restructure components tests

tests/components/test_components_generate_snapshot.py

@@ -0,0 +1,140 @@
+"""Test generate a snapshot"""
+
+import json
+from pathlib import Path
+from unittest.mock import MagicMock
+
+import pytest
+
+from nf_core.components.components_test import ComponentsTest
+from nf_core.utils import set_wd
+
+from ..test_components import TestComponents
+from ..utils import GITLAB_NFTEST_BRANCH, GITLAB_URL
+
+
+class TestTestComponentsUtils(TestComponents):
+    def test_generate_snapshot_module(self):
+        """Generate the snapshot for a module in nf-core/modules clone"""
+        with set_wd(self.nfcore_modules):
+            snap_generator = ComponentsTest(
+                component_type="modules",
+                component_name="fastqc",
+                no_prompts=True,
+                remote_url=GITLAB_URL,
+                branch=GITLAB_NFTEST_BRANCH,
+            )
+            snap_generator.run()
+
+            snap_path = Path("modules", "nf-core-test", "fastqc", "tests", "main.nf.test.snap")
+            assert snap_path.exists()
+
+            with open(snap_path) as fh:
+                snap_content = json.load(fh)
+            assert "versions" in snap_content
+            assert "content" in snap_content["versions"]
+            assert "versions.yml:md5,e1cc25ca8af856014824abd842e93978" in snap_content["versions"]["content"][0]
+
+    def test_generate_snapshot_subworkflow(self):
+        """Generate the snapshot for a subworkflows in nf-core/modules clone"""
+        with set_wd(self.nfcore_modules):
+            snap_generator = ComponentsTest(
+                component_type="subworkflows",
+                component_name="bam_sort_stats_samtools",
+                no_prompts=True,
+                remote_url=GITLAB_URL,
+                branch=GITLAB_NFTEST_BRANCH,
+            )
+            snap_generator.run()
+
+            snap_path = Path("subworkflows", "nf-core-test", "bam_sort_stats_samtools", "tests", "main.nf.test.snap")
+            assert snap_path.exists()
+
+            with open(snap_path) as fh:
+                snap_content = json.load(fh)
+            assert "test_bam_sort_stats_samtools_paired_end_flagstats" in snap_content
+            assert (
+                "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783"
+                in snap_content["test_bam_sort_stats_samtools_paired_end_flagstats"]["content"][0][0]
+            )
+            assert "test_bam_sort_stats_samtools_paired_end_idxstats" in snap_content
+            assert (
+                "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2"
+                in snap_content["test_bam_sort_stats_samtools_paired_end_idxstats"]["content"][0][0]
+            )
+
+    def test_generate_snapshot_once(
+        self,
+    ):
+        """Generate the snapshot for a module in nf-core/modules clone only once"""
+        with set_wd(self.nfcore_modules):
+            snap_generator = ComponentsTest(
+                component_type="modules",
+                component_name="fastqc",
+                once=True,
+                no_prompts=True,
+                remote_url=GITLAB_URL,
+                branch=GITLAB_NFTEST_BRANCH,
+            )
+            snap_generator.repo_type = "modules"
+            snap_generator.generate_snapshot = MagicMock()
+            snap_generator.run()
+            snap_generator.generate_snapshot.assert_called_once()
+
+    def test_update_snapshot_module(self):
+        """Update the snapshot of a module in nf-core/modules clone"""
+
+        with set_wd(self.nfcore_modules):
+            snap_path = Path("modules", "nf-core-test", "bwa", "mem", "tests", "main.nf.test.snap")
+            with open(snap_path) as fh:
+                snap_content = json.load(fh)
+            original_timestamp = snap_content["Single-End"]["timestamp"]
+            # delete the timestamp in json
+            snap_content["Single-End"]["timestamp"] = ""
+            with open(snap_path, "w") as fh:
+                json.dump(snap_content, fh)
+            snap_generator = ComponentsTest(
+                component_type="modules",
+                component_name="bwa/mem",
+                no_prompts=True,
+                remote_url=GITLAB_URL,
+                branch=GITLAB_NFTEST_BRANCH,
+                update=True,
+            )
+            snap_generator.run()
+
+            with open(snap_path) as fh:
+                snap_content = json.load(fh)
+            assert "Single-End" in snap_content
+            assert snap_content["Single-End"]["timestamp"] != original_timestamp
+
+    def test_test_not_found(self):
+        """Generate the snapshot for a module in nf-core/modules clone which doesn't contain tests"""
+        with set_wd(self.nfcore_modules):
+            snap_generator = ComponentsTest(
+                component_type="modules",
+                component_name="fastp",
+                no_prompts=True,
+                remote_url=GITLAB_URL,
+                branch=GITLAB_NFTEST_BRANCH,
+            )
+            test_file = Path("modules", "nf-core-test", "fastp", "tests", "main.nf.test")
+            test_file.rename(test_file.parent / "main.nf.test.bak")
+            with pytest.raises(UserWarning) as e:
+                snap_generator.run()
+            assert "Test file 'main.nf.test' not found" in str(e.value)
+            Path(test_file.parent / "main.nf.test.bak").rename(test_file)
+
+    def test_unstable_snapshot(self):
+        """Generate the snapshot for a module in nf-core/modules clone with unstable snapshots"""
+        with set_wd(self.nfcore_modules):
+            snap_generator = ComponentsTest(
+                component_type="modules",
+                component_name="kallisto/quant",
+                no_prompts=True,
+                remote_url=GITLAB_URL,
+                branch=GITLAB_NFTEST_BRANCH,
+            )
+            with pytest.raises(UserWarning) as e:
+                snap_generator.run()
+            assert "nf-test snapshot is not stable" in str(e.value)

tests/components/test_components_snapshot_test.py

@@ -0,0 +1,41 @@
+"""Test the 'modules test' or 'subworkflows test' command which runs nf-test test."""
+
+import shutil
+from pathlib import Path
+
+import pytest
+
+from nf_core.components.components_test import ComponentsTest
+from nf_core.utils import set_wd
+
+from ..test_components import TestComponents
+
+
+class TestTestComponentsUtils(TestComponents):
+    def test_components_test_check_inputs(self):
+        """Test the check_inputs() function - raise UserWarning because module doesn't exist"""
+        with set_wd(self.nfcore_modules):
+            meta_builder = ComponentsTest(component_type="modules", component_name="none", no_prompts=True)
+            with pytest.raises(UserWarning) as excinfo:
+                meta_builder.check_inputs()
+        assert "Cannot find directory" in str(excinfo.value)
+
+    def test_components_test_no_name_no_prompts(self):
+        """Test the check_inputs() function - raise UserWarning prompts are deactivated and module name is not provided."""
+        with set_wd(self.nfcore_modules):
+            meta_builder = ComponentsTest(component_type="modules", component_name=None, no_prompts=True)
+            with pytest.raises(UserWarning) as excinfo:
+                meta_builder.check_inputs()
+        assert "Module name not provided and prompts deactivated." in str(excinfo.value)
+
+    def test_components_test_no_installed_modules(self):
+        """Test the check_inputs() function - raise UserWarning because installed modules were not found"""
+        with set_wd(self.nfcore_modules):
+            module_dir = Path(self.nfcore_modules, "modules")
+            shutil.rmtree(module_dir)
+            module_dir.mkdir()
+            meta_builder = ComponentsTest(component_type="modules", component_name=None, no_prompts=False)
+            meta_builder.repo_type = "modules"
+            with pytest.raises(LookupError) as excinfo:
+                meta_builder.check_inputs()
+        assert "Nothing installed from" in str(excinfo.value)

tests/test_components.py

@@ -36,21 +36,3 @@ def tearDown(self):
     @pytest.fixture(autouse=True)
     def _use_caplog(self, caplog):
         self.caplog = caplog
-
-    ############################################
-    # Test of the individual components commands. #
-    ############################################
-
-    from .components.generate_snapshot import (  # type: ignore[misc]
-        test_generate_snapshot_module,
-        test_generate_snapshot_once,
-        test_generate_snapshot_subworkflow,
-        test_test_not_found,
-        test_unstable_snapshot,
-        test_update_snapshot_module,
-    )
-    from .components.snapshot_test import (  # type: ignore[misc]
-        test_components_test_check_inputs,
-        test_components_test_no_installed_modules,
-        test_components_test_no_name_no_prompts,
-    )