Merge pull request #2911 from nf-core/update-api-docs-3.1.1

Update nf-core/tools API docs for 3.1.1

sites/docs/src/content/api_reference/3.1.1/_static/autodoc_pydantic.css

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+.autodoc_pydantic_validator_arrow {
+  padding-left: 8px;
+  }
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+.autodoc_pydantic_collapsable_json {
+  cursor: pointer;
+  }
+
+.autodoc_pydantic_collapsable_erd {
+  cursor: pointer;
+  }

sites/docs/src/content/api_reference/3.1.1/api/index.md

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+# 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 reference]()

sites/docs/src/content/api_reference/3.1.1/api/pipelines/bump_version.md

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+# nf_core.pipelines.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.handle_error(message: str, required: bool){:python}`
+
+### `nf_core.pipelines.bump_version.log_change(old_content: str, new_content: str){:python}`
+
+### `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]], required: bool = True, yaml_key: List[str] | None = None) → None{:python}`
+
+Updates a file with a new version number.
+
+- **Parameters:**
+  - **filename** (_str_) – The name of the file to update.
+  - **pipeline_obj** ([_nf_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information
+    about the pipeline contents.
+  - **patterns** (_List_ \*\[\*_Tuple_ \*\[\*_str_ _,_ _str_ _]_ _]_) – A list of tuples containing the regex patterns to
+    match and the replacement strings.
+  - **required** (_bool_ _,_ _optional_) – Whether the file is required to exist. Defaults to True.
+  - **yaml_key** (_Optional_ \*\[\*_List_ \*\[\*_str_ _]_ _]_ _,_ _optional_) – The YAML key to update. Defaults to None.
+
+### `nf_core.pipelines.bump_version.update_text_file(fn: Path, patterns: List[Tuple[str, str]], required: bool){:python}`
+
+Updates a text file with a new version number.
+
+- **Parameters:**
+  - **fn** (_Path_) – The name of the file to update.
+  - **patterns** (_List_ \*\[\*_Tuple_ \*\[\*_str_ _,_ _str_ _]_ _]_) – A list of tuples containing the regex patterns to
+    match and the replacement strings.
+  - **required** (_bool_) – Whether the file is required to exist.
+
+### `nf_core.pipelines.bump_version.update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[str], required: bool){:python}`
+
+Updates a YAML file with a new version number.
+
+- **Parameters:**
+  - **fn** (_Path_) – The name of the file to update.
+  - **patterns** (_List_ \*\[\*_Tuple_ \*\[\*_str_ _,_ _str_ _]_ _]_) – A list of tuples containing the regex patterns to
+    match and the replacement strings.
+  - **yaml_key** (_List_ \*\[\*_str_ _]_) – The YAML key to update.
+  - **required** (_bool_) – Whether the file is required to exist.