[automated] Update nf-core/tools API docs for dev

package.json

@@ -17,9 +17,11 @@
         "update": "for dir in sites/*; do (cd $dir && npx ncu --interactive --format group); done",
         "test-all": "for dir in sites/*; do (cd $dir && npm run test); done"
     },
-    "devDependencies": {
-    },
     "workspaces": [
         "sites/*"
-    ]
+    ],
+    "dependencies": {
+        "remark": "^15.0.1",
+        "unist-util-visit": "^5.0.0"
+    }
 }

sites/docs/src/content/api_reference/dev/api/index.md

@@ -1,15 +1,11 @@
-# API Reference
+# nf-core/tools documentation
 
-- [nf_core.bump_version](bump_version)
-- [nf_core.create](create)
-- [nf_core.download](download)
-- [nf_core.launch](launch)
-- [nf_core.licences](licences)
-- [nf_core.lint](lint)
-- [nf_core.list](list)
-- [nf_core.modules](modules)
-- [nf_core.params_file](params-file)
-- [nf_core.schema](schema)
-- [nf_core.subworkflows](subworkflows)
-- [nf_core.sync](sync)
-- [nf_core.utils](utils)
+This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.
+
+## Contents
+
+- [Pipeline commands]() (run by `nf-core pipelines lint`)
+- [Module commands]() (run by `nf-core modules lint`)
+- [Subworkflow commands]() (run by `nf-core subworkflows lint`)
+- [nf-core/tools Python package API reference]()
+  - [nf-core/tools pipeline commands API referece]()

sites/docs/src/content/api_reference/dev/api/lint.md

@@ -127,8 +127,10 @@ Helper function to take a list of filenames and format with markdown.
 
 - **Returns:**
   Formatted string of paths separated by word `or`, eg:
+
   ```default
   `foo` or bar` or `baz`
   ```
+
 - **Return type:**
   markdown (str)

sites/docs/src/content/api_reference/dev/api/pipelines/bump_version.md

@@ -0,0 +1,34 @@
+# nf_core.bump_version
+
+Bumps the version number in all appropriate files for
+a nf-core pipeline.
+
+### `nf_core.pipelines.bump_version.bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) → None{:python}`
+
+Bumps the required Nextflow version number of a pipeline.
+
+- **Parameters:**
+  - **pipeline_obj** (_nf_core.utils.Pipeline_) – A Pipeline 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.pipelines.bump_version.bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) → None{:python}`
+
+Bumps a pipeline version number.
+
+- **Parameters:**
+  - **pipeline_obj** (_nf_core.utils.Pipeline_) – A Pipeline 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.pipelines.bump_version.update_file_version(filename: str | Path, pipeline_obj: Pipeline, patterns: List[Tuple[str, str]]) → None{:python}`
+
+Updates the version number in a requested file.
+
+- **Parameters:**
+  - **filename** (_str_) – File to scan.
+  - **pipeline_obj** (_nf_core.pipelines.lint.PipelineLint_) – A PipelineLint object that holds information
+    about the pipeline contents and build files.
+  - **pattern** (_str_) – Regex pattern to apply.
+- **Raises:**
+  **ValueError**\*\*,\*\* **if the version number cannot be found.** –