Release version 1 #51
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Pull Request Overview
This PR prepares the project for Release version 1 by updating license headers, upgrading the Gradle distribution version, and aligning Java versions in workflows. Additionally, minor text improvements were made in the README to reflect current project details and remove outdated information.
- Added SPDX license headers to both Windows and Unix wrapper scripts.
- Upgraded the Gradle distribution URL and set the Java version to 21 in the workflows.
- Revised the README content for clarity and updated project links.
Reviewed Changes
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Show a summary per file
| File | Description |
|---|---|
| gradlew.bat | Added SPDX license headers and updated the Gradle execution command to use the -jar option. |
| gradlew | Added SPDX license header and modified the execution command, including an updated CLASSPATH assignment. |
| gradle/wrapper/gradle-wrapper.properties | Upgraded the Gradle distribution URL to use Gradle 8.14.1. |
| README.md | Updated project description and links, removed deprecated text. |
| .github/workflows/run-tests-on-pr.yml | Updated Java version from 17 to 21. |
| .github/workflows/run-publish-maven.yml | Updated Java version from 17 to 21. |
Comments suppressed due to low confidence (1)
gradlew:117
- The assignment of CLASSPATH to an escaped empty string may be incorrect. Consider setting it to a simple empty string or properly referencing the gradle-wrapper.jar to ensure that the classpath is correctly configured.
CLASSPATH="\"\""
| @@ -68,11 +70,11 @@ goto fail | |||
| :execute | |||
| @rem Setup the command line | |||
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| set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar | |||
| set CLASSPATH= | |||
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This file and the other gradle files were autogenerated by this command. We didn't code that.
./gradlew wrapper --gradle-version 8.14.1 --distribution-type bin
README.md
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| [develop](https://bitbucket.org/bucklerlab/biokotlin/branch/develop) and associated branches | ||
| * Main website for [BioKotlin](https://www.biokotlin.org) | ||
| * [Source Code](https://github.com/maize-genetics/BioKotlin) on GitHub | ||
| * [Documentation (API)](https://javadoc.io/doc/org.biokotlin/biokotlin/latest/index.html) | ||
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| ### How do I get set up? ### |
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What is this section supposed to convey? If I was a new user, this section would be very confusing. You should add simple Gradle/Maven instructions to set this up in a JVM project and magic instructions for Jupyter notebooks running the Kotlin kernel.
README.md
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| protein sequence manipulation, fast sequence IO, alignment, motif, pathway support. | ||
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| BioKotlin leverages the performance and type safety of the JVM languages with ease of Python like scripting. | ||
| Because the Kotlin language is compiled on the fly it can be thousands of times faster for | ||
| Because the Kotlin language is compiled, it can be thousands of times faster for |
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...it can be thousands of times faster...
I would back these claims up. You should add a link to the initial comparisons on BioKotlin site.
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Ed made those claims
| * We follow a Git-Flow branching structure | ||
| * Since we are in early development, most of the code is in the | ||
| [develop](https://bitbucket.org/bucklerlab/biokotlin/branch/develop) and associated branches | ||
| * Main website for [BioKotlin](https://www.biokotlin.org) |
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This should also be linked to in the "About" section along with a short description and some tags.
README.md
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| * Since we are in early development, most of the code is in the | ||
| [develop](https://bitbucket.org/bucklerlab/biokotlin/branch/develop) and associated branches | ||
| * Main website for [BioKotlin](https://www.biokotlin.org) | ||
| * [Source Code](https://github.com/maize-genetics/BioKotlin) on GitHub |
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This seems redundant since if you are reading this, you are already looking at the source code.
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