From febbf8c3d1cba72a89adbce7a1193157d7498c23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Semid=C3=A1n=20Robaina=20Est=C3=A9vez?= Date: Fri, 19 Jun 2026 00:06:20 +0100 Subject: [PATCH] docs: make Pynteny pip-only (remove bioconda) and drop conda recipes The package is distributed via pip only now, so remove the remaining conda / bioconda references that described the old build: - README.md: drop the four Anaconda/Bioconda badges, remove the "install with conda" block, and remove `conda activate pynteny` from the usage snippet. Update the Python badge to 3.9 | 3.12. - docs/index.md: remove the conda install block. - Installation now points to `pip install git+https://github.com/Robaina/Pynteny.git` with a note that `pip install pynteny` will work once published to PyPI (the package is not on PyPI yet, so the plain `pip install pynteny` line was not actually installable). The Colab example uses the git install too. - Remove the obsolete conda packaging recipes (.conda/, .bioconda/). Co-Authored-By: Claude Opus 4.8 --- .bioconda/meta.yaml | 55 --------------------------- .conda/conda_build_config.yaml | 6 --- .conda/meta.yaml | 51 ------------------------- README.md | 17 +++------ docs/examples/example_api_colab.ipynb | 2 +- docs/index.md | 9 ++--- 6 files changed, 10 insertions(+), 130 deletions(-) delete mode 100644 .bioconda/meta.yaml delete mode 100644 .conda/conda_build_config.yaml delete mode 100644 .conda/meta.yaml diff --git a/.bioconda/meta.yaml b/.bioconda/meta.yaml deleted file mode 100644 index 08bb1f7..0000000 --- a/.bioconda/meta.yaml +++ /dev/null @@ -1,55 +0,0 @@ -{% set name = "pynteny" %} -{% set version = "1.0.0" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/Robaina/pynteny/archive/v{{ version }}.tar.gz - sha256: 51ffa50eee508f6e09bcb707bbaac6e69365aad1d5bb2f2d203017b739369b95 - -build: - number: 0 - entry_points: - - pynteny = pynteny.cli:main - skip: True # [win] - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . - -requirements: - build: - - {{ compiler('c') }} - host: - - python >=3.8 - - poetry - - pip - run: - - pyhmmer >=0.10 - - pyrodigal >=3.0 - - pyfastx >=0.8 - - biopython - - numpy - - pandas - - psutil - - requests - - tqdm - -test: - imports: - - pynteny - commands: - - pynteny --help - -about: - home: http://github.com/robaina/Pynteny - license: Apache-2.0 license - description: "Multiple HMM - search via synteny structures in Python" - summary: "Multiple HMM - search via synteny structures in Python" - doc_url: https://robaina.github.io/Pynteny/ - dev_url: http://github.com/robaina/Pynteny - -extra: - recipe-maintainers: - - Robaina - identifiers: - - DOI:10.5281/zenodo.7082448 \ No newline at end of file diff --git a/.conda/conda_build_config.yaml b/.conda/conda_build_config.yaml deleted file mode 100644 index 3521102..0000000 --- a/.conda/conda_build_config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -numpy: - - 1.16 - -target_platform: - - osx-64 - - linux-64 \ No newline at end of file diff --git a/.conda/meta.yaml b/.conda/meta.yaml deleted file mode 100644 index b682176..0000000 --- a/.conda/meta.yaml +++ /dev/null @@ -1,51 +0,0 @@ -{% set name = "pynteny" %} -{% set version = "1.0.0" %} - -package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: https://github.com/Robaina/pynteny/archive/v{{ version }}.tar.gz - -build: - number: 0 - entry_points: - - pynteny = pynteny.cli:main - script: {{ PYTHON }} -m pip install --no-deps --ignore-installed . - -requirements: - build: - - {{ compiler('c') }} - host: - - python >=3.8 - - poetry - - pip - run: - - pyhmmer >=0.10 - - pyrodigal >=3.0 - - pyfastx >=0.8 - - biopython >=1.8 - - numpy - - pandas - - psutil >=5.9 - - requests - - tqdm - -test: - imports: - - pynteny - commands: - - pynteny --help - -about: - home: "http://github.com/robaina/Pynteny" - license: Apache-2.0 license - summary: "Multiple HMM - search via synteny structures in Python" - doc_url: "https://robaina.github.io/Pynteny/" - -extra: - recipe-maintainers: - - Robaina - identifiers: - - DOI:10.5281/zenodo.7082448 diff --git a/README.md b/README.md index 8752ebe..548ca6a 100644 --- a/README.md +++ b/README.md @@ -8,17 +8,12 @@ [![docs](https://github.com/Robaina/Pynteny/actions/workflows/docs.yml/badge.svg)](https://github.com/Robaina/Pynteny/actions/workflows/docs.yml) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![Anaconda-Server Badge](https://anaconda.org/bioconda/pynteny/badges/latest_release_date.svg)](https://anaconda.org/bioconda/pynteny) ![license](https://img.shields.io/github/license/Robaina/Pynteny) ![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4) -[![Bioconda](https://img.shields.io/conda/vn/bioconda/pynteny?logo=anaconda&style=flat-square&maxAge=3600)](https://anaconda.org/bioconda/pynteny) -[![Anaconda-Server Badge](https://anaconda.org/bioconda/pynteny/badges/downloads.svg)](https://anaconda.org/bioconda/pynteny) [![GitHub release](https://img.shields.io/github/release/Robaina/Pynteny.svg)](https://GitHub.com/Robaina/Pynteny/releases/) - -[![Anaconda-Server Badge](https://anaconda.org/bioconda/pynteny/badges/platforms.svg)](https://anaconda.org/bioconda/pynteny) -![python](https://img.shields.io/badge/Python-3.10-blue) +![python](https://img.shields.io/badge/Python-3.9%20|%203.12-blue) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/67) @@ -41,17 +36,16 @@ binaries). All dependencies, including the HMMER and Prodigal engines, are provided by the pip packages [pyhmmer](https://github.com/althonos/pyhmmer) and [pyrodigal](https://github.com/althonos/pyrodigal). -Install with pip: +Install the latest development version directly from GitHub: ```bash -pip install pynteny +pip install git+https://github.com/Robaina/Pynteny.git ``` -Or with conda (from bioconda): +Once released on PyPI, Pynteny will also be installable with: ```bash -conda create -n pynteny -c bioconda -c conda-forge python=3.10 pynteny -conda activate pynteny +pip install pynteny ``` Check that the installation worked fine: @@ -78,7 +72,6 @@ Here, we are interested in four genes which colocate according to the pattern ab Pynteny can be run either as a command line tool or as a Python module. To run pynteny in the command line, execute: ```bash -conda activate pynteny pynteny ``` diff --git a/docs/examples/example_api_colab.ipynb b/docs/examples/example_api_colab.ipynb index 6308683..435fcb4 100644 --- a/docs/examples/example_api_colab.ipynb +++ b/docs/examples/example_api_colab.ipynb @@ -45,7 +45,7 @@ "try:\n", " import google.colab\n", " # Pynteny is a pure-pip package (no conda / external binaries required).\n", - " !pip install -q pynteny\n", + " !pip install -q git+https://github.com/Robaina/Pynteny.git\n", " # Grab the bundled test data used throughout this example.\n", " !git clone -q https://github.com/Robaina/Pynteny.git\n", " !cp -r Pynteny/tests/ . && rm -rf Pynteny\n", diff --git a/docs/index.md b/docs/index.md index 03034bf..f5a9bd1 100644 --- a/docs/index.md +++ b/docs/index.md @@ -18,17 +18,16 @@ binaries). The HMMER and Prodigal engines are provided by the pip packages [pyhmmer](https://github.com/althonos/pyhmmer) and [pyrodigal](https://github.com/althonos/pyrodigal). -Install with pip: +Install the latest development version directly from GitHub: ```bash -pip install pynteny +pip install git+https://github.com/Robaina/Pynteny.git ``` -Or with conda (from bioconda): +Once released on PyPI, Pynteny will also be installable with: ```bash -conda create -n pynteny -c bioconda -c conda-forge python=3.10 pynteny -conda activate pynteny +pip install pynteny ``` Check that installation worked fine: