actions_ci pytests - more granular

Author: ewels

tests/lint/actions_ci.py

@@ -21,16 +21,36 @@ def test_actions_ci_pass(self):
     assert len(results.get("ignored", [])) == 0
 
 
-def test_actions_ci_fail(self):
-    """Lint test: actions_actions_ci - FAIL"""
+def test_actions_ci_fail_wrong_nf(self):
+    """Lint test: actions_ci - FAIL - wrong minimum version of Nextflow tested"""
+    self.lint_obj._load()
+    self.lint_obj.minNextflowVersion = "1.2.3"
+    results = self.lint_obj.actions_ci()
+    assert results["failed"] == ["Minimum NF version in '.github/workflows/ci.yml' different to pipeline's manifest"]
+
+
+def test_actions_ci_fail_wrong_docker_ver(self):
+    """Lint test: actions_actions_ci - FAIL - wrong pipeline version used for docker commands"""
+
+    self.lint_obj._load()
+    self.lint_obj.nf_config["process.container"] = "'nfcore/tools:0.4'"
+    results = self.lint_obj.actions_ci()
+    assert results["failed"] == [
+        "CI is not building the correct docker image. Should be: `docker build --no-cache . -t nfcore/tools:0.4`",
+        "CI is not pulling the correct docker image. Should be: `docker pull nfcore/tools:dev`",
+        "CI is not tagging docker image correctly. Should be: `docker tag nfcore/tools:dev nfcore/tools:0.4`",
+    ]
+
+
+def test_actions_ci_fail_wrong_trigger(self):
+    """Lint test: actions_actions_ci - FAIL - workflow triggered incorrectly, NF ver not checked at all"""
 
     # Edit .github/workflows/actions_ci.yml to mess stuff up!
     new_pipeline = self._make_pipeline_copy()
     with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml"), "r") as fh:
         ci_yml = yaml.safe_load(fh)
     ci_yml[True]["push"] = ["dev", "patch"]
-    ci_yml["jobs"]["test"]["strategy"]["matrix"]["nxf_ver"] = ["foo", ""]
-    ci_yml["jobs"]["test"]["steps"] = [{"name": "Check out pipeline code", "uses": "actions/checkout@v2"}]
+    ci_yml["jobs"]["test"]["strategy"]["matrix"] = {"nxf_versionnn": ["foo", ""]}
     with open(os.path.join(new_pipeline, ".github", "workflows", "ci.yml"), "w") as fh:
         yaml.dump(ci_yml, fh)
 
@@ -41,11 +61,5 @@ def test_actions_ci_fail(self):
     results = lint_obj.actions_ci()
     assert results["failed"] == [
         "'.github/workflows/ci.yml' is not triggered on expected events",
-        "CI is not building the correct docker image. Should be: `docker build --no-cache . -t nfcore/testpipeline:dev`",
-        "CI is not pulling the correct docker image. Should be: `docker pull nfcore/testpipeline:dev`",
-        "CI is not tagging docker image correctly. Should be: `docker tag nfcore/testpipeline:dev nfcore/testpipeline:dev`",
-        "Minimum NF version in '.github/workflows/ci.yml' different to pipeline's manifest"
+        "'.github/workflows/ci.yml' does not check minimum NF version",
     ]
-    assert len(results.get("warned", [])) == 0
-    assert len(results.get("passed", [])) == 0
-    assert len(results.get("ignored", [])) == 0

tests/test_lint.py

@@ -187,7 +187,12 @@ def test_sphinx_rst_files(self):
         test_actions_branch_protection_fail,
         test_actions_branch_protection_ignore,
     )
-    from lint.actions_ci import test_actions_ci_pass, test_actions_ci_fail
+    from lint.actions_ci import (
+        test_actions_ci_pass,
+        test_actions_ci_fail_wrong_nf,
+        test_actions_ci_fail_wrong_docker_ver,
+        test_actions_ci_fail_wrong_trigger,
+    )
 
 
 #    def test_critical_missingfiles_example(self):
@@ -236,52 +241,6 @@ def test_sphinx_rst_files(self):
 #        bad_lint_obj = nf_core.lint.PipelineLint("/non/existant/path")
 #        bad_lint_obj.check_nextflow_config()
 #
-#    def test_actions_wf_branch_pass(self):
-#        """Tests that linting for GitHub Actions workflow for branch protection works for a good example"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-#        lint_obj.pipeline_name = "tools"
-#        lint_obj.check_actions_branch_protection()
-#        expectations = {"failed": 0, "warned": 0, "passed": 2}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
-#    def test_actions_wf_branch_fail(self):
-#        """Tests that linting for GitHub Actions workflow for branch protection fails for a bad example"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
-#        lint_obj.pipeline_name = "tools"
-#        lint_obj.check_actions_branch_protection()
-#        expectations = {"failed": 2, "warned": 0, "passed": 0}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
-#    def test_actions_wf_ci_pass(self):
-#        """Tests that linting for GitHub Actions CI workflow works for a good example"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-#        lint_obj.minNextflowVersion = "20.04.0"
-#        lint_obj.pipeline_name = "tools"
-#        lint_obj.config["process.container"] = "'nfcore/tools:0.4'"
-#        lint_obj.check_actions_ci()
-#        expectations = {"failed": 0, "warned": 0, "passed": 5}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
-#    def test_actions_wf_ci_fail(self):
-#        """Tests that linting for GitHub Actions CI workflow fails for a bad example"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
-#        lint_obj.minNextflowVersion = "20.04.0"
-#        lint_obj.pipeline_name = "tools"
-#        lint_obj.config["process.container"] = "'nfcore/tools:0.4'"
-#        lint_obj.check_actions_ci()
-#        expectations = {"failed": 5, "warned": 0, "passed": 0}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
-#    def test_actions_wf_ci_fail_wrong_NF_version(self):
-#        """Tests that linting for GitHub Actions CI workflow fails for a bad NXF version"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-#        lint_obj.minNextflowVersion = "0.28.0"
-#        lint_obj.pipeline_name = "tools"
-#        lint_obj.config["process.container"] = "'nfcore/tools:0.4'"
-#        lint_obj.check_actions_ci()
-#        expectations = {"failed": 1, "warned": 0, "passed": 4}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
 #    def test_actions_wf_lint_pass(self):
 #        """Tests that linting for GitHub Actions linting wf works for a good example"""
 #        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
@@ -296,20 +255,6 @@ def test_sphinx_rst_files(self):
 #        expectations = {"failed": 3, "warned": 0, "passed": 0}
 #        self.assess_lint_status(lint_obj, **expectations)
 #
-#    def test_actions_wf_awstest_pass(self):
-#        """Tests that linting for GitHub Actions AWS test wf works for a good example"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
-#        lint_obj.check_actions_awstest()
-#        expectations = {"failed": 0, "warned": 0, "passed": 1}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
-#    def test_actions_wf_awstest_fail(self):
-#        """Tests that linting for GitHub Actions AWS test wf fails for a bad example"""
-#        lint_obj = nf_core.lint.PipelineLint(PATH_FAILING_EXAMPLE)
-#        lint_obj.check_actions_awstest()
-#        expectations = {"failed": 1, "warned": 0, "passed": 0}
-#        self.assess_lint_status(lint_obj, **expectations)
-#
 #    def test_wrong_license_examples_with_failed(self):
 #        """Tests for checking the license test behavior"""
 #        for example in PATHS_WRONG_LICENSE_EXAMPLE: