Update GitHub Actions (#4389)

renovate[bot] · mashehu · web-flow · commit facc0352102e · 2026-07-14T21:24:46.000+02:00
* Update GitHub Actions * Apply suggestion from @mashehu * add fuller integration bench mark (cherry picked from commit 4d109c3) * fix test --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com>
diff --git a/.github/workflows/codspeed.yml b/.github/workflows/codspeed.yml
@@ -24,16 +24,16 @@ jobs:
     name: Run start-up benchmarks
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6
         name: Check out source-code repository
 
       - name: Set up Python
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
+        uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6
         with:
           python-version: "3.10"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
@@ -44,7 +44,7 @@ jobs:
       # import/start-up cost, which CodSpeed's instruction-counting
       # "simulation" instrument can't see. Use "walltime" mode instead.
       - name: Run start-up benchmarks
-        uses: CodSpeedHQ/action@a4a36bb07c0638b0b4ca52bf1f3dad1b4289e52f # v4.18.1
+        uses: CodSpeedHQ/action@9f3a37ece7abc84992501a7fcd54d1704f3458fa # v4.18.4
         with:
           mode: walltime
           run: uv run pytest benchmarks/test_startup_benchmarks.py --codspeed
diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
@@ -52,7 +52,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -64,7 +64,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -50,7 +50,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/deploy-pypi.yml b/.github/workflows/deploy-pypi.yml
@@ -22,7 +22,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/nextflow-source-test.yml b/.github/workflows/nextflow-source-test.yml
@@ -50,7 +50,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -82,7 +82,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
@@ -82,7 +82,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/update-template-snapshots.yml b/.github/workflows/update-template-snapshots.yml
@@ -61,7 +61,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml
@@ -42,7 +42,7 @@ jobs:
           python-version: "3.14"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
         with:
           enable-cache: true
 
diff --git a/benchmarks/test_startup_benchmarks.py b/benchmarks/test_startup_benchmarks.py
@@ -13,26 +13,74 @@
 import subprocess
 import sys
 
+import pytest
+
 IMPORT_CMD = [sys.executable, "-c", "import nf_core.__main__"]
 HELP_CMD = [sys.executable, "-m", "nf_core", "--help"]
+COMMAND_GROUPS = ["pipelines", "modules", "subworkflows", "test-datasets"]
 
 # Keep the help invocation offline and deterministic.
 _ENV = {**os.environ, "NFCORE_NO_VERSION_CHECK": "1"}
 
 
-def test_import_main_startup(benchmark):
-    """Wall-time cost of importing the CLI entry point in a fresh interpreter."""
-
+def _benchmark_command(benchmark, command):
     def run():
-        subprocess.run(IMPORT_CMD, check=True, capture_output=True)
+        subprocess.run(command, check=True, capture_output=True, env=_ENV)
 
     benchmark.pedantic(run, rounds=10, warmup_rounds=2)
 
 
+def _cli_script(setup, args):
+    return f"{setup}\nimport sys\nsys.argv = {args!r}\nfrom nf_core.__main__ import run_nf_core\nrun_nf_core()"
+
+
+def test_import_main_startup(benchmark):
+    """Wall-time cost of importing the CLI entry point in a fresh interpreter."""
+    _benchmark_command(benchmark, IMPORT_CMD)
+
+
 def test_cli_help_startup(benchmark):
     """Wall-time cost of a full `nf-core --help` invocation."""
+    _benchmark_command(benchmark, HELP_CMD)
 
-    def run():
-        subprocess.run(HELP_CMD, check=True, capture_output=True, env=_ENV)
 
-    benchmark.pedantic(run, rounds=10, warmup_rounds=2)
+@pytest.mark.parametrize("command_group", COMMAND_GROUPS)
+def test_cli_command_group_help_startup(benchmark, command_group):
+    """Wall-time cost of loading each top-level command tree and rendering its help."""
+    _benchmark_command(benchmark, [sys.executable, "-m", "nf_core", command_group, "--help"])
+
+
+def test_pipelines_create_startup(benchmark, tmp_path):
+    """Start the create command, stubbing only template generation and other writes."""
+    args = [
+        "nf-core",
+        "pipelines",
+        "create",
+        "--name",
+        "benchmark",
+        "--description",
+        "benchmark pipeline",
+        "--author",
+        "nf-core",
+        "--outdir",
+        str(tmp_path / "pipeline"),
+    ]
+    setup = (
+        "from nf_core.pipelines.create.create import PipelineCreate\nPipelineCreate.init_pipeline = lambda self: None"
+    )
+    _benchmark_command(benchmark, [sys.executable, "-c", _cli_script(setup, args)])
+
+
+def test_modules_install_startup(benchmark, tmp_path):
+    """Start module installation, stubbing only the remote clone and resulting writes."""
+    args = ["nf-core", "modules", "install", "fastp", "-d", str(tmp_path)]
+    setup = """import nf_core.modules.install as install_module
+install_module.ModuleInstall = type(
+    "ModuleInstall",
+    (),
+    {
+        "__init__": lambda self, *args, **kwargs: None,
+        "install": lambda self, *args, **kwargs: True,
+    },
+)"""
+    _benchmark_command(benchmark, [sys.executable, "-c", _cli_script(setup, args)])
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -34,7 +34,7 @@ jobs:
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@f98e06938123ccabd21905ea5d0069192241f9f1 # v8.3.1
+        uses: astral-sh/setup-uv@11f9893b081a58869d3b5fccaea48c9e9e46f990 # v8.3.2
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
diff --git a/nf_core/pipelines/download/download.py b/nf_core/pipelines/download/download.py
@@ -703,12 +703,18 @@ def run_nextflow_inspect(params_file: Path | None = None) -> dict[str, Any]:
         try:
             out_json = run_nextflow_inspect()
         except RuntimeError as e:
-            # Extract Nextflow stdout from the chained CalledProcessError (errors go to stdout in NF)
-            nf_stdout = getattr(e.__cause__, "output", None) or b""
+            # Nextflow's error text is embedded in the RuntimeError message by run_cmd;
+            # a chained CalledProcessError (if any) may carry it in stdout/stderr instead.
+            nf_error_parts = [str(e), getattr(e.__cause__, "output", None), getattr(e.__cause__, "stderr", None)]
+            nf_error = "\n".join(
+                part.decode("utf-8", errors="replace") if isinstance(part, bytes) else part
+                for part in nf_error_parts
+                if part
+            )
 
             # Nextflow >= 26.04 enforces strict process directive syntax and rejects old-style
             # if/else container blocks with "Invalid process directive". Users need an older NF.
-            if b"Invalid process directive" in nf_stdout:
+            if "Invalid process directive" in nf_error:
                 raise DownloadError(
                     "nextflow inspect failed because the pipeline uses old-style process syntax "
                     "that the default strict syntax of Nextflow >= 26.04 no longer accepts.\n"
@@ -720,7 +726,7 @@ def run_nextflow_inspect(params_file: Path | None = None) -> dict[str, Any]:
             # only issue, retry inspect with an ephemeral params file that provides one.
             if re.search(
                 r"missing required parameter\s*:\s*(?:--outdir|params\.outdir|outdir)\b",
-                nf_stdout.decode("utf-8", errors="replace"),
+                nf_error,
                 flags=re.IGNORECASE,
             ):
                 try:
