new way to generate api docs

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

@@ -2,6 +2,14 @@ name: nf-core/tools release API docs
 on:
   release:
     types: [published]
+  push:
+    branches: dev
+  workflow_dispatch:
+    inputs:
+      release_version:
+        description: "Release version"
+        required: true
+        default: "dev"
 
 # Cancel if a newer run is started
 concurrency:
@@ -10,39 +18,41 @@ concurrency:
 
 jobs:
   api-docs:
-    name: Build & push Sphinx API docs
+    # checkout the nf-core/website repo, generate the docs with lazydocs and copy to `src/content/tools/$release_version` and open a PR with the changes on the website repo
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        dir:
-          - latest
-          - ${{ github.event.release.tag_name }}
     steps:
-      - name: Check out source-code repository
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      - name: Checkout nf-core/website
         uses: actions/checkout@v3
+        with:
+          repository: nf-core/website
+          token: ${{ secrets.nf_core_bot_auth_token }}
+          path: website
 
-      - name: Set up Python 3.11
+      - name: setup python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
+          cache: "pip"
 
-      - name: Install python dependencies
-        run: |
-          pip install --upgrade pip
-          pip install -r ./docs/api/requirements.txt
-          pip install .
+      - name: Install lazydocs
+        run: pip install lazydocs
 
-      - name: Build HTML docs
-        run: make --directory ./docs/api html
+      - name: Generate API docs
+        run: |
+          lazydocs nf-core/tools -o website/src/content/tools/${{github.ref_name}} --force \
+            --src-base-url="https://github.com/nf-core/tools/blob/${{github.ref_name}}/" \
+            --overview-file="index.md"
 
-      - name: Sync release docs
-        if: github.repository == 'nf-core/tools'
-        uses: SamKirkland/FTP-Deploy-Action@4.0.0
-        with:
-          server: ${{ secrets.ftp_server }}
-          username: ${{ secrets.ftp_username}}
-          password: ${{ secrets.ftp_password }}
-          local-dir: "./docs/api/_build/html/"
-          server-dir: ${{ secrets.ftp_server_old_site_dir }}/${{ matrix.dir }}/
-          protocol: ${{ secrets.ftp_protocol }}
-          port: ${{ secrets.ftp_port }}
+      - name: Commit and push changes
+        run: |
+          cd website
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git checkout -b update-tools-api-docs
+          git add src/content/tools/${{github.ref_name}}
+          git remote add nf-core-website https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/nf-core/website.git
+          git push nf-core-website update-tools-api-docs

docs/api/_src/conf.py

@@ -58,15 +58,15 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-# pygments_style = None
+pygments_style = "sphinx"
 
 
 # -- Options for HTML output -------------------------------------------------

nf_core/download.py

@@ -754,33 +754,49 @@ def find_container_images(self, workflow_directory):
         self.containers = self.prioritize_direct_download(previous_findings + config_findings + module_findings)
 
     def rectify_raw_container_matches(self, raw_findings):
-        """Helper function to rectify the raw extracted container matches into fully qualified container names.
+        """
+        Helper function to rectify the raw extracted container matches into fully qualified container names.
         If multiple containers are found, any prefixed with http for direct download is prioritized
 
         Example syntax:
 
         Early DSL2:
+
+        .. code-block:: groovy
+
             if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-                container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0"
+                container 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0'
             } else {
-                container "quay.io/biocontainers/fastqc:0.11.9--0"
+                container 'quay.io/biocontainers/fastqc:0.11.9--0'
             }
 
         Later DSL2:
+
+        .. code-block:: groovy
+
             container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
                 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
                 'biocontainers/fastqc:0.11.9--0' }"
 
+
         Later DSL2, variable is being used:
+
+        .. code-block:: groovy
+
             container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-                "https://depot.galaxyproject.org/singularity/${container_id}" :
-                "quay.io/biocontainers/${container_id}" }"
+                'https://depot.galaxyproject.org/singularity/${container_id}' :
+                'quay.io/biocontainers/${container_id}' }"
 
             container_id = 'mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:afaaa4c6f5b308b4b6aa2dd8e99e1466b2a6b0cd-0'
 
         DSL1 / Special case DSL2:
+
+        .. code-block:: groovy
+
             container "nfcore/cellranger:6.0.2"
+
         """
+
         cleaned_matches = []
 
         # Thanks Stack Overflow for the regex: https://stackoverflow.com/a/3809435/713980
@@ -830,6 +846,7 @@ def rectify_raw_container_matches(self, raw_findings):
             or a plain URL like in the old DSL2 convention
 
             """
+
             direct_match = re.match(either_url_or_docker, container_value.strip())
             if direct_match:
                 cleaned_matches.append(direct_match.group(0))
@@ -852,6 +869,7 @@ def rectify_raw_container_matches(self, raw_findings):
             example result:
             ['https://depot.galaxyproject.org/singularity/scanpy:1.7.2--pyhdfd78af_0', 'biocontainers/scanpy:1.7.2--pyhdfd78af_0']
             """
+
             container_value_defs = [
                 capture for _, capture in container_value_defs[:] if not capture in ["singularity", "apptainer"]
             ]

nf_core/lint/multiqc_config.py

@@ -20,6 +20,7 @@ def multiqc_config(self):
 
         export_plots: true
     """
+
     passed = []
     failed = []
 

nf_core/lint/nextflow_config.py

@@ -114,6 +114,7 @@ def nextflow_config(self):
     * A ``test`` configuration profile should exist.
 
     """
+
     passed = []
     warned = []
     failed = []