major refactoring and increased test coverage

.gitignore

@@ -29,4 +29,5 @@ site/
 # Tests
 test/test_protein_L/tmp/
 ## pytest
-.pytest_cache
+.pytest_cache
+.coverage

Makefile

@@ -1,7 +1,8 @@
 .PHONY: coverage
 
 coverage:
-	coverage run -m pytest test/test_core.py test/test_main.py test/test_fit.py test/test_cli.py
+	#coverage run -m pytest test/test_core.py test/test_main.py test/test_fit.py test/test_cli.py
+	coverage run -m pytest test/test_fitting.py test/test_lineshapes.py test/test_io.py test/test_utils.py test/test_main.py test/test_cli.py
 
 coverage-html:
 	coverage html

peakipy/cli/check_panel.py

@@ -69,7 +69,7 @@ def create_plotly_pane(cluster, plane):
         data_path=data.data_path,
         clusters=[cluster],
         plane=[plane],
-        config_path=data.config_path,
+        # config_path=data.config_path,
         plotly=True,
     )
 

peakipy/cli/edit.py

@@ -34,7 +34,8 @@
 from bokeh.plotting.contour import contour_data
 from bokeh.palettes import PuBuGn9, Category20, Viridis256, RdGy11, Reds256, YlOrRd9
 
-from peakipy.core import LoadData, update_args_with_values_from_config_file, StrucEl
+from peakipy.io import LoadData, StrucEl
+from peakipy.utils import update_args_with_values_from_config_file
 
 log_style = "overflow:scroll;"
 log_div = """<div style=%s>%s</div>"""

peakipy/cli/edit_panel.py

@@ -102,9 +102,12 @@ def fit_peaks_button_click(event):
     button.on_click(fit_peaks_button_click)
 
     def update_source_selected_indices(event):
-        # print(event)
         # print(bs.tablulator_widget.selection)
+        # hack to make current selection however, only allows one selection
+        # at a time
+        bs.tablulator_widget._update_selection([event.value])
         bs.source.selected.indices = bs.tablulator_widget.selection
+        # print(bs.tablulator_widget.selection)
 
     bs.tablulator_widget.on_click(update_source_selected_indices)
     bs.tablulator_widget.on_edit(update_peakipy_data_on_edit_of_table)

peakipy/cli/fit.py

@@ -14,15 +14,17 @@
 from lmfit import Model, Parameter, Parameters
 from lmfit.model import ModelResult
 
-from peakipy.core import (
-    fix_params,
+from peakipy.lineshapes import (
     Lineshape,
     pvoigt2d,
     voigt2d,
     pv_pv,
+    get_lineshape_function,
+)
+from peakipy.fitting import (
+    fix_params,
     to_prefix,
     get_limits_for_axis_in_points,
-    get_lineshape_function,
     deal_with_peaks_on_edge_of_spectrum,
     select_planes_above_threshold_from_masked_data,
     select_reference_planes_using_indices,