Revert "move pipeline subcommands for v3.0"

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -24,7 +24,7 @@ body:
       description: Steps to reproduce the behaviour. Please paste the command and output from your terminal.
       render: console
       placeholder: |
-        $ nf-core pipelines lint ...
+        $ nf-core lint ...
 
         Some output where something broke
 

.github/actions/create-lint-wf/action.yml

@@ -30,9 +30,9 @@ runs:
         nf-core --log-file log.txt pipelines create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"
 
     # Try syncing it before we change anything
-    - name: nf-core pipelines sync
+    - name: nf-core sync
       shell: bash
-      run: nf-core --log-file log.txt pipelines sync --dir nf-core-testpipeline/
+      run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
       working-directory: create-lint-wf
 
     # Run code style linting
@@ -59,20 +59,20 @@ runs:
       run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;
       working-directory: create-lint-wf
 
-    # Run nf-core pipelines linting
-    - name: nf-core pipelines lint
+    # Run nf-core linting
+    - name: nf-core lint
       shell: bash
-      run: nf-core --verbose --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+      run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
       working-directory: create-lint-wf
 
-    - name: nf-core pipelines bump-version to release
+    - name: nf-core bump-version to release
       shell: bash
-      run: nf-core --log-file log.txt pipelines bump-version --dir nf-core-testpipeline/ 1.1
+      run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
       working-directory: create-lint-wf
 
-    - name: nf-core pipelines lint in release mode
+    - name: nf-core lint in release mode
       shell: bash
-      run: nf-core --log-file log.txt --hide-progress pipelines lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
+      run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release
       working-directory: create-lint-wf
 
     - name: Upload log file artifact

.github/workflows/create-lint-wf.yml

@@ -79,12 +79,12 @@ jobs:
         working-directory: create-lint-wf
 
       # Run the other nf-core commands
-      - name: nf-core pipelines list
-        run: nf-core --log-file log.txt pipelines list
+      - name: nf-core list
+        run: nf-core --log-file log.txt list
         working-directory: create-lint-wf
 
-      - name: nf-core pipelines schema
-        run: nf-core --log-file log.txt pipelines schema build --dir nf-core-testpipeline/ --no-prompts
+      - name: nf-core schema
+        run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts
         working-directory: create-lint-wf
 
       - name: Cleanup work directory

.github/workflows/create-test-lint-wf-template.yml

@@ -119,8 +119,8 @@ jobs:
           rm -rf create-test-lint-wf/results
 
       # Try syncing it before we change anything
-      - name: nf-core pipelines sync
-        run: nf-core --log-file log.txt pipelines sync --dir create-test-lint-wf/my-prefix-testpipeline/
+      - name: nf-core sync
+        run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
       - name: Run pre-commit
@@ -138,18 +138,18 @@ jobs:
         working-directory: create-test-lint-wf
 
       # Run nf-core linting
-      - name: nf-core pipelines lint
-        run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned
+      - name: nf-core lint
+        run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned
         working-directory: create-test-lint-wf
 
       # Run bump-version
-      - name: nf-core pipelines bump-version
-        run: nf-core --log-file log.txt pipelines bump-version --dir my-prefix-testpipeline/ 1.1
+      - name: nf-core bump-version
+        run: nf-core --log-file log.txt bump-version --dir my-prefix-testpipeline/ 1.1
         working-directory: create-test-lint-wf
 
       # Run nf-core linting in release mode
-      - name: nf-core pipelines lint in release mode
-        run: nf-core --log-file log.txt --hide-progress pipelines lint --dir my-prefix-testpipeline --fail-warned --release
+      - name: nf-core lint in release mode
+        run: nf-core --log-file log.txt --hide-progress lint --dir my-prefix-testpipeline --fail-warned --release
         working-directory: create-test-lint-wf
 
       - name: Tar files

CHANGELOG.md

@@ -24,7 +24,6 @@
 - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988))
 - Add no clobber and put bash options on their own line ([#2991](https://github.com/nf-core/tools/pull/2991))
 - update minimal textual version and snapshots ([#2998](https://github.com/nf-core/tools/pull/2998))
-- move pipeline subcommands for v3.0 ([#2983](https://github.com/nf-core/tools/pull/2983))
 - return directory if base_dir is the root directory ([#3003](https://github.com/nf-core/tools/pull/3003))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.6 ([#3006](https://github.com/nf-core/tools/pull/3006))
 - Create: allow more special characters on the pipeline name for non-nf-core pipelines ([#3008](https://github.com/nf-core/tools/pull/3008))
@@ -34,6 +33,7 @@
 - Update python:3.12-slim Docker digest to e3ae8cf ([#3020](https://github.com/nf-core/tools/pull/3020))
 - Update python:3.12-slim Docker digest to 2fba8e7 ([#3023](https://github.com/nf-core/tools/pull/3023))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 ([#3031](https://github.com/nf-core/tools/pull/3031))
+- Revert "move pipeline subcommands for v3.0" ([#3035](https://github.com/nf-core/tools/pull/3035))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 

CONTRIBUTING.md

@@ -107,8 +107,8 @@ This ensures that any changes we make to either the linting or the template stay
 You can replicate this process locally with the following commands:
 
 ```bash
-nf-core pipelines create -n testpipeline -d "This pipeline is for testing"
-nf-core pipelines lint nf-core-testpipeline
+nf-core create -n testpipeline -d "This pipeline is for testing"
+nf-core lint nf-core-testpipeline
 ```
 
 ## GitHub Codespaces

docs/api/_src/index.md

@@ -16,7 +16,6 @@ This documentation is for the `nf-core/tools` package.
 
 ## Contents
 
-- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core pipelines lint`)
-- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules 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)
+- [Pipeline code lint tests](pipeline_lint_tests/) (run by `nf-core lint`)
+- [Module code lint tests](module_lint_tests/) (run by `nf-core modules lint`)
+- [Subworkflow code lint tests](subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)

docs/api/make_lint_md.py

@@ -3,8 +3,8 @@
 import fnmatch
 import os
 
+import nf_core.lint
 import nf_core.modules.lint
-import nf_core.pipelines.lint
 import nf_core.subworkflows.lint
 
 
@@ -31,11 +31,11 @@ def make_docs(docs_basedir, lint_tests, md_template):
 pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests")
 make_docs(
     pipeline_docs_basedir,
-    nf_core.pipelines.lint.PipelineLint._get_all_lint_tests(True),
+    nf_core.lint.PipelineLint._get_all_lint_tests(True),
     """# {0}
 
 ```{{eval-rst}}
-.. automethod:: nf_core.pipelines.lint.PipelineLint.{0}
+.. automethod:: nf_core.lint.PipelineLint.{0}
 ```
 """,
 )