add tools api docs to content collection

.github/workflows/add-tools-api-docs.yml

@@ -0,0 +1,80 @@
+name: Open PR with tools API docs based on webhook call
+on:
+  workflow_dispatch:
+    inputs:
+      ref_name:
+        description: 'The name of the release branch'
+        required: true
+        default: 'dev'
+
+jobs:
+  api-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Checkout tools code
+        uses: actions/checkout@v4
+        with:
+          repository: 'nf-core/tools'
+          ref: ${{ inputs.ref_name }}
+          path: 'tools'
+
+      - name: setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        run: |
+          npm install remark unist-util-visit
+
+      - name: run API generation script
+        run: |
+          cd tools
+          bash docs/api/generate-api-docs.sh --release ${{ inputs.ref_name }}
+
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
+
+      # install prettier plugins
+      - uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
+        with:
+          node-version: 20
+
+      - run: npm install --only=dev
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
+
+      - name: Commit & push changes
+        id: commit-and-push
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Update nf-core/tools API docs for ${{ inputs.ref_name }}"
+          git push
+
+      - name: Create PR
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Update nf-core/tools API docs for ${{github.ref_name}}
+          title: Update nf-core/tools API docs for ${{github.ref_name}}
+          body: |
+            This PR updates the nf-core/tools API docs for ${{github.ref_name}}.
+            Please review the changes and merge if they look good.
+          branch: 'update-api-docs-${{github.ref_name}}'
+          delete-branch: true
+          base: 'main'
+          draft: false

astro.config.mjs

@@ -30,34 +30,40 @@ import icon from "astro-icon";
 const latestToolsRelease = await fetch('https://api.github.com/repos/nf-core/tools/releases/latest')
     .then((res) => res.json())
     .then((json) => json.tag_name);
-let latestPipelineReleases = {};
 
+let latestPipelineReleases = {};
 pipelines_json.remote_workflows.map(
     (pipeline) => (latestPipelineReleases[pipeline.name] = `/${pipeline.name}/${pipeline.releases[0].tag_name}/`),
 );
-const latestTollsURL = `/tools/docs/'+${latestToolsRelease}`;
 // https://astro.build/config
 export default defineConfig({
     site: 'https://nf-co.re/',
     output: 'hybrid',
     adapter: netlify(),
     redirects: {
-        [latestTollsURL]: 'https://oldsite.nf-co.re/tools/docs/latest/',
         ...latestPipelineReleases,
     },
     integrations: [
         svelte(),
         icon({
-            include:{
-            // only include a subset of icons
-            "file-icons":["nextflow"],
-            logos:["twitter","mastodon-icon","slack-icon","aws","microsoft-azure","github-actions", "youtube-icon"],
-            fa:["github"],
-            "fa-brands":["github"],
-            "line-md":["check-list-3-twotone"],
-            "mdi":["aws","slack","youtube"],
-            octicon:["link-external-16","table-16"],
-            }
+            include: {
+                // only include a subset of icons
+                'file-icons': ['nextflow'],
+                logos: [
+                    'twitter',
+                    'mastodon-icon',
+                    'slack-icon',
+                    'aws',
+                    'microsoft-azure',
+                    'github-actions',
+                    'youtube-icon',
+                ],
+                fa: ['github'],
+                'fa-brands': ['github'],
+                'line-md': ['check-list-3-twotone'],
+                mdi: ['aws', 'slack', 'youtube'],
+                octicon: ['link-external-16', 'table-16'],
+            },
         }),
         sitemap(),
         prefetch(),
@@ -190,7 +196,7 @@ export default defineConfig({
                     theme: {
                         dark: 'github-dark',
                         light: 'github-light',
-                    }
+                    },
                 },
             ],
             rehypeKatex,

public/_redirects

@@ -3,9 +3,6 @@
 
 # Temporary oldsite redirections
 /logo/*  https://oldsite.nf-co.re/logo/:splat 200
-
-/tools-docs/lint_tests/* https://oldsite.nf-co.re/tools/docs/latest/pipeline_lint_tests/:splat
-/tools/docs/* https://oldsite.nf-co.re/tools/docs/:splat
 /pipeline_schema_builder/* https://oldsite.nf-co.re/pipeline_schema_builder/:splat 200
 /launch/* https://oldsite.nf-co.re/launch/:splat 200
 /assets/* https://oldsite.nf-co.re/assets/:splat 200
@@ -16,4 +13,5 @@
 /developers/* /docs/contributing/:splat
 /contributing/* /docs/contributing/:splat
 /assets/img/* /images/:splat
+/tools-docs/lint_tests/* /tools/docs/latest/pipeline_lint_tests/:splat
 

src/components/navbar/Navbar.astro

@@ -107,6 +107,9 @@ newBlogPost = await getCollection('blog').then((posts) => {
                         <li><span class="dropdown-header">Configs & tools</span></li>
                         <li><a class="dropdown-item" href="/configs/">Shared configs</a></li>
                         <li><a class="dropdown-item" href="/tools/">Tools</a></li>
+                        <li>
+                            <a class="dropdown-item" href="/tools/docs/latest/index">Linting Errors</a>
+                        </li>
                     </ul>
                 </li>
                 <li class="nav-item p-1 px-3 px-xl-1">

src/components/sidebar/SidebarNav.astro

@@ -1,5 +1,5 @@
 ---
-const { items, minimal } = Astro.props;
+const { items, minimal, accordion } = Astro.props;
 
 export interface Props {
     items: {
@@ -12,13 +12,14 @@ export interface Props {
         }[];
     }[];
     minimal?: boolean;
+    accordion?: boolean;
 }
 
 let url = Astro.url.pathname.endsWith('/') ? Astro.url.pathname.slice(0, -1) : Astro.url.pathname;
 url = url.replace(/\.html$/, '');
 ---
 
-<div class="nav">
+<div class:list={['nav', { accordion: accordion }]}>
     <div class="w-100 sticky-top-under">
         {
             items &&
@@ -68,9 +69,8 @@ url = url.replace(/\.html$/, '');
                                                             'stretched-link',
                                                         ]}
                                                         href={child.slug}
-                                                    >
-                                                        {child.title}
-                                                    </a>
+                                                    />
+                                                    <span set:html={child.title} />
                                                 </li>
                                             );
                                         })}
@@ -185,4 +185,17 @@ url = url.replace(/\.html$/, '');
             }
         }
     }
+    // show only the active section
+    .nav.accordion {
+        ul {
+            display: none;
+        }
+        h6:has(.active) ~ ul,
+        ul:has(.active) {
+            display: block;
+        }
+        div.mb-3:not(:has(.active)) {
+            margin-bottom: 0 !important;
+        }
+    }
 </style>

src/components/sidebar/SidebarToc.svelte

@@ -24,7 +24,7 @@
     // make margin classes from min to max heading depth
     let headingMargin = {};
     for (let i = minHeadingDepth; i <= 4; i++) {
-        headingMargin[i] = 'ps-' + (i - minHeadingDepth) * 2;
+        headingMargin[i] = 'ps-' + (i - minHeadingDepth);
     }
     let activeHeading = {};
     onMount(() => {
@@ -47,7 +47,7 @@
 </script>
 
 <div class="nav flex-column sticky-top-under align-items-end pt-1">
-    <div class="d-none d-md-inline">
+    <div class="d-none d-md-block w-100">
         {#if headings.length > 1}
             <strong class="h6 my-2 text-body">On this page</strong>
         {/if}
@@ -57,7 +57,7 @@
                 <ul class="mb-0 mt-1">
                     {#each headings as heading (heading)}
                         <li
-                            class={'nav-item ' + headingMargin[heading.depth]}
+                            class={'nav-item' + headingMargin[heading.depth]}
                             class:active={heading.slug === activeHeading}
                             class:collapse={heading.hidden && !$showHidden}
                         >

src/content/config.ts

@@ -124,10 +124,13 @@ const blog = defineCollection({
 
 const pipelines = defineCollection({});
 
+const tools = defineCollection({});
+
 export const collections = {
     events: events,
     docs: docs,
     about: about,
     pipelines: pipelines,
     blog: blog,
+    tools: tools,
 };

src/content/tools/docs/1.10.1/bump_version.md

@@ -0,0 +1,36 @@
+# nf_core.bump_version
+
+Bumps the version number in all appropriate files for
+a nf-core pipeline.
+
+### `nf_core.bump_version.bump_nextflow_version(lint_obj, new_version){:python}`
+
+Bumps the required Nextflow version number of a pipeline.
+
+- **Parameters:**
+  - **lint_obj** ([_nf_core.lint.PipelineLint_](lint#nf_core.lint.PipelineLint)) – A PipelineLint object that holds information
+    about the pipeline contents and build files.
+  - **new_version** (_str_) – The new version tag for the required Nextflow version.
+
+### `nf_core.bump_version.bump_pipeline_version(lint_obj, new_version){:python}`
+
+Bumps a pipeline version number.
+
+- **Parameters:**
+  - **lint_obj** ([_nf_core.lint.PipelineLint_](lint#nf_core.lint.PipelineLint)) – A PipelineLint object that holds information
+    about the pipeline contents and build files.
+  - **new_version** (_str_) – The new version tag for the pipeline. Semantic versioning only.
+
+### `nf_core.bump_version.update_file_version(filename, lint_obj, pattern, newstr, allow_multiple=False){:python}`
+
+Updates the version number in a requested file.
+
+- **Parameters:**
+  - **filename** (_str_) – File to scan.
+  - **lint_obj** ([_nf_core.lint.PipelineLint_](lint#nf_core.lint.PipelineLint)) – A PipelineLint object that holds information
+    about the pipeline contents and build files.
+  - **pattern** (_str_) – Regex pattern to apply.
+  - **newstr** (_str_) – The replaced string.
+  - **allow_multiple** (_bool_) – Replace all pattern hits, not only the first. Defaults to False.
+- **Raises:**
+  **SyntaxError**\*\*,\*\* **if the version number cannot be found.** –

src/content/tools/docs/1.10.1/create.md

@@ -0,0 +1 @@
+# nf_core.create

src/content/tools/docs/1.10.1/download.md

@@ -0,0 +1,68 @@
+# nf_core.download
+
+Downloads a nf-core pipeline to the local file system.
+
+### _`class{:python}`_`nf_core.download.DownloadWorkflow(pipeline, release=None, singularity=False, outdir=None, compress_type='tar.gz'){:python}`
+
+Downloads a nf-core workflow from GitHub to the local file system.
+
+Can also download its Singularity container image if required.
+
+- **Parameters:**
+  - **pipeline** (_str_) – A nf-core pipeline name.
+  - **release** (_str_) – The workflow release version to download, like 1.0. Defaults to None.
+  - **singularity** (_bool_) – Flag, if the Singularity container should be downloaded as well. Defaults to False.
+  - **outdir** (_str_) – Path to the local download directory. Defaults to None.
+
+#### `compress_download(){:python}`
+
+Take the downloaded files and make a compressed .tar.gz archive.
+
+#### `download_configs(){:python}`
+
+Downloads the centralised config profiles from nf-core/configs to `self.outdir`.
+
+#### `download_wf_files(){:python}`
+
+Downloads workflow files from GitHub to the `self.outdir`.
+
+#### `download_workflow(){:python}`
+
+Starts a nf-core workflow download.
+
+#### `fetch_workflow_details(wfs){:python}`
+
+Fetches details of a nf-core workflow to download.
+
+- **Parameters:**
+  **wfs** ([_nf_core.list.Workflows_](list#nf_core.list.Workflows)) – A nf_core.list.Workflows object
+- **Raises:**
+  **LockupError**\*\*,\*\* **if the pipeline can not be found.** –
+
+#### `find_container_images(){:python}`
+
+Find container image names for workflow
+
+#### `pull_singularity_image(container){:python}`
+
+Uses a local installation of singularity to pull an image from Docker Hub.
+
+- **Parameters:**
+  **container** (_str_) – A pipeline’s container name. Usually it is of similar format
+  to nfcore/name:dev.
+- **Raises:**
+  **Various exceptions possible from subprocess execution** **of** **Singularity.** –
+
+#### `validate_md5(fname, expected=None){:python}`
+
+Calculates the md5sum for a file on the disk and validate with expected.
+
+- **Parameters:**
+  - **fname** (_str_) – Path to a local file.
+  - **expected** (_str_) – The expected md5sum.
+- **Raises:**
+  **IOError**\*\*,\*\* **if the md5sum does not match the remote sum.** –
+
+#### `wf_use_local_configs(){:python}`
+
+Edit the downloaded nextflow.config file to use the local config files