don't allow to re-run aligner

DEV-GUIDE.md

@@ -12,16 +12,19 @@ This supersedes [Fragalysis-API](https://github.com/xchem/fragalysis-api).
 
 Project dependencies are defined in the `pyproject.toml` file.
 
-You will need to use Python 3.10 or later (a requirement of the `pyproject.toml` file).
+You will need to use Python 3.10 or 3.11 (a requirement of the `pyproject.toml` file).
+Python 3.12 cannot currently be used.
+
 If you prefer to use [conda] you can create a Python 3.10 environment using the
-`environment.yaml` in this project, otherwise, if you have Python 3.10 or later,
+`environment.yaml` in this project, otherwise, if you have Python 3.10 or 3.11,
 you can create an environment using the built-in `venv` module: -
 
     python -m venv venv
     source venv/bin/activate
     pip install --upgrade pip
 
-Make sure you create the venv using Python 3.10 (or later).
+Make sure you create the venv using Python 3.10 or 3.11 (e.g. change the first command to `python3.11 -m venv venv`
+if needed).
 
 From your clean virtual environment you can now install the run-time and development
 dependencies like this: -

src/xchemalign/aligner.py

@@ -20,7 +20,6 @@
 import gemmi
 
 from rich.traceback import install
-install(show_locals=True)
 
 # Local alignment imports
 from ligand_neighbourhood_alignment import constants as lna_constants
@@ -66,6 +65,8 @@
 from xchemalign.utils import Constants
 from xchemalign.pdb_xtal import PDBXtal
 
+install(show_locals=True)
+
 
 def try_make(path):
     if not Path(path).exists():
@@ -215,6 +216,14 @@ def validate(self):
         elif not self.version_dir.is_dir():
             self._log_error("version dir {} is not a directory".format(self.version_dir))
         else:
+            output_meta_path = self.version_dir / Constants.METADATA_ALIGN_FILENAME
+            if output_meta_path.exists():
+                self._log_error(
+                    "aligner output {} already exists. You must run aligner on clean output from collator.".format(
+                        str(output_meta_path)
+                    )
+                )
+
             p = self.metadata_file
             if not p.exists():
                 self._log_error("metadata file {} does not exist. Did the collator step run successfully?".format(p))
@@ -447,23 +456,16 @@ def _perform_alignments(self, meta):
             working_fs_model = fs_model
 
         if working_fs_model.assembly_landmarks.exists():
-            assembly_landmarks = ah.load_yaml(
-                working_fs_model.assembly_landmarks,
-                ah.dict_to_assembly_landmarks
-            )
+            assembly_landmarks = ah.load_yaml(working_fs_model.assembly_landmarks, ah.dict_to_assembly_landmarks)
         else:
             assembly_landmarks = {}
 
         # Get the assembly transforms
         if working_fs_model.assembly_landmarks.exists():
-            assembly_transforms = ah.load_yaml(
-                working_fs_model.assembly_landmarks,
-                lambda x: x
-            )
+            assembly_transforms = ah.load_yaml(working_fs_model.assembly_landmarks, lambda x: x)
         else:
             assembly_transforms = {}
 
-
         # Run the update
         updated_fs_model = _update(
             fs_model,
@@ -485,7 +487,6 @@ def _perform_alignments(self, meta):
             assembly_landmarks,
             assembly_transforms,
             self.version_dir.name[7:],
-
         )
 
         # Update the metadata_file with aligned file locations and site information
@@ -650,9 +651,13 @@ def _perform_alignments(self, meta):
                             aligned_xmap_path = version_output.aligned_xmaps[site_id]
                             aligned_diff_map_path = version_output.aligned_diff_maps[site_id]
 
-                            aligned_crystallographic_event_map_path = version_output.aligned_event_maps_crystallographic[site_id]
+                            aligned_crystallographic_event_map_path = (
+                                version_output.aligned_event_maps_crystallographic[site_id]
+                            )
                             aligned_crystallographic_xmap_path = version_output.aligned_xmaps_crystallographic[site_id]
-                            aligned_crystallographic_diff_map_path = version_output.aligned_diff_maps_crystallographic[site_id]
+                            aligned_crystallographic_diff_map_path = version_output.aligned_diff_maps_crystallographic[
+                                site_id
+                            ]
 
                             aligned_version_output[site_id] = {
                                 Constants.META_AIGNED_STRUCTURE: aligned_structure_path,