Fix package/dependency creation bugs

src/packagedcode/alpine.py

@@ -129,7 +129,7 @@ def compute_normalized_license(cls, package):
 
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
-        cls.assign_package_to_parent_tree(
+        super().assign_package_to_parent_tree(
             package=package,
             resource=resource,
             codebase=codebase,

src/packagedcode/build.py

@@ -51,7 +51,7 @@ def parse(cls, location):
 
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
-        cls.assign_package_to_parent_tree(
+        super().assign_package_to_parent_tree(
             package=package,
             resource=resource,
             codebase=codebase,
@@ -376,7 +376,7 @@ def compute_normalized_license(cls, package):
 
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
-        cls.assign_package_to_parent_tree(
+        super().assign_package_to_parent_tree(
             package_=package,
             resource=resource,
             codebase=codebase,

src/packagedcode/build_gradle.py

@@ -35,7 +35,7 @@ def parse(cls, location):
     # TODO: handle complex cases of nested builds with many packages
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
-        cls.assign_package_to_parent_tree(
+        super().assign_package_to_parent_tree(
             package=package,
             resource=resource,
             codebase=codebase,

src/packagedcode/debian.py

@@ -142,7 +142,7 @@ def assign_package_to_resources(cls, package, resource, codebase):
         # two levels up
         root = resource.parent(codebase).parent(codebase)
         if root:
-            return cls.assign_package_to_resources(package, root, codebase)
+            return super().assign_package_to_resources(package, root, codebase)
 
 
 # TODO: also look into neighboring copyright files!!!
@@ -169,7 +169,7 @@ def assign_package_to_resources(cls, package, resource, codebase):
         # two levels up
         root = resource.parent(codebase).parent(codebase)
         if root:
-            return cls.assign_package_to_resources(package, root, codebase)
+            return super().assign_package_to_resources(package, root, codebase)
 
 
 class DebianDscFileHandler(models.DatafileHandler):
@@ -489,7 +489,7 @@ def assign_package_to_resources(cls, package, resource, codebase):
         # two levels up
         root = resource.parent(codebase).parent(codebase)
         if root:
-            return cls.assign_package_to_resources(package, root, codebase)
+            return super().assign_package_to_resources(package, root, codebase)
 
 
 def build_package_data_from_package_filename(filename, datasource_id, package_type,):

src/packagedcode/models.py

@@ -436,12 +436,17 @@ def from_dependent_packages(
         """
         dependent_packages = dependent_packages or []
         for dependent_package in dependent_packages:
-            yield Dependency.from_dependent_package(
-                dependent_package=dependent_package,
-                datafile_path=datafile_path,
-                datasource_id=datasource_id,
-                package_uid=package_uid,
-            )
+            if dependent_package.purl:
+                yield Dependency.from_dependent_package(
+                    dependent_package=dependent_package,
+                    datafile_path=datafile_path,
+                    datasource_id=datasource_id,
+                    package_uid=package_uid,
+                )
+            else:
+                if TRACE:
+                    logger_debug(f' Dependency.from_dependent_packages: dependent_package (does not have purl): {dependent_package}')
+                pass
 
 
 @attr.attributes(slots=True)

src/packagedcode/npm.py

@@ -53,11 +53,18 @@ def assemble(cls, package_data, resource, codebase):
         else:
             dir_resource=resource
 
-        yield from cls.assemble_from_many_datafiles(
+        for assembled in cls.assemble_from_many_datafiles(
             datafile_name_patterns=datafile_name_patterns,
             directory=dir_resource,
             codebase=codebase,
-        )
+        ):
+            if isinstance(assembled, models.Package):
+                cls.assign_package_to_resources(
+                    package=assembled,
+                    resource=resource,
+                    codebase=codebase,
+                )
+            yield assembled
 
     @classmethod
     def walk_npm(cls, resource, codebase, depth=0):

src/packagedcode/pypi.py

@@ -71,6 +71,14 @@ class BasePypiHandler(models.DatafileHandler):
     def compute_normalized_license(cls, package):
         return compute_normalized_license(package.declared_license)
 
+    @classmethod
+    def assign_package_to_resources(cls, package, resource, codebase):
+        return models.DatafileHandler.assign_package_to_resources(package, resource, codebase)
+
+    @classmethod
+    def assign_package_to_parent_tree(cls, package, resource, codebase):
+        return models.DatafileHandler.assign_package_to_parent_tree(package, resource, codebase)
+
 
 class PythonEggPkgInfoFile(BasePypiHandler):
     datasource_id = 'pypi_egg_pkginfo'
@@ -93,7 +101,7 @@ def assign_package_to_resources(cls, package, resource, codebase):
         # two levels up
         root = resource.parent(codebase).parent(codebase)
         if root:
-            return cls.assign_package_to_resources(package, root, codebase)
+            return super().assign_package_to_resources(package, root, codebase)
 
 
 class PythonEditableInstallationPkgInfoFile(BasePypiHandler):
@@ -115,7 +123,7 @@ def parse(cls, location):
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
         # only the parent for now... though it can be more complex
-        return cls.assign_package_to_parent_tree(package, resource, codebase)
+        return super().assign_package_to_parent_tree(package, resource, codebase)
 
 
 class BaseExtractedPythonLayout(BasePypiHandler):
@@ -144,7 +152,7 @@ def assemble(cls, package_data, resource, codebase):
 
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
-        return cls.assign_package_to_parent_tree(package, resource, codebase)
+        return super().assign_package_to_parent_tree(package, resource, codebase)
 
 
 class PythonSdistPkgInfoFile(BaseExtractedPythonLayout):

src/packagedcode/rubygems.py

@@ -123,7 +123,7 @@ def assemble(cls, package_data, resource, codebase):
 
     @classmethod
     def assign_package_to_resources(cls, package, resource, codebase):
-        return cls.assign_package_to_parent_tree(package, resource, codebase)
+        return super().assign_package_to_parent_tree(package, resource, codebase)
 
 
 class GemspecHandler(BaseGemHandler):

tests/packagedcode/data/pypi/requirements_txt/docs/pip-22.0.4-docs-requirements.txt

@@ -0,0 +1,11 @@
+sphinx ~= 4.2, != 4.4.0
+towncrier
+furo
+myst_parser
+sphinx-copybutton
+sphinx-inline-tabs
+sphinxcontrib-towncrier >= 0.2.0a0
+
+# `docs.pipext` uses pip's internals to generate documentation. So, we install
+# the current directory to make it work.
+.