Changes assignment of 'Notes' from 0 to NaN in densimeters.py.

[cljdevitre]

Changes assignment to 'Notes' from 0 to NaN. Was causing invalid value error in notebook Step 4 at cell [12]:
df=pf.calculate_density_ucb(df_combo=df_combo_sec_phase,
Ne_pickle_str='Neon_corr_model.pkl', temp='SupCrit', CI_split=0.67, CI_neon=0.67)
df.head()

If not NaN, replace with something else, like a str (could be "0", if the 0 is important later). 'Notes' is a string column that won't accept integer as assignment.

Error traceback below....

TypeError Traceback (most recent call last)
Cell In[42], line 1
----> 1 df=pf.calculate_density_ucb(df_combo=df_combo_sec_phase,
2 Ne_pickle_str='Neon_corr_model.pkl', temp='SupCrit', CI_split=0.67, CI_neon=0.67)
3 df.head()

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/DiadFit/densimeters.py:1245, in calculate_density_ucb(Ne_line_combo, df_combo, temp, CI_split, CI_neon, Ne_pickle_str, Ar_pickle_str, pref_Ne, Ne_err, corrected_split, split_err)
1243 Imposs_upper_end=(df['Corrected_Splitting']<105.3438707618937+offset)# & (df['Splitting']>103.88+offset)
1244 df.loc[zero, 'Preferred D']=0
-> 1245 df.loc[zero, 'Notes']=0
1247 # Assign to the right type to avoid annoying pandas 2 warning
1248 # Ensure the columns are of type float64
1249 df['Preferred D'] = df['Preferred D'].astype('float64', errors='ignore')

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/indexing.py:938, in _LocationIndexer.setitem(self, key, value)
933 self._has_valid_setitem_indexer(key)
935 iloc: _iLocIndexer = (
936 cast("_iLocIndexer", self) if self.name == "iloc" else self.obj.iloc
937 )
--> 938 iloc._setitem_with_indexer(indexer, value, self.name)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/indexing.py:1953, in _iLocIndexer._setitem_with_indexer(self, indexer, value, name)
1950 # align and set the values
1951 if take_split_path:
1952 # We have to operate column-wise
-> 1953 self._setitem_with_indexer_split_path(indexer, value, name)
1954 else:
1955 self._setitem_single_block(indexer, value, name)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/indexing.py:2044, in _iLocIndexer._setitem_with_indexer_split_path(self, indexer, value, name)
2041 else:
2042 # scalar value
2043 for loc in ilocs:
-> 2044 self._setitem_single_column(loc, value, pi)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/indexing.py:2181, in _iLocIndexer._setitem_single_column(self, loc, value, plane_indexer)
2171 if dtype == np.void:
2172 # This means we're expanding, with multiple columns, e.g.
2173 # df = pd.DataFrame({'A': [1,2,3], 'B': [4,5,6]})
(...) 2176 # Here, we replace those temporary np.void columns with
2177 # columns of the appropriate dtype, based on value.
2178 self.obj.iloc[:, loc] = construct_1d_array_from_inferred_fill_value(
2179 value, len(self.obj)
2180 )
-> 2181 self.obj._mgr.column_setitem(loc, plane_indexer, value)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/internals/managers.py:1520, in BlockManager.column_setitem(self, loc, idx, value, inplace_only)
1518 col_mgr.setitem_inplace(idx, value)
1519 else:
-> 1520 new_mgr = col_mgr.setitem((idx,), value)
1521 self.iset(loc, new_mgr._block.values, inplace=True)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/internals/managers.py:604, in BaseBlockManager.setitem(self, indexer, value)
600 # No need to split if we either set all columns or on a single block
601 # manager
602 self = self.copy(deep=True)
--> 604 return self.apply("setitem", indexer=indexer, value=value)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/internals/managers.py:442, in BaseBlockManager.apply(self, f, align_keys, **kwargs)
440 applied = b.apply(f, **kwargs)
441 else:
--> 442 applied = getattr(b, f)(**kwargs)
443 result_blocks = extend_blocks(applied, result_blocks)
445 out = type(self).from_blocks(result_blocks, [ax.view() for ax in self.axes])

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/internals/blocks.py:1667, in EABackedBlock.setitem(self, indexer, value)
1664 check_setitem_lengths(indexer, value, values)
1666 try:
-> 1667 values[indexer] = value
1668 except (ValueError, TypeError):
1669 if isinstance(self.dtype, IntervalDtype):
1670 # see TestSetitemFloatIntervalWithIntIntervalValues

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/arrays/string_.py:863, in StringArray.setitem(self, key, value)
860 if self._readonly:
861 raise ValueError("Cannot modify read-only array")
--> 863 value = self._maybe_convert_setitem_value(value)
865 key = check_array_indexer(self, key)
866 scalar_key = lib.is_scalar(key)

File /opt/anaconda3/envs/thermoengine_env/lib/python3.12/site-packages/pandas/core/arrays/string_.py:837, in StringArray._maybe_convert_setitem_value(self, value)
835 value = self.dtype.na_value
836 elif not isinstance(value, str):
--> 837 raise TypeError(
838 f"Invalid value '{value}' for dtype '{self.dtype}'. Value should "
839 f"be a string or missing value, got '{type(value).name}' "
840 "instead."
841 )
842 else:
843 value = extract_array(value, extract_numpy=True)

TypeError: Invalid value '0' for dtype 'str'. Value should be a string or missing value, got 'int' instead.

[cljdevitre]

the third commit, is to fix an issue with secondary phase plotting. just added .values[0] instead of .values to ensure correct assignment. I wasn't able to run the notebooks with the refits without these changes.

This is the traceback.
TypeError Traceback (most recent call last)
TypeError: only 0-dimensional arrays can be converted to Python scalars

The above exception was the direct cause of the following exception:

ValueError Traceback (most recent call last)
Cell In[13], line 6
2 height_carb=10
3 width_carb=1
4 threshold_carb=1
5
----> 6 Carb_peaks_scipy, x_data_scipy, y_data_scipy, fig=pf.plot_secondary_peaks(
7 Diad_Files=Diad_Files, path=spectra_path,
8 filetype=spectra_filetype, find_peaks_filter=True,
9 xlim_plot=[1050, 1150], xlim_peaks=[1070, 1100], yscale=0.3,

File ~/Documents/Python_dev/DiadFit/src/DiadFit/diads.py:4262, in plot_secondary_peaks(Diad_Files, path, filetype, xlim_plot, xlim_peaks, height, threshold, distance, prominence, width, prominence_filter, sigma, sigma_window, find_peaks_filter, just_plot, yscale, gaussian_smooth, smoothing_window, smooth_std)
4259 if len(df_peak_sort>=1):
4261 df_peak_sort_short=df_peak_sort[0:1]
-> 4262 peak_pos_saved[i]=df_peak_sort_short['pos'].values
4263 peak_height_saved[i]=df_peak_sort_short['height'].values
4264 else:

ValueError: setting an array element with a sequence.