From e30fc378b33ce860a7a61df2aaf896684c6c49d0 Mon Sep 17 00:00:00 2001 From: Brad Langhorst Date: Mon, 20 Sep 2021 07:43:49 -0400 Subject: [PATCH 1/3] Create CONTRIBUTING.md This proposal includes only small chances from the IUC's contributing document. --- CONTRIBUTING.md | 51 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 CONTRIBUTING.md diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 000000000..4b01c3f2d --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,51 @@ +# Contributing + +This document describes how to contribute to this repository. Pull +requests containing bug fixes, updates, and extensions to the existing +tools and tool suites in this repository will be considered for +inclusion. + +## How to Contribute + +* Make sure you have a [GitHub account](https://github.com/signup/free) +* Make sure you have git [installed](https://help.github.com/articles/set-up-git) +* Fork the repository on [GitHub](https://github.com/galaxyproject/tools-iuc/fork) +* Make the desired modifications - consider using a [feature branch](https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches). +* Make sure you have added the necessary tests for your changes and they pass. +* Open a [pull request](https://help.github.com/articles/using-pull-requests) + with these changes. + +## What to contribute + +* Galaxy workflows using [OSI licensed](https://opensource.org/licenses/alphabetical) tools +* Bug fixes +* Documentation improvements +* New test cases + +## What not to contribute + +* Things already wrapped and currently maintained by other users +* Worklows without tests + +## Tests + +Contributed tools should include reasonable tests with small example data. + +The IWC strongly recommends testing with [planemo](https://github.com/galaxyproject/planemo/), which provides a simple command line utility for testing functionality + +```console +$ planemo test --install_galaxy my_tool.xml (todo: fix this...) +``` + +## Requirements for Contributions + +Before a PR will be accepted, meaningful review for correctnessa and quality will need to be established. + +* Tools must contain tests (and test-data) +* Continuous integration tests must pass: + * The tests must pass (`planemo test --install_galaxy my_tool.xml`) + * The tools must pass linting by planemo (`planemo lint my_tool.xml`) + * Any Python or R script must pass linting with `flake8` and `lintr`, respectively +* If there's a relevant paper for the tool, it should be cited in a [citation](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-citations) block +* The tool must be licensed to allow use by anyone. The OSI maintains a [list of appropriate](https://opensource.org/licenses/alphabetical) licenses +* At least one approving review by an IWC member From 5f95f405dc3b83279352af7ac3063f4f6bcefce9 Mon Sep 17 00:00:00 2001 From: Simon Bray <32272674+simonbray@users.noreply.github.com> Date: Fri, 26 Nov 2021 17:36:33 +0100 Subject: [PATCH 2/3] some changes --- CONTRIBUTING.md | 35 ++++++++++++++++++++--------------- 1 file changed, 20 insertions(+), 15 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 4b01c3f2d..8c4a96fd7 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -2,14 +2,13 @@ This document describes how to contribute to this repository. Pull requests containing bug fixes, updates, and extensions to the existing -tools and tool suites in this repository will be considered for -inclusion. +workflows in this repository will be considered for inclusion. -## How to Contribute +## How to contribute * Make sure you have a [GitHub account](https://github.com/signup/free) * Make sure you have git [installed](https://help.github.com/articles/set-up-git) -* Fork the repository on [GitHub](https://github.com/galaxyproject/tools-iuc/fork) +* Fork the repository on [GitHub](https://github.com/galaxyproject/iwc/fork) * Make the desired modifications - consider using a [feature branch](https://github.com/Kunena/Kunena-Forum/wiki/Create-a-new-branch-with-git-and-manage-branches). * Make sure you have added the necessary tests for your changes and they pass. * Open a [pull request](https://help.github.com/articles/using-pull-requests) @@ -25,27 +24,33 @@ inclusion. ## What not to contribute * Things already wrapped and currently maintained by other users -* Worklows without tests +* Workflows without tests ## Tests -Contributed tools should include reasonable tests with small example data. +Contributed workflows should include reasonable tests with small example data. -The IWC strongly recommends testing with [planemo](https://github.com/galaxyproject/planemo/), which provides a simple command line utility for testing functionality +The IWC strongly recommends testing with [planemo](https://github.com/galaxyproject/planemo/), which provides a simple command line utility for testing functionality. ```console -$ planemo test --install_galaxy my_tool.xml (todo: fix this...) +$ planemo test my_workflow.ga +``` + +In some cases, you might find it simpler to run tests against an external Galaxy server: + + +```console +$ planemo test my_workflow.ga --galaxy_url https://usegalaxy.org --galaxy_user_key API_KEY ``` ## Requirements for Contributions -Before a PR will be accepted, meaningful review for correctnessa and quality will need to be established. +Before a PR will be accepted, meaningful review for correctness and quality will need to be established. -* Tools must contain tests (and test-data) +* Tests (and test-data) must be provided for all workflows * Continuous integration tests must pass: - * The tests must pass (`planemo test --install_galaxy my_tool.xml`) - * The tools must pass linting by planemo (`planemo lint my_tool.xml`) - * Any Python or R script must pass linting with `flake8` and `lintr`, respectively -* If there's a relevant paper for the tool, it should be cited in a [citation](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-citations) block -* The tool must be licensed to allow use by anyone. The OSI maintains a [list of appropriate](https://opensource.org/licenses/alphabetical) licenses + * The tests must pass (`planemo test my_workflow.ga`) + * The workflows must pass linting by planemo (`planemo lint my_workflow.ga`) +* If there's a relevant paper for the workflow, it should be cited in a the READMe file. +* The workflow must be licensed to allow use by anyone. The OSI maintains a [list of appropriate](https://opensource.org/licenses/alphabetical) licenses * At least one approving review by an IWC member From b20a5aa4de9f9f3b85f3ae43629c301c10fc491a Mon Sep 17 00:00:00 2001 From: Simon Bray <32272674+simonbray@users.noreply.github.com> Date: Fri, 26 Nov 2021 17:37:13 +0100 Subject: [PATCH 3/3] caps --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 8c4a96fd7..f5b5b3881 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -51,6 +51,6 @@ Before a PR will be accepted, meaningful review for correctness and quality will * Continuous integration tests must pass: * The tests must pass (`planemo test my_workflow.ga`) * The workflows must pass linting by planemo (`planemo lint my_workflow.ga`) -* If there's a relevant paper for the workflow, it should be cited in a the READMe file. +* If there's a relevant paper for the workflow, it should be cited in a the README file. * The workflow must be licensed to allow use by anyone. The OSI maintains a [list of appropriate](https://opensource.org/licenses/alphabetical) licenses * At least one approving review by an IWC member