chore: add minor changes and fixes

Author: David Wallace

src/raman_fitting/config/base_settings.py

@@ -11,13 +11,21 @@
 from raman_fitting.models.deconvolution.base_model import (
     get_models_and_peaks_from_definitions,
 )
-from raman_fitting.models.deconvolution.spectrum_regions import get_default_regions_from_toml_files
+from raman_fitting.models.deconvolution.spectrum_regions import (
+    get_default_regions_from_toml_files,
+)
+from .default_models import load_config_from_toml_files
 from .path_settings import create_default_package_dir_or_ask, InternalPathSettings
 
 
+def get_default_models_and_peaks_from_definitions():
+    models_and_peaks_definitions = load_config_from_toml_files()
+    return get_models_and_peaks_from_definitions(models_and_peaks_definitions)
+
+
 class Settings(BaseSettings):
     default_models: Dict[str, Dict[str, BaseLMFitModel]] = Field(
-        default_factory=get_models_and_peaks_from_definitions,
+        default_factory=get_default_models_and_peaks_from_definitions,
         alias="my_default_models",
         init_var=False,
         validate_default=False,
@@ -28,7 +36,5 @@ class Settings(BaseSettings):
         init_var=False,
         validate_default=False,
     )
-    destination_dir: Path = Field(
-        default_factory=create_default_package_dir_or_ask
-    )
+    destination_dir: Path = Field(default_factory=create_default_package_dir_or_ask)
     internal_paths: InternalPathSettings = Field(default_factory=InternalPathSettings)

src/raman_fitting/config/path_settings.py

@@ -71,6 +71,8 @@ class RunModes(StrEnum):
 def get_run_mode_paths(run_mode: RunModes, user_package_home: Path = None):
     if user_package_home is None:
         user_package_home = USER_HOME_PACKAGE
+    if isinstance(run_mode, str):
+        run_mode = RunModes(run_mode)
 
     RUN_MODE_PATHS = {
         RunModes.PYTEST.name: {

src/raman_fitting/delegating/main_delegator.py

@@ -2,19 +2,16 @@
 from dataclasses import dataclass, field
 from typing import Dict, List, Sequence, Any
 
-
 from raman_fitting.config.path_settings import (
     RunModes,
     ERROR_MSG_TEMPLATE,
     initialize_run_mode_paths,
 )
+from raman_fitting.config import settings
 
 from raman_fitting.imports.models import RamanFileInfo
 
 from raman_fitting.models.deconvolution.base_model import BaseLMFitModel
-from raman_fitting.models.deconvolution.base_model import (
-    get_models_and_peaks_from_definitions,
-)
 from raman_fitting.models.splitter import RegionNames
 from raman_fitting.exports.exporter import ExportManager
 from raman_fitting.imports.files.file_indexer import (
@@ -32,7 +29,7 @@
     prepare_aggregated_spectrum_from_files,
 )
 from raman_fitting.types import LMFitModelCollection
-from .run_fit_spectrum import run_fit_over_selected_models
+from raman_fitting.delegating.run_fit_spectrum import run_fit_over_selected_models
 
 
 from loguru import logger
@@ -51,7 +48,7 @@ class MainDelegator:
     run_mode: RunModes
     use_multiprocessing: bool = False
     lmfit_models: LMFitModelCollection = field(
-        default_factory=get_models_and_peaks_from_definitions
+        default_factory=lambda: settings.default_models
     )
     fit_model_region_names: Sequence[RegionNames] = field(
         default=(RegionNames.first_order, RegionNames.second_order)
@@ -60,7 +57,6 @@ class MainDelegator:
     sample_ids: Sequence[str] = field(default_factory=list)
     sample_groups: Sequence[str] = field(default_factory=list)
     index: RamanFileIndex = None
-
     selection: Sequence[RamanFileInfo] = field(init=False)
     selected_models: Sequence[RamanFileInfo] = field(init=False)
 
@@ -191,7 +187,7 @@ def get_results_over_selected_models(
 def make_examples():
     # breakpoint()
     _main_run = MainDelegator(
-        run_mode="pytest", fit_model_specific_names=["2peaks", "4peaks"]
+        run_mode="pytest", fit_model_specific_names=["2peaks", "3peaks", "2nd_4peaks"]
     )
     _main_run.main_run()
     return _main_run

src/raman_fitting/imports/files/file_indexer.py

@@ -22,6 +22,8 @@
 from raman_fitting.imports.models import RamanFileInfo
 from tablib import Dataset
 
+from raman_fitting.imports.spectrum import SPECTRUM_FILETYPE_PARSERS
+
 RamanFileInfoSet: TypeAlias = Sequence[RamanFileInfo]
 
 
@@ -180,7 +182,16 @@ def collect_raman_file_index_info(
     raman_files: Sequence[Path] | None = None, **kwargs
 ) -> RamanFileInfoSet:
     """loops over the files and scrapes the index data from each file"""
-    index, files = collect_raman_file_infos(raman_files, **kwargs)
+    raman_files = list(raman_files)
+    total_files = []
+    dirs = [i for i in raman_files if i.is_dir()]
+    files = [i for i in raman_files if i.is_file()]
+    total_files += files
+    suffixes = [i.lstrip(".") for i in SPECTRUM_FILETYPE_PARSERS.keys()]
+    for d1 in dirs:
+        paths = [path for i in suffixes for path in d1.glob(f"*.{i}")]
+        total_files += paths
+    index, files = collect_raman_file_infos(total_files, **kwargs)
     logger.info(f"successfully made index {len(index)} from {len(files)} files")
     return index
 
@@ -191,6 +202,7 @@ def initialize_index_from_source_files(
     force_reindex: bool = False,
 ) -> RamanFileIndex:
     raman_files = collect_raman_file_index_info(raman_files=files)
+    # breakpoint()
     raman_index = RamanFileIndex(
         index_file=index_file, raman_files=raman_files, force_reindex=force_reindex
     )

src/raman_fitting/imports/samples/sample_id_helpers.py

@@ -6,7 +6,7 @@
 
 def parse_string_to_sample_id_and_position(
     string: str, seps=("_", " ", "-")
-) -> Tuple[str, str]:
+) -> Tuple[str, int]:
     """
     Parser for the filenames -> finds SampleID and sample position
 
@@ -48,6 +48,7 @@ def parse_string_to_sample_id_and_position(
     elif len(split) >= 3:
         sample_id = "_".join(split[0:-1])
         position = int("".join(filter(str.isdigit, split[-1])))
+    position = position or 0
     return (sample_id, position)
 
 

src/raman_fitting/imports/spectrum/__init__.py

@@ -15,5 +15,3 @@
         "method": read_file_with_tablib,
     },
 }
-
-supported_filetypes = [".txt"]

src/raman_fitting/utils/string_operations.py

@@ -4,7 +4,7 @@
 def join_prefix_suffix(prefix: str, suffix: str) -> str:
     prefix_ = prefix.rstrip("_")
     suffix_ = suffix.lstrip("_")
-    if prefix.endswith(suffix_):
+    if suffix_ in prefix:
         return prefix_
     return f"{prefix_}_{suffix_}"