Merge pull request #2779 from nf-core/update-api-docs-3.0.1

Update nf-core/tools API docs for 3.0.1

sites/docs/src/content/api_reference/3.0.1/_static/autodoc_pydantic.css

@@ -0,0 +1,11 @@
+.autodoc_pydantic_validator_arrow {
+  padding-left: 8px;
+  }
+
+.autodoc_pydantic_collapsable_json {
+  cursor: pointer;
+  }
+
+.autodoc_pydantic_collapsable_erd {
+  cursor: pointer;
+  }

sites/docs/src/content/api_reference/3.0.1/api/index.md

@@ -0,0 +1,11 @@
+# nf-core/tools documentation
+
+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/3.0.1/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:{:python}`[`Pipeline{:python}`](../utils#nf_core.utils.Pipeline)`, new_version: str) → None{:python}`
+
+Bumps the required Nextflow version number of a pipeline.
+
+- **Parameters:**
+  - **pipeline_obj** ([_nf_core.utils.Pipeline_](../utils#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:{:python}`[`Pipeline{:python}`](../utils#nf_core.utils.Pipeline)`, new_version: str) → None{:python}`
+
+Bumps a pipeline version number.
+
+- **Parameters:**
+  - **pipeline_obj** ([_nf_core.utils.Pipeline_](../utils#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:{:python}`[`Pipeline{:python}`](../utils#nf_core.utils.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.** –