Fix installing specs from yaml file (#6906)

The feature added in #4611 is currently broken. This commit fixes the
behavior of the command and adds unit tests to ensure the basic semantic
is maintained.

It also changes slightly the behavior of Spec.concretized to avoid
copying caches before the concretization (as this may result in a
wrong hash computation for the DAG).

lib/spack/spack/cmd/install.py

@@ -417,11 +417,20 @@ def install(parser, args, **kwargs):
     if args.file:
         for file in args.package:
             with open(file, 'r') as f:
-                specs.append(spack.spec.Spec.from_yaml(f))
+                s = spack.spec.Spec.from_yaml(f)
+
+            if s.concretized().dag_hash() != s.dag_hash():
+                msg = 'skipped invalid file "{0}". '
+                msg += 'The file does not contain a concrete spec.'
+                tty.warn(msg.format(file))
+                continue
+
+            specs.append(s.concretized())
+
     else:
         specs = spack.cmd.parse_specs(args.package, concretize=True)
     if len(specs) == 0:
-        tty.error('The `spack install` command requires a spec to install.')
+        tty.die('The `spack install` command requires a spec to install.')
 
     if args.overwrite:
         # If we asked to overwrite an existing spec we must ensure that:

lib/spack/spack/cmd/spec.py

@@ -69,7 +69,7 @@ def spec(parser, args):
     for spec in spack.cmd.parse_specs(args.specs):
         # With -y, just print YAML to output.
         if args.yaml:
-            if spec.name in spack.repo:
+            if spec.name in spack.repo or spec.virtual:
                 spec.concretize()
             print(spec.to_yaml())
             continue

lib/spack/spack/spec.py

@@ -1897,7 +1897,7 @@ def concretized(self):
         """This is a non-destructive version of concretize().  First clones,
            then returns a concrete version of this package without modifying
            this package. """
-        clone = self.copy()
+        clone = self.copy(caches=False)
         clone.concretize()
         return clone
 

lib/spack/spack/test/cmd/install.py

@@ -245,3 +245,24 @@ def test_install_conflicts(conflict_spec):
         install(conflict_spec)
 
     assert install.returncode == 1
+
+
+@pytest.mark.usefixtures('noop_install', 'config')
+@pytest.mark.parametrize('spec,concretize,error_code', [
+    (Spec('mpi'), False, 1),
+    (Spec('mpi'), True, 0),
+    (Spec('boost'), False, 1),
+    (Spec('boost'), True, 0)
+])
+def test_install_from_file(spec, concretize, error_code, tmpdir):
+
+    if concretize:
+        spec.concretize()
+
+    with fs.working_dir(str(tmpdir)):
+        # A non-concrete spec will fail to be installed
+        with open('spec.yaml', 'w') as f:
+            spec.to_yaml(f)
+        install('-f', 'spec.yaml', fail_on_error=False)
+
+    assert install.returncode == error_code