Add shellcheck linter

bioconda_utils/bioconda_utils-requirements.txt

@@ -26,6 +26,7 @@ anaconda-client=1.6.*  # anaconda_upload
 involucro=1.1.*        # mulled test and container build
 skopeo=0.1.35          # docker upload
 git=2.14.*             # well - git
+shellcheck=0.7.*       # shellcheck linter
 
 # hosters - special regex not supported by RE
 regex=2018.08.29

bioconda_utils/lint/__init__.py

@@ -87,6 +87,7 @@
    check_noarch
    check_policy
    check_repo
+   check_shellcheck
    check_syntax
 
 """

bioconda_utils/lint/check_shellcheck.py

@@ -0,0 +1,73 @@
+import json
+import os
+from subprocess import run
+import warnings
+
+from . import LintCheck, LintMessage, ERROR, WARNING, INFO
+
+class shellcheck(LintCheck):
+    """The recipe uses shell scripts with portability/reliability issues
+
+    The shell scripts should be checked and either fixed or annotated with
+    # shellcheck disable=<error-code>
+    tags
+    """
+
+    _SEVERITY_MAP = {
+        "error": ERROR,
+        "warning": WARNING,
+        "info": INFO,
+        "style": None
+    }
+
+    def _run_shellcheck(self, recipe):
+        sh_files = [x for x in os.listdir(recipe.dir) if x.ends_with(".sh") and os.path.isfile(x)]
+        if not sh_files:
+            return None
+        try:
+            res = run(["shellcheck", "-f", "json1"] + sh_files, capture_output = True, check = False)
+        except FileNotFoundError:
+            warnings.warn("Skipping shellcheck linter because it could not be found")
+            return None
+        if res.returncode == 0:
+            return None
+        try:
+            errors = json.loads(res.stdout)
+        except json.JSONDecodeError:
+            print("Skipping shellcheck it returned unexpected output: " + res.stdout)
+            return None
+        return errors["comments"]
+
+    def fix(self, error):
+        # shellcheck may provide in error["fix"] suggestions to fix the error, but
+        # we don't implement them here. The error message is usually helpful enough
+        return False
+
+    @classmethod
+    def _shellcheck_msg(cls, recipe, error):
+        error_severity = cls._SEVERITY_MAP[error["level"]]
+        if error_severity is None:
+            return None
+        return LintMessage(
+            recipe=recipe,
+            check=cls,
+            severity=error_severity,
+            title="shellcheck",
+            body=error["message"],
+            fname=error["file"],
+            start_line=error["line"],
+            end_line=error["endLine"],
+            canfix=False
+    )
+
+    def check_recipe(self, recipe):
+        errors = self._run_shellcheck(recipe)
+        if errors is None:
+            return
+        for error in errors:
+            if self.try_fix and error.get("fix", None):
+                if self.fix(error):
+                    continue
+            msg = self._shellcheck_msg(recipe, error)
+            if msg is not None:
+                self.messages.append(msg)