feat!: adjust linting to new outputs structure

.gitignore

@@ -12,6 +12,8 @@ docs/recipes/
 *~
 _bioconda_recipes
 docs/source/developer/_autosummary
+# user-specific VSCode configs
+.vscode
 
 # Mac OS Files
 .DS_Store

bioconda_utils/lint/__init__.py

@@ -257,8 +257,20 @@ def run(self, recipe: _recipe.Recipe, fix: bool = False) -> list[LintMessage]:
                 if isinstance(src, dict):
                     self.check_source(cast(dict[str, Any], src), f"source/{num}")
 
-        # Run depends checks
-        self.check_deps(recipe.get_deps_dict())
+        # Run depends checks, per outputs: package if necessary
+        outputs = recipe.get("outputs", dict())
+        deps = recipe.get_deps_dict()
+        if outputs:
+            for i in range(len(outputs)):
+                output_location = f"outputs/{i}/"
+                # filter down to dependencies for this outputs: package
+                output_deps = dict()
+                for dep in deps:
+                    if any(output_location in d for d in deps[dep]):
+                        output_deps[dep] = deps[dep]
+                self.check_deps(output_deps, output_location)
+        else:
+            self.check_deps(deps, "")
 
         return self.messages
 
@@ -281,7 +293,7 @@ def check_source(self, source: dict[str, Any], section: str) -> None:
                    ``source/0`` (1,2,3...).
         """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         """Execute check on recipe dependencies
 
         Example format for **deps**::
@@ -298,6 +310,12 @@ def check_deps(self, deps: dict[str, list[str]]) -> None:
         Args:
           deps: Dictionary mapping requirements occurring in the recipe
                 to their locations within the recipe.
+          package_location: Path to the main location for the build and
+                            requirements sections. Empty string for the top
+                            level in single-package recipes, something like
+                            ``outputs/0/`` for recipes with packages specified
+                            in an outputs section.
+
         """
 
     def fix(self, _message, _data, /) -> bool:

bioconda_utils/lint/check_build_help.py

@@ -41,7 +41,7 @@ class should_use_compilers(LintCheck):
         "rust",
     )
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         for compiler in self.compilers:
             for location in deps.get(compiler, []):
                 self.message(section=location)
@@ -55,7 +55,7 @@ class compilers_must_be_in_build(LintCheck):
 
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         for dep in deps:
             if dep.startswith("compiler_"):
                 for location in deps[dep]:
@@ -70,7 +70,7 @@ class compiler_needs_stdlib_c(LintCheck):
     ``requirements: build:`` section.
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         compiler = False
         stdlib = False
         for dep, locations in deps.items():
@@ -124,7 +124,7 @@ def _check_line(line: str) -> bool:
             return True
         return False
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "setuptools" not in deps:
             return  # no setuptools, no problem
 
@@ -150,7 +150,7 @@ class cython_must_be_in_host(LintCheck):
           - cython
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "cython" in deps:
             if any("host" not in location for location in deps["cython"]):
                 self.message()
@@ -169,13 +169,13 @@ class cython_needs_compiler(LintCheck):
 
     severity = WARNING
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "cython" in deps and "compiler_c" not in deps and "compiler_cxx" not in deps:
             self.message()
 
 
 class missing_run_exports(LintCheck):
-    """Recipe should have a run_exports statement that ensures correct pinning in downstream packages
+    """Recipe should have a run_exports statement for each package, ensuring correct pinning in downstream packages
 
     This ensures that the package is automatically pinned to a compatible version if
     it is used as a dependency in another recipe.
@@ -186,6 +186,15 @@ class missing_run_exports(LintCheck):
     libraries) but also for e.g. Python packages, as those might also
     introduce breaking changes in their APIs or command line interfaces.
 
+    A ``run_exports:`` specification should be specified in the relevant
+    ``build:`` section for all packages that are built. This means either:
+    (i) in the main ``build`` section, if only one package is built from this
+        recipe, or:
+    (ii) in each outputs' ``build:`` section, if multiple ``outputs:`` are
+        specified. In this case, the main recipe ``build:`` section does not
+        refer to a package that is being built, but only to the recipe, so a
+        ``run_exports:`` section for it does not make sense.
+
     We distinguish between four cases.
 
     **Case 1:** If the software follows semantic versioning (or it has at least a normal version string (like 1.2.3) and the actual strategy of the devs is unknown), add run_exports to the recipe like this::
@@ -233,6 +242,33 @@ class missing_run_exports(LintCheck):
     """
 
     def check_recipe(self, recipe: _recipe.Recipe) -> None:
-        build = recipe.meta.get("build", dict())
-        if "run_exports" not in build:
-            self.message()
+        build_sections = recipe.get_all_section_occurrences(
+            section="build",
+            outputs_exclusive=True,
+            missing_as_empty=True,
+        )
+        for build in build_sections:
+            if "run_exports" not in build_sections[build]:
+                self.message()
+
+
+class unnecessary_run_exports_in_main_build_section_with_multiple_outputs(LintCheck):
+    """Recipe should not have a run_exports statement in main build section if it specifies multiple outputs.
+
+    A ``run_exports:`` specification should be specified in the relevant
+    ``build:`` section for all packages that are built. This means either:
+    (i) in the main ``build`` section, if only one package is built from this
+        recipe, or:
+    (ii) in each outputs' ``build:`` section, if multiple ``outputs:`` are
+        specified.
+
+    This recipe specifies multiple ``outputs:``, so the main recipe ``build:``
+    section does not refer to a package that is being built, but only to the
+    recipe. Thus, a ``run_exports:`` section for it does not make sense.
+    """
+
+    def check_recipe(self, recipe):
+        outputs = recipe.get("outputs", dict())
+        if outputs:
+            if "run_exports" in recipe.meta.get("build", dict()):
+                self.message()

bioconda_utils/lint/check_completeness.py

@@ -16,6 +16,11 @@ class missing_build_number(LintCheck):
 
         build:
             number: 0
+
+    Currently, bioconda-utils does not support specifying build numbers
+    under outputs, so only a single global build number in the top-level
+    build section is supported.
+
     """
 
     def check_recipe(self, recipe: _recipe.Recipe) -> None:
@@ -24,6 +29,29 @@ def check_recipe(self, recipe: _recipe.Recipe) -> None:
 
 
 class missing_home(LintCheck):
+    """The recipe is missing an ``about/home`` entry with a homepage URL.
+
+    If the recipe specifies just one package, please add::
+
+        about:
+            home: <URL to homepage>
+
+    If the recipe specifies multiple `outputs:` packages, each needs to have
+    an `about: summary:` defined. Each package can either inherit this from the
+    global recipe (if it has this section!), or specify its own. For example,
+    package `one` inherits and package `two` specifies its own::
+
+        outputs:
+            one:
+                ...
+            two:
+                about:
+                    home: <URL to other homepage>
+        about:
+            home: <URL to homepage>
+
+    """
+
     """The recipe is missing a homepage URL
 
     Please add::
@@ -34,38 +62,69 @@ class missing_home(LintCheck):
     """
 
     def check_recipe(self, recipe: _recipe.Recipe) -> None:
-        if not recipe.get("about/home", ""):
-            self.message(section="about")
+        missing_section = recipe.check_for_missing_inherited_section("about/home")
+        if missing_section:
+            self.message(section=missing_section)
 
 
 class missing_summary(LintCheck):
-    """The recipe is missing a summary
+    """The recipe is missing an ``about/summary`` section.
 
-    Please add::
+    If the recipe specifies just one package, please add::
 
-       about:
-         summary: One line briefly describing package
+        about:
+            summary: One line briefly describing package
+
+    If the recipe specifies multiple `outputs:` packages, each needs to have
+    an `about: summary:` defined. Each package can either inherit this from the
+    global recipe (if it has this section!), or specify its own. For example,
+    package `one` inherits and package `two` specifies its own::
+
+        outputs:
+            one:
+                ...
+            two:
+                about:
+                    summary: Another one-liner
+        about:
+            summary: Some one-liner
 
     """
 
     def check_recipe(self, recipe: _recipe.Recipe) -> None:
-        if not recipe.get("about/summary", ""):
-            self.message(section="about")
+        missing_section = recipe.check_for_missing_inherited_section("about/summary")
+        if missing_section:
+            self.message(section=missing_section)
 
 
 class missing_license(LintCheck):
-    """The recipe is missing the ``about/license`` key.
+    """The recipe is missing an ``about/license`` section.
 
-    Please add::
+    If the recipe specifies just one package, please add::
 
         about:
-           license: <name of license>
+            license: <name of license>
+
+    If the recipe specifies multiple `outputs:` packages, each needs to have
+    an `about: license:` defined. Each package can either inherit this from the
+    global recipe (if it has this section!), or specify its own. For example,
+    package `one` inherits and package `two` specifies its own::
+
+        outputs:
+            one:
+                ...
+            two:
+            about:
+                license: <name of license>
+        about:
+            license: <name of license>
 
     """
 
     def check_recipe(self, recipe: _recipe.Recipe) -> None:
-        if not recipe.get("about/license", ""):
-            self.message(section="about")
+        missing_section = recipe.check_for_missing_inherited_section("about/license")
+        if missing_section:
+            self.message(section=missing_section)
 
 
 class missing_tests(LintCheck):

bioconda_utils/lint/check_deprecation.py

@@ -12,7 +12,7 @@ class uses_perl_threaded(LintCheck):
 
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "perl-threaded" in deps:
             self.message(data=True)
 
@@ -29,7 +29,7 @@ class uses_javajdk(LintCheck):
 
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "java-jdk" in deps:
             self.message(data=True)
 
@@ -45,7 +45,7 @@ class deprecated_numpy_spec(LintCheck):
 
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "numpy" not in deps:
             return
         for path in deps["numpy"]:
@@ -66,7 +66,7 @@ class uses_matplotlib(LintCheck):
 
     """
 
-    def check_deps(self, deps: dict[str, list[str]]) -> None:
+    def check_deps(self, deps: dict[str, list[str]], package_location: str) -> None:
         if "matplotlib" in deps:
             self.message(data=True)