wip: more work

.envrc

@@ -0,0 +1 @@
+use nix

.github/workflows/test.yml

@@ -26,6 +26,3 @@ jobs:
       - run: npm run test
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - uses: codecov/codecov-action@v3
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

CHANGELOG.md

@@ -7,12 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [1.4.0] - 2023-08-12
-
 ## Changed
 
 - If `fs.renameSync` fails (e.g. because source and destination files are on different partitions), try `fs.copySync` and `fs.unlinkSync` instead (#14).
-- Fail instead of warn, when `nextflow help`` doesn't work (#23).
 
 ## Fixed
 
@@ -58,8 +55,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - GitHub Actions workflow to test Nextflow installation and downstream usage
 - Documentation and license files
 
-[unreleased]: https://github.com/nf-core/setup-nextflow/compare/v1.4.0...HEAD
-[1.4.0]: https://github.com/nf-core/setup-nextflow/compare/v1.3.0...v1.4.0
+[unreleased]: https://github.com/nf-core/setup-nextflow/compare/v1.3.0...HEAD
 [1.3.0]: https://github.com/nf-core/setup-nextflow/compare/v1.2.0...v1.3.0
 [1.2.0]: https://github.com/nf-core/setup-nextflow/compare/v1.1.1...v1.2.0
 [1.1.0]: https://github.com/nf-core/setup-nextflow/compare/v1.0.1...v1.1.0

README.md

@@ -1,7 +1,6 @@
 # ![nf-core/setup-nextflow](docs/images/nfcore-setupnextflow_logo.png#gh-light-mode-only) ![nf-core/setup-nextflow](docs/images/nfcore-setupnextflow_logo_dark.png#gh-dark-mode-only)
 
 [![Testing](https://github.com/nf-core/setup-nextflow/actions/workflows/example.yml/badge.svg)](https://github.com/nf-core/setup-nextflow/actions/workflows/example.yml)
-[![codecov](https://codecov.io/gh/nf-core/setup-nextflow/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/setup-nextflow)
 [![MIT License](https://img.shields.io/github/license/nf-core/setup-nextflow?logo=opensourceinitiative)](https://github.com/nf-core/setup-nextflow/blob/master/LICENSE)
 [![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/nf-core/setup-nextflow?logo=github)](https://github.com/nf-core/setup-nextflow/releases/latest)
 [![Get from GitHub Actions](https://img.shields.io/static/v1?label=actions&message=marketplace&color=green&logo=githubactions)](https://github.com/marketplace/actions/setup-nextflow)

default.nix

@@ -0,0 +1,8 @@
+{ pkgs ? import (fetchTarball "channel:nixos-23.05") {} }:
+
+
+pkgs.mkShell {
+  buildInputs = [
+    pkgs.nodejs
+  ];
+}

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "install-nextflow-action",
-  "version": "1.4.0",
+  "version": "1.3.0",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "install-nextflow-action",
-      "version": "1.4.0",
+      "version": "1.3.0",
       "license": "MIT",
       "dependencies": {
         "@actions/core": "^1.8.2",
@@ -433,9 +433,9 @@
       }
     },
     "node_modules/@types/istanbul-lib-coverage": {
-      "version": "2.0.5",
-      "resolved": "https://registry.npmjs.org/@types/istanbul-lib-coverage/-/istanbul-lib-coverage-2.0.5.tgz",
-      "integrity": "sha512-zONci81DZYCZjiLe0r6equvZut0b+dBRPBN5kBDjsONnutYNtJMoWQ9uR2RkL1gLG9NMTzvf+29e5RFfPbeKhQ==",
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/@types/istanbul-lib-coverage/-/istanbul-lib-coverage-2.0.4.tgz",
+      "integrity": "sha512-z/QT1XN4K4KYuslS23k62yDIDLwLFkzxOuMplDtObz0+y7VqJCaO2o+SPwHCvLFZh7xazvvoor2tA/hPz9ee7g==",
       "dev": true
     },
     "node_modules/@types/json-schema": {
@@ -4875,9 +4875,9 @@
       }
     },
     "node_modules/v8-to-istanbul/node_modules/@jridgewell/trace-mapping": {
-      "version": "0.3.20",
-      "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.20.tgz",
-      "integrity": "sha512-R8LcPeWZol2zR8mmH3JeKQ6QRCFb7XgUhV9ZlGhHLGyg4wpPiPZNQOOWhFZhxKw8u//yTbNGI42Bx/3paXEQ+Q==",
+      "version": "0.3.19",
+      "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.19.tgz",
+      "integrity": "sha512-kf37QtfW+Hwx/buWGMPcR60iF9ziHa6r/CZJIHbmcm4+0qrXiVdxegAH0F6yddEVQ7zdkjcGCgCzUu+BcbhQxw==",
       "dev": true,
       "dependencies": {
         "@jridgewell/resolve-uri": "^3.1.0",
@@ -5445,9 +5445,9 @@
       }
     },
     "@types/istanbul-lib-coverage": {
-      "version": "2.0.5",
-      "resolved": "https://registry.npmjs.org/@types/istanbul-lib-coverage/-/istanbul-lib-coverage-2.0.5.tgz",
-      "integrity": "sha512-zONci81DZYCZjiLe0r6equvZut0b+dBRPBN5kBDjsONnutYNtJMoWQ9uR2RkL1gLG9NMTzvf+29e5RFfPbeKhQ==",
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/@types/istanbul-lib-coverage/-/istanbul-lib-coverage-2.0.4.tgz",
+      "integrity": "sha512-z/QT1XN4K4KYuslS23k62yDIDLwLFkzxOuMplDtObz0+y7VqJCaO2o+SPwHCvLFZh7xazvvoor2tA/hPz9ee7g==",
       "dev": true
     },
     "@types/json-schema": {
@@ -8556,9 +8556,9 @@
       },
       "dependencies": {
         "@jridgewell/trace-mapping": {
-          "version": "0.3.20",
-          "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.20.tgz",
-          "integrity": "sha512-R8LcPeWZol2zR8mmH3JeKQ6QRCFb7XgUhV9ZlGhHLGyg4wpPiPZNQOOWhFZhxKw8u//yTbNGI42Bx/3paXEQ+Q==",
+          "version": "0.3.19",
+          "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.19.tgz",
+          "integrity": "sha512-kf37QtfW+Hwx/buWGMPcR60iF9ziHa6r/CZJIHbmcm4+0qrXiVdxegAH0F6yddEVQ7zdkjcGCgCzUu+BcbhQxw==",
           "dev": true,
           "requires": {
             "@jridgewell/resolve-uri": "^3.1.0",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "install-nextflow-action",
-  "version": "1.4.0",
+  "version": "1.3.0",
   "description": "An action to install Nextflow into a GitHub Actions workflow and make it available for subsequent steps.",
   "main": "lib/src/main.js",
   "scripts": {

src/NextflowRelease.ts

@@ -2,10 +2,10 @@
  * Houses the pertinent data that GitHub exposes for each Nextflow release
  */
 export type NextflowRelease = {
-  versionNumber: string
-  isEdge: boolean
-  binaryURL: string
-  allBinaryURL: string
+  versionNumber: string;
+  isEdge: boolean;
+  binaryURL: string;
+  allBinaryURL: string;
 }
 
 /**

src/OctokitWrapper.ts

@@ -9,9 +9,9 @@ const NEXTFLOW_REPO = { owner: "nextflow-io", repo: "nextflow" }
 export async function setup_octokit(
   github_token: string
 ): Promise<InstanceType<typeof GitHub>> {
-  let octokit = {} as InstanceType<typeof GitHub>
+    let octokit = {} as InstanceType<typeof GitHub>
   try {
-    octokit = github.getOctokit(github_token)
+      octokit = github.getOctokit(github_token)
   } catch (e: unknown) {
     if (e instanceof Error) {
       core.setFailed(
@@ -19,7 +19,7 @@ export async function setup_octokit(
       )
     }
   }
-  return octokit
+    return octokit
 }
 
 export async function pull_releases(
@@ -43,20 +43,3 @@ export async function all_nf_release_data(
     response => response.data
   )
 }
-
-export async function latest_stable_release_data(
-  ok: InstanceType<typeof GitHub>
-): Promise<object> {
-  const { data: stable_release } = await ok.rest.repos.getLatestRelease(
-    NEXTFLOW_REPO
-  )
-
-  return stable_release
-}
-
-export async function pull_latest_stable_release(
-  ok: InstanceType<typeof GitHub>
-): Promise<NextflowRelease> {
-  const latest_release = await latest_stable_release_data(ok)
-  return nextflow_release(latest_release)
-}

src/functions.ts

@@ -25,11 +25,13 @@ function tag_filter(version: string): (NextflowRelease) => Boolean {
       filter = (r: NextflowRelease) => {
         return r.versionNumber.endsWith("-edge")
       }
+
     } else {
       filter = (r: NextflowRelease) => {
         return !r.isEdge
       }
     }
+
   }
   return filter
 }
@@ -39,7 +41,7 @@ export async function get_nextflow_release(
   releases: Array<NextflowRelease>
 ): Promise<NextflowRelease> {
   // Filter the releases
-  const filter = tag_filter(version)
+  const filter = tag_filter(version);
   const matching_releases = releases.filter(filter)
 
   matching_releases.sort((x, y) => {

src/main.ts

@@ -34,8 +34,8 @@ async function run(): Promise<void> {
   const releases = await pull_releases(octokit)
 
   // Get the release info for the desired release
-  let release = {} as NextflowRelease
-  let resolved_version = ""
+  let release = {} as NextflowRelease;
+  let resolved_version = "";
   try {
     release = await get_nextflow_release(version, releases)
     resolved_version = release.versionNumber
@@ -50,6 +50,7 @@ async function run(): Promise<void> {
     }
   }
 
+  // Get the download url for the desired release
   try {
     // Download Nextflow and add it to path
     if (!check_cache(resolved_version)) {
@@ -76,8 +77,9 @@ async function run(): Promise<void> {
     await exec.exec("nextflow", ["help"])
   } catch (e: unknown) {
     if (e instanceof Error) {
-      // fail workflow if Nextflow run does not succeed
-      core.setFailed(`Could not run 'nextflow help'. Error: ${e.message}`)
+      core.warning(
+        "Nextflow appears to have installed correctly, but an error was thrown while running it."
+      )
     }
   }
 }