Merge pull request #3323 from mashehu/fix-api-doc-headers

mashehu · web-flow · commit 98285e3480cd · 2024-12-09T12:03:18.000+01:00
fix headers in api docs
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -49,6 +49,7 @@
 - Update GitHub Actions ([#3237](https://github.com/nf-core/tools/pull/3237))
 - add `--dir/-d` option to schema commands ([#3247](https://github.com/nf-core/tools/pull/3247))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.1 ([#3250](https://github.com/nf-core/tools/pull/3250))
+- fix headers in api docs ([#3323](https://github.com/nf-core/tools/pull/3323))
 - handle new schema structure in `nf-core pipelines create-params-file` ([#3276](https://github.com/nf-core/tools/pull/3276))
 - Update Gitpod image to use Miniforge instead of Miniconda([#3274](https://github.com/nf-core/tools/pull/3274))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.3 ([#3275](https://github.com/nf-core/tools/pull/3275))
diff --git a/docs/api/_src/api/pipelines/bump_version.md b/docs/api/_src/api/pipelines/bump_version.md
@@ -1,4 +1,4 @@
-# nf_core.bump_version
+# nf_core.pipelines.bump_version
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.bump_version
diff --git a/docs/api/_src/api/pipelines/create.md b/docs/api/_src/api/pipelines/create.md
@@ -1,4 +1,4 @@
-# nf_core.create
+# nf_core.pipelines.create
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.create
diff --git a/docs/api/_src/api/pipelines/download.md b/docs/api/_src/api/pipelines/download.md
@@ -1,4 +1,4 @@
-# nf_core.download
+# nf_core.pipelines.download
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.download
diff --git a/docs/api/_src/api/pipelines/launch.md b/docs/api/_src/api/pipelines/launch.md
@@ -1,4 +1,4 @@
-# nf_core.launch
+# nf_core.pipelines.launch
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.launch
diff --git a/docs/api/_src/api/pipelines/lint.md b/docs/api/_src/api/pipelines/lint.md
@@ -1,4 +1,4 @@
-# nf_core.lint
+# nf_core.pipelines.lint
 
 :::{seealso}
 See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.
diff --git a/docs/api/_src/api/pipelines/list.md b/docs/api/_src/api/pipelines/list.md
@@ -1,4 +1,4 @@
-# nf_core.list
+# nf_core.pipelines.list
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.list
diff --git a/docs/api/_src/api/pipelines/params-file.md b/docs/api/_src/api/pipelines/params-file.md
@@ -1,4 +1,4 @@
-# nf_core.params_file
+# nf_core.pipelines.params_file
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.params_file
diff --git a/docs/api/_src/api/pipelines/schema.md b/docs/api/_src/api/pipelines/schema.md
@@ -1,4 +1,4 @@
-# nf_core.schema
+# nf_core.pipelines.schema
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.schema
diff --git a/docs/api/_src/api/pipelines/sync.md b/docs/api/_src/api/pipelines/sync.md
@@ -1,4 +1,4 @@
-# nf_core.sync
+# nf_core.pipelines.sync
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.sync
diff --git a/docs/api/_src/api/pipelines/utils.md b/docs/api/_src/api/pipelines/utils.md
@@ -1,4 +1,4 @@
-# nf_core.utils
+# nf_core.pipelines.utils
 
 ```{eval-rst}
 .. automodule:: nf_core.pipelines.utils

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.bump_version`
	`1`	`+# nf_core.pipelines.bump_version`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.bump_version`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.create`
	`1`	`+# nf_core.pipelines.create`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.create`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.download`
	`1`	`+# nf_core.pipelines.download`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.download`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.launch`
	`1`	`+# nf_core.pipelines.launch`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.launch`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.lint`
	`1`	`+# nf_core.pipelines.lint`
`2`	`2`
`3`	`3`	`:::{seealso}`
`4`	`4`	`See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.list`
	`1`	`+# nf_core.pipelines.list`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.list`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.params_file`
	`1`	`+# nf_core.pipelines.params_file`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.params_file`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.schema`
	`1`	`+# nf_core.pipelines.schema`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.schema`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# nf_core.sync`
	`1`	`+# nf_core.pipelines.sync`
`2`	`2`
`3`	`3`	```{eval-rst}
`4`	`4`	`.. automodule:: nf_core.pipelines.sync`