handle float values correctly in default value comparison

CHANGELOG.md

@@ -16,6 +16,7 @@
 ### General
 
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 ([#2705](https://github.com/nf-core/tools/pull/2705))
+- handle float values correctly in default value comparison ([#2711](https://github.com/nf-core/tools/pull/2711))
 - fix changelog titles ([#2708](https://github.com/nf-core/tools/pull/2708))
 - Print relative path not absolute path in logo cmd log output ([#2709](https://github.com/nf-core/tools/pull/2709))
 

nf_core/lint/nextflow_config.py

@@ -388,18 +388,27 @@ def nextflow_config(self):
             ignored.append(f"Config default ignored: {param}")
         elif param in self.nf_config.keys():
             if str(self.nf_config[param]) == schema_default:
-                passed.append(f"Config default value correct: {param}")
+                passed.append(f"Config default value correct: {param}= {schema_default}")
             else:
                 # Handle "number" type
                 if schema_default.endswith(".0") and str(self.nf_config[param]) == schema_default[:-2]:
-                    passed.append(f"Config default value correct: {param}")
+                    passed.append(f"Config default value correct: {param}= {schema_default}")
                 else:
-                    failed.append(
-                        f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
-                    )
+                    # try to convert to float
+                    try:
+                        if float(self.nf_config[param]) == float(schema_default):
+                            passed.append(f"Config default value correct: {param}= {schema_default}")
+                        else:
+                            failed.append(
+                                f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
+                            )
+                    except ValueError:
+                        failed.append(
+                            f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
+                        )
         else:
             failed.append(
-                f"Default value from the Nextflow schema '{param} = {self._wrap_quotes(schema_default)}' not found in `nextflow.config`."
+                f"Default value from the Nextflow schema `{param} = {self._wrap_quotes(schema_default)}` not found in `nextflow.config`."
             )
 
     return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

nf_core/list.py

@@ -39,7 +39,7 @@ def list_workflows(filter_by=None, sort_by="release", as_json=False, show_archiv
         return wfs.print_summary()
 
 
-def get_local_wf(workflow, revision=None):
+def get_local_wf(workflow, revision=None) -> str:
     """
     Check if this workflow has a local copy and use nextflow to pull it if not
     """

tests/lint/nextflow_config.py

@@ -64,8 +64,8 @@ def test_default_values_match(self):
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
     assert len(result["warned"]) == 0
-    assert "Config default value correct: params.max_cpus" in result["passed"]
-    assert "Config default value correct: params.validate_params" in result["passed"]
+    assert "Config default value correct: params.max_cpus" in str(result["passed"])
+    assert "Config default value correct: params.validate_params" in str(result["passed"])
 
 
 def test_default_values_fail(self):
@@ -75,7 +75,7 @@ def test_default_values_fail(self):
     nf_conf_file = Path(new_pipeline) / "nextflow.config"
     with open(nf_conf_file) as f:
         content = f.read()
-        fail_content = re.sub(r"\bmax_cpus                   = 16\b", "max_cpus                   = 0", content)
+        fail_content = re.sub(r"\bmax_cpus\s*=\s*16\b", "max_cpus = 0", content)
     with open(nf_conf_file, "w") as f:
         f.write(fail_content)
     # Change the default value of max_memory in nextflow_schema.json
@@ -115,5 +115,68 @@ def test_default_values_ignored(self):
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) == 0
     assert len(result["ignored"]) == 1
-    assert "Config default value correct: params.max_cpus" not in result["passed"]
-    assert "Config default ignored: params.max_cpus" in result["ignored"]
+    assert "Config default value correct: params.max_cpu" not in str(result["passed"])
+    assert "Config default ignored: params.max_cpus" in str(result["ignored"])
+
+
+def test_default_values_float(self):
+    """Test comparing two float values."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
+    nf_conf_file = Path(new_pipeline) / "nextflow.config"
+    with open(nf_conf_file) as f:
+        content = f.read()
+        fail_content = re.sub(
+            r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+        )
+    with open(nf_conf_file, "w") as f:
+        f.write(fail_content)
+    # Add a float value `dummy` to the nextflow_schema.json
+    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
+    with open(nf_schema_file) as f:
+        content = f.read()
+        fail_content = re.sub(
+            r'"validate_params": {',
+            '    "dummy": {"type": "float","default":0.000000001},\n"validate_params": {',
+            content,
+        )
+    with open(nf_schema_file, "w") as f:
+        f.write(fail_content)
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+    assert len(result["warned"]) == 0
+    assert "Config default value correct: params.dummy" in str(result["passed"])
+
+
+def test_default_values_float_fail(self):
+    """Test comparing two float values."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
+    nf_conf_file = Path(new_pipeline) / "nextflow.config"
+    with open(nf_conf_file) as f:
+        content = f.read()
+        fail_content = re.sub(
+            r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+        )
+    with open(nf_conf_file, "w") as f:
+        f.write(fail_content)
+    # Add a float value `dummy` to the nextflow_schema.json
+    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
+    with open(nf_schema_file) as f:
+        content = f.read()
+        fail_content = re.sub(
+            r'"validate_params": {', '    "dummy": {"type": "float","default":0.000001},\n"validate_params": {', content
+        )
+    with open(nf_schema_file, "w") as f:
+        f.write(fail_content)
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+
+    assert len(result["failed"]) == 1
+    assert len(result["warned"]) == 0
+    assert "Config default value incorrect: `params.dummy" in str(result["failed"])

tests/test_lint.py

@@ -222,6 +222,8 @@ def test_sphinx_md_files(self):
     )
     from .lint.nextflow_config import (  # type: ignore[misc]
         test_default_values_fail,
+        test_default_values_float,
+        test_default_values_float_fail,
         test_default_values_ignored,
         test_default_values_match,
         test_nextflow_config_bad_name_fail,