Merge pull request #1166 from ErikDanielsson/refactor-tests

Refactor tests

CHANGELOG.md

@@ -43,6 +43,7 @@
 #### Tests
 
 * Added a test for the `version_consistency` lint check
+* Refactored modules tests into separate files, and removed direct comparisons with number of tests in `lint` tests ([#1158](https://github.com/nf-core/tools/issues/1158))
 
 ## [v1.14 - Brass Chicken :chicken:](https://github.com/nf-core/tools/releases/tag/1.14) - [2021-05-11]
 

tests/lint/files_unchanged.py

@@ -24,6 +24,6 @@ def test_files_unchanged_fail(self):
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
     lint_obj._load()
     results = lint_obj.files_unchanged()
-    assert len(results["failed"]) == 1
+    assert len(results["failed"]) > 0
     assert failing_file in results["failed"][0]
     assert results["could_fix"]

tests/lint/modules_json.py

@@ -1,9 +1,9 @@
 import nf_core.lint
 
 
-def test_modules_json_fail(self):
+def test_modules_json_pass(self):
     self.lint_obj._load()
     results = self.lint_obj.modules_json()
     assert len(results.get("warned", [])) == 0
     assert len(results.get("failed", [])) == 0
-    assert len(results.get("passed", [])) == 1
+    assert len(results.get("passed", [])) > 0

tests/lint/nextflow_config.py

@@ -24,7 +24,7 @@ def test_nextflow_config_bad_name_fail(self):
 
     lint_obj.nf_config["manifest.name"] = "bad_name"
     result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 1
+    assert len(result["failed"]) > 0
     assert len(result["warned"]) == 0
 
 
@@ -37,5 +37,5 @@ def test_nextflow_config_dev_in_release_mode_failed(self):
     lint_obj.release_mode = True
     lint_obj.nf_config["manifest.version"] = "dev_is_bad_name"
     result = lint_obj.nextflow_config()
-    assert len(result["failed"]) == 1
+    assert len(result["failed"]) > 0
     assert len(result["warned"]) == 0

tests/modules/bump_versions.py

@@ -0,0 +1,49 @@
+import os
+import re
+import pytest
+
+import nf_core.modules
+from nf_core.modules.module_utils import ModuleException
+
+
+def test_modules_bump_versions_single_module(self):
+    """Test updating a single module"""
+    # Change the star/align version to an older version
+    main_nf_path = os.path.join(self.nfcore_modules, "software", "star", "align", "main.nf")
+    with open(main_nf_path, "r") as fh:
+        content = fh.read()
+    new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=2.6.1d", content)
+    with open(main_nf_path, "w") as fh:
+        fh.write(new_content)
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+    version_bumper.bump_versions(module="star/align")
+    assert len(version_bumper.failed) == 0
+
+
+def test_modules_bump_versions_all_modules(self):
+    """Test updating all modules"""
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+    version_bumper.bump_versions(all_modules=True)
+    assert len(version_bumper.failed) == 0
+
+
+def test_modules_bump_versions_fail(self):
+    """Fail updating a module with wrong name"""
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+    with pytest.raises(ModuleException) as excinfo:
+        version_bumper.bump_versions(module="no/module")
+    assert "Could not find the specified module:" in str(excinfo.value)
+
+
+def test_modules_bump_versions_fail_unknown_version(self):
+    """Fail because of an unknown version"""
+    # Change the star/align version to an older version
+    main_nf_path = os.path.join(self.nfcore_modules, "software", "star", "align", "main.nf")
+    with open(main_nf_path, "r") as fh:
+        content = fh.read()
+    new_content = re.sub(r"bioconda::star=\d.\d.\d\D?", r"bioconda::star=xxx", content)
+    with open(main_nf_path, "w") as fh:
+        fh.write(new_content)
+    version_bumper = nf_core.modules.ModuleVersionBumper(pipeline_dir=self.nfcore_modules)
+    version_bumper.bump_versions(module="star/align")
+    assert "Conda package had unknown version" in version_bumper.failed[0][0]

tests/modules/create.py

@@ -0,0 +1,42 @@
+import os
+import pytest
+
+import nf_core.modules
+
+
+def test_modules_create_succeed(self):
+    """Succeed at creating the TrimGalore! module"""
+    module_create = nf_core.modules.ModuleCreate(
+        self.pipeline_dir, "trimgalore", "@author", "process_low", True, True, conda_name="trim-galore"
+    )
+    module_create.create()
+    assert os.path.exists(os.path.join(self.pipeline_dir, "modules", "local", "trimgalore.nf"))
+
+
+def test_modules_create_fail_exists(self):
+    """Fail at creating the same module twice"""
+    module_create = nf_core.modules.ModuleCreate(
+        self.pipeline_dir, "trimgalore", "@author", "process_low", False, False, conda_name="trim-galore"
+    )
+    module_create.create()
+    with pytest.raises(UserWarning) as excinfo:
+        module_create.create()
+    assert "Module file exists already" in str(excinfo.value)
+
+
+def test_modules_create_nfcore_modules(self):
+    """Create a module in nf-core/modules clone"""
+    module_create = nf_core.modules.ModuleCreate(self.nfcore_modules, "fastqc", "@author", "process_low", False, False)
+    module_create.create()
+    assert os.path.exists(os.path.join(self.nfcore_modules, "software", "fastqc", "main.nf"))
+    assert os.path.exists(os.path.join(self.nfcore_modules, "tests", "software", "fastqc", "main.nf"))
+
+
+def test_modules_create_nfcore_modules_subtool(self):
+    """Create a tool/subtool module in a nf-core/modules clone"""
+    module_create = nf_core.modules.ModuleCreate(
+        self.nfcore_modules, "star/index", "@author", "process_medium", False, False
+    )
+    module_create.create()
+    assert os.path.exists(os.path.join(self.nfcore_modules, "software", "star", "index", "main.nf"))
+    assert os.path.exists(os.path.join(self.nfcore_modules, "tests", "software", "star", "index", "main.nf"))

tests/modules/create_test_yml.py

@@ -0,0 +1,59 @@
+import os
+import tempfile
+import pytest
+
+import nf_core.modules
+
+
+def test_modules_custom_yml_dumper(self):
+    """Try to create a yml file with the custom yml dumper"""
+    out_dir = tempfile.mkdtemp()
+    yml_output_path = os.path.join(out_dir, "test.yml")
+    meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", False, "./", False, True)
+    meta_builder.test_yml_output_path = yml_output_path
+    meta_builder.tests = [{"testname": "myname"}]
+    meta_builder.print_test_yml()
+    assert os.path.isfile(yml_output_path)
+
+
+def test_modules_test_file_dict(self):
+    """Creat dict of test files and create md5 sums"""
+    test_file_dir = tempfile.mkdtemp()
+    meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", False, "./", False, True)
+    with open(os.path.join(test_file_dir, "test_file.txt"), "w") as fh:
+        fh.write("this line is just for testing")
+    test_files = meta_builder.create_test_file_dict(test_file_dir)
+    assert len(test_files) == 1
+    assert test_files[0]["md5sum"] == "2191e06b28b5ba82378bcc0672d01786"
+
+
+def test_modules_create_test_yml_get_md5(self):
+    """Get md5 sums from a dummy output"""
+    test_file_dir = tempfile.mkdtemp()
+    meta_builder = nf_core.modules.ModulesTestYmlBuilder("test/tool", False, "./", False, True)
+    with open(os.path.join(test_file_dir, "test_file.txt"), "w") as fh:
+        fh.write("this line is just for testing")
+    test_files = meta_builder.get_md5_sums(
+        entry_point="dummy", command="dummy", results_dir=test_file_dir, results_dir_repeat=test_file_dir
+    )
+    assert test_files[0]["md5sum"] == "2191e06b28b5ba82378bcc0672d01786"
+
+
+def test_modules_create_test_yml_entry_points(self):
+    """Test extracting test entry points from a main.nf file"""
+    meta_builder = nf_core.modules.ModulesTestYmlBuilder("star/align", False, "./", False, True)
+    meta_builder.module_test_main = os.path.join(self.nfcore_modules, "tests", "software", "star", "align", "main.nf")
+    meta_builder.scrape_workflow_entry_points()
+    assert meta_builder.entry_points[0] == "test_star_align"
+
+
+def test_modules_create_test_yml_check_inputs(self):
+    """Test the check_inputs() function - raise UserWarning because test.yml exists"""
+    cwd = os.getcwd()
+    os.chdir(self.nfcore_modules)
+    meta_builder = nf_core.modules.ModulesTestYmlBuilder("star/align", False, "./", False, True)
+    meta_builder.module_test_main = os.path.join(self.nfcore_modules, "tests", "software", "star", "align", "main.nf")
+    with pytest.raises(UserWarning) as excinfo:
+        meta_builder.check_inputs()
+    os.chdir(cwd)
+    assert "Test YAML file already exists!" in str(excinfo.value)

tests/modules/install.py

@@ -0,0 +1,42 @@
+import tempfile
+import pytest
+import os
+
+
+def test_modules_install_nopipeline(self):
+    """Test installing a module - no pipeline given"""
+    self.mods_install.dir = None
+    assert self.mods_install.install("foo") is False
+
+
+def test_modules_install_emptypipeline(self):
+    """Test installing a module - empty dir given"""
+    self.mods_install.dir = tempfile.mkdtemp()
+    with pytest.raises(UserWarning) as excinfo:
+        self.mods_install.install("foo")
+    assert "Could not find a 'main.nf' or 'nextflow.config' file" in str(excinfo.value)
+
+
+def test_modules_install_nomodule(self):
+    """Test installing a module - unrecognised module given"""
+    assert self.mods_install.install("foo") is False
+
+
+def test_modules_install_trimgalore(self):
+    """Test installing a module - TrimGalore!"""
+    assert self.mods_install.install("trimgalore") is not False
+    module_path = os.path.join(self.mods_install.dir, "modules", "nf-core", "software", "trimgalore")
+    assert os.path.exists(module_path)
+
+
+def test_modules_install_trimgalore_alternative_source(self):
+    """Test installing a module from a different source repository - TrimGalore!"""
+    assert self.mods_install_alt.install("trimgalore") is not False
+    module_path = os.path.join(self.mods_install.dir, "modules", "external", "trimgalore")
+    assert os.path.exists(module_path)
+
+
+def test_modules_install_trimgalore_twice(self):
+    """Test installing a module - TrimGalore! already there"""
+    self.mods_install.install("trimgalore")
+    assert self.mods_install.install("trimgalore") is True

tests/modules/lint.py

@@ -0,0 +1,31 @@
+import nf_core.modules
+
+
+def test_modules_lint_trimgalore(self):
+    """Test linting the TrimGalore! module"""
+    self.mods_install.install("trimgalore")
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+    module_lint.lint(print_results=False, module="trimgalore")
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) == 0
+    assert len(module_lint.failed) == 0
+
+
+def test_modules_lint_empty(self):
+    """Test linting a pipeline with no modules installed"""
+    self.mods_remove.remove("fastqc")
+    self.mods_remove.remove("multiqc")
+    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
+    module_lint.lint(print_results=False, all_modules=True)
+    assert len(module_lint.passed) == 0
+    assert len(module_lint.warned) == 0
+    assert len(module_lint.failed) == 0
+
+
+def test_modules_lint_new_modules(self):
+    """lint all modules in nf-core/modules repo clone"""
+    module_lint = nf_core.modules.ModuleLint(dir=self.nfcore_modules)
+    module_lint.lint(print_results=True, all_modules=True)
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
+    assert len(module_lint.failed) == 0

tests/modules/list.py

@@ -0,0 +1,34 @@
+import nf_core.modules
+from rich.console import Console
+
+
+def test_modules_list_remote(self):
+    """Test listing available modules"""
+    mods_list = nf_core.modules.ModuleList(None)
+    listed_mods = mods_list.list_modules()
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "fastqc" in output
+
+
+def test_modules_list_pipeline(self):
+    """Test listing locally installed modules"""
+    mods_list = nf_core.modules.ModuleList(self.pipeline_dir)
+    listed_mods = mods_list.list_modules()
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "fastqc" in output
+    assert "multiqc" in output
+
+
+def test_modules_install_and_list_pipeline(self):
+    """Test listing locally installed modules"""
+    self.mods_install.install("trimgalore")
+    mods_list = nf_core.modules.ModuleList(self.pipeline_dir)
+    listed_mods = mods_list.list_modules()
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "trimgalore" in output

tests/modules/remove.py

@@ -0,0 +1,22 @@
+import os
+
+
+def test_modules_remove_trimgalore(self):
+    """Test removing TrimGalore! module after installing it"""
+    self.mods_install.install("trimgalore")
+    module_path = os.path.join(self.mods_install.dir, "modules", "nf-core", "software", "trimgalore")
+    assert self.mods_remove.remove("trimgalore")
+    assert os.path.exists(module_path) is False
+
+
+def test_modules_remove_trimgalore_alternative_source(self):
+    """Test removing TrimGalore! module after installing it from an alternative source"""
+    self.mods_install_alt.install("trimgalore")
+    module_path = os.path.join(self.mods_install.dir, "modules", "external", "trimgalore")
+    assert self.mods_remove_alt.remove("trimgalore")
+    assert os.path.exists(module_path) is False
+
+
+def test_modules_remove_trimgalore_uninstalled(self):
+    """Test removing TrimGalore! module without installing it"""
+    assert self.mods_remove.remove("trimgalore") is False

tests/test_lint.py

@@ -128,8 +128,8 @@ def test_json_output(self):
         # Load created JSON file and check its contents
         with open(json_fn, "r") as fh:
             saved_json = json.load(fh)
-        assert saved_json["num_tests_pass"] == 2
-        assert saved_json["num_tests_warned"] == 1
+        assert saved_json["num_tests_pass"] > 0
+        assert saved_json["num_tests_warned"] > 0
         assert saved_json["num_tests_ignored"] == 0
         assert saved_json["num_tests_failed"] == 0
         assert saved_json["has_tests_pass"]
@@ -215,15 +215,15 @@ def test_sphinx_rst_files(self):
 
     from lint.version_consistency import test_version_consistency
 
-    from lint.modules_json import test_modules_json_fail
+    from lint.modules_json import test_modules_json_pass
 
 
 # TODO nf-core: Assess and strip out if no longer required for DSL2
 
 #    def test_critical_missingfiles_example(self):
 #        """Tests for missing nextflow config and main.nf files"""
 #        lint_obj = nf_core.lint.run_linting(PATH_CRITICAL_EXAMPLE, False)
-#        assert len(lint_obj.failed) == 1
+#        assert len(lint_obj.failed) > 0
 #
 #    def test_failing_missingfiles_example(self):
 #        """Tests for missing files like Dockerfile or LICENSE"""