move fix_module_version to environment.yml file and fix test fixture

Author: mashehu

nf_core/modules/lint/__init__.py

@@ -28,7 +28,7 @@
 
 log = logging.getLogger(__name__)
 
-from .environment_yml import environment_yml
+from .environment_yml import lint_environment_yml
 from .main_nf import main_nf
 from .meta_yml import meta_yml, meta_yml_containers, obtain_inputs, obtain_outputs, obtain_topics, read_meta_yml
 from .module_changes import module_changes
@@ -46,7 +46,7 @@ class ModuleLint(ComponentLint):
     """
 
     # Import lint functions
-    environment_yml = environment_yml
+    environment_yml = lint_environment_yml
     main_nf = main_nf
     meta_yml = meta_yml
     obtain_inputs = obtain_inputs

nf_core/modules/lint/environment_yml.py

@@ -18,7 +18,17 @@
 yaml.indent(mapping=2, sequence=2, offset=2)
 
 
-def environment_yml(
+def _fix_module_version(self, current_version, latest_version, response):
+    """Update the conda package version in environment.yml."""
+    with open(self.environment_yml) as source:
+        content = source.read()
+    new_content = content.replace(f"={current_version}", f"={latest_version}", 1)
+    with open(self.environment_yml, "w") as source:
+        source.write(new_content)
+    return True
+
+
+def lint_environment_yml(
     module_lint_object: ComponentLint,
     module: NFCoreComponent,
     allow_missing: bool = False,
@@ -340,8 +350,6 @@ def sort_key(x):
                         package, ver = bp.split("=", 1)
                         if fix_version:
                             try:
-                                from nf_core.modules.lint.main_nf import _fix_module_version
-
                                 fixed = _fix_module_version(module, bioconda_version, last_ver, response)
                             except FileNotFoundError as e:
                                 fixed = False

nf_core/modules/lint/main_nf.py

@@ -780,20 +780,6 @@ def _is_empty(line):
     return empty
 
 
-def _fix_module_version(self, current_version, latest_version, response):
-    """Updates the module conda version in environment.yml."""
-
-    with open(self.environment_yml) as source:
-        content = source.read()
-
-    new_content = content.replace(f"={current_version}", f"={latest_version}", 1)
-
-    with open(self.environment_yml, "w") as source:
-        source.write(new_content)
-
-    return True
-
-
 def _get_build(response):
     """Get the latest build of the container version"""
     build_times = []

tests/modules/lint/test_environment_yml.py

@@ -7,7 +7,7 @@
 import nf_core.modules.lint
 from nf_core.components.lint import ComponentLint
 from nf_core.components.nfcore_component import NFCoreComponent
-from nf_core.modules.lint.environment_yml import environment_yml
+from nf_core.modules.lint.environment_yml import lint_environment_yml as environment_yml
 
 from ...test_modules import TestModules
 
@@ -25,6 +25,7 @@ class DummyModule(NFCoreComponent):
     def __init__(self, path):
         self.environment_yml = path
         self.component_dir = path.parent
+        self.base_dir = path.parent
         self.component_name = "dummy"
         self.passed = []
         self.failed = []
@@ -266,7 +267,7 @@ def test_fix_version_fix_fails(tmp_path):
 
     with (
         patch("nf_core.utils.anaconda_package", return_value=fake_response),
-        patch("nf_core.modules.lint.main_nf._fix_module_version", return_value=False),
+        patch("nf_core.modules.lint.environment_yml._fix_module_version", return_value=False),
     ):
         environment_yml(lint, module, fix_version=True)
 

tests/test_modules.py

@@ -70,15 +70,20 @@ def create_modules_repo_dummy(tmp_dir):
         name="quay.io/biocontainers/bpipe:0.9.13--hdfd78af_0", build_id="", scan_id=""
     )
     sing = MetaYmlContainers.SingularityContainer(
-        name="https://depot.galaxyproject.org/singularity/bpipe:0.9.13--hdfd78af_0",
+        name="oras://community.wave.seqera.io/library/bpipe:0.9.13--hdfd78af_0",
         build_id="",
         https="https://depot.galaxyproject.org/singularity/bpipe:0.9.13--hdfd78af_0",
     )
-    conda = MetaYmlContainers.CondaEnvironment(lock_file="")
+    conda_amd64 = MetaYmlContainers.CondaEnvironment(
+        lock_file="modules/nf-core/bpipe/test/.conda-lock/linux_amd64-bd-dummy_1.txt"
+    )
+    conda_arm64 = MetaYmlContainers.CondaEnvironment(
+        lock_file="modules/nf-core/bpipe/test/.conda-lock/linux_arm64-bd-dummy_1.txt"
+    )
     containers = MetaYmlContainers(
         docker={"linux/amd64": docker, "linux/arm64": docker},
         singularity={"linux/amd64": sing, "linux/arm64": sing},
-        conda={"linux/amd64": conda, "linux/arm64": conda},
+        conda={"linux/amd64": conda_amd64, "linux/arm64": conda_arm64},
     )
     meta_yml["containers"] = containers.model_dump()
     with open(str(meta_yml_path), "w") as fh: