Set of commits to be tagged v0.19

Changelog

With the supporting features from TaggingBackends!11 (merged), if predict is called on a directory instead of a file:

• a primary input file is guessed among the files with extensions: .spine, .outline, .csv, .mat or .hdf5;
• only the files related to the primary input file are taken as input, in addition to the primary input file.

As a consequence, the extra files in the input directory are no longer listed in the dependencies section of the resulting .label file.

Additional change:

• the path specified by the training_dataset element in the clf_config.json file of a tagger is now relative;
• a requirements.txt file is shipped to freeze the version number of most Python dependencies.

src/maggotuba/models/modules.py

@@ -184,7 +184,7 @@ class MaggotEncoder(MaggotModule):
                 _reason = e
                 config['load_state'] = False # for `was_pretrained` to properly work
             else:
-                logging.debug(f"loading neural network state: {path}")
+                logging.debug(f"neural network state loaded: {path}")
         else:
             _reason = '"load_state" is set to false'
         # if state file not found or config option "load_state" is False,
@@ -336,8 +336,8 @@ class DeepLinear(nn.Module):
         return self.layers(x)
 
     def load(self, path):
-        logging.debug(f"loading neural network state: {path}")
         self.load_state_dict(torch.load(path))
+        logging.debug(f"neural network state loaded: {path}")
 
     def save(self, path):
         logging.debug(f"saving neural network state to file: {path}")