Merge branch 'master' into issue_1674

Author: tdudgeon

src/xchemalign/aligner.py

@@ -424,7 +424,7 @@ def _perform_alignments(self, meta):
 
         # Get the dataset assignments
         if source_fs_model:
-            dataset_assignments = _load_dataset_assignments(Path(self.base_dir / source_fs_model.dataset_assignments))
+            dataset_assignments = _load_dataset_assignments(Path(source_fs_model.dataset_assignments))
         else:
             dataset_assignments = _load_dataset_assignments(Path(fs_model.dataset_assignments))
 

src/xchemalign/collator.py

@@ -192,6 +192,8 @@ def __init__(self, working_dir, log_file=None, log_level=0, include_git_info=Fal
                 else:
                     excluded_datasets = []
 
+                self.logger.info("Excluded datasets:", excluded_datasets)
+
                 input_path = utils.find_path(input, Constants.CONFIG_DIR)
                 type = utils.find_property(input, Constants.CONFIG_TYPE)
                 code_prefix = utils.find_property(input, Constants.CONFIG_CODE_PREFIX)
@@ -613,6 +615,9 @@ def _validate_manual_input(self, input, crystals):
         self.logger.info("found {} manual inputs".format(len(items)))
 
         for key, item in items.items():
+            if key in input.exclude:
+                self.logger.info("excluding manual crystal", key)
+                continue
             pdb = item[0]
             mtz = item[1]
             cif = item[2]