Update viash (#51)

* update viash

* update readme

* update changelog

* update changelog

* fix incorrect heading detection

* update again

* clean up readme

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

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:

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
 

_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']