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

Pegas #49759

Merged
merged 19 commits into from
Oct 23, 2024
Merged

Pegas #49759

Changes from all commits
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
8462ad7
added meta.yaml
liviurotiul Aug 2, 2024
a0f8f63
added sha sum
liviurotiul Aug 2, 2024
a11c9fc
added run exports
liviurotiul Aug 2, 2024
bc0b071
Merge branch 'master' into pegas
liviurotiul Aug 2, 2024
969253e
changed meta
liviurotiul Aug 2, 2024
ddbbe76
Merge branch 'pegas' of https://github.com/liviurotiul/bioconda-recip…
liviurotiul Aug 2, 2024
dabe2d7
Merge branch 'bioconda:master' into pegas
liviurotiul Aug 6, 2024
c76205c
Merge branch 'bioconda:master' into pegas
liviurotiul Aug 6, 2024
1e5fa2d
solved linting errors
liviurotiul Aug 6, 2024
cf267e4
changed git to source
liviurotiul Aug 6, 2024
3ebc55e
Merge branch 'master' into pegas
liviurotiul Aug 6, 2024
1030457
version 0.2.13
liviurotiul Oct 18, 2024
810a3c5
Merge branch 'pegas' of https://github.com/liviurotiul/bioconda-recip…
liviurotiul Oct 18, 2024
4f34548
fixed meta
liviurotiul Oct 18, 2024
2e58da7
Merge branch 'master' into pegas
liviurotiul Oct 18, 2024
855f109
fixed liniting errors
liviurotiul Oct 18, 2024
f602251
fixed linting errors
liviurotiul Oct 18, 2024
790cee0
Merge branch 'master' into pegas
liviurotiul Oct 18, 2024
3e4b96e
clean up recipe
mencian Oct 22, 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
52 changes: 52 additions & 0 deletions recipes/pegas/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
{% set name = "pegas" %}
{% set version = "0.2.13" %}

package:
name: {{ name }}
version: {{ version }}

source:
url: https://github.com/liviurotiul/PeGAS/archive/refs/tags/v{{ version }}.tar.gz
sha256: 2c028caa90bb8825e1c64f2ca5bd5e80f82f6db1cb5c4609bed86157c954c1f8

build:
number: 0
noarch: python
script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
run_exports:
- {{ pin_subpackage(name, max_pin="x.x") }}

requirements:
build:
- python >=3.10
- pip
- setuptools
run:
- python >=3.10
- plotly >=5.0.0
- pandas >=1.3.5
- tqdm >=4.66.5
- matplotlib-base >=3.9.2
- networkx >=3.2
- snakemake-minimal >=7.32.4
- beautifulsoup4 >=4.12.3

test:
commands:
- {{ name }} --help
Comment on lines +34 to +36
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

Enhance test coverage for better package validation.

While running the help command is a good basic test to ensure the package is installed correctly, it doesn't verify the package's functionality.

Consider adding more comprehensive tests, such as:

  1. Running a simple analysis with sample data.
  2. Importing and testing key functions or classes.
  3. Verifying the presence of important files or directories.

For example:

test:
  commands:
    - {{ name }} --help
    - {{ name }} --version
    - python -c "from pegas import some_key_function; assert some_key_function() == expected_output"
  files:
    - path/to/test/data/sample.fastq

These additional tests would provide more confidence in the package's functionality after installation. Please adjust the suggested tests according to your package's specific features and requirements.


about:
home: https://github.com/liviurotiul/PeGAS
license: GPL-2.0-or-later
license_family: GPL
license_file: LICENSE
summary: "PeGAS is a Snakemake pipeline for genome analysis"
description: |
PeGAS is a Snakemake pipeline for genome analysis. It is designed to be
lightweight, easy to install, and easy to use.
doc_url: https://github.com/liviurotiul/PeGAS#readme
dev_url: https://github.com/liviurotiul/PeGAS/issues

extra:
recipe-maintainers:
- liviurotiul