Merge branch 'dev' into remove-python-linting-template

.github/workflows/changelog.yml

@@ -36,7 +36,7 @@ jobs:
           fi
           gh pr checkout $PR_NUMBER
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 
@@ -65,7 +65,7 @@ jobs:
           echo "File changed: ${{ env.changed }}"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: "pip"

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

@@ -53,7 +53,7 @@ jobs:
 
       # Set up nf-core/tools
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: pip

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

@@ -65,7 +65,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

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

@@ -52,7 +52,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/deploy-pypi.yml

@@ -17,7 +17,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/fix-linting.yml

@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/lint-code.yml

@@ -21,7 +21,7 @@ jobs:
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: "pip"

.github/workflows/pytest.yml

@@ -91,7 +91,7 @@ jobs:
         name: Check out source-code repository
 
       - name: Set up Python ${{ needs.setup.outputs.python-version }}
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: ${{ needs.setup.outputs.python-version }}
           cache: "pip"
@@ -160,7 +160,7 @@ jobs:
 
       - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         env:
           AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/
         with:
@@ -184,7 +184,7 @@ jobs:
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@54bcd8715eee62d40e33596ef5e8f0f48dbbccab # v4
+      - uses: codecov/codecov-action@c16abc29c95fcf9174b58eb7e1abf4c866893bc8 # v4
         with:
           files: coverage.xml
         env:

.github/workflows/rich-codex.yml

@@ -8,7 +8,7 @@ jobs:
       - name: Check out the repo
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
       - name: Set up Python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: 3.x
           cache: pip

.github/workflows/sync.yml

@@ -57,7 +57,7 @@ jobs:
           fetch-depth: "0"
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
 

.github/workflows/update_components_template.yml

@@ -14,7 +14,7 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.x"
 

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.3.4
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

CHANGELOG.md

@@ -42,6 +42,11 @@
 - Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862))
 - Fix schema docs console output truncating ([#2880](https://github.com/nf-core/tools/pull/2880))
 - fix: ensure path object converted to string before stripping quotes ([#2878](https://github.com/nf-core/tools/pull/2878))
+- Fix incorrect assertions for called_with on mocks ([#2891](https://github.com/nf-core/tools/pull/2891))
+- Make cli-provided module/subworkflow names case insensitive ([#2869](https://github.com/nf-core/tools/pull/2869))
+- Update gitpod/workspace-base Docker digest to 168d78b ([#2899](https://github.com/nf-core/tools/pull/2899))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.4 ([#2894](https://github.com/nf-core/tools/pull/2894))
+- Update GitHub Actions ([#2902](https://github.com/nf-core/tools/pull/2902))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
 
@@ -52,6 +57,7 @@
 - Fix topic extraction step for hashtags in toots ([#2810](https://github.com/nf-core/tools/pull/2810))
 - Update modules and subworkflows in the template ([#2811](https://github.com/nf-core/tools/pull/2811))
 - Unpin setup-nextflow and action-tower-launch ([#2806](https://github.com/nf-core/tools/pull/2806))
+- Add nf-core-version to `.nf-core.yml` ([#2874](https://github.com/nf-core/tools/pull/2874))
 
 ### Download
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim
+FROM python:3.12-slim@sha256:5dc6f84b5e97bfb0c90abfb7c55f3cacc2cb6687c8f920b64a833a2219875997
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"
 

docs/api/_src/pipeline_lint_tests/nfcore_yml.md

@@ -0,0 +1,5 @@
+# nfcore_yml
+
+```{eval-rst}
+.. automethod:: nf_core.lint.PipelineLint.nfcore_yml
+```

nf_core/__main__.py

@@ -103,6 +103,14 @@ def selective_traceback_hook(exctype, value, traceback):
 sys.excepthook = selective_traceback_hook
 
 
+# Define callback function to normalize the case of click arguments,
+# which is used to make the module/subworkflow names, provided by the
+# user on the cli, case insensitive.
+def normalize_case(ctx, param, component_name):
+    if component_name is not None:
+        return component_name.casefold()
+
+
 def run_nf_core():
     # print nf-core header if environment variable is not set
     if os.environ.get("_NF_CORE_COMPLETE") is None:
@@ -786,7 +794,7 @@ def modules_list_local(ctx, keywords, json, dir):  # pylint: disable=redefined-b
 # nf-core modules install
 @modules.command("install")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -838,7 +846,7 @@ def modules_install(ctx, tool, dir, prompt, force, sha):
 # nf-core modules update
 @modules.command("update")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -930,7 +938,7 @@ def modules_update(
 # nf-core modules patch
 @modules.command()
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -967,7 +975,7 @@ def patch(ctx, tool, dir, remove):
 # nf-core modules remove
 @modules.command("remove")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1121,7 +1129,7 @@ def create_module(
 # nf-core modules test
 @modules.command("test")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1180,7 +1188,7 @@ def test_module(ctx, tool, dir, no_prompts, update, once, profile):
 # nf-core modules lint
 @modules.command("lint")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1267,7 +1275,7 @@ def modules_lint(ctx, tool, dir, registry, key, all, fail_warned, local, passed,
 # nf-core modules info
 @modules.command("info")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1306,7 +1314,7 @@ def modules_info(ctx, tool, dir):
 # nf-core modules bump-versions
 @modules.command()
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.argument("tool", type=str, callback=normalize_case, required=False, metavar="<tool> or <tool/subtool>")
 @click.option(
     "-d",
     "--dir",
@@ -1392,7 +1400,7 @@ def create_subworkflow(ctx, subworkflow, dir, author, force, migrate_pytest):
 # nf-core subworkflows test
 @subworkflows.command("test")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1519,7 +1527,7 @@ def subworkflows_list_local(ctx, keywords, json, dir):  # pylint: disable=redefi
 # nf-core subworkflows lint
 @subworkflows.command("lint")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1600,15 +1608,15 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo
 # nf-core subworkflows info
 @subworkflows.command("info")
 @click.pass_context
-@click.argument("tool", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
     type=click.Path(exists=True),
     default=".",
     help=r"Pipeline directory. [dim]\[default: Current working directory][/]",
 )
-def subworkflows_info(ctx, tool, dir):
+def subworkflows_info(ctx, subworkflow, dir):
     """
     Show developer usage information about a given subworkflow.
 
@@ -1625,7 +1633,7 @@ def subworkflows_info(ctx, tool, dir):
     try:
         subworkflow_info = SubworkflowInfo(
             dir,
-            tool,
+            subworkflow,
             ctx.obj["modules_repo_url"],
             ctx.obj["modules_repo_branch"],
             ctx.obj["modules_repo_no_pull"],
@@ -1639,7 +1647,7 @@ def subworkflows_info(ctx, tool, dir):
 # nf-core subworkflows install
 @subworkflows.command("install")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1697,7 +1705,7 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
 # nf-core subworkflows remove
 @subworkflows.command("remove")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",
@@ -1727,7 +1735,7 @@ def subworkflows_remove(ctx, dir, subworkflow):
 # nf-core subworkflows update
 @subworkflows.command("update")
 @click.pass_context
-@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.argument("subworkflow", type=str, callback=normalize_case, required=False, metavar="subworkflow name")
 @click.option(
     "-d",
     "--dir",

nf_core/components/components_command.py

@@ -245,7 +245,7 @@ def check_patch_paths(self, patch_path: Path, module_name: str) -> None:
                 # Update path in modules.json if the file is in the correct format
                 modules_json = ModulesJson(self.dir)
                 modules_json.load()
-                if modules_json.has_git_url_and_modules():
+                if modules_json.has_git_url_and_modules() and modules_json.modules_json is not None:
                     modules_json.modules_json["repos"][self.modules_repo.remote_url]["modules"][
                         self.modules_repo.repo_path
                     ][module_name]["patch"] = str(patch_path.relative_to(Path(self.dir).resolve()))

nf_core/gitpod/gitpod.Dockerfile

@@ -1,7 +1,7 @@
 # Test build locally before making a PR
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
-FROM gitpod/workspace-base@sha256:1e133e5691add6c19443672594b9f3d7d9c3372ead4c86a4490c2701dbfa32e3
+FROM gitpod/workspace-base@sha256:168d78bc249332f9437b11a1844819308ac7ec1bc6bab61bf5adf8cbe53bf8e6
 
 USER root