diff --git a/README.md b/README.md index 11e020bd..ef279d0d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,9 @@ -# pyranges +# pyranges0 -[![Coverage Status](https://img.shields.io/coveralls/github/biocore-ntnu/pyranges.svg)](https://coveralls.io/github/biocore-ntnu/pyranges?branch=master) [![hypothesis tested](graphs/hypothesis-tested-brightgreen.svg)](http://hypothesis.readthedocs.io/) [![PyPI version](https://badge.fury.io/py/pyranges.svg)](https://badge.fury.io/py/pyranges) [![MIT](https://img.shields.io/pypi/l/pyranges.svg?color=green)](https://opensource.org/licenses/MIT) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyranges.svg) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pyranges/README.html) +## Deprecation note! + +This repo currently hosts the "version 0" of pyranges. A redesigned, faster version 1 is available at https://github.com/pyranges/pyranges1 +Version 1 will soon replace version 0. We encourage existing v0 users to migrate to v1 (see guide at https://pyranges1.readthedocs.io/en/latest/migration_guide.html), and new users to directly adopt v1. Read about v1 in our preprint at https://doi.org/10.64898/2025.12.11.693639 ## Introduction @@ -10,14 +13,9 @@ The library is optimized for fast querying and manipulation of genomic annotatio *"Finally ... This was what Python badly needed for years."* - Heng Li -## Deprecation note! -This repo currently hosts the "version 0" of pyranges. A redesigned, faster version1 is available at https://github.com/pyranges/pyranges_1.x -Version 1 will soon replace version 0. We encourage existing v0 users to migrate to v1 (see guide at https://pyranges1.readthedocs.io/en/latest/migration_guide.html), and new users to directly adopt v1. Read about v1 in our preprint at https://doi.org/10.64898/2025.12.11.693639 - - ## Documentation -The pyranges documentation, including installation instructions, API, tutorial, and how-to-pages, of version 0 is available at +The pyranges0 documentation, including installation instructions, API, tutorial, and how-to pages, is available at ## Features @@ -41,10 +39,9 @@ Stovner EB, Sætrom P (2020) PyRanges: efficient comparison of genomic intervals ## Asking for help -If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues +If you encounter bugs, or the documentation is not enough and you cannot accomplish a specific task of interest, or if you'd like new features implemented, open an issue on GitHub: https://github.com/pyranges/pyranges0/issues ## Contributing to pyranges -Pyranges accepts code contributions in form of pull request. For details, visit [https://pyranges.readthedocs.io/developer_guide.html](https://pyranges.readthedocs.io/en/latest/developer_guide.html) - +Pyranges accepts code contributions in the form of pull requests. For details, visit [https://pyranges0.readthedocs.io/en/latest/developer_guide.html](https://pyranges0.readthedocs.io/en/latest/developer_guide.html) diff --git a/book/index.Rmd b/book/index.Rmd index 46e30c35..a30c586e 100644 --- a/book/index.Rmd +++ b/book/index.Rmd @@ -45,5 +45,4 @@ The PyRanges documentation is structured in three parts: 1. The tutorial, on the next page, recommended for all new users 2. The how-to pages, further below, where functionalities are grouped by topic -3. The [API reference](https://pyranges.readthedocs.io/), where all methods are explained in detail - +3. The [API reference](https://pyranges0.readthedocs.io/en/latest/), where all methods are explained in detail diff --git a/docs/developer_guide.rst b/docs/developer_guide.rst index 1faf854a..7dabbaf9 100644 --- a/docs/developer_guide.rst +++ b/docs/developer_guide.rst @@ -3,7 +3,7 @@ Developer guide PyRanges is mainly developed by Endre Bakken Stovner and by the Comparative Genomics lab of Marco Mariotti. It follows the guidelines for open source software, and external contributors -are welcome. The code is centralized on github, at https://github.com/pyranges/pyranges +are welcome. The code is centralized on GitHub, at https://github.com/pyranges/pyranges0 Bugs and feature requests can be reported as github issues. You may also contribute by submitting your own code edits, either to deal with issues or to add new functionalities. The code will be @@ -38,8 +38,8 @@ Documentation: docstrings Python docstrings are widely used to document the rationale, input arguments, and returned values of all functions and methods. The use of a consistent docstring style allows the automatic generation -of API documentation, as seen in pyranges documentation at `https://pyranges.readthedocs.io/ -`_, built through the Sphynx software. +of API documentation, as seen in the pyranges0 documentation at `https://pyranges0.readthedocs.io/ +`_, built through the Sphinx software. Pyranges adopts the NumPy/SciPy-style: `https://numpydoc.readthedocs.io/en/latest/format.html `_. It is important that code contributors @@ -90,8 +90,8 @@ automated documentation: 2. Create and setup your own PyRanges fork ------------------------------------------ -The easiest way to do this is through github. Login into the github website if you aren't already, -then visit `https://github.com/pyranges/pyranges `_, and +The easiest way to do this is through GitHub. Login into the GitHub website if you aren't already, +then visit `https://github.com/pyranges/pyranges0 `_, and click "Fork" on the top right. Fill the form and confirm. In the page of your new fork, find the **<> Code** button, and copy the https address. On your computer, create a new folder dedicated to the project, then clone your fork inside it: @@ -102,14 +102,14 @@ to the project, then clone your fork inside it: cd pr_debug git clone PASTE_GITHUB_HTTPS -Next, cd into your pyranges fork, and install it locally with pip as shown below. By using pip +Next, cd into your pyranges0 fork, and install it locally with pip as shown below. By using pip option ``-e``, your installation is in "editable" mode: any changes you make to your pyranges code will be immediately reflected in your environment. In other words, you won't need to re-run pip install every time you change something in the code. .. code:: bash - cd pyranges + cd pyranges0 pip install -e . @@ -125,7 +125,7 @@ imports pyranges, making sure you're in the prdev conda environment. 4. Format and lint code ----------------------- -Run these commands from inside your pyranges folder (which has a pyranges subfolder): +Run these commands from inside your pyranges0 folder (which has a pyranges subfolder): .. code:: bash @@ -139,7 +139,7 @@ Run these commands from inside your pyranges folder (which has a pyranges subfol Your code edits may warrant edits in the pyranges docstrings. In this case, it is compelling to locally check that the automatically generated documentation is built appropriately. Inside the -pyranges folder, run these commands: +pyranges0 folder, run these commands: .. code:: bash @@ -148,7 +148,7 @@ pyranges folder, run these commands: cd - If the "make" command has no major errors, it will generate the full pyranges documentation in the -form of html pages, identical to `https://pyranges.readthedocs.io/ `_. +form of html pages, identical to `https://pyranges0.readthedocs.io/ `_. Open the file docs/build/html/index.html with a browser to inspect all the parts that may have been affected by your changes, and fix any potential problems. To know more about its inner workings, read about the Sphynx system. @@ -229,19 +229,19 @@ Finally, push to your remote repository, i.e. update your online fork at github, git push -You will be requested your github credentials. Note that your online password may not work; in this -case, google how to set up a github token that you can use. +You will be requested your GitHub credentials. Note that your online password may not work; in this +case, search how to set up a GitHub token that you can use. 9. Open a pull request ---------------------- The easiest way to open a pull request is through the github website. Go to **your** -pyranges fork on github, then find the "Contribute" button (near the **<> Code** button). Click +pyranges fork on GitHub, then find the "Contribute" button (near the **<> Code** button). Click it, and select **Open pull request**. In the newly opened page, carefully check that source and destination are correctly selected. The -Base repository should be pyranges/pyranges (i.e. the main pyranges repo), and the Head repository +Base repository should be pyranges/pyranges0 (i.e. the main pyranges repo), and the Head repository should be your fork. If you worked on non-master git branches, select them here. In the comments, write a summary of the introduced changes and their rationale, tagging any related @@ -256,7 +256,7 @@ Every now and then, the core development team considers that a new pyranges vers released. To do so: - Update the version number in the pyproject.toml file -- Find the "Build and upload to PyPI" workflow in the left menu of the github actions at `https://github.com/pyranges/pyranges/actions/ `_ +- Find the "Build and upload to PyPI" workflow in the left menu of the GitHub actions at `https://github.com/pyranges/pyranges0/actions/ `_ - Click the "Run workflow" button on the right Next, check that everything worked correctly, by confirming that a new pyranges installation via diff --git a/docs/how_to_book_old_version.rst b/docs/how_to_book_old_version.rst index 048a41b7..8d96e8e2 100644 --- a/docs/how_to_book_old_version.rst +++ b/docs/how_to_book_old_version.rst @@ -6,7 +6,7 @@ How-to-book Introduction to PyRanges ~~~~~~~~~~~~~~~~~~~~~~~~ -This is the PyRanges tutorial. For docs, see: `https://pyranges.readthedocs.io/en/latest/` +This is the PyRanges tutorial. For docs, see: `https://pyranges0.readthedocs.io/en/latest/` .. contents:: Contents of How-to pages @@ -1316,4 +1316,3 @@ RLEs: run length encodings [outline as advanced usage. Put everything related to RLEs in a single chapter; keep as last even if you add further chapters] - diff --git a/docs/index.rst b/docs/index.rst index 77d989f5..47d16c70 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -9,7 +9,7 @@ PyRanges is a Python library specifically designed for efficient and intuitive m particularly genomic intervals (like genes, genomic features, or reads). The library is optimized for fast querying and manipulation of genomic annotations. -PyRanges is open source, and hosted at github: https://github.com/pyranges/pyranges +PyRanges is open source, and hosted at GitHub: https://github.com/pyranges/pyranges0 Citation @@ -30,7 +30,7 @@ Documentation outline Asking for help ~~~~~~~~~~~~~~~ -If you encounter bugs, or the documentation is not enough a cannot accomplish a specific task of interest, or if you'd like new features implemented, open an Issue at github: https://github.com/pyranges/pyranges/issues +If you encounter bugs, or the documentation is not enough and you cannot accomplish a specific task of interest, or if you'd like new features implemented, open an issue on GitHub: https://github.com/pyranges/pyranges0/issues .. toctree:: diff --git a/pyproject.toml b/pyproject.toml index 16f04b58..04de8068 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,4 +33,4 @@ where = ["."] inputs = ['pyranges'] [project.urls] -Homepage="http://github.com/pyranges/pyranges" +Homepage="https://github.com/pyranges/pyranges0"