MIRP Release Version 2.4.1 A Comprehensive Guide

by Felix Dubois 49 views

Hey guys! We're super stoked to walk you through the release process for version 2.4.1. This guide will cover all the steps necessary to ensure a smooth and successful release of MIRP (Molecular Interaction and Recognition Package). Let's dive right in and make sure everything is shipshape!

Updating Version Information

First things first, we need to update the version number across various files. This ensures consistency and helps users identify the correct version they are working with. This is a critical step in the release process to maintain clarity and avoid confusion. Here’s how we’ll tackle it:

Updating mirp\pyproject.toml

The pyproject.toml file is crucial as it contains project metadata, including the version number. It’s the first place we need to update to reflect the new release. To update the version, open the file in a text editor and locate the version field. Change the value to 2.4.1. This file serves as the central source of truth for the project's version, influencing how the package is built and distributed. It's also used by various tools for dependency management and package installation. Ensuring this file is accurate is vital for the overall integrity of the release. The pyproject.toml file not only specifies the version but also includes other essential metadata such as project name, description, authors, and dependencies. These details are used by packaging tools like build and twine to create and upload the package to PyPI. A well-maintained pyproject.toml file is a cornerstone of a successful Python project, facilitating collaboration and distribution. By meticulously updating the version here, we ensure that all subsequent processes will correctly identify the release as 2.4.1, preventing potential issues with dependency resolution or installation.

Updating mirp\docs_source\source\conf.py

The conf.py file is used by Sphinx, the documentation generator, to build the project’s documentation. Updating the version here ensures that the documentation correctly reflects the current release. This is particularly important for users who rely on the documentation to understand the features and usage of the package. Open the conf.py file and find the version and release variables. Set both to 2.4.1. The version variable typically refers to the short X.Y version, while release refers to the full version, including patch numbers. Keeping these in sync is crucial for the documentation to align with the codebase. Documentation is often the first point of contact for new users, and accurate versioning in the documentation helps them quickly grasp the current state of the project. Moreover, versioned documentation allows users to access historical documentation, which can be invaluable for those using older versions of the software. By updating conf.py, we ensure that the generated documentation accurately represents the 2.4.1 release, providing users with a reliable resource for understanding and using MIRP.

Updating mirp\conda\meta.yaml (if building for conda)

If you’re building a Conda package, the meta.yaml file contains metadata necessary for Conda to manage the package. This includes the version number, dependencies, and build instructions. Open meta.yaml and update the version field to 2.4.1. Conda is a popular package and environment management system, especially in the scientific computing community. Updating the version in meta.yaml ensures that users installing MIRP through Conda receive the correct version. This file also specifies dependencies, which Conda uses to ensure that all required libraries are installed along with MIRP. A correctly configured meta.yaml file is essential for seamless installation and usage within Conda environments. Additionally, meta.yaml can include build instructions and test scripts, which are executed during the package creation process. This allows for automated testing of the package within the Conda environment, ensuring that it functions correctly across different platforms. By meticulously updating the version in meta.yaml, we guarantee that Conda users will receive and use the 2.4.1 release without any version conflicts or dependency issues.

Unit Testing

Next up, we need to ensure that all our unit tests pass successfully. This step is crucial for verifying that the new version doesn't introduce any regressions or break existing functionality. Comprehensive unit tests provide confidence in the stability of the codebase. We want to catch any issues early on, so let’s get this done!

Running Unit Tests

To run the unit tests, open a terminal, navigate to the root directory of the MIRP project, and execute the command python -m pytest test. This command will run the pytest testing framework, which will discover and execute all the test functions in the test directory. pytest is a powerful testing framework that simplifies the process of writing and running tests. It provides features such as test discovery, fixtures, and detailed reporting. Running unit tests is a cornerstone of software development best practices, ensuring that the codebase behaves as expected. The output from pytest will indicate whether all tests have passed or if any have failed. If any tests fail, it’s essential to investigate the cause, fix the bugs, and re-run the tests until all pass. This iterative process helps maintain the quality and reliability of the software. Unit tests serve as a safety net, preventing regressions and ensuring that new features don't inadvertently break existing functionality. Moreover, a comprehensive suite of unit tests provides valuable documentation of the expected behavior of the code. By ensuring that all unit tests pass, we can confidently proceed with the release, knowing that the core functionality of MIRP is solid and reliable.

Updating Documentation and Changelog

Now, let's keep our users in the loop! Updating the changelog and documentation is essential for communicating the changes and improvements in the new release. Users rely on these resources to understand what’s new and how to use the updated features. A well-maintained changelog and documentation enhance user satisfaction and adoption.

Updating NEWS.md

The NEWS.md file serves as the changelog for MIRP. It provides a human-readable summary of the changes, bug fixes, and new features included in the release. This file is essential for users to quickly understand what’s new in version 2.4.1. Open NEWS.md and add a new section for version 2.4.1, detailing the key changes and improvements. Be specific and concise, using bullet points or a similar format to make the information easily digestible. The changelog should highlight the most significant changes, such as new features, bug fixes, performance improvements, and any breaking changes that users should be aware of. A well-structured changelog helps users quickly assess whether the new release is relevant to them and understand how to upgrade. Additionally, the changelog serves as a historical record of the project's evolution, which can be valuable for developers and users alike. By meticulously updating NEWS.md, we ensure that users have a clear and accurate understanding of the changes in version 2.4.1, fostering transparency and trust in the project.

Updating README.md (if required)

The README.md file is the first thing users see when they visit the project’s repository. It provides an overview of the project, including installation instructions, usage examples, and other essential information. Review README.md and update it if necessary. This might involve updating installation instructions, adding information about new features, or clarifying existing documentation. The goal is to ensure that README.md provides an accurate and up-to-date overview of MIRP. A well-crafted README.md file is crucial for attracting new users and helping them get started with the project. It should clearly communicate the purpose of the project, its key features, and how to install and use it. Including examples and quick start guides can significantly enhance the user experience. Moreover, README.md can serve as a central hub for links to more detailed documentation, tutorials, and community resources. By keeping README.md up-to-date, we ensure that users have a positive first impression of MIRP and can quickly grasp its value and functionality.

Checking Long-Form Documentation Locally

Before we ship this, let's make sure our long-form documentation is on point! This ensures that users have a comprehensive resource to refer to for in-depth information and guidance. Accurate and complete documentation is vital for user adoption and satisfaction.

Building Documentation Locally

To check the documentation locally, we need to build it using Sphinx. Follow these steps:

  1. Open a terminal.
  2. Navigate to mirp\docs_source. This is where the source files for the documentation are located.
  3. Run the make script: Execute the command .\make html. This command tells Sphinx to build the HTML documentation.

The make script automates the process of generating the documentation from the source files. It uses Sphinx to convert the reStructuredText files into HTML pages, which can then be viewed in a web browser. Building the documentation locally allows us to preview it and identify any issues before deploying it to the live site. This step is crucial for ensuring that the documentation is accurate, complete, and easy to navigate. The make html command is the standard way to build Sphinx documentation, and it’s essential to have Sphinx installed and configured correctly for this to work. The process involves parsing the reStructuredText files, resolving cross-references, and generating the HTML output. Any errors or warnings during the build process should be addressed to ensure the quality of the documentation.

Checking Locally Built HTML Pages

Once the documentation is built, you’ll find the HTML files in the mirp\docs_source\build\html directory. Open the index.html file in your web browser and navigate through the pages. Check for any obvious errors, such as broken links, formatting issues, or missing content. Pay close attention to the new sections or updates related to version 2.4.1. Reviewing the locally built HTML pages provides a realistic preview of how the documentation will appear to users. It allows us to catch any visual or structural issues that might not be apparent in the source files. Checking for broken links is particularly important, as they can frustrate users and hinder their ability to find the information they need. Similarly, formatting issues can make the documentation difficult to read and understand. By thoroughly reviewing the HTML pages, we can ensure that the documentation is polished and professional, providing a positive user experience. This step is a critical quality control measure, ensuring that the documentation is a valuable resource for users.

Copying Updated Documentation

Alright, the documentation looks good locally! Now, let's get it ready for the world to see. We need to copy the updated documentation to the mirp\docs directory, which is where GitHub Pages will serve it from. This ensures that users can access the latest documentation online.

Preparing the docs Directory

First, we need to prepare the docs directory by emptying it, except for the .nojekyll file. This file prevents GitHub Pages from processing the documentation files again, which can cause issues. Here’s how to do it:

  1. Empty the docs directory: Delete all files and folders inside mirp\docs, except for .nojekyll.
  2. Keep .nojekyll: Make sure the .nojekyll file remains in the directory. This file is crucial for preventing GitHub Pages from reprocessing the documentation.

The .nojekyll file is a simple but essential component of GitHub Pages deployments. It tells GitHub Pages to serve the files in the docs directory as static assets, without attempting to process them using Jekyll, a static site generator. This is important because we are using Sphinx to generate the documentation, and we want GitHub Pages to serve the generated HTML files directly. By emptying the docs directory and keeping .nojekyll, we ensure that the directory is clean and ready to receive the updated documentation files. This prevents any conflicts or issues that might arise from old files or incorrect processing by GitHub Pages. The process of cleaning the directory is a standard practice in documentation deployments, ensuring that the latest version is served without interference from previous builds.

Copying Documentation Files

Next, copy the contents of mirp\docs_source\build\html into mirp\docs. Ensure that index.html is in the root of the docs folder, as GitHub will use this as the landing page. This step makes the documentation accessible via GitHub Pages. The index.html file serves as the entry point to the documentation, so it must be located in the root of the docs directory. Copying the entire contents of the build\html directory ensures that all the generated HTML files, CSS stylesheets, and JavaScript files are included in the deployment. This step is a straightforward file transfer operation, but it’s crucial for making the documentation live. Once the files are copied, GitHub Pages will automatically deploy the documentation, making it accessible to users online. This process leverages the static site hosting capabilities of GitHub Pages, providing a simple and efficient way to serve the documentation directly from the repository.

Packaging for PyPI

Time to package MIRP for PyPI, the Python Package Index! This makes it easy for users to install MIRP using pip. Getting the packaging right is crucial for ensuring a smooth installation experience for our users. Let's get this packaged up and ready for distribution!

Building the Package

First, we need to build the package. Follow these steps:

  1. Open a terminal.
  2. Navigate to the mirp root directory.
  3. Build the package: Run the command python -m build.

The python -m build command uses the build package to create distribution packages from the project's source code. It reads the pyproject.toml file to determine the project metadata and build settings. This command generates two types of packages: a source distribution (.tar.gz) and a wheel (.whl). The source distribution contains the project's source code and build scripts, while the wheel is a pre-built distribution format that can be installed more quickly. Building the package is a fundamental step in the PyPI release process, preparing the code for distribution. The build package is the recommended tool for building Python packages, as it follows the latest standards and best practices. The output from the build command will include messages indicating the progress and any errors encountered. Successful completion of this step results in the creation of the distribution packages in the dist directory.

Checking Package Content

After building the package, check the package content in mirp\dist\*.tar.gz. This step ensures that all necessary files are included and that the package is structured correctly. Unpack the .tar.gz file and verify that the source code, documentation, and any other required assets are present. Checking the package content is a critical quality control measure, preventing issues during installation and usage. Verifying the package structure and contents ensures that users will receive a complete and functional package. This step also helps identify any accidental inclusion of sensitive information or unnecessary files. A well-structured package is easier to install, maintain, and use, contributing to a positive user experience. This meticulous check can save significant time and effort in the long run by preventing common packaging errors.

Uploading to TestPyPI

Before we push it to the real PyPI, let’s test it out on TestPyPI. This allows us to ensure that the package installs correctly and functions as expected in a real-world environment, without affecting the live PyPI repository. Testing on TestPyPI is a best practice for preventing issues with the main PyPI repository.

Uploading the Package

  1. Run the upload command: Execute python -m twine upload --repository testpypi dist\*.
  2. Username: Use __token__.
  3. Password: Use your TestPyPI API token.

Twine is a tool for securely uploading packages to PyPI and TestPyPI. The twine upload command takes the distribution packages from the dist directory and uploads them to the specified repository. The --repository testpypi option tells Twine to upload to TestPyPI. Using an API token for authentication is more secure than using a password, as it limits the scope of access. Uploading to TestPyPI allows us to simulate the installation process and verify that the package dependencies are correctly specified and that the package installs without errors. This step is crucial for ensuring a smooth installation experience for users. The output from Twine will indicate the progress of the upload and any errors encountered. Successful upload to TestPyPI means that the package is ready for further testing.

Checking the Package on TestPyPI

  1. Check the landing page: Visit the TestPyPI website and check the landing page for any obvious errors.
  2. Create a virtual environment or temporary Conda environment.
  3. Install MIRP: Run pip install mirp --index-url https://test.pypi.org/mirp/ --no-deps.

Checking the package on TestPyPI involves both visual inspection of the landing page and practical installation testing. The landing page provides a summary of the package metadata, such as the version, description, and dependencies. Checking this page for errors ensures that the package information is displayed correctly. Creating a virtual environment or Conda environment provides an isolated environment for testing the package installation. The pip install command with the --index-url option tells pip to install the package from TestPyPI. The --no-deps option prevents pip from installing dependencies, allowing us to verify that the package correctly specifies its dependencies. Successful installation and usage within a virtual environment demonstrate that the package is functioning correctly and is ready for release to the main PyPI repository. This thorough testing on TestPyPI minimizes the risk of issues for users who install the package from PyPI.

Uploading to PyPI

We’ve tested on TestPyPI, and everything looks good! Now it’s time to upload to the real PyPI, making MIRP available to the world. This is the final step in the distribution process, so let’s make sure it goes smoothly.

Uploading the Package

  1. Run the upload command: Execute python -m twine upload dist\*.
  2. Username: Use __token__.
  3. Password: Use your PyPI API token.

This process is similar to uploading to TestPyPI, but this time we are targeting the main PyPI repository. The twine upload command securely uploads the distribution packages to PyPI, making them available for installation via pip. Using an API token for authentication is essential for security, as it prevents the need to store or transmit your PyPI password. Uploading to PyPI makes the package accessible to a wide audience of Python developers and users. The output from Twine will indicate the progress of the upload and any errors encountered. Successful upload to PyPI means that the package is live and ready for use.

Merging with the Main Branch

Before creating the release, let's merge our changes into the main branch. This ensures that the main branch reflects the latest state of the codebase, including all the changes and improvements in version 2.4.1. Merging with the main branch is a crucial step in maintaining a clean and consistent codebase.

Creating the Release

We’re in the home stretch! Let's create the release on GitHub. This step makes the new version official and provides users with a stable release to use. Creating a release on GitHub allows users to easily access the packaged files and release notes.

Finalizing the Release

  1. Copy NEWS.md: Copy the contents of NEWS.md into the release notes.
  2. Attach package and wheel files: Attach the .tar.gz and .whl files from mirp\dist as binary files.

Copying the contents of NEWS.md into the release notes provides users with a concise summary of the changes in the new release. This helps users quickly understand what’s new and whether the release is relevant to them. Attaching the .tar.gz and .whl files as binary files allows users to easily download and install the package. These files are the distribution packages that we built earlier, and they are essential for users who want to install MIRP without using pip. Creating a release on GitHub provides a convenient way for users to access the release notes and the distribution packages, making it easier for them to adopt the new version. This also helps in version control and makes it easier to track the project's history.

Conclusion

And there you have it! We’ve successfully walked through the release process for version 2.4.1. By following these steps, we ensure a smooth, consistent, and well-documented release. Great job, team! Now, let’s get this out there and make some magic happen! If you guys encounter any issues or have suggestions, feel free to reach out. Happy coding!