE

# Also verify the license in the source repository
gh repo view HUPO-PSI/mzPAF --json licenseInfo

Length of output: 7218

dev_url: https://github.com/HUPO-PSI/mzPAF/implementations/python
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doc_url: https://mzpaf.readthedocs.io/en/latest/

extra:
recipe-maintainers:
- hechth
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