Add new flavor definition style, add bioinformatics flavor

.automation/build.py

@@ -157,8 +157,8 @@ def generate_all_flavors():
 # Automatically generate Dockerfile , action.yml and upgrade all_flavors.json
 def generate_flavor(flavor, flavor_info):
     descriptor_and_linters = []
-    flavor_descriptors = []
-    flavor_linters = []
+    flavor_descriptors = flavor_info.get("descriptors", [])
+    flavor_linters = flavor_info.get("linters", [])
     # Get install instructions at descriptor level
     descriptor_files = megalinter.linter_factory.list_descriptor_files()
     for descriptor_file in descriptor_files:
@@ -179,6 +179,11 @@ def generate_flavor(flavor, flavor_info):
             flavor_linters += [linter.name]
             if linter.cli_docker_image is not None:
                 requires_docker = True
+
+    # Remove duplicate entries without sorting
+    flavor_descriptors = list(dict.fromkeys(flavor_descriptors))
+    flavor_linters = list(dict.fromkeys(flavor_linters))
+
     # Initialize Dockerfile
     if flavor == "all":
         dockerfile = f"{REPO_HOME}/Dockerfile"
@@ -621,6 +626,12 @@ def match_flavor(item, flavor, flavor_info):
         and flavor in item["descriptor_flavors_exclude"]
     ):
         return False
+
+    elif (item.get("descriptor_id") in flavor_info.get("descriptors", [])
+          or item.get("name") in flavor_info.get("linters", [])):
+        # Short-circuit if the flavor explicitly supplied these details
+        return True
+
     # Flavor all
     elif flavor == "all":
         return True

CHANGELOG.md

@@ -9,6 +9,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 Note: Can be used with `oxsecurity/megalinter@beta` in your GitHub Action mega-linter.yml file, or with `oxsecurity/megalinter:beta` docker image
 
 - Core
+  - Allow flavors to be completely defined in `flavor_factory.py`
 
 - New linters
 
@@ -36,6 +37,7 @@ Note: Can be used with `oxsecurity/megalinter@beta` in your GitHub Action mega-l
   - Update DevSkim documentation to show a valid exclusion config file
 
 - Flavors
+  - Add bioinformatics flavor
 
 - CI
   - Also prune volumes before pulling and pushing to docker hub

megalinter/flavor_factory.py

@@ -65,6 +65,21 @@ def list_megalinter_flavors():
         "security": {"label": "Optimized for security", "strict": True},
         "swift": {"label": "Optimized for SWIFT based projects"},
         "terraform": {"label": "Optimized for TERRAFORM based projects"},
+        "bioinformatics": {
+            "label": "Optimized for bioinformatics projects",
+            "strict": True,
+            "descriptors": [
+                "ACTION",
+                "BASH",
+                "GROOVY",
+                "JAVASCRIPT",
+                "JSON",
+                "PERL",
+                "PYTHON",
+                "R",
+                "YAML",
+            ]
+        },
     }
     return flavors