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Add rna-seqc python utilities and qtl package #51344

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Add rna-seqc python utilities and qtl package #51344

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d6b2f35
enh: Add rna-seqc python utilities and qtl package
lrvdijk Oct 11, 2024
324d35f
fix: Include home, license and run_exports
lrvdijk Oct 11, 2024
01655f1
fix: Fix incorrect package name in qtl
lrvdijk Oct 11, 2024
624351d
fix: Template variable name in rna-seqc-python
lrvdijk Oct 11, 2024
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49 changes: 49 additions & 0 deletions recipes/qtl/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
{% set name = "qtl" %}
{% set version = "0.1.8" %}

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

source:
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/qtl-{{ version }}.tar.gz
sha256: 8fdb99cda1ceff578a233db6c15a944fa57b43a2826af41c292e36848906117b

build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
run_exports:
- {{ pin_subpackage("rna-seqc-python", max_pin="x.x") }}
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💡 Codebase verification

The run_exports section appears unnecessary as no dependencies on rna-seqc-python were found. Please remove it to simplify the build configuration.

  • No imports or references to rna-seqc-python detected in the qtl package.
  • rna-seqc-python is not listed in setup.py or pyproject.toml.
🔗 Analysis chain

Build configuration looks good, but please verify the run_exports section.

The build configuration is well-structured:

  • noarch: python is correctly set for a pure Python package.
  • The pip install script uses the recommended flags for Conda builds.
  • The build number is correctly set to 0 for a new package.

However, the run_exports section is unusual for a Python package. Please verify if this is intentional and necessary. If it is, consider adding a comment explaining why this pinning is required.

To verify the relationship between qtl and rna-seqc-python, you can run the following script:

This script will help determine if there's a strong dependency between qtl and rna-seqc-python that justifies the run_exports pinning.

[/run_scripts]

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for dependencies between qtl and rna-seqc-python

# Search for imports of rna-seqc-python in qtl package
echo "Searching for imports of rna-seqc-python in qtl package:"
rg --type python 'import.*rna[-_]seqc' || echo "No direct imports found"

# Search for other references to rna-seqc-python
echo "\nSearching for other references to rna-seqc-python:"
rg --type python 'rna[-_]seqc' || echo "No other references found"

# Check if rna-seqc-python is listed in setup.py or pyproject.toml
echo "\nChecking for rna-seqc-python in setup.py or pyproject.toml:"
rg --type python 'rna[-_]seqc' -g 'setup.py' -g 'pyproject.toml' || echo "Not found in setup files"

Length of output: 777

Script:

#!/bin/bash
# Description: Check for dependencies between qtl and rna-seqc-python

# Search for imports of rna-seqc-python in qtl package
echo "Searching for imports of rna-seqc-python in qtl package:"
rg 'import.*rna[-_]seqc' --glob '*.py' || echo "No direct imports found"

# Search for other references to rna-seqc-python
echo "\nSearching for other references to rna-seqc-python:"
rg 'rna[-_]seqc' --glob '*.py' || echo "No other references found"

# Check if rna-seqc-python is listed in setup.py or pyproject.toml
echo "\nChecking for rna-seqc-python in setup.py or pyproject.toml:"
rg 'rna[-_]seqc' --glob 'setup.py' --glob 'pyproject.toml' || echo "Not found in setup files"

Length of output: 678


requirements:
host:
- python
- pip
run:
- python
- numpy
- pandas
- scipy
- matplotlib-base
- seaborn
- pybigwig
- bx-python

test:
imports:
- qtl
commands:
- pip check
requires:
- pip

about:
home: https://github.com/broadinstitute/pyqtl
summary: Utilities for analyzing and visualizing QTL data
license: BSD-3-Clause
license_file: LICENSE

extra:
recipe-maintainers:
- lrvdijk
48 changes: 48 additions & 0 deletions recipes/rna-seqc-python/meta.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
{% set pypi_name = "rnaseqc" %}
{% set version = "0.0.3" %}

package:
name: "rna-seqc-python"
version: {{ version }}

source:
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/rnaseqc-{{ version }}.tar.gz
sha256: 857ad1ad54f2b563163d75ff8c5f2439208d06980b7c8ded279bd59d19c48a0f

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

requirements:
host:
- python
- pip
run:
- python
- numpy
- pandas
- matplotlib-base
- seaborn
- qtl
- nbformat

test:
imports:
- rnaseqc
commands:
- pip check
requires:
- pip

about:
home: https://github.com/broadinstitute/rnaseqc
summary: Multi-sample visualization of metrics from RNA-SeQC
license: BSD 3-clause
license_family: BSD

extra:
recipe-maintainers:
- lrvdijk
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