Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add mzpaf as requirement for mzSpecLib #52166

Merged
merged 7 commits into from
Nov 19, 2024
Merged

Add mzpaf as requirement for mzSpecLib #52166

Changes from 4 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
0340111
added mzpaf recipe
hechth Nov 18, 2024
cf9965b
added run_exports
hechth Nov 18, 2024
716c6de
fixed max pin
hechth Nov 18, 2024
faf23bd
added recipe metadata
hechth Nov 18, 2024
35f7d3a
added further test following coderabbit's advice
hechth Nov 18, 2024
e79ac4a
added license file
hechth Nov 19, 2024
601e2ae
removed version check
hechth Nov 19, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
46 changes: 46 additions & 0 deletions recipes/mzpaf/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
{% 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") }}
Comment on lines +16 to +17
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🛠️ 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
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🛠️ 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
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
Comment on lines +38 to +40
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 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
hechth marked this conversation as resolved.
Show resolved Hide resolved
doc_url: https://mzpaf.readthedocs.io/en/latest/

extra:
recipe-maintainers:
- hechth
Loading