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.

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 gene-trajectory-python recipe #51476

Merged
merged 10 commits into from
Oct 19, 2024
Merged
Show file tree
Hide file tree
Changes from 8 commits
Commits
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
21 changes: 21 additions & 0 deletions recipes/gene-trajectory-python/LICENSE
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
MIT License

Copyright (c) 2024 PCMGF-Limited

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
61 changes: 61 additions & 0 deletions recipes/gene-trajectory-python/meta.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
{% set name = "gene-trajectory-python" %}
{% set version = "1.0.4" %}

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

source:
url: https://pypi.org/packages/source/{{ name[0] }}/gene-trajectory/gene_trajectory-{{ version }}.tar.gz
sha256: 133e22dd167cbc83b8d4ecffa98bfc623f98584b91d2ecf31b915aeb11072b73

build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
number: 0
run_exports:
- {{ pin_subpackage(name|lower, max_pin="x") }}
Comment on lines +12 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 a more flexible pinning strategy.

The build section is well-defined, but the run_exports pinning strategy might be too strict. For most Python packages, it's recommended to use a more flexible pinning strategy to allow for minor version updates.

Consider updating the run_exports section as follows:

run_exports:
  - {{ pin_subpackage(name|lower, max_pin='x.x') }}

This allows for minor version updates while still maintaining compatibility.


requirements:
host:
- python >=3.9,<4.0a0
- flit-core >=3.2,<4
- pip
run:
- python >=3.9
- python-igraph >=0.10
- matplotlib-base >=3.6
- numpy >=1.25
- pandas >=1.5
- pot >=0.8.2
- scanpy >=1.9.3
- scikit-misc >=0.1.3
- scikit-learn >=0.24
- scipy >=1.8
- seaborn >=0.13
- tqdm >=4.64.1

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

about:
home: https://github.com/KlugerLab/GeneTrajectory-python
summary: Compute gene trajectories
description: |
Gene Trajectory is a Python package that computes and analyzes gene trajectories in single-cell data.
It provides tools for trajectory inference, gene expression analysis along trajectories, and visualization of results.

license: MIT
license_file: LICENSE
doc_url: https://github.com/KlugerLab/GeneTrajectory-python
dev_url: https://github.com/KlugerLab/GeneTrajectory-python
Comment on lines +47 to +57
Copy link
Contributor

Choose a reason for hiding this comment

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

⚠️ Potential issue

LGTM: About section is comprehensive.

The about section provides all necessary information about the package, including its purpose, license, and relevant URLs.

The license_file is specified, but it's not included in the recipe. To ensure compliance with Conda packaging guidelines, you should include the LICENSE file in the recipe directory. Please add the following steps:

  1. Download the LICENSE file from the GitHub repository.
  2. Add it to the recipe directory (next to meta.yaml).
  3. Update the meta.yaml to reference the local LICENSE file:
about:
  ...
  license_file: LICENSE
  ...

This ensures that the license is properly packaged with the Conda package.



extra:
recipe-maintainers:
- fra-pcmgf