Merge pull request #2 from KevinMenden/lint-refactoring

Some additions

nf_core/lint/__init__.py

@@ -205,7 +205,7 @@ def _lint_pipeline(self):
                 "Running lint checks", total=len(self.lint_tests), func_name=self.lint_tests[0]
             )
             for fun_name in self.lint_tests:
-                if self.lint_config.get(fun_name) is False:
+                if self.lint_config.get(fun_name, {}) is False:
                     log.debug("Skipping lint test '{}'".format(fun_name))
                     self.ignored.append((fun_name, fun_name))
                     continue

nf_core/lint/files_exist.py

@@ -51,6 +51,7 @@ def files_exist(self):
     passed = []
     warned = []
     failed = []
+    ignored = []
 
     # NB: Should all be files, not directories
     # List of lists. Passes if any of the files in the sublist are found.
@@ -85,6 +86,9 @@ def files_exist(self):
     ]
     files_warn_ifexists = [".travis.yml"]
 
+    # Remove files that should be ignored according to the linting config
+    ignore_files = self.lint_config.get('files_exist', [])
+
     def pf(file_path):
         return os.path.join(self.wf_path, file_path)
 
@@ -95,30 +99,42 @@ def pf(file_path):
 
     # Files that cause an error if they don't exist
     for files in files_fail:
+        if any([f in ignore_files for f in files]):
+            continue
         if any([os.path.isfile(pf(f)) for f in files]):
             passed.append("File found: {}".format(self._wrap_quotes(files)))
         else:
             failed.append("File not found: {}".format(self._wrap_quotes(files)))
 
     # Files that cause a warning if they don't exist
     for files in files_warn:
+        if any([f in ignore_files for f in files]):
+            continue
         if any([os.path.isfile(pf(f)) for f in files]):
             passed.append("File found: {}".format(self._wrap_quotes(files)))
         else:
             warned.append("File not found: {}".format(self._wrap_quotes(files)))
 
     # Files that cause an error if they exist
     for file in files_fail_ifexists:
+        if file in ignore_files:
+            continue
         if os.path.isfile(pf(file)):
             failed.append("File must be removed: {}".format(self._wrap_quotes(file)))
         else:
             passed.append("File not found check: {}".format(self._wrap_quotes(file)))
 
     # Files that cause a warning if they exist
     for file in files_warn_ifexists:
+        if file in ignore_files:
+            continue
         if os.path.isfile(pf(file)):
             warned.append("File should be removed: {}".format(self._wrap_quotes(file)))
         else:
             passed.append("File not found check: {}".format(self._wrap_quotes(file)))
 
-    return {"passed": passed, "warned": warned, "failed": failed}
+    # Files that are ignoed
+    for file in ignore_files:
+        ignored.append("File is ignored: {}".format(self._wrap_quotes(file)))
+
+    return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

nf_core/lint/nextflow_config.py

@@ -16,6 +16,7 @@ def nextflow_config(self):
     passed = []
     warned = []
     failed = []
+    ignored = []
 
     # Fail tests if these are missing
     config_fail = [
@@ -52,21 +53,31 @@ def nextflow_config(self):
         "params.igenomesIgnore",
     ]
 
+    # Remove field that should be ignored according to the linting config
+    ignore_configs = self.lint_config.get('nextflow_config', [])
+
+
     for cfs in config_fail:
         for cf in cfs:
+            if cf in ignore_configs:
+                continue
             if cf in self.nf_config.keys():
                 passed.append("Config variable found: {}".format(self._wrap_quotes(cf)))
                 break
         else:
             failed.append("Config variable not found: {}".format(self._wrap_quotes(cfs)))
     for cfs in config_warn:
         for cf in cfs:
+            if cf in ignore_configs:
+                continue
             if cf in self.nf_config.keys():
                 passed.append("Config variable found: {}".format(self._wrap_quotes(cf)))
                 break
         else:
             warned.append("Config variable not found: {}".format(self._wrap_quotes(cfs)))
     for cf in config_fail_ifdefined:
+        if cf in ignore_configs:
+            continue
         if cf not in self.nf_config.keys():
             passed.append("Config variable (correctly) not found: {}".format(self._wrap_quotes(cf)))
         else:
@@ -183,4 +194,7 @@ def nextflow_config(self):
                     self.nf_config["manifest.version"]
                 )
             )
-    return {"passed": passed, "warned": warned, "failed": failed}
+
+    for config in ignore_configs:
+        ignored.append("Config ignored: {}".format(self._wrap_quotes(config)))
+    return {"passed": passed, "warned": warned, "failed": failed, "ignored":ignored}

tests/lint/actions_branch_protection.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 import nf_core.lint
 import os
 import yaml

tests/lint/files_exist.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+
+import os
+import yaml
+import nf_core.lint
+
+def test_files_exist_missing_config(self):
+    """Lint test: critical files missing FAIL"""
+    new_pipeline = self._make_pipeline_copy()
+
+    os.remove(os.path.join(new_pipeline, "nextflow.config"))
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    results = lint_obj.files_exist()
+    assert results["failed"] == ["File not found: `nextflow.config`"]
+
+def test_files_exist_missing_main(self):
+    """Check if missing main issues warning"""
+    new_pipeline = self._make_pipeline_copy()
+
+    os.remove(os.path.join(new_pipeline, "main.nf"))
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    results = lint_obj.files_exist()
+    assert results["warned"] == ["File not found: `main.nf`"] 
+
+def test_files_exist_depreciated_file(self):
+    """Check whether depreciated file issues warning"""
+    new_pipeline = self._make_pipeline_copy()
+
+    nf = os.path.join(new_pipeline, "parameters.settings.json")
+    os.system("touch {}".format(nf))
+
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    results = lint_obj.files_exist()
+    assert results["failed"] == ["File must be removed: `parameters.settings.json`"]
+
+def test_files_exist_pass(self):
+    """Lint check should pass if all files are there"""
+
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    results = lint_obj.files_exist()
+    assert results["failed"] == []
+

tests/lint/licence.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+
+import os
+import yaml
+import nf_core.lint
+
+def test_licence_pass(self):
+    """Lint test: check a valid MIT licence"""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    results = lint_obj.licence()
+    assert results["passed"] == ["Licence check passed"]
+
+def test_licence_fail(self):
+    """Lint test: invalid MIT licence"""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load()
+
+    fh = open(os.path.join(new_pipeline, "LICENSE"), "a")
+    fh.write("[year]")
+    fh.close()
+
+    results = lint_obj.licence()
+    assert results["failed"] == ["Licence file contains placeholders: {}".format(os.path.join(new_pipeline, "LICENSE"))]

tests/test_lint.py

@@ -182,6 +182,16 @@ def test_sphinx_rst_files(self):
         test_actions_awsfulltest_fail,
     )
     from lint.actions_awstest import test_actions_awstest_pass, test_actions_awstest_fail
+    from lint.files_exist import (
+        test_files_exist_missing_config,
+        test_files_exist_missing_main, 
+        test_files_exist_depreciated_file,
+        test_files_exist_pass
+    )
+    from lint.licence import (
+        test_licence_pass, 
+        test_licence_fail
+    )
     from lint.actions_branch_protection import (
         test_actions_branch_protection_pass,
         test_actions_branch_protection_fail,