Merge pull request #49 from molssi-seamm/dev

Starting switch to standard structure handling
molssi-seamm · Nov 2, 2023 · 5951119 · 5951119
2 parents 444e31a + c386fce
commit 5951119
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Showing 3 changed files with 5 additions and 8 deletions.
diff --git a/read_structure_step/read_structure.py b/read_structure_step/read_structure.py
@@ -79,7 +79,6 @@ def create_parser(self):
         # Remember if the parser exists ... this type of step may have been
         # found before
         parser_exists = parser.exists(parser_name)
-        print(f"{parser_exists=}")
 
         # Create the standard options, e.g. log-level
         result = super().create_parser(name=parser_name)
@@ -212,9 +211,7 @@ def run(self):
 
             # Read the file into the system
             system_db = self.get_variable("_system_db")
-            system, configuration = self.get_system_configuration(
-                P, structure_handling=True
-            )
+            system, configuration = self.get_system_configuration(P, same_as=None)
 
             configurations = read(
                 filename,
@@ -327,7 +324,7 @@ def read_tarfile(self, tarfile_path, P):
                     # Read the file into the system
                     system_db = self.get_variable("_system_db")
                     system, configuration = self.get_system_configuration(
-                        P, structure_handling=True
+                        P, same_as=None
                     )
 
                     read(

diff --git a/read_structure_step/write_structure.py b/read_structure_step/write_structure.py
@@ -181,7 +181,7 @@ def run(self):
 
         # Write the file into the system
         system_db = self.get_variable("_system_db")
-        system, configuration = self.get_system_configuration(P)
+        system, configuration = self.get_system_configuration()
 
         structures = P["structures"]
         configs = P["configurations"]

diff --git a/versioneer.py b/versioneer.py
@@ -339,9 +339,9 @@ def get_config_from_root(root):
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
     setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
+    parser = configparser.ConfigParser()
     with open(setup_cfg, "r") as f:
-        parser.readfp(f)
+        parser.read_file(f)
     VCS = parser.get("versioneer", "VCS")  # mandatory
 
     def get(parser, name):