From 2117d343206613917c177726aedec0564224cdfc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 27 Jul 2023 14:37:27 +0200 Subject: [PATCH 1/2] update function names to get lint tests in make_lint_md.py --- docs/api/make_lint_md.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py index 6c804db0f2..35e38a55ca 100644 --- a/docs/api/make_lint_md.py +++ b/docs/api/make_lint_md.py @@ -45,8 +45,8 @@ def make_docs(docs_basedir, lint_tests, md_template): make_docs( modules_docs_basedir, list( - set(nf_core.modules.lint.ModuleLint.get_all_lint_tests(is_pipeline=True)).union( - nf_core.modules.lint.ModuleLint.get_all_lint_tests(is_pipeline=False) + set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union( + nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False) ) ), """# {0} @@ -62,8 +62,8 @@ def make_docs(docs_basedir, lint_tests, md_template): make_docs( subworkflows_docs_basedir, list( - set(nf_core.subworkflows.lint.SubworkflowLint.get_all_lint_tests(is_pipeline=True)).union( - nf_core.subworkflows.lint.SubworkflowLint.get_all_lint_tests(is_pipeline=False) + set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union( + nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False) ) ), """# {0} From 3878f44a9a1ac2c1bb62d0e6befe42c2f35c56b4 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 27 Jul 2023 15:05:55 +0200 Subject: [PATCH 2/2] fix subworkflow API docs file names - still not working --- docs/api/_src/index.md | 3 ++- docs/api/_src/subworkflow_lint_tests/module_changes.md | 5 ----- docs/api/_src/subworkflow_lint_tests/module_tests.md | 5 ----- docs/api/_src/subworkflow_lint_tests/module_todos.md | 5 ----- docs/api/_src/subworkflow_lint_tests/module_version.md | 5 ----- docs/api/_src/subworkflow_lint_tests/subworkflow_changes.md | 5 +++++ docs/api/_src/subworkflow_lint_tests/subworkflow_tests.md | 5 +++++ docs/api/_src/subworkflow_lint_tests/subworkflow_todos.md | 5 +++++ docs/api/_src/subworkflow_lint_tests/subworkflow_version.md | 5 +++++ 9 files changed, 22 insertions(+), 21 deletions(-) delete mode 100644 docs/api/_src/subworkflow_lint_tests/module_changes.md delete mode 100644 docs/api/_src/subworkflow_lint_tests/module_tests.md delete mode 100644 docs/api/_src/subworkflow_lint_tests/module_todos.md delete mode 100644 docs/api/_src/subworkflow_lint_tests/module_version.md create mode 100644 docs/api/_src/subworkflow_lint_tests/subworkflow_changes.md create mode 100644 docs/api/_src/subworkflow_lint_tests/subworkflow_tests.md create mode 100644 docs/api/_src/subworkflow_lint_tests/subworkflow_todos.md create mode 100644 docs/api/_src/subworkflow_lint_tests/subworkflow_version.md diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md index dfa21f467e..cb455986d7 100644 --- a/docs/api/_src/index.md +++ b/docs/api/_src/index.md @@ -8,6 +8,7 @@ pipeline_lint_tests/index.rst module_lint_tests/index.rst +subworkflow_lint_tests/index.rst api/index.rst ``` @@ -17,7 +18,7 @@ This documentation is for the `nf-core/tools` package. - [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core lint`) - [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`) -- [Subworkflow code lint tests](subworkflow_lint_test/index.mf) (run by `nf-core subworkflows lint`) +- [Subworkflow code lint tests](subworkflow_lint_tests/index.md) (run by `nf-core subworkflows lint`) - [nf-core/tools Python package API reference](api/index.md) - {ref}`genindex` - {ref}`modindex` diff --git a/docs/api/_src/subworkflow_lint_tests/module_changes.md b/docs/api/_src/subworkflow_lint_tests/module_changes.md deleted file mode 100644 index 33934490f9..0000000000 --- a/docs/api/_src/subworkflow_lint_tests/module_changes.md +++ /dev/null @@ -1,5 +0,0 @@ -# module_changes - -```{eval-rst} -.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.module_changes -``` diff --git a/docs/api/_src/subworkflow_lint_tests/module_tests.md b/docs/api/_src/subworkflow_lint_tests/module_tests.md deleted file mode 100644 index a6e4385c61..0000000000 --- a/docs/api/_src/subworkflow_lint_tests/module_tests.md +++ /dev/null @@ -1,5 +0,0 @@ -# module_tests - -```{eval-rst} -.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.module_tests -``` diff --git a/docs/api/_src/subworkflow_lint_tests/module_todos.md b/docs/api/_src/subworkflow_lint_tests/module_todos.md deleted file mode 100644 index 114a1f81a2..0000000000 --- a/docs/api/_src/subworkflow_lint_tests/module_todos.md +++ /dev/null @@ -1,5 +0,0 @@ -# module_todos - -```{eval-rst} -.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.module_todos -``` diff --git a/docs/api/_src/subworkflow_lint_tests/module_version.md b/docs/api/_src/subworkflow_lint_tests/module_version.md deleted file mode 100644 index 5296d6017b..0000000000 --- a/docs/api/_src/subworkflow_lint_tests/module_version.md +++ /dev/null @@ -1,5 +0,0 @@ -# module_version - -```{eval-rst} -.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.module_version -``` diff --git a/docs/api/_src/subworkflow_lint_tests/subworkflow_changes.md b/docs/api/_src/subworkflow_lint_tests/subworkflow_changes.md new file mode 100644 index 0000000000..adb40dd4e4 --- /dev/null +++ b/docs/api/_src/subworkflow_lint_tests/subworkflow_changes.md @@ -0,0 +1,5 @@ +# subworkflow_changes + +```{eval-rst} +.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.subworkflow_changes +``` diff --git a/docs/api/_src/subworkflow_lint_tests/subworkflow_tests.md b/docs/api/_src/subworkflow_lint_tests/subworkflow_tests.md new file mode 100644 index 0000000000..56be858b64 --- /dev/null +++ b/docs/api/_src/subworkflow_lint_tests/subworkflow_tests.md @@ -0,0 +1,5 @@ +# subworkflow_tests + +```{eval-rst} +.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.subworkflow_tests +``` diff --git a/docs/api/_src/subworkflow_lint_tests/subworkflow_todos.md b/docs/api/_src/subworkflow_lint_tests/subworkflow_todos.md new file mode 100644 index 0000000000..30eab69d47 --- /dev/null +++ b/docs/api/_src/subworkflow_lint_tests/subworkflow_todos.md @@ -0,0 +1,5 @@ +# subworkflow_todos + +```{eval-rst} +.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.subworkflow_todos +``` diff --git a/docs/api/_src/subworkflow_lint_tests/subworkflow_version.md b/docs/api/_src/subworkflow_lint_tests/subworkflow_version.md new file mode 100644 index 0000000000..b5ec7aace0 --- /dev/null +++ b/docs/api/_src/subworkflow_lint_tests/subworkflow_version.md @@ -0,0 +1,5 @@ +# subworkflow_version + +```{eval-rst} +.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.subworkflow_version +```