XspecT 0.5.3__py3-none-any.whl → 0.5.4__py3-none-any.whl

xspect/classify.py

@@ -1,11 +1,13 @@
+"""Classification module"""
+
 from pathlib import Path
-from xspect.mlst_feature.mlst_helper import pick_scheme_from_models_dir
+from importlib import import_module
 import xspect.model_management as mm
-from xspect.models.probabilistic_filter_mlst_model import (
-    ProbabilisticFilterMlstSchemeModel,
-)
 from xspect.file_io import prepare_input_output_paths
 
+# inline imports lead to "invalid name" issues
+# pylint: disable=invalid-name
+
 
 def classify_genus(
     model_genus: str, input_path: Path, output_path: Path, step: int = 1
@@ -22,7 +24,12 @@ def classify_genus(
         output_path (Path): The path to the output file where results will be saved.
         step (int): The amount of kmers to be skipped.
     """
-    model = mm.get_genus_model(model_genus)
+    ProbabilisticSingleFilterModel = import_module(
+        "xspect.models.probabilistic_single_filter_model"
+    ).ProbabilisticSingleFilterModel
+
+    model_path = mm.get_genus_model_path(model_genus)
+    model = ProbabilisticSingleFilterModel.load(model_path)
     input_paths, get_output_path = prepare_input_output_paths(input_path)
 
     for idx, current_path in enumerate(input_paths):
@@ -34,7 +41,11 @@ def classify_genus(
 
 
 def classify_species(
-    model_genus: str, input_path: Path, output_path: Path, step: int = 1
+    model_genus: str,
+    input_path: Path,
+    output_path: Path,
+    step: int = 1,
+    display_name: bool = False,
 ):
     """
     Classify the species of sequences.
@@ -47,12 +58,18 @@ def classify_species(
         input_path (Path): The path to the input file/directory containing sequences.
         output_path (Path): The path to the output file where results will be saved.
         step (int): The amount of kmers to be skipped.
+        display_name (bool): Includes a display name for each tax_ID.
     """
-    model = mm.get_species_model(model_genus)
+    ProbabilisticFilterSVMModel = import_module(
+        "xspect.models.probabilistic_filter_svm_model"
+    ).ProbabilisticFilterSVMModel
+
+    model_path = mm.get_species_model_path(model_genus)
+    model = ProbabilisticFilterSVMModel.load(model_path)
     input_paths, get_output_path = prepare_input_output_paths(input_path)
 
     for idx, current_path in enumerate(input_paths):
-        result = model.predict(current_path, step=step)
+        result = model.predict(current_path, step=step, display_name=display_name)
         result.input_source = current_path.name
         cls_path = get_output_path(idx, output_path)
         result.save(cls_path)
@@ -68,6 +85,12 @@ def classify_mlst(input_path: Path, output_path: Path, limit: bool):
         output_path (Path): The path to the output file where results will be saved.
         limit (bool): A limit for the highest allele_id results that are shown.
     """
+    pick_scheme_from_models_dir = import_module(
+        "xspect.mlst_feature.mlst_helper"
+    ).pick_scheme_from_models_dir
+    ProbabilisticFilterMlstSchemeModel = import_module(
+        "xspect.models.probabilistic_filter_mlst_model"
+    ).ProbabilisticFilterMlstSchemeModel
 
     scheme_path = pick_scheme_from_models_dir()
     model = ProbabilisticFilterMlstSchemeModel.load(scheme_path)

xspect/definitions.py

@@ -11,8 +11,9 @@ def get_xspect_root_path() -> Path:
     """
     Return the root path for XspecT data.
 
-    Returns the path to the XspecT data directory, which can be located either in the user's home directory or in the current working directory.
-    If neither exists, it creates the directory in the user's home directory.
+    Returns the path to the XspecT data directory, which can be located either in the user's home
+    directory or in the current working directory. If neither exists, it creates the directory in
+    the user's home directory.
 
     Returns:
         Path: The path to the XspecT data directory.
@@ -34,8 +35,8 @@ def get_xspect_model_path() -> Path:
     """
     Return the path to the XspecT models.
 
-    Returns the path to the XspecT models directory, which is located within the XspecT data directory.
-    If the directory does not exist, it creates the directory.
+    Returns the path to the XspecT models directory, which is located within the XspecT data
+    directory. If the directory does not exist, it creates the directory.
 
     Returns:
         Path: The path to the XspecT models directory.
@@ -49,8 +50,8 @@ def get_xspect_upload_path() -> Path:
     """
     Return the path to the XspecT upload directory.
 
-    Returns the path to the XspecT uploads directory, which is located within the XspecT data directory.
-    If the directory does not exist, it creates the directory.
+    Returns the path to the XspecT uploads directory, which is located within the XspecT data
+    directory. If the directory does not exist, it creates the directory.
 
     Returns:
         Path: The path to the XspecT uploads directory.
@@ -64,8 +65,8 @@ def get_xspect_runs_path() -> Path:
     """
     Return the path to the XspecT runs directory.
 
-    Returns the path to the XspecT runs directory, which is located within the XspecT data directory.
-    If the directory does not exist, it creates the directory.
+    Returns the path to the XspecT runs directory, which is located within the XspecT data
+    directory. If the directory does not exist, it creates the directory.
 
     Returns:
         Path: The path to the XspecT runs directory.
@@ -79,8 +80,8 @@ def get_xspect_mlst_path() -> Path:
     """
     Return the path to the XspecT MLST directory.
 
-    Returns the path to the XspecT MLST directory, which is located within the XspecT data directory.
-    If the directory does not exist, it creates the directory.
+    Returns the path to the XspecT MLST directory, which is located within the XspecT data
+    directory. If the directory does not exist, it creates the directory.
 
     Returns:
         Path: The path to the XspecT MLST directory.

xspect/file_io.py

@@ -113,7 +113,8 @@ def concatenate_metagenome(fasta_dir: Path, meta_path: Path) -> None:
     Concatenate all fasta files in a directory into one file.
 
     This function searches for all fasta files in the specified directory and writes their contents
-    into a single output file. The output file will contain the concatenated sequences from all fasta files.
+    into a single output file. The output file will contain the concatenated sequences from all
+    fasta files.
 
     Args:
         fasta_dir (Path): Path to the directory with the fasta files.

xspect/filter_sequences.py

@@ -1,7 +1,13 @@
+"""Sequence filtering module"""
+
 from pathlib import Path
-from xspect.model_management import get_genus_model, get_species_model
+from importlib import import_module
+from xspect.model_management import get_genus_model_path, get_species_model_path
 from xspect.file_io import filter_sequences, prepare_input_output_paths
 
+# inline imports lead to "invalid name" issues
+# pylint: disable=invalid-name
+
 
 def filter_species(
     model_genus: str,
@@ -31,7 +37,12 @@ def filter_species(
             available species scores.
         sparse_sampling_step (int): The step size for sparse sampling. Defaults to 1.
     """
-    species_model = get_species_model(model_genus)
+    ProbabilisticFilterSVMModel = import_module(
+        "xspect.models.probabilistic_filter_svm_model"
+    ).ProbabilisticFilterSVMModel
+
+    species_model_path = get_species_model_path(model_genus)
+    species_model = ProbabilisticFilterSVMModel.load(species_model_path)
     input_paths, get_output_path = prepare_input_output_paths(input_path)
 
     for idx, current_path in enumerate(input_paths):
@@ -82,11 +93,16 @@ def filter_genus(
         sparse_sampling_step (int): The step size for sparse sampling. Defaults to 1.
 
     """
-    model = get_genus_model(model_genus)
+    ProbabilisticSingleFilterModel = import_module(
+        "xspect.models.probabilistic_single_filter_model"
+    ).ProbabilisticSingleFilterModel
+
+    genus_model_path = get_genus_model_path(model_genus)
+    genus_model = ProbabilisticSingleFilterModel.load(genus_model_path)
     input_paths, get_output_path = prepare_input_output_paths(input_path)
 
     for idx, current_path in enumerate(input_paths):
-        result = model.predict(current_path, step=sparse_sampling_step)
+        result = genus_model.predict(current_path, step=sparse_sampling_step)
         result.input_source = current_path.name
 
         if classification_output_path:

xspect/main.py

@@ -2,25 +2,12 @@
 
 from pathlib import Path
 from uuid import uuid4
+from importlib import import_module
 import click
-import uvicorn
-from xspect import classify
-from xspect.web import app
-from xspect.download_models import download_test_models
-from xspect import filter_sequences
-from xspect.train import train_from_directory, train_from_ncbi
-from xspect.definitions import (
-    get_xspect_model_path,
-)
-from xspect.mlst_feature.mlst_helper import pick_scheme
-from xspect.mlst_feature.pub_mlst_handler import PubMLSTHandler
-from xspect.models.probabilistic_filter_mlst_model import (
-    ProbabilisticFilterMlstSchemeModel,
-)
-from xspect.model_management import (
-    get_model_metadata,
-    get_models,
-)
+from xspect.model_management import get_models
+
+# inline imports lead to "invalid name" issues
+# pylint: disable=invalid-name
 
 
 @click.group()
@@ -32,7 +19,10 @@ def cli():
 @cli.command()
 def web():
     """Open the XspecT web application."""
-    uvicorn.run(app, host="0.0.0.0", port=8000)
+    app = import_module("xspect.web").app
+    run = import_module("uvicorn").run
+
+    run(app, host="0.0.0.0", port=8000)
 
 
 # # # # # # # # # # # # # # #
@@ -49,6 +39,8 @@ def models():
 def download():
     """Download models."""
     click.echo("Downloading models, this may take a while...")
+    download_test_models = import_module("xspect.download_models").download_test_models
+
     download_test_models(
         "https://assets.adrianromberg.com/science/xspect-models-07-08-2025.zip"
     )
@@ -64,7 +56,6 @@ def list_models():
     if not available_models:
         click.echo("No models found.")
         return
-    # todo: make this machine readable
     click.echo("Models found:")
     click.echo("--------------")
     for model_type, names in available_models.items():
@@ -100,6 +91,8 @@ def train_ncbi(model_genus, svm_steps, author, author_email):
     """Train a species and a genus model based on NCBI data."""
     click.echo(f"Training {model_genus} species and genus metagenome model.")
     try:
+        train_from_ncbi = import_module("xspect.train").train_from_ncbi
+
         train_from_ncbi(model_genus, svm_steps, author, author_email)
     except ValueError as e:
         click.echo(f"Error: {e}")
@@ -143,6 +136,8 @@ def train_ncbi(model_genus, svm_steps, author, author_email):
 def train_directory(model_genus, input_path, svm_steps, meta, author, author_email):
     """Train a model based on data from a directory for a given genus."""
     click.echo(f"Training {model_genus} model with {svm_steps} SVM steps.")
+    train_from_directory = import_module("xspect.train").train_from_directory
+
     train_from_directory(
         model_genus,
         Path(input_path),
@@ -167,12 +162,28 @@ def train_directory(model_genus, input_path, svm_steps, meta, author, author_ema
 def train_mlst(choose_schemes):
     """Download alleles and train bloom filters."""
     click.echo("Updating alleles")
+    mlst_helper = import_module("xspect.mlst_feature.mlst_helper")
+    pick_scheme = mlst_helper.pick_scheme
+
+    pub_mlst_handler = import_module("xspect.mlst_feature.pub_mlst_handler")
+    PubMLSTHandler = pub_mlst_handler.PubMLSTHandler
+
+    probabilistic_filter_mlst_model = import_module(
+        "xspect.models.probabilistic_filter_mlst_model"
+    )
+    ProbabilisticFilterMlstSchemeModel = (
+        probabilistic_filter_mlst_model.ProbabilisticFilterMlstSchemeModel
+    )
+
+    definitions = import_module("xspect.definitions")
+    get_xspect_model_path = definitions.get_xspect_model_path
+
     handler = PubMLSTHandler()
     handler.download_alleles(choose_schemes)
     click.echo("Download finished")
     scheme_path = pick_scheme(handler.get_scheme_paths())
     species_name = str(scheme_path).split("/")[-2]
-    scheme_name = str(scheme_path).split("/")[-1]
+    scheme_name = str(scheme_path).rsplit("/", maxsplit=1)[-1]
     scheme_url = handler.scheme_mapping[str(scheme_path)]
     model = ProbabilisticFilterMlstSchemeModel(
         31, f"{species_name}:{scheme_name}", get_xspect_model_path(), scheme_url
@@ -230,6 +241,8 @@ def classify_seqs():
 def classify_genus(model_genus, input_path, output_path, sparse_sampling_step):
     """Classify samples using a genus model."""
     click.echo("Classifying...")
+    classify = import_module("xspect.classify")
+
     classify.classify_genus(
         model_genus, Path(input_path), Path(output_path), sparse_sampling_step
     )
@@ -268,11 +281,25 @@ def classify_genus(model_genus, input_path, output_path, sparse_sampling_step):
     help="Sparse sampling step (e. g. only every 500th kmer for '--sparse-sampling-step 500').",
     default=1,
 )
-def classify_species(model_genus, input_path, output_path, sparse_sampling_step):
+@click.option(
+    "-n",
+    "--display-names",
+    help="Includes the display names next to taxonomy-IDs.",
+    is_flag=True,
+)
+def classify_species(
+    model_genus, input_path, output_path, sparse_sampling_step, display_names
+):
     """Classify samples using a species model."""
     click.echo("Classifying...")
+    classify = import_module("xspect.classify")
+
     classify.classify_species(
-        model_genus, Path(input_path), Path(output_path), sparse_sampling_step
+        model_genus,
+        Path(input_path),
+        Path(output_path),
+        sparse_sampling_step,
+        display_names,
     )
 
 
@@ -301,6 +328,8 @@ def classify_species(model_genus, input_path, output_path, sparse_sampling_step)
 def classify_mlst(input_path, output_path, limit):
     """MLST classify a sample."""
     click.echo("Classifying...")
+    classify = import_module("xspect.classify")
+
     classify.classify_mlst(Path(input_path), Path(output_path), limit)
 
 
@@ -372,6 +401,7 @@ def filter_genus(
 ):
     """Filter samples using a genus model."""
     click.echo("Filtering...")
+    filter_sequences = import_module("xspect.filter_sequences")
 
     filter_sequences.filter_genus(
         model_genus,
@@ -426,14 +456,16 @@ def filter_genus(
     "-t",
     "--threshold",
     type=float,
-    help="Threshold for filtering (default: 0.7). Use -1 to filter for the highest scoring species.",
+    help="Threshold for filtering (default: 0.7). Use -1 to filter for the highest scoring "
+    "species.",
     default=0.7,
     prompt=True,
 )
 @click.option(
     "--sparse-sampling-step",
     type=int,
-    help="Sparse sampling step (e. g. only every 500th kmer for '--sparse-sampling-step 500').",
+    help="Sparse sampling step (e. g. only every 500th kmer for "
+    "'--sparse-sampling-step 500').",
     default=1,
 )
 def filter_species(
@@ -449,9 +481,12 @@ def filter_species(
 
     if threshold != -1 and (threshold < 0 or threshold > 1):
         raise click.BadParameter(
-            "Threshold must be between 0 and 1, or -1 for filtering by the highest scoring species."
+            "Threshold must be between 0 and 1, or -1 for filtering by the highest "
+            "scoring species."
         )
 
+    get_model_metadata = import_module("xspect.model_management").get_model_metadata
+
     available_species = get_model_metadata(f"{model_genus}-species")["display_names"]
     available_species = {
         id: name.replace(f"{model_genus} ", "")
@@ -476,6 +511,8 @@ def filter_species(
     ][0]
 
     click.echo("Filtering...")
+    filter_sequences = import_module("xspect.filter_sequences")
+
     filter_sequences.filter_species(
         model_genus,
         model_species,

xspect/mlst_feature/mlst_helper.py

@@ -2,10 +2,10 @@
 
 __author__ = "Cetin, Oemer"
 
-import requests
 import json
-from io import StringIO
 from pathlib import Path
+from io import StringIO
+import requests
 from Bio import SeqIO
 from xspect.definitions import get_xspect_model_path
 
@@ -29,7 +29,7 @@ def create_fasta_files(locus_path: Path, fasta_batch: str) -> None:
         output_fasta_file = locus_path / f"Allele_ID_{number}.fasta"
         if output_fasta_file.exists():
             continue  # Ignore existing ones
-        with open(output_fasta_file, "w") as allele:
+        with open(output_fasta_file, "w", encoding="utf-8") as allele:
             SeqIO.write(record, allele, "fasta")
 
 
@@ -59,10 +59,9 @@ def pick_species_number_from_db(available_species: dict) -> str:
             if int(choice) in available_species.keys():
                 chosen_species = available_species.get(int(choice))
                 return chosen_species
-            else:
-                print(
-                    "Wrong input! Try again with a number that is available in the list above."
-                )
+            print(
+                "Wrong input! Try again with a number that is available in the list above."
+            )
         except ValueError:
             print(
                 "Wrong input! Try again with a number that is available in the list above."
@@ -95,10 +94,9 @@ def pick_scheme_number_from_db(available_schemes: dict) -> str:
             if int(choice) in available_schemes.keys():
                 chosen_scheme = available_schemes.get(int(choice))[1]
                 return chosen_scheme
-            else:
-                print(
-                    "Wrong input! Try again with a number that is available in the above list."
-                )
+            print(
+                "Wrong input! Try again with a number that is available in the above list."
+            )
         except ValueError:
             print(
                 "Wrong input! Try again with a number that is available in the above list."
@@ -162,12 +160,12 @@ def pick_scheme(available_schemes: dict) -> Path:
     for counter, scheme in available_schemes.items():
         # For Strain Typing with an API-POST Request to the db
         if str(scheme).startswith("http"):
-            scheme_json = requests.get(scheme).json()
+            scheme_json = requests.get(scheme, timeout=10).json()
             print(str(counter) + ":" + scheme_json["description"])
 
         # To pick a scheme after download for fitting
         else:
-            print(str(counter) + ":" + str(scheme).split("/")[-1])
+            print(str(counter) + ":" + str(scheme).rsplit("/", maxsplit=1)[-1])
 
     print("\nPick a scheme for strain type prediction")
     while True:
@@ -176,10 +174,9 @@ def pick_scheme(available_schemes: dict) -> Path:
             if int(choice) in available_schemes.keys():
                 chosen_scheme = available_schemes.get(int(choice))
                 return chosen_scheme
-            else:
-                print(
-                    "Wrong input! Try again with a number that is available in the above list."
-                )
+            print(
+                "Wrong input! Try again with a number that is available in the above list."
+            )
         except ValueError:
             print(
                 "Wrong input! Try again with a number that is available in the above list."
@@ -209,8 +206,7 @@ class MlstResult:
         Returns:
             dict: The result dictionary with s sequence ID as key and the Strain type as value.
         """
-        results = {seq_id: result for seq_id, result in self.hits.items()}
-        return results
+        return dict(self.hits.items())
 
     def to_dict(self) -> dict:
         """

xspect/mlst_feature/pub_mlst_handler.py

@@ -2,8 +2,8 @@
 
 __author__ = "Cetin, Oemer"
 
-import requests
 import json
+import requests
 from xspect.mlst_feature.mlst_helper import (
     create_fasta_files,
     pick_species_number_from_db,
@@ -51,7 +51,7 @@ class PubMLSTHandler:
         counter = 1
         # retrieve all available species
         species_url = PubMLSTHandler.base_url
-        for species_databases in requests.get(species_url).json():
+        for species_databases in requests.get(species_url, timeout=10).json():
             for database in species_databases["databases"]:
                 if database["name"].endswith("seqdef"):
                     available_species[counter] = database["name"]
@@ -61,7 +61,7 @@ class PubMLSTHandler:
 
         counter = 1
         scheme_url = f"{species_url}/{chosen_species}/schemes"
-        for scheme in requests.get(scheme_url).json()["schemes"]:
+        for scheme in requests.get(scheme_url, timeout=10).json()["schemes"]:
             # scheme["description"] stores the name of a scheme.
             # scheme["scheme"] stores the URL that is needed for downloading all loci.
             available_schemes[counter] = [scheme["description"], scheme["scheme"]]
@@ -70,11 +70,8 @@ class PubMLSTHandler:
         # Selection process of available scheme from a species for download (doubles are caught!)
         while True:
             chosen_scheme = pick_scheme_number_from_db(available_schemes)
-            (
+            if chosen_scheme not in chosen_schemes:
                 chosen_schemes.append(chosen_scheme)
-                if chosen_scheme not in chosen_schemes
-                else None
-            )
             choice = input(
                 "Do you want to pick another scheme to download? (y/n):"
             ).lower()
@@ -97,7 +94,7 @@ class PubMLSTHandler:
             self.choose_schemes()  # changes the scheme_list attribute
 
         for scheme in self.scheme_list:
-            scheme_json = requests.get(scheme).json()
+            scheme_json = requests.get(scheme, timeout=10).json()
             # We only want the name and the respective featured loci of a scheme
             scheme_name = scheme_json["description"]
             locus_list = scheme_json["loci"]
@@ -117,7 +114,7 @@ class PubMLSTHandler:
                 if not locus_path.exists():
                     locus_path.mkdir(exist_ok=True, parents=True)
 
-                alleles = requests.get(f"{locus_url}/alleles_fasta").text
+                alleles = requests.get(f"{locus_url}/alleles_fasta", timeout=10).text
                 create_fasta_files(locus_path, alleles)
 
     def assign_strain_type_by_db(self) -> None:
@@ -132,13 +129,15 @@ class PubMLSTHandler:
             str(pick_scheme(scheme_list_to_dict(self.scheme_list))) + "/sequence"
         )
         fasta_file = get_xspect_upload_path() / "Test.fna"
-        with open(fasta_file, "r") as file:
+        with open(fasta_file, "r", encoding="utf-8") as file:
             data = file.read()
             payload = {  # Essential API-POST-Body
                 "sequence": data,
                 "filetype": "fasta",
             }
-        response = requests.post(scheme_url, data=json.dumps(payload)).json()
+        response = requests.post(
+            scheme_url, data=json.dumps(payload), timeout=10
+        ).json()
 
         for locus, meta_data in response["exact_matches"].items():
             # meta_data is a list containing a dictionary, therefore [0] and then key value.
@@ -170,18 +169,16 @@ class PubMLSTHandler:
             }
         }
 
-        response = requests.post(post_url + "/designations", json=payload)
+        response = requests.post(post_url + "/designations", json=payload, timeout=10)
 
         if response.status_code == 200:
             data = response.json()
             if "fields" in data:
                 post_response = data["fields"]
                 return post_response
-            else:
-                post_response = "No matching Strain Type found in the database. "
-                post_response += "Possibly a novel Strain Type."
-                return post_response
-        else:
-            post_response = "Error:" + str(response.status_code)
-            post_response += response.text
+            post_response = "No matching Strain Type found in the database. "
+            post_response += "Possibly a novel Strain Type."
             return post_response
+        post_response = "Error:" + str(response.status_code)
+        post_response += response.text
+        return post_response

xspect/model_management.py

@@ -2,45 +2,41 @@
 
 from json import loads, dumps
 from pathlib import Path
-from xspect.models.probabilistic_single_filter_model import (
-    ProbabilisticSingleFilterModel,
-)
-from xspect.models.probabilistic_filter_svm_model import ProbabilisticFilterSVMModel
 from xspect.definitions import get_xspect_model_path
 
 
-def get_genus_model(genus) -> ProbabilisticSingleFilterModel:
+def get_genus_model_path(genus) -> Path:
     """
-    Get a genus model for the specified genus.
+    Get a genus model path for the specified genus.
 
-    This function retrieves a pre-trained genus classification model based on the provided genus name.
+    This function retrieves the path of a pre-trained genus classification model based on the
+    provided genus name.
 
     Args:
         genus (str): The genus name for which the model is to be retrieved.
 
     Returns:
-        ProbabilisticSingleFilterModel: An instance of the genus classification model.
+        Path: The file path of the genus classification model.
     """
     genus_model_path = get_xspect_model_path() / (genus.lower() + "-genus.json")
-    genus_filter_model = ProbabilisticSingleFilterModel.load(genus_model_path)
-    return genus_filter_model
+    return genus_model_path
 
 
-def get_species_model(genus) -> ProbabilisticFilterSVMModel:
+def get_species_model_path(genus) -> Path:
     """
-    Get a species classification model for the specified genus.
+    Get a species model path for the specified genus.
 
-    This function retrieves a pre-trained species classification model based on the provided genus name.
+    This function retrieves the path of a pre-trained species classification model based on the
+    provided genus name.
 
     Args:
         genus (str): The genus name for which the species model is to be retrieved.
 
     Returns:
-        ProbabilisticFilterSVMModel: An instance of the species classification model.
+        Path: The file path of the species classification model.
     """
     species_model_path = get_xspect_model_path() / (genus.lower() + "-species.json")
-    species_filter_model = ProbabilisticFilterSVMModel.load(species_model_path)
-    return species_filter_model
+    return species_model_path
 
 
 def get_model_metadata(model: str | Path) -> dict:
@@ -121,7 +117,8 @@ def get_models() -> dict[str, list[dict]]:
     This function scans the model directory for JSON files and organizes them by their model type.
 
     Returns:
-        dict[str, list[dict]]: A dictionary where keys are model types and values are lists of model display names.
+        dict[str, list[dict]]: A dictionary where keys are model types and values are lists of
+        model display names.
     """
     model_dict = {}
     for model_file in get_xspect_model_path().glob("*.json"):

xspect/models/probabilistic_filter_mlst_model.py

@@ -2,14 +2,14 @@
 
 __author__ = "Cetin, Oemer"
 
-import cobs_index
 import json
 from pathlib import Path
+from collections import defaultdict
+import cobs_index
+from cobs_index import DocumentList
 from Bio import SeqIO
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
-from cobs_index import DocumentList
-from collections import defaultdict
 from xspect.file_io import get_record_iterator
 from xspect.mlst_feature.mlst_helper import MlstResult
 from xspect.mlst_feature.pub_mlst_handler import PubMLSTHandler
@@ -100,11 +100,11 @@ class ProbabilisticFilterMlstSchemeModel:
                 "Scheme not found. Please make sure to download the schemes prior!"
             )
 
-        scheme = str(scheme_path).split("/")[-1]
+        scheme = str(scheme_path).rsplit("/", maxsplit=1)[-1]
         cobs_path = ""
         # COBS structure for every locus (default = 7 for Oxford or Pasteur scheme)
         for locus_path in sorted(scheme_path.iterdir()):
-            locus = str(locus_path).split("/")[-1]
+            locus = str(locus_path).rsplit("/", maxsplit=1)[-1]
             # counts all fasta files that belong to a locus
             self.loci[locus] = sum(
                 (1 for _ in locus_path.iterdir() if not str(_).endswith("cache"))
@@ -112,7 +112,7 @@ class ProbabilisticFilterMlstSchemeModel:
 
             # determine the avg base pair size of alleles
             fasta_file = next(locus_path.glob("*.fasta"), None)
-            with open(fasta_file, "r") as handle:
+            with open(fasta_file, "r", encoding="utf-8") as handle:
                 record = next(SeqIO.parse(handle, "fasta"))
             self.avg_locus_bp_size.append(len(record.seq))
 
@@ -134,7 +134,8 @@ class ProbabilisticFilterMlstSchemeModel:
 
     def save(self) -> None:
         """Saves the model to disk"""
-        scheme = str(self.scheme_path).split("/")[-1]  # [-1] contains the scheme name
+        # [-1] contains the scheme name
+        scheme = str(self.scheme_path).rsplit("/", maxsplit=1)[-1]
         json_path = self.base_path / scheme / f"{scheme}.json"
         json_object = json.dumps(self.to_dict(), indent=4)
 
@@ -152,7 +153,7 @@ class ProbabilisticFilterMlstSchemeModel:
         Returns:
             ProbabilisticFilterMlstSchemeModel: A trained model from the disk in JSON format.
         """
-        scheme_name = str(scheme_path).split("/")[-1]
+        scheme_name = str(scheme_path).rsplit("/", maxsplit=1)[-1]
         json_path = scheme_path / f"{scheme_name}.json"
         with open(json_path, "r", encoding="utf-8") as file:
             json_object = file.read()
@@ -221,7 +222,7 @@ class ProbabilisticFilterMlstSchemeModel:
         for entry in sorted(cobs_path.iterdir()):
             if str(entry).endswith(".json"):
                 continue
-            file_name = str(entry).split("/")[-1]  # file_name = locus
+            file_name = str(entry).rsplit("/", maxsplit=1)[-1]  # file_name = locus
             scheme_path_list.append(file_name.split(".")[0])  # without the file ending
 
         result_dict = {}
@@ -442,7 +443,7 @@ class ProbabilisticFilterMlstSchemeModel:
         Returns:
             bool: True if any locus score >= 0.5 * its avg base pair size, False otherwise.
         """
-        for i, (locus, allele_score_dict) in enumerate(highest_results.items()):
+        for i, (_, allele_score_dict) in enumerate(highest_results.items()):
             if not allele_score_dict:
                 continue  # skip empty values
 

xspect/models/probabilistic_filter_model.py

@@ -135,8 +135,8 @@ class ProbabilisticFilterModel:
             display_names (dict | None): A dictionary mapping file names to display names.
                 If None, uses file names as display names.
             training_accessions (dict[str, list[str]] | None): A dictionary mapping filter IDs to
-                lists of accession numbers used for training the model. If None, no training accessions
-                are set.
+                lists of accession numbers used for training the model. If None, no training
+                accessions are set.
         Raises:
             ValueError: If the directory path is invalid, does not exist, or is not a directory.
         """
@@ -230,6 +230,7 @@ class ProbabilisticFilterModel:
         ),
         filter_ids: list[str] = None,
         step: int = 1,
+        display_name: bool = False,
     ) -> ModelResult:
         """
         Returns a model result object for the sequence(s) based on the filters in the model
@@ -246,6 +247,7 @@ class ProbabilisticFilterModel:
             filter_ids (list[str]): A list of filter IDs to filter the results. If None,
                 all results are returned.
             step (int): The step size for the k-mer search. Default is 1.
+            display_name (bool): Includes a display name for each tax_ID.
 
         Returns:
             ModelResult: An object containing the hits for each sequence, the number of kmers,
@@ -253,11 +255,12 @@ class ProbabilisticFilterModel:
 
         Raises:
             ValueError: If the input sequence is not valid, or if it is not a Seq object,
-                        a list of Seq objects, a SeqIO iterator, or a Path object to a fasta/fastq file.
+                        a list of Seq objects, a SeqIO iterator, or a Path object to a fasta/fastq
+                        file.
         """
         if isinstance(sequence_input, (SeqRecord)):
             return ProbabilisticFilterModel.predict(
-                self, [sequence_input], filter_ids, step=step
+                self, [sequence_input], filter_ids, step=step, display_name=display_name
             )
 
         if self._is_sequence_list(sequence_input) | self._is_sequence_iterator(
@@ -272,12 +275,25 @@ class ProbabilisticFilterModel:
                 num_kmers[individual_sequence.id] = self._count_kmers(
                     individual_sequence, step=step
                 )
+                if display_name:
+                    individual_hits.update(
+                        {
+                            f"{key} -{self.display_names.get(key, 'Unknown').replace( 
+                                self.model_display_name, '', 1)}": individual_hits.pop(
+                                key
+                            )
+                            for key in list(individual_hits.keys())
+                        }
+                    )
                 hits[individual_sequence.id] = individual_hits
             return ModelResult(self.slug(), hits, num_kmers, sparse_sampling_step=step)
 
         if isinstance(sequence_input, Path):
             return ProbabilisticFilterModel.predict(
-                self, get_record_iterator(sequence_input), step=step
+                self,
+                get_record_iterator(sequence_input),
+                step=step,
+                display_name=display_name,
             )
 
         raise ValueError(

xspect/models/probabilistic_filter_svm_model.py

@@ -55,10 +55,14 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
             base_path (Path): The base path where the model will be stored.
             kernel (str): The kernel type for the SVM (e.g., 'linear', 'rbf').
             c (float): Regularization parameter for the SVM.
-            fpr (float, optional): False positive rate for the probabilistic filter. Defaults to 0.01.
-            num_hashes (int, optional): Number of hashes for the probabilistic filter. Defaults to 7.
-            training_accessions (dict[str, list[str]] | None, optional): Accessions used for training the probabilistic filter. Defaults to None.
-            svm_accessions (dict[str, list[str]] | None, optional): Accessions used for training the SVM. Defaults to None.
+            fpr (float, optional): False positive rate for the probabilistic filter.
+            Defaults to 0.01.
+            num_hashes (int, optional): Number of hashes for the probabilistic filter.
+            Defaults to 7.
+            training_accessions (dict[str, list[str]] | None, optional): Accessions used for
+            training the probabilistic filter. Defaults to None.
+            svm_accessions (dict[str, list[str]] | None, optional): Accessions used for
+            training the SVM. Defaults to None.
         """
         super().__init__(
             k=k,
@@ -112,17 +116,18 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
         """
         Fit the SVM to the sequences and labels.
 
-        This method first trains the probabilistic filter model and then
-        calculates scores for the SVM training. It expects the sequences to be in
-        the specified directory and the SVM training sequences to be in the
-        specified SVM path. The scores are saved in a CSV file for later use.
+        This method first trains the probabilistic filter model and then calculates scores for
+        the SVM training. It expects the sequences to be in the specified directory and the SVM
+        training sequences to be in the specified SVM path. The scores are saved in a CSV file
+        for later use.
 
         Args:
             dir_path (Path): The directory containing the training sequences.
             svm_path (Path): The directory containing the SVM training sequences.
             display_names (dict[str, str] | None): A mapping of accession IDs to display names.
             svm_step (int): Step size for sparse sampling in SVM training.
-            training_accessions (dict[str, list[str]] | None): Accessions used for training the probabilistic filter.
+            training_accessions (dict[str, list[str]] | None): Accessions used for training the
+            probabilistic filter.
             svm_accessions (dict[str, list[str]] | None): Accessions used for training the SVM.
         """
 
@@ -178,6 +183,7 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
         ),
         filter_ids: list[str] = None,
         step: int = 1,
+        display_name: bool = False,
     ) -> ModelResult:
         """
         Predict the labels of the sequences.
@@ -187,25 +193,33 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
         with the probabilistic filter model, and it will return a `ModelResult`.
 
         Args:
-            sequence_input (SeqRecord | list[SeqRecord] | SeqIO.FastaIO.FastaIterator | SeqIO.QualityIO.FastqPhredIterator | Path): The input sequences to predict.
-            filter_ids (list[str], optional): A list of IDs to filter the predictions. Defaults to None.
+            sequence_input (SeqRecord | list[SeqRecord] | SeqIO.FastaIO.FastaIterator |
+            SeqIO.QualityIO.FastqPhredIterator | Path): The input sequences to predict.
+            filter_ids (list[str], optional): A list of IDs to filter the predictions.
             step (int, optional): Step size for sparse sampling. Defaults to 1.
+            display_name (bool): Includes a display name for each tax_ID.
 
         Returns:
-            ModelResult: The result of the prediction containing hits, number of kmers, and the predicted label.
+            ModelResult: The result of the prediction containing hits, number of kmers, and the
+            predicted label.
         """
         # get scores and format them for the SVM
-        res = super().predict(sequence_input, filter_ids, step=step)
+        res = super().predict(sequence_input, filter_ids, step, display_name)
         svm_scores = dict(sorted(res.get_scores()["total"].items()))
         svm_scores = [list(svm_scores.values())]
 
         svm = self._get_svm(filter_ids)
+        svm_prediction = str(svm.predict(svm_scores)[0])
+        if display_name:
+            svm_prediction = f"{svm_prediction} -{self.display_names.get(svm_prediction, 'Unknown')}".replace(
+                self.model_display_name, "", 1
+            )
         return ModelResult(
             self.slug(),
             res.hits,
             res.num_kmers,
             sparse_sampling_step=step,
-            prediction=str(svm.predict(svm_scores)[0]),
+            prediction=svm_prediction,
         )
 
     def _get_svm(self, id_keys) -> SVC:
@@ -217,7 +231,8 @@ class ProbabilisticFilterSVMModel(ProbabilisticFilterModel):
         training data to only include those keys.
 
         Args:
-            id_keys (list[str] | None): A list of IDs to filter the training data. If None, all data is used.
+            id_keys (list[str] | None): A list of IDs to filter the training data.
+                If None, all data is used.
 
         Returns:
             SVC: The trained SVM model.

xspect/models/probabilistic_single_filter_model.py

@@ -34,8 +34,8 @@ class ProbabilisticSingleFilterModel(ProbabilisticFilterModel):
     ) -> None:
         """Initialize probabilistic single filter model.
 
-        This model uses a Bloom filter to store k-mers from the training sequences. It is designed to
-        be used with a single filter, which is suitable e.g. for genus-level classification.
+        This model uses a Bloom filter to store k-mers from the training sequences. It is designed
+        to be used with a single filter, which is suitable e.g. for genus-level classification.
 
         Args:
             k (int): Length of the k-mers to use for filtering
@@ -45,7 +45,7 @@ class ProbabilisticSingleFilterModel(ProbabilisticFilterModel):
             model_type (str): Type of the model, e.g. "probabilistic_single_filter"
             base_path (Path): Base path where the model will be saved
             fpr (float): False positive rate for the Bloom filter, default is 0.01
-            training_accessions (list[str] | None): List of accessions used for training, default is None
+            training_accessions (list[str] | None): List of accessions used for training
         """
         super().__init__(
             k=k,
@@ -75,7 +75,7 @@ class ProbabilisticSingleFilterModel(ProbabilisticFilterModel):
         Args:
             file_path (Path): Path to the file containing sequences in FASTA format
             display_name (str): Display name for the model
-            training_accessions (list[str] | None): List of accessions used for training, default is None
+            training_accessions (list[str] | None): List of accessions used for training
         """
         self.training_accessions = training_accessions
 
@@ -104,7 +104,7 @@ class ProbabilisticSingleFilterModel(ProbabilisticFilterModel):
         Calculates the number of k-mers in the sequence that are present in the Bloom filter.
 
         Args:
-            sequence (Seq | SeqRecord): Sequence to calculate hits for, can be a Bio.Seq or Bio.SeqRecord object
+            sequence (Seq | SeqRecord): Sequence to calculate hits for
             filter_ids (list[str] | None): List of filter IDs to use, default is None
             step (int): Step size for generating k-mers, default is 1
         Returns:
@@ -162,13 +162,15 @@ class ProbabilisticSingleFilterModel(ProbabilisticFilterModel):
         """
         Generate kmers from the sequence
 
-        Generates k-mers from the sequence, considering both the forward and reverse complement strands.
+        Generates k-mers from the sequence, considering both the forward and reverse complement
+        strands.
 
         Args:
             sequence (Seq): Sequence to generate k-mers from
             step (int): Step size for generating k-mers, default is 1
         Yields:
-            str: The minimizer k-mer (the lexicographically smallest k-mer between the forward and reverse complement)
+            str: The minimizer k-mer (the lexicographically smallest k-mer between the forward and
+                reverse complement)
         """
         num_kmers = ceil((len(sequence) - self.k + 1) / step)
         for i in range(num_kmers):

xspect/models/result.py

@@ -50,7 +50,8 @@ class ModelResult:
 
         Returns:
             dict: A dictionary where keys are subsequence names and values are dictionaries
-                with labels as keys and scores as values. Also includes a 'total' key for overall scores.
+                with labels as keys and scores as values. Also includes a 'total' key for
+                overall scores.
         """
         scores = {
             subsequence: {
@@ -78,7 +79,8 @@ class ModelResult:
         The total hits are calculated by summing the hits for each label across all subsequences.
 
         Returns:
-            dict: A dictionary where keys are labels and values are the total number of hits for that label.
+            dict: A dictionary where keys are labels and values are the total number of hits for
+            that label.
         """
         total_hits = {label: 0 for label in list(self.hits.values())[0]}
         for _, subsequence_hits in self.hits.items():
@@ -97,8 +99,8 @@ class ModelResult:
 
         Args:
             label (str): The label for which to filter the subsequences.
-            filter_threshold (float): The threshold for filtering subsequences. Must be between 0 and 1,
-                or -1 to return the subsequence with the maximum score for the label.
+            filter_threshold (float): The threshold for filtering subsequences. Must be between 0
+                and 1, or -1 to return the subsequence with the maximum score for the label.
 
         Returns:
             dict[str, bool]: A dictionary where keys are subsequence names and values are booleans
@@ -114,11 +116,10 @@ class ModelResult:
                 subsequence: score[label] >= filter_threshold
                 for subsequence, score in scores.items()
             }
-        else:
-            return {
-                subsequence: score[label] == max(score.values())
-                for subsequence, score in scores.items()
-            }
+        return {
+            subsequence: score[label] == max(score.values())
+            for subsequence, score in scores.items()
+        }
 
     def get_filtered_subsequence_labels(
         self, label: str, filter_threshold: float = 0.7
@@ -126,15 +127,17 @@ class ModelResult:
         """
         Return the labels of filtered subsequences.
 
-        This method filters subsequences based on the scores for a given label and a filter threshold.
+        This method filters subsequences based on the scores for a given label and a filter
+        threshold.
 
         Args:
             label (str): The label for which to filter the subsequences.
-            filter_threshold (float): The threshold for filtering subsequences. Must be between 0 and 1,
-                or -1 to return the subsequence with the maximum score for the label.
+            filter_threshold (float): The threshold for filtering subsequences. Must be between 0
+                and 1, or -1 to return the subsequence with the maximum score for the label.
 
         Returns:
-            list[str]: A list of subsequence names that meet the filter criteria for the given label.
+            list[str]: A list of subsequence names that meet the filter criteria for the given
+                label.
         """
         return [
             subsequence
@@ -148,11 +151,13 @@ class ModelResult:
         """
         Return the result as a dictionary.
 
-        This method converts the ModelResult object into a dictionary format suitable for serialization.
+        This method converts the ModelResult object into a dictionary format suitable for
+        serialization.
 
         Returns:
             dict: A dictionary representation of the ModelResult object, including model slug,
-            sparse sampling step, hits, scores, number of k-mers, input source, and prediction if available.
+            sparse sampling step, hits, scores, number of k-mers, input source, and prediction if
+            available.
         """
         res = {
             "model_slug": self.model_slug,

xspect/web.py

@@ -1,17 +1,26 @@
 """FastAPI-based web application for XspecT."""
 
+# pylint: disable=too-many-arguments,too-many-positional-arguments
+
+
 from uuid import uuid4
 import json
 from shutil import copyfileobj
 import importlib.resources as pkg_resources
-from fastapi import APIRouter, FastAPI, HTTPException, UploadFile, BackgroundTasks
+from fastapi import (
+    APIRouter,
+    BackgroundTasks,
+    FastAPI,
+    HTTPException,
+    UploadFile,
+)
 from fastapi.responses import FileResponse, RedirectResponse
+from fastapi.staticfiles import StaticFiles
 from xspect.definitions import get_xspect_runs_path, get_xspect_upload_path
 from xspect.download_models import download_test_models
 import xspect.model_management as mm
 from xspect.train import train_from_ncbi
 from xspect import classify, filter_sequences
-from fastapi.staticfiles import StaticFiles
 
 app = FastAPI()
 app.mount(
@@ -72,7 +81,7 @@ def classify_post(
         )
         return {"message": "Classification started.", "uuid": uuid}
 
-    elif classification_type == "Species":
+    if classification_type == "Species":
         background_tasks.add_task(
             classify.classify_species,
             model,
@@ -119,7 +128,7 @@ def filter_post(
         )
         return {"message": "Genus filtering started.", "uuid": uuid}
 
-    elif filter_type == "Species":
+    if filter_type == "Species":
         if not filter_species:
             raise ValueError("filter_species must be provided for species filtering.")
         background_tasks.add_task(

{xspect-0.5.3.dist-info → xspect-0.5.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: XspecT
-Version: 0.5.3
+Version: 0.5.4
 Summary: Tool to monitor and characterize pathogens using Bloom filters.
 License: MIT License
         

{xspect-0.5.3.dist-info → xspect-0.5.4.dist-info}/RECORD

@@ -1,23 +1,23 @@
 xspect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/classify.py,sha256=4E95JCMdLIaWQOlTVzWeNi3J4kAYsek__wMK8iiV_mI,3122
-xspect/definitions.py,sha256=FpdY1lzWG8mOLUIvL6YVCJX_jV_qdRSItk2yoodCQMg,2730
+xspect/classify.py,sha256=SOTfUsEarZVbVtBuwNTlOYQ_MvoW0ADAqH7rTASWEI8,3936
+xspect/definitions.py,sha256=8PpU8bpzcwv8PPacncywz-Na_MicMl-JsvjiX3e46yo,2734
 xspect/download_models.py,sha256=VALcnowzkUpR-OAvgB5BUdEq9WnyNbli0CxH3OT40Rc,1121
-xspect/file_io.py,sha256=Y9BX5O2Ni-EEhWxq2Nh0zn0mzWfai-6s5f6ASE83eUA,8116
-xspect/filter_sequences.py,sha256=LOmhvK7SmUVpx5zsrCSySDFB1n6wbemBKysK34b4N-s,4574
-xspect/main.py,sha256=Dt4ji-NgAUoR5DCcVXFxT0ZJSKgw7DJG8of3U9R6THw,13088
-xspect/model_management.py,sha256=KhWL_TtbqZNIM8sakm_QPZAJMFgAFUwConqYKM7ekMk,5290
+xspect/file_io.py,sha256=QX2nBtlLAexBdfUr7rtHLlWOuXiaKvfRdpn1Dn0avnY,8120
+xspect/filter_sequences.py,sha256=QKjgUCk3RBY3U9hHmyvSQeQt8n1voBna-NjOoTqdp3A,5196
+xspect/main.py,sha256=vRCsSH_QVKY6usU5d5pjehPAhk4WJfZ_eyl_0xUGu5E,14137
+xspect/model_management.py,sha256=yWbCk6tUn7-OYpzH0BViX2oWr4cdNkEBjrvnaw5GPdQ,4893
 xspect/ncbi.py,sha256=VRbFvtfGR4WTsc3buZE9UCabE3OJUTRphDRY20g63-E,11704
 xspect/train.py,sha256=jxjK4OqzTywmd5KGPou9A-doH8Nwhlv_xF4X7M6X_jI,11588
-xspect/web.py,sha256=XD5G232DvGxVzX56-cWgAkss7m2dxk8t7-7WSuNXCIA,6949
+xspect/web.py,sha256=kM4BZ3fA0f731EEXScAaiGrJZvjjfep1iC1iZemfazw,7039
 xspect/mlst_feature/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/mlst_feature/mlst_helper.py,sha256=MsBzMtqz2KW_YnLYOqfYdFTPkx2gC2T8chY9E_2JgLU,8236
-xspect/mlst_feature/pub_mlst_handler.py,sha256=t84obSvp0FUccUEsmNBjVxBj42kbzblJo41AYTvHfUk,7686
+xspect/mlst_feature/mlst_helper.py,sha256=pxRX_nRbrTSIFPf_FDV3dxR_FonmGtxttFgqNS7sIxE,8130
+xspect/mlst_feature/pub_mlst_handler.py,sha256=gX0bgAqXTaW9weWgxcbsiD7UtMGuDD9veE9mj42Ffm8,7685
 xspect/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/models/probabilistic_filter_mlst_model.py,sha256=s6JnqEHvh38Wg8qLD3-J_aU51REDolCY5DNAQtGAjGc,17630
-xspect/models/probabilistic_filter_model.py,sha256=3fAdQlOLvMZba9T-ej_qeGuhO_Fri8vAY_aG2vlvPFw,18350
-xspect/models/probabilistic_filter_svm_model.py,sha256=kzHYdkGFRD-ICviFc8EyawBi8P_9dzjiq0dOJc2rXys,10708
-xspect/models/probabilistic_single_filter_model.py,sha256=CoJeVe3Xw-DDbiBaFPGCpO3CPgiwG7i1Remz01uipSA,6880
-xspect/models/result.py,sha256=gKuyTUPEeXCPoVhj3T6J9LrWXG2usy91nzqeVNKcNTk,7028
+xspect/models/probabilistic_filter_mlst_model.py,sha256=w9ibUkAYA-DSOEkU8fBenlENrs8JwRRLaF5KO1HVKoM,17716
+xspect/models/probabilistic_filter_model.py,sha256=pUgkN4E2EO-gePVR4BMndgMhJcyvOfVzfjVypjIz2JA,19047
+xspect/models/probabilistic_filter_svm_model.py,sha256=n_HMARvcUMP1i-csiW8uvskcocrvhWMjue7kfsaKPpI,11146
+xspect/models/probabilistic_single_filter_model.py,sha256=vJvKZrAybYHq_UdKQ2GvvVwgTYwqRrL-nDDQZxb6RRc,6828
+xspect/models/result.py,sha256=Wpsm9EYrvMazDO0JAqF51Sb8BJqAZwYx4G6-SUOt5-c,7070
 xspect/xspect-web/.gitignore,sha256=_nGOe6uxTzy60tl_CIibnOUhXtP-DkOyuM-_s7m4ROg,253
 xspect/xspect-web/README.md,sha256=Fa5cCk66ohbqD_AAVgnXUZLhuzshnLxhlUFhxyscScc,1942
 xspect/xspect-web/components.json,sha256=5emhfq5JRW9J8Zga-1N5jAcj4B-r8VREXnH7Z6tZGNk,425
@@ -78,9 +78,9 @@ xspect/xspect-web/src/components/ui/switch.tsx,sha256=uIqRXtd41ba0eusIEUWVyYZv82
 xspect/xspect-web/src/components/ui/table.tsx,sha256=M2-TIHKwPFWuXrwysSufdQRSMJT-K9jPzGOokfU6PXo,2463
 xspect/xspect-web/src/components/ui/tabs.tsx,sha256=BImHKcdDCtrS3CCV1AGgn8qg0b65RB5P-QdH49IAhx0,1955
 xspect/xspect-web/src/lib/utils.ts,sha256=66ibdQiEHKftZBq1OMLmOKqWma1BkO-O60rc1IQYwLE,165
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-xspect-0.5.3.dist-info/RECORD,,
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+xspect-0.5.4.dist-info/RECORD,,