Add ns build (#5)

* Add ns build action

* add node modules Y_Y

* update documentation

---------

Co-authored-by: Dries Schaumont <[email protected]>

CHANGELOG.md

@@ -2,7 +2,9 @@
 
 ## New Features
 
-* Added [build-nextflow-schemas](build-nextflow-schemas) - Build schemas from a viash config to use with nf-tower
+* Added [ns-build](ns-build) - Build a namespace from many viash config files.
+
+* Added [build_nextflow_schemas](build_nextflow_schemas) - Build schemas from a viash config to use with nf-tower
 
 * Added [build-nextflow-params](build-nextflow-params) - build nextflow parameter file templates (see nextflow's -params-file option) from viash configs
 

README.md

@@ -3,9 +3,10 @@
 This repository stores [Github Actions](https://github.com/features/actions) useful for building and publishing [Viash](https://viash.io) documents.
 
 1. [viash-io/viash-actions/setup](setup) - Install Viash
-1. [viash-io/viash-actions/ns-list](ns-list) - List Viash components in a repository
+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.
 
-We recommend using `v1` for your actions.
+We recommend using `v2` for your actions.
 
 ## Release Management
 

ns-build/README.md

@@ -0,0 +1,60 @@
+ns-build
+================
+
+Build a namespace from many viash config files.
+
+## Usage
+
+This action will run `viash ns build`. See the reference documentation
+on [ns build](https://viash.io/reference/viash/ns.html) for more info on
+each of the arguments.
+
+We recommend using a Linux or MacOS runner if possible.
+
+### Inputs available
+
+- `query`: - *optional*. Filter which components get selected by
+  component and namespace name. Can be a regex. Example:
+  “^mynamespace/component1\$”.
+- `query_namespace`: - *optional*. Filter which namespaces get selected
+  by namespace name. Can be a regex. Example: “^mynamespace\$”.
+- `query_name`: - *optional*. Filter which components get selected by
+  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.
+- `parallel`: - *optional*. Whether or not to run the process in
+  parallel.
+- `config_mod`: - *optional*. Modify a viash config at runtime using
+  dynamic config modding.
+- `target`: - *optional*. A target directory to build the executables
+  into. Default: target/.
+- `setup`: - *optional*. Which setup strategy for creating the container
+  to use \[Docker Platform only\].
+
+## Examples
+
+``` yaml
+name: demo of viash ns build
+
+on: 
+  branch: main
+
+jobs:
+  viash-linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: viash-io/viash-actions/setup@v1
+
+      - uses: viash-io/viash-actions/ns-build@v1
+  viash-macos:
+    runs-on: macos-latest
+    steps:
+      - uses: viash-io/viash-actions/setup@v1
+
+      - uses: viash-io/viash-actions/ns-build@v1
+```

ns-build/README.qmd

@@ -0,0 +1,55 @@
+---
+title: ns-build
+format: gfm
+---
+
+```{r}
+#| include: false
+library(tidyverse)
+# action <- yaml::read_yaml("ns-build/action.yml")
+action <- yaml::read_yaml("action.yml")
+```
+
+`r action$description`
+
+## Usage
+
+This action will run `viash ns build`. See the reference documentation on [ns build](https://viash.io/reference/viash/ns.html) for more info on each of the arguments.
+
+We recommend using a Linux or MacOS runner if possible.
+
+### Inputs available
+
+```{r}
+#| echo: false
+lines <- map_chr(names(action$inputs), function(name) {
+  input <- action$inputs[[name]]
+  required <- ifelse (input$required %||% FALSE, "required", "optional")
+  glue::glue("* `{name}`: - _{required}_. {input$description}")
+})
+knitr::asis_output(paste0(lines, collapse = "\n"))
+```
+
+## Examples
+
+```yaml
+name: demo of viash ns build
+
+on: 
+  branch: main
+
+jobs:
+  viash-linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: viash-io/viash-actions/setup@v1
+
+      - uses: viash-io/viash-actions/ns-build@v1
+  viash-macos:
+    runs-on: macos-latest
+    steps:
+      - uses: viash-io/viash-actions/setup@v1
+
+      - uses: viash-io/viash-actions/ns-build@v1
+```
+

ns-build/action.yml

@@ -0,0 +1,41 @@
+name: viash ns build
+description: Build a namespace from many viash config files.
+inputs:
+  query:
+    description: 'Filter which components get selected by component and namespace
+      name. Can be a regex. Example: "^mynamespace/component1$".'
+    required: false
+  query_namespace:
+    description: 'Filter which namespaces get selected by namespace name. Can be a
+      regex. Example: "^mynamespace$".'
+    required: false
+  query_name:
+    description: 'Filter which components get selected by component name. Can be a
+      regex. Example: "^component1".'
+    required: false
+  src:
+    description: ' A source directory containing viash config files, possibly structured
+      in a hierarchical folder structure. Default: src/.'
+    required: false
+  platform:
+    description: 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.
+    required: false
+  parallel:
+    description: Whether or not to run the process in parallel.
+    required: false
+  config_mod:
+    description: Modify a viash config at runtime using dynamic config modding.
+    required: false
+  target:
+    description: 'A target directory to build the executables into. Default: target/.'
+    required: false
+  setup:
+    description: Which setup strategy for creating the container to use [Docker Platform
+      only].
+    required: false
+runs:
+  using: node16
+  main: index.js

ns-build/generate_yml.R

@@ -0,0 +1,71 @@
+# This script generates a github action given a Viash schema
+
+library(tidyverse)
+
+# parameters
+skip_args <- c("push", "flatten")
+dest_file <- "ns-build/action.yml"
+subcommands <- c("ns", "build")
+
+#################### common code
+# fetch schema
+out <- system("viash export cli_schema", intern = TRUE)
+schema <- jsonlite::fromJSON(out, simplifyVector = FALSE)
+
+# go down schema to find the right command
+for (i in seq_along(subcommands)) {
+  subcommand <- subcommands[[i]]
+  schema <- schema[[which(sapply(schema, function(li) li$name == subcommand))]]
+
+  if (i != length(subcommands)) {
+    schema <- schema$subcommands
+  }
+}
+
+# construct yaml
+selected_opts <- schema$opts[sapply(schema$opts, function(x) !x$name %in% skip_args)]
+input_values <- sapply(selected_opts, function(opt) {
+  descr <- opt$descr %>%
+    str_replace_all("@\\[[^]]*\\]\\(([^\\)]*)\\)", "\\1") %>%
+    str_replace_all(". *$", ".")
+
+  choices_str <-
+    if (!is.null(opt$choices)) {
+      paste0(" Possible values are: \"", paste(opt$choices, collapse = "\", \""), "\".")
+    } else {
+      ""
+    }
+  out <- list(
+    description = paste0(descr, choices_str),
+    required = opt$required
+  )
+  setNames(list(out), opt$name)
+})
+out <- list(
+  name = schema$bannerCommand,
+  description = schema$bannerDescription,
+  inputs = input_values,
+  # outputs = list(
+  #   output = list(
+  #     description = "A list of all of the components found. By default this will be a yaml, unless the format argument was set to 'json'."
+  #   )
+  # ),
+  runs = list(
+    using = "node16",
+    main = "index.js"
+  )
+)
+
+# write github action
+handlers <- list(
+  logical = function(x) {
+    result <- ifelse(x, "true", "false")
+    class(result) <- "verbatim"
+    return(result)
+  }
+)
+yaml::write_yaml(
+  out,
+  dest_file,
+  handlers = handlers
+)

ns-build/index.js

@@ -0,0 +1,54 @@
+const core = require("@actions/core");
+const exec = require("@actions/exec");
+
+async function run() {
+  try {
+    // set up listeners
+    let myOutput = "";
+    let myError = "";
+
+    const options = {};
+    options.listeners = {
+      stdout: (data) => {
+        myOutput += data.toString();
+      },
+      stderr: (data) => {
+        myError += data.toString();
+      }
+    };
+
+    // fetch arguments for command
+    // skip "parallel"
+    // todo: can I extract these inputNames from the action.yml?
+    const inputNames = [
+      "query", "query_namespace", "query_name", "src", "platform",
+      "parallel", "config_mod", "target", "setup"
+    ]
+    const booleanInputs = ["parallel"]
+    const inputArgs = inputNames.flatMap(function(argName) {
+      const value = core.getInput(argName)
+      if (value == "") {
+        return [];
+      } else if (booleanInputs.indexOf(argName) >= 0) {
+        if (value.toLowerCase() == "true") {
+          return ["--" + argName];
+        } else {
+          return [];
+        }
+      } else {
+        return ["--" + argName, value];
+      }
+    })
+    let args = ["ns", "build"].concat(inputArgs);
+
+    // run command
+    await exec.exec("viash", args, options);
+
+    // pass output
+    core.setOutput("output", myOutput);
+  } catch (error) {
+    core.setFailed(error.message);
+  }
+}
+
+run();