From 7f59bb8006af18034d6e766a3bb249a37dc5cbfe Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 22 May 2024 10:58:56 +0200 Subject: [PATCH] Update viash (#51) * update viash * update readme * update changelog * update changelog * fix incorrect heading detection * update again * clean up readme --- CHANGELOG.md | 2 ++ README.md | 41 ++++++++++++++++------------------------- README.qmd | 17 ++++++----------- _viash.yaml | 2 +- 4 files changed, 25 insertions(+), 37 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95c0451e..f52a6d02 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -56,6 +56,8 @@ * Update to Viash 0.8.5 (PR #25). +* Update to Viash 0.9.0-RC3 (PR #51). + ## DOCUMENTATION ## BUG FIXES diff --git a/README.md b/README.md index 1639481f..ecf807ca 100644 --- a/README.md +++ b/README.md @@ -26,34 +26,25 @@ We encourage contributions from the community. To contribute: ## Contribution Guidelines -- **Documentation of Functionality**: The purpose and functionality of - each component should be adequately described. -- **Documentation of Inputs and Outputs**: All input and output - arguments should have a description and example (with extension). -- **Docker Image**: A Docker image (with optional additional - dependencies) should be provided. -- **Write unit tests**: A unit test with possibly test resources needs - to be provided. -- **Provide test resources**: If the unit test requires test resources, - these should be provided in the `test_resources` section of the - component. -- **Versioning**: If the component uses custom software (not installed - via Apt, Apk, Yum, Pip, Conda, or R), a Bash script `version.sh` needs - to be provided that outputs the version of the software. -- **File format specifications**: If a component returns a directory or - data structure such as AnnData or MuData, a specification of the file - format should be provided. +The contribution guidelines describes which steps you should follow to +contribute a component to this repository. + +1. Find a component to contribute +2. Add config template +3. Fill in the metadata +4. Find a suitable container +5. Create help file +6. Create or fetch test data +7. Add arguments for the input files +8. Add arguments for the output files +9. Add arguments for the other arguments +10. Add a Docker engine +11. Write a runner script +12. Create test script +13. Create a `/var/software_versions.txt` file See the [CONTRIBUTING](CONTRIBUTING.md) file for more details. -## Repository Structure - -… - -## Installation and Usage - -… - ## Support and Community For support, questions, or to join our community: diff --git a/README.qmd b/README.qmd index f7e5139b..656cdac7 100644 --- a/README.qmd +++ b/README.qmd @@ -21,29 +21,24 @@ We encourage contributions from the community. To contribute: ## Contribution Guidelines +The contribution guidelines describes which steps you should follow to contribute a component to this repository. + ```{r echo=FALSE} lines <- readr::read_lines("CONTRIBUTING.md") -index_start <- grep("^## ", lines) +index_start <- grep("^### Step [0-9]*:", lines) + index_end <- c(index_start[-1] - 1, length(lines)) -name <- gsub("^## ", "", lines[index_start]) -description <- lines[index_start + 2] +name <- gsub("^### Step [0-9]*: *", "", lines[index_start]) knitr::asis_output( - paste(paste0(" * **", name, "**: ", description, "\n"), collapse = "") + paste(paste0(" 1. ", name, "\n"), collapse = "") ) ``` See the [CONTRIBUTING](CONTRIBUTING.md) file for more details. -## Repository Structure - -... - -## Installation and Usage - -... ## Support and Community diff --git a/_viash.yaml b/_viash.yaml index 6d658e2d..397a8d69 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -7,7 +7,7 @@ links: issue_tracker: https://github.com/viash-hub/biobase/issues repository: https://github.com/viash-hub/biobase -viash_version: 0.9.0-RC2 +viash_version: 0.9.0-RC3 config_mods: | .requirements.commands := ['ps']