Fixes for Viash 0.9 (#27)

* Update action.yml * Update jq query * update for viash 0.9 * add matrix to output of ns list * update docs * fix description * add more actions * update action * update readme * remove functionality * remove variable * update action * update * fix action * fix action * fix ci * pin versions * fix action * fix ci * fix ci * fix ci * fix ci * fix ci * fix ci * fix ci * add matrix to output * fix ci * fix action * fix action * fix action * improve readability * fix action * clean up action * move update docker engine * remove viash hub deploy * arguments `components` and `workflows` were removed in favour for the `target_dir` argument. * uniformize documentation pages * add changelog * update docs * update changelog * update mentioned viash versions to v6 * fix platform description * fix indentation * update readme * simplify readme * fix check-concurrent-pr * fix fallback * add paste * fix flag * add entry to changelog
viash-io · Jun 28, 2024 · 9706ce0 · 9706ce0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,32 @@
+# viash-actions v6.0.0
+
+## Breaking changes
+
+* `update-docker-engine` was moved to `project/update-docker-engine` (PR #27).
+
+* `pro/build-nextflow-params`: Arguments `components` and `workflows` were removed in favour for the `target_dir` argument (PR #27).
+
+* `pro/build-nextflow-schemas`: Arguments `components` and `workflows` were removed in favour for the `target_dir` argument (PR #27).
+
+* Removed `viash-hub/deploy`: Viash Hub pulls source code from GitHub and builds Viash packages accordingly, as opposed to pushing deployments using GitHub Actions (PR #27).
+
+## New functionality
+
+* `project/build-target`: Created an action for building a target directory using `viash ns build` and generating a matrix of the components for which Docker images need to be built and pushed (PR #27).
+
+* `project/check-concurrent-pr`: Created an action for checking if a push event is concurrent with a pull request (PR #27).
+
+## Major changes
+
+* All actions were updated to work with Viash 0.9 and later (PR #27).
+
+## Documentation
+
+* Updated all READMEs to be more consistent (PR #27).
+
+* Added a Makefile for generating READMEs more efficiently (PR #27).
+
+
 # viash-actions v5.3.1
 
 ## Bug fixes
@@ -20,13 +49,13 @@
 
 ## Minor changes
 
-* `project/detect-changed-components`: bump `tj-actions/changed-files` to `42.0.2` (PR #24)
+* `project/detect-changed-components`: bump `tj-actions/changed-files` to `42.0.2` (PR #24).
 
 # viash-actions v5.1.0
 
 ## New functionality
 
-* `pro/build-nextflow-schemas`: Add optional flag to allow dataset input for nf-tower (PR #23)
+* `pro/build-nextflow-schemas`: Add optional flag to allow dataset input for nf-tower (PR #23).
 
 # viash-actions v5.0.0
 

diff --git a/Makefile b/Makefile
@@ -0,0 +1,15 @@
+# Set up some variables for consistency
+QMD_FILES := $(shell find . -name "README.qmd")  # Find all README.qmd files
+MD_FILES := $(patsubst %.qmd,%.md,$(QMD_FILES)) # Corresponding MD filenames
+
+# Default target: build all MD files
+all: $(MD_FILES)
+
+README.md: README.qmd
+	quarto render $<
+%/README.md: %/README.qmd %/action.yml
+	quarto render $<
+
+# Clean up generated MD files
+clean:
+	rm -f $(MD_FILES) 
diff --git a/README.md b/README.md
@@ -1,23 +1,50 @@
 # Github Actions for Viash
 
-This repository stores [Github Actions](https://github.com/features/actions) useful for building and publishing [Viash](https://viash.io) components:
 
-1. [viash-io/viash-actions/setup](setup) - Install Viash
-2. [viash-io/viash-actions/ns-list](ns-list) - List Viash components in a repository
-3. [viash-io/viash-actions/ns-build](ns-build) - Build a namespace from many viash config files
+This repository stores Github Actions useful for building and publishing
+[Viash](https://viash.io) components:
 
-There are also a few actions that are commonly used in Viash projects:
+1.  [`ns-build`](ns-build) - viash ns build
+2.  [`ns-list`](ns-list) - viash ns list
+3.  [`setup`](setup) - Setup Viash
 
-1. [viash-io/viash-actions/project/cache-and-sync-s3](project/cache-and-sync-s3) - Sync and cache an S3 bucket
-2. [viash-io/viash_actions/project/detect-changed-components](project/detect-changed-components) - Detect changed Viash components
+There are also some actions that are commonly used in Viash projects:
 
-We recommend using `v3` for your actions.
+1.  [`project/build-target`](project/build-target) - Build target
+    directory
+2.  [`project/detect-changed-components`](project/detect-changed-components) -
+    Detect components with changed files
+3.  [`project/is-pr`](project/is-pr) - Is PR
+4.  [`project/sync-and-cache-s3`](project/sync-and-cache-s3) - Sync and
+    cache an S3 bucket
+5.  [`project/update-docker-engine`](project/update-docker-engine) -
+    Update Docker Engine
 
-## Release Management
+Finally, there are some [Viash
+Pro](https://www.data-intuitive.com/services/viashpro.html) actions:
+
+1.  [`pro/build-nextflow-params`](pro/build-nextflow-params) - Build
+    parameter yaml
+2.  [`pro/build-nextflow-schemas`](pro/build-nextflow-schemas) - Build
+    nf-tower schemas
+3.  [`pro/generate-documentation-qmd`](pro/generate-documentation-qmd) -
+    Build and publish qmd
 
-This repository uses [GitHub's recommended release management for actions](https://docs.github.com/en/actions/creating-actions/about-custom-actions#using-release-management-for-actions): 
+We recommend using `v6` for your actions.
+
+## Release Management
 
-* GitHub releases with tags are used for updates on the actions. 
-* Semantic versioning is used, with major, minor and possibly patch release. 
-* Major versions (such as `v1`) will always point to the last minor or patch release for this major version. (when `v1.0.2` is out, `v1` will point to this update to). This means using `viash-io/viash-actions/setup@v1` in your workflow file will automatically get the updated versions. Using `viash-io/viash-actions/[email protected]` will pin a specific release.
-* Major version changes (`v1` to `v2`) will often come with breaking changes, and workflows might require manual updates.
+This repository uses [GitHub’s recommended release management for
+actions](https://docs.github.com/en/actions/creating-actions/about-custom-actions#using-release-management-for-actions):
+
+- GitHub releases with tags are used for updates on the actions.
+- Semantic versioning is used, with major, minor and possibly patch
+  release.
+- Major versions (such as `v1`) will always point to the last minor or
+  patch release for this major version. (when `v1.0.2` is out, `v1` will
+  point to this update to). This means using
+  `viash-io/viash-actions/setup@v1` in your workflow file will
+  automatically get the updated versions. Using
+  `viash-io/viash-actions/[email protected]` will pin a specific release.
+- Major version changes (`v1` to `v2`) will often come with breaking
+  changes, and workflows might require manual updates.
diff --git a/README.qmd b/README.qmd
@@ -0,0 +1,54 @@
+---
+title: Github Actions for Viash
+format: gfm
+---
+
+```{r}
+#| include: false
+library(tidyverse)
+
+repo_name <- "viash-io/viash-actions"
+latest_stable_version <- "v6"
+
+actions <- tibble(
+  file = list.files(".", full.names = TRUE, recursive = TRUE, pattern = "action.yml"),
+  path = gsub("^\\./(.*)/action.yml$", "\\1", file),
+  action = map(file, yaml::read_yaml),
+  action_name = map_chr(action, "name"),
+  namespace = ifelse(grepl("/", path), gsub("/.*", "", path), ""),
+  str = paste0("1. [`", path, "`](", path, ") - ", action_name, "\n")
+)
+```
+
+
+This repository stores Github Actions useful for building and publishing [Viash](https://viash.io) components:
+
+```{r output="asis"}
+#| echo: false
+cat(actions %>% filter(namespace == "") %>% pull(str) %>% paste(collapse = ""))
+```
+
+There are also some actions that are commonly used in Viash projects:
+
+```{r output="asis"}
+#| echo: false
+cat(actions %>% filter(namespace == "project") %>% pull(str) %>% paste(collapse = ""))
+```
+
+Finally, there are some [Viash Pro](https://www.data-intuitive.com/services/viashpro.html) actions:
+
+```{r output="asis"}
+#| echo: false
+cat(actions %>% filter(namespace == "pro") %>% pull(str) %>% paste(collapse = ""))
+```
+
+We recommend using ``r latest_stable_version`` for your actions.
+
+## Release Management
+
+This repository uses [GitHub's recommended release management for actions](https://docs.github.com/en/actions/creating-actions/about-custom-actions#using-release-management-for-actions): 
+
+* GitHub releases with tags are used for updates on the actions. 
+* Semantic versioning is used, with major, minor and possibly patch release. 
+* Major versions (such as `v1`) will always point to the last minor or patch release for this major version. (when `v1.0.2` is out, `v1` will point to this update to). This means using `viash-io/viash-actions/setup@v1` in your workflow file will automatically get the updated versions. Using `viash-io/viash-actions/[email protected]` will pin a specific release.
+* Major version changes (`v1` to `v2`) will often come with breaking changes, and workflows might require manual updates.
diff --git a/ns-build/README.md b/ns-build/README.md
@@ -1,5 +1,11 @@
-ns-build
-================
+
+
+# ns-build
+
+<!--
+DO NOT EDIT THIS FILE MANUALLY!
+This README was generated by running `make`
+-->
 
 Build a namespace from many viash config files.
 
@@ -11,7 +17,7 @@ each of the arguments.
 
 We recommend using a Linux or MacOS runner if possible.
 
-### Inputs available
+### Inputs
 
 - `query`: - *optional*. Filter which components get selected by
   component and namespace name. Can be a regex. Example:
@@ -22,39 +28,55 @@ We recommend using a Linux or MacOS runner if possible.
   component name. Can be a regex. Example: “^component1”.
 - `src`: - *optional*. A source directory containing viash config files,
   possibly structured in a hierarchical folder structure. Default: src/.
-- `platform`: - *optional*. Acts as a regular expression to filter the
-  platform ids specified in the found config files. If this is not
-  provided, all platforms will be used. If no platforms are defined in a
-  config, the native platform will be used. In addition, the path to a
-  platform yaml file can also be specified.
+- `platform`: - *optional*. (viash \< 0.9.0) Acts as a regular
+  expression to filter the platform ids specified in the found config
+  files. If this is not provided, all platforms will be used. If no
+  platforms are defined in a config, the native platform will be used.
+  In addition, the path to a platform yaml file can also be specified.
+- `runner`: - *optional*. (viash \>= 0.9.0) Acts as a regular expression
+  to filter the runner ids specified in the found config files. If this
+  is not provided, all runners will be used. If no runners are defined
+  in a config, the executable runner will be used.
+- `engine`: - *optional*. (viash \>= 0.9.0) Acts as a regular expression
+  to filter the engine ids specified in the found config files. If this
+  is not provided, all engines will be used. If no engines are defined
+  in a config, the native engine will be used.
 - `parallel`: - *optional*. Whether or not to run the process in
   parallel.
 - `config_mod`: - *optional*. Modify a viash config at runtime using
-  dynamic config modding.
+  config_mod.
 - `target`: - *optional*. A target directory to build the executables
   into. Default: target/.
-- `setup`: - *optional*. Which setup strategy for creating the container
-  to use \[Docker Platform only\].
+- `colorize`: - *optional*. Specify whether the console output should be
+  colorized. If not specified, we attempt to detect this automatically.
+  Possible values are: “true”, “false”, “auto”.
+- `loglevel`: - *optional*. Specify the log level in us. Possible values
+  are: “error”, “warn”, “info”, “debug”, “trace”.
+- `setup`: - *optional*. Which docker_setup_strategy for creating the
+  container to use \[Docker Engine only\].
+
+### Outputs
+
+- `output`: The output of ‘viash ns build’.
 
 ## Examples
 
 ``` yaml
-name: demo of viash ns build
+name: Demo of ns-build
 
 on: 
-  branch: main
+  push:
 
 jobs:
   viash-linux:
     runs-on: ubuntu-latest
     steps:
-      - uses: viash-io/viash-actions/setup@v3
+      - name: Check out repository
+        uses: actions/checkout@v3
 
-      - uses: viash-io/viash-actions/ns-build@v3
-  viash-macos:
-    runs-on: macos-latest
-    steps:
-      - uses: viash-io/viash-actions/setup@v3
+      - name: Install Viash
+        uses: viash-io/viash-actions/setup@v6
 
-      - uses: viash-io/viash-actions/ns-build@v3
+      - name: viash ns build
+        uses: viash-io/viash-actions/ns-build@v6
 ```
diff --git a/ns-build/README.qmd b/ns-build/README.qmd
@@ -1,15 +1,21 @@
 ---
-title: ns-build
 format: gfm
 ---
 
 ```{r}
 #| include: false
 library(tidyverse)
-# action <- yaml::read_yaml("ns-build/action.yml")
 action <- yaml::read_yaml("action.yml")
+action_name <- basename(getwd())
 ```
 
+# `r action_name`
+
+<!--
+DO NOT EDIT THIS FILE MANUALLY!
+This README was generated by running `make`
+-->
+
 `r action$description`
 
 ## Usage
@@ -18,7 +24,7 @@ This action will run `viash ns build`. See the reference documentation on [ns bu
 
 We recommend using a Linux or MacOS runner if possible.
 
-### Inputs available
+### Inputs
 
 ```{r}
 #| echo: false
@@ -30,26 +36,36 @@ lines <- map_chr(names(action$inputs), function(name) {
 knitr::asis_output(paste0(lines, collapse = "\n"))
 ```
 
+### Outputs
+
+```{r}
+#| echo: false
+lines <- map_chr(names(action$outputs), function(name) {
+  output <- action$outputs[[name]]
+  glue::glue("* `{name}`: {output$description}")
+})
+knitr::asis_output(paste0(lines, collapse = "\n"))
+```
+
 ## Examples
 
 ```yaml
-name: demo of viash ns build
+name: Demo of `r action_name`
 
 on: 
-  branch: main
+  push:
 
 jobs:
   viash-linux:
     runs-on: ubuntu-latest
     steps:
-      - uses: viash-io/viash-actions/setup@v3
+      - name: Check out repository
+        uses: actions/checkout@v3
 
-      - uses: viash-io/viash-actions/ns-build@v3
-  viash-macos:
-    runs-on: macos-latest
-    steps:
-      - uses: viash-io/viash-actions/setup@v3
+      - name: Install Viash
+        uses: viash-io/viash-actions/setup@v6
 
-      - uses: viash-io/viash-actions/ns-build@v3
+      - name: `r action$name`
+        uses: viash-io/viash-actions/ns-build@v6
 ```