revert bumping specfile version

Signed-off-by: Gregory Becker <becker33@llnl.gov>

lib/spack/spack/database.py

@@ -778,7 +778,7 @@ def _assign_dependencies(
             spec_node_dict = spec_node_dict[spec.name]
         if "dependencies" in spec_node_dict:
             yaml_deps = spec_node_dict["dependencies"]
-            for dname, dhash, dtypes, _, virtuals in spec_reader.read_specfile_dep_specs(
+            for dname, dhash, dtypes, _, virtuals, direct in spec_reader.read_specfile_dep_specs(
                 yaml_deps
             ):
                 # It is important that we always check upstream installations in the same order,
@@ -797,7 +797,9 @@ def _assign_dependencies(
                     )
                     continue
 
-                spec._add_dependency(child, depflag=dt.canonicalize(dtypes), virtuals=virtuals)
+                spec._add_dependency(
+                    child, depflag=dt.canonicalize(dtypes), virtuals=virtuals, direct=direct
+                )
 
     def _read_from_file(self, filename: pathlib.Path, *, reindex: bool = False) -> None:
         """Fill database from file, do not maintain old data.

lib/spack/spack/environment/__init__.py

@@ -543,7 +543,6 @@
         },
       }
     }
-
 """
 
 from .environment import (

lib/spack/spack/environment/environment.py

@@ -2230,9 +2230,14 @@ def filter_specs(self, reader, json_specs_by_hash, order_concretized):
         # and add them to the spec, including build specs
         for lockfile_key, node_dict in json_specs_by_hash.items():
             name, data = reader.name_and_data(node_dict)
-            for _, dep_hash, deptypes, _, virtuals in reader.dependencies_from_node_dict(data):
+            for _, dep_hash, deptypes, _, virtuals, direct in reader.dependencies_from_node_dict(
+                data
+            ):
                 specs_by_hash[lockfile_key]._add_dependency(
-                    specs_by_hash[dep_hash], depflag=dt.canonicalize(deptypes), virtuals=virtuals
+                    specs_by_hash[dep_hash],
+                    depflag=dt.canonicalize(deptypes),
+                    virtuals=virtuals,
+                    direct=direct,
                 )
 
             if "build_spec" in node_dict:

lib/spack/spack/spec.py

@@ -2383,6 +2383,7 @@ def to_node_dict(self, hash=ht.dag_hash):
                     "parameters": {
                         "deptypes": dt.flag_to_tuple(dspec.depflag),
                         "virtuals": dspec.virtuals,
+                        "direct": dspec.direct,
                     },
                 }
                 for name, edges_for_name in sorted(deps.items())
@@ -4890,7 +4891,7 @@ def _load(cls, data):
 
         # Pass 0: Determine hash type
         for node in nodes:
-            for _, _, _, dhash_type, _ in cls.dependencies_from_node_dict(node):
+            for _, _, _, dhash_type, _, _ in cls.dependencies_from_node_dict(node):
                 any_deps = True
                 if dhash_type:
                     hash_type = dhash_type
@@ -4921,11 +4922,12 @@ def _load(cls, data):
         # Pass 2: Finish construction of all DAG edges (including build specs)
         for node_hash, node in hash_dict.items():
             node_spec = node["node_spec"]
-            for _, dhash, dtype, _, virtuals in cls.dependencies_from_node_dict(node):
+            for _, dhash, dtype, _, virtuals, direct in cls.dependencies_from_node_dict(node):
                 node_spec._add_dependency(
                     hash_dict[dhash]["node_spec"],
                     depflag=dt.canonicalize(dtype),
                     virtuals=virtuals,
+                    direct=direct,
                 )
             if "build_spec" in node.keys():
                 _, bhash, _ = cls.extract_build_spec_info_from_node_dict(node, hash_type=hash_type)
@@ -4966,9 +4968,9 @@ def load(cls, data):
         for node in nodes:
             # get dependency dict from the node.
             name, data = cls.name_and_data(node)
-            for dname, _, dtypes, _, virtuals in cls.dependencies_from_node_dict(data):
+            for dname, _, dtypes, _, virtuals, direct in cls.dependencies_from_node_dict(data):
                 deps[name]._add_dependency(
-                    deps[dname], depflag=dt.canonicalize(dtypes), virtuals=virtuals
+                    deps[dname], depflag=dt.canonicalize(dtypes), virtuals=virtuals, direct=direct
                 )
 
         reconstruct_virtuals_on_edges(result)
@@ -5006,7 +5008,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
                     raise spack.error.SpecError("Couldn't parse dependency spec.")
             else:
                 raise spack.error.SpecError("Couldn't parse dependency types in spec.")
-            yield dep_name, dep_hash, list(deptypes), hash_type, list(virtuals)
+            yield dep_name, dep_hash, list(deptypes), hash_type, list(virtuals), True
 
 
 class SpecfileV2(SpecfileReaderBase):
@@ -5043,13 +5045,15 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
                 # new format: elements of dependency spec are keyed.
                 for h in ht.HASHES:
                     if h.name in elt:
-                        dep_hash, deptypes, hash_type, virtuals = cls.extract_info_from_dep(elt, h)
+                        dep_hash, deptypes, hash_type, virtuals, direct = (
+                            cls.extract_info_from_dep(elt, h)
+                        )
                         break
                 else:  # We never determined a hash type...
                     raise spack.error.SpecError("Couldn't parse dependency spec.")
             else:
                 raise spack.error.SpecError("Couldn't parse dependency types in spec.")
-            result.append((dep_name, dep_hash, list(deptypes), hash_type, list(virtuals)))
+            result.append((dep_name, dep_hash, list(deptypes), hash_type, list(virtuals), direct))
         return result
 
     @classmethod
@@ -5057,7 +5061,8 @@ def extract_info_from_dep(cls, elt, hash):
         dep_hash, deptypes = elt[hash.name], elt["type"]
         hash_type = hash.name
         virtuals = []
-        return dep_hash, deptypes, hash_type, virtuals
+        direct = True
+        return dep_hash, deptypes, hash_type, virtuals, direct
 
     @classmethod
     def extract_build_spec_info_from_node_dict(cls, node, hash_type=ht.dag_hash.name):
@@ -5078,7 +5083,8 @@ def extract_info_from_dep(cls, elt, hash):
         deptypes = elt["parameters"]["deptypes"]
         hash_type = hash.name
         virtuals = elt["parameters"]["virtuals"]
-        return dep_hash, deptypes, hash_type, virtuals
+        direct = True
+        return dep_hash, deptypes, hash_type, virtuals, direct
 
     @classmethod
     def load(cls, data):
@@ -5092,6 +5098,15 @@ class SpecfileV5(SpecfileV4):
     def legacy_compiler(cls, node):
         raise RuntimeError("The 'compiler' option is unexpected in specfiles at v5 or greater")
 
+    @classmethod
+    def extract_info_from_dep(cls, elt, hash):
+        dep_hash = elt[hash.name]
+        deptypes = elt["parameters"]["deptypes"]
+        hash_type = hash.name
+        virtuals = elt["parameters"]["virtuals"]
+        direct = elt["parameters"].get("direct", True)
+        return dep_hash, deptypes, hash_type, virtuals, direct
+
 
 #: Alias to the latest version of specfiles
 SpecfileLatest = SpecfileV5

lib/spack/spack/test/spec_yaml.py

@@ -494,6 +494,10 @@ def test_anchorify_2():
         "hdf5~~mpi++shared",
         "hdf5 cflags==-g foo==bar cxxflags==-O3",
         "hdf5 cflags=-g foo==bar cxxflags==-O3",
+        "hdf5%gcc",
+        "hdf5%cmake",
+        "hdf5^gcc",
+        "hdf5^cmake",
     ],
 )
 def test_pickle_roundtrip_for_abstract_specs(spec_str):