lime-stable 2.2.dev6__tar.gz → 2.4.1__tar.gz

{lime_stable-2.2.dev6/src/lime_stable.egg-info → lime_stable-2.4.1}/PKG-INFO

@@ -1,39 +1,39 @@
 Metadata-Version: 2.4
 Name: lime-stable
-Version: 2.2.dev6
+Version: 2.4.1
 Summary: Line measuring algorithm for astronomical spectra
 Author-email: Vital Fernández <vgf@stsci.edu>
 License: GPL-3.0-or-later
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE.rst
-Requires-Dist: astropy~=7.1
-Requires-Dist: lmfit~=1.3
+Requires-Dist: astropy~=8.0.0
+Requires-Dist: lmfit~=1.3.4
 Requires-Dist: matplotlib~=3.10
-Requires-Dist: numpy~=2.3
-Requires-Dist: pandas~=2.2
-Requires-Dist: scipy~=1.16
-Requires-Dist: tomli>=2.0.0; python_version < "3.11"
+Requires-Dist: numpy~=2.5
+Requires-Dist: pandas~=3.0.3
+Requires-Dist: scipy~=1.18
 Provides-Extra: full
 Requires-Dist: asdf~=4.1; extra == "full"
-Requires-Dist: aspect-stable~=0.7.dev3; extra == "full"
-Requires-Dist: bokeh~=3.8; extra == "full"
+Requires-Dist: aspect-stable~=0.8; extra == "full"
+Requires-Dist: bokeh~=3.9.1; extra == "full"
 Requires-Dist: mplcursors~=0.6; extra == "full"
 Requires-Dist: openpyxl~=3.1; extra == "full"
 Requires-Dist: PyLaTeX~=1.4; extra == "full"
 Requires-Dist: toml~=0.10; extra == "full"
 Provides-Extra: docs
-Requires-Dist: sphinx-rtd-theme~=3.0; extra == "docs"
-Requires-Dist: sphinx_togglebutton~=0.3; extra == "docs"
-Requires-Dist: sphinx_book_theme~=1.1; extra == "docs"
-Requires-Dist: ipympl~=0.9; extra == "docs"
-Requires-Dist: myst-nb~=1.3; extra == "docs"
+Requires-Dist: sphinx~=9.1.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme~=3.1; extra == "docs"
+Requires-Dist: sphinx_togglebutton~=0.4.5; extra == "docs"
+Requires-Dist: sphinx_book_theme~=1.2; extra == "docs"
+Requires-Dist: ipympl~=0.10; extra == "docs"
+Requires-Dist: myst-nb~=1.4; extra == "docs"
 Provides-Extra: tests
-Requires-Dist: pytest~=8.4; extra == "tests"
-Requires-Dist: pytest-cov~=7.0; extra == "tests"
-Requires-Dist: pytest-mpl~=0.17; extra == "tests"
+Requires-Dist: pytest~=9.1.1; extra == "tests"
+Requires-Dist: pytest-cov~=7.1.0; extra == "tests"
+Requires-Dist: pytest-mpl~=0.19.0; extra == "tests"
 Dynamic: license-file
 
 [![Line Measurer (LiMe) library.](https://github.com/Vital-Fernandez/lime/blob/0afedb150b0169deec6c7f159def99750a3a30da/docs/source/_static/logo_transparent.png?raw=true)]()

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/pyproject.toml

@@ -4,42 +4,42 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lime-stable"
-version = "2.2.dev6"
+version = "2.4.1"
 readme = { file = "README.md", content-type = "text/markdown" }
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 license = {text = "GPL-3.0-or-later"}
 classifiers = ["License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
-               "Programming Language :: Python :: 3.11"]
+               "Programming Language :: Python :: 3.12"]
 
 authors = [{name = "Vital Fernández", email = "vgf@stsci.edu"}]
 description = "Line measuring algorithm for astronomical spectra"
 
-dependencies = ["astropy~=7.1",
-                "lmfit~=1.3",
+dependencies = ["astropy~=8.0.0",
+                "lmfit~=1.3.4",
                 "matplotlib~=3.10",
-                "numpy~=2.3",
-                "pandas~=2.2",
-                "scipy~=1.16",
-                "tomli >= 2.0.0 ; python_version < '3.11'"]
+                "numpy~=2.5",
+                "pandas~=3.0.3",
+                "scipy~=1.18"]
 
 [project.optional-dependencies]
 full = ["asdf~=4.1",
-        "aspect-stable~=0.7.dev3",
-        "bokeh~=3.8",
+        "aspect-stable~=0.8",
+        "bokeh~=3.9.1",
         "mplcursors~=0.6",
         "openpyxl~=3.1",
         "PyLaTeX~=1.4",
         "toml~=0.10",]
 
-docs = ["sphinx-rtd-theme~=3.0",
-        "sphinx_togglebutton~=0.3",
-        "sphinx_book_theme~=1.1",
-        "ipympl~=0.9",
-        "myst-nb~=1.3"]
+docs = ["sphinx~=9.1.0",
+        "sphinx-rtd-theme~=3.1",
+        "sphinx_togglebutton~=0.4.5",
+        "sphinx_book_theme~=1.2",
+        "ipympl~=0.10",
+        "myst-nb~=1.4"]
 
-tests = ["pytest~=8.4",
-         "pytest-cov~=7.0",
-         "pytest-mpl~=0.17"]
+tests = ["pytest~=9.1.1",
+         "pytest-cov~=7.1.0",
+         "pytest-mpl~=0.19.0"]
 
 [tool.pytest.ini_options]
 pythonpath = ["src"]
@@ -48,3 +48,7 @@ mpl-results-path = 'tests/outputs'
 mpl-results-always = false
 markers = ["mpl: matplotlib image comparison tests"]
 addopts = "-p no:asdf_schema_tester"
+
+[tool.coverage.run]
+omit = ["src/lime/resources/generator_db.py",
+        "src/lime/resources/generator_logo.py"]

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/archives/read_fits.py

@@ -610,11 +610,89 @@ class OpenFits:
         pixel_mask = np.isnan(flux_array) | np.isnan(err_array)
 
         # Spectrum properties
-        params_dict = SPECTRUM_FITS_PARAMS['nirspec']
-        params_dict['pixel_mask'] = pixel_mask
+        params_dict = {**SPECTRUM_FITS_PARAMS['nirspec'], 'pixel_mask': pixel_mask}
 
         return wave_array, flux_array, err_array, header_list, params_dict
 
+
+    @staticmethod
+    def lzlcs_miri_merged(fits_address, data_ext_list=(1), hdr_ext_list=(1), **kwargs):
+
+        """
+
+        This method returns the spectrum array data and headers from a MUSE observation.
+
+        The function returns numpy arrays with the wavelength, flux and uncertainty flux (if available this is the
+        standard deviation available), a list with the requested headers and a dictionary with the parameters to
+        construct a LiMe Cube. These parameters include the observation wavelength/flux units, normalization and wcs
+        from the input fits file.
+
+        :param fits_address: File location address for the observation .fits file.
+        :type fits_address: str, Path
+
+        :param data_ext_list: Data extension number or name to extract from the .fits file.
+        :type fits_address: int, str or list of either, optional
+
+        :param hdr_ext_list: header extension number or name to extract from the .fits file.
+        :type hdr_ext_list: int, str or list of either, optional
+
+        :return: wavelength array, flux array, uncertainty array, header list, observation parameter dict
+
+        """
+
+        # Get data table and header dict lists
+        data_list, header_list = load_fits(fits_address, data_ext_list, hdr_ext_list, url_check=False)
+
+        # Re-construct spectrum arrays
+        wave_array = data_list[0]['WAVE']
+        flux_array = data_list[0]['FLUX']
+        err_array = data_list[0]['FLUX_ERROR']
+
+        # Fits properties
+        fits_params = {**SPECTRUM_FITS_PARAMS['lzlcs_miri_merged'], 'pixel_mask': None}
+
+        return wave_array, flux_array, err_array, header_list, fits_params
+
+    @staticmethod
+    def lzlcs_miri_x1d(fits_address, data_ext_list=(1), hdr_ext_list=(1), **kwargs):
+
+        """
+
+        This method returns the spectrum array data and headers from a MUSE observation.
+
+        The function returns numpy arrays with the wavelength, flux and uncertainty flux (if available this is the
+        standard deviation available), a list with the requested headers and a dictionary with the parameters to
+        construct a LiMe Cube. These parameters include the observation wavelength/flux units, normalization and wcs
+        from the input fits file.
+
+        :param fits_address: File location address for the observation .fits file.
+        :type fits_address: str, Path
+
+        :param data_ext_list: Data extension number or name to extract from the .fits file.
+        :type fits_address: int, str or list of either, optional
+
+        :param hdr_ext_list: header extension number or name to extract from the .fits file.
+        :type hdr_ext_list: int, str or list of either, optional
+
+        :return: wavelength array, flux array, uncertainty array, header list, observation parameter dict
+
+        """
+
+        # Get data table and header dict lists
+        data_list, header_list = load_fits(fits_address, data_ext_list, hdr_ext_list, url_check=False)
+
+        # Re-construct spectrum arrays
+        wave_array = data_list[0]['WAVELENGTH']
+        flux_array = data_list[0]['FLUX']
+        err_array = data_list[0]['FLUX_ERROR']
+
+        # Fits properties
+        fits_params = {**SPECTRUM_FITS_PARAMS['lzlcs_miri_x1d'], 'pixel_mask': None}
+
+        return wave_array, flux_array, err_array, header_list, fits_params
+
+
+
     @staticmethod
     def nirspec_grizli(fits_address, data_ext_list=1, hdr_ext_list=(0, 1), **kwargs):
 
@@ -649,8 +727,7 @@ class OpenFits:
         pixel_mask = np.isnan(flux_array) | np.isnan(err_array)
 
         # Spectrum properties
-        params_dict = SPECTRUM_FITS_PARAMS['nirspec_grizli']
-        params_dict['pixel_mask'] = pixel_mask
+        params_dict = {**SPECTRUM_FITS_PARAMS['nirspec_grizli'], 'pixel_mask': pixel_mask}
 
         return wave_array, flux_array, err_array, header_list, params_dict
 
@@ -695,7 +772,7 @@ class OpenFits:
             flux_array, err_array = data_list[0], None
 
         # Spectrum properties
-        params_dict = SPECTRUM_FITS_PARAMS['isis']
+        params_dict = {**SPECTRUM_FITS_PARAMS['isis']}
 
         return wave_array, flux_array, err_array, header_list, params_dict
 
@@ -776,7 +853,7 @@ class OpenFits:
             flux_array, err_array = data_list[0], None
 
         # Spectrum properties
-        params_dict = SPECTRUM_FITS_PARAMS['osiris']
+        params_dict = {**SPECTRUM_FITS_PARAMS['osiris']}
 
         return wave_array, flux_array, err_array, header_list, params_dict
 
@@ -843,7 +920,7 @@ class OpenFits:
             #     # print(key_arr, np.any(np.isnan(cont_arr)))
 
         # Spectrum properties
-        params_dict = SPECTRUM_FITS_PARAMS['cos']
+        params_dict = {**SPECTRUM_FITS_PARAMS['cos']}
 
         return wave_arr, flux_arr, err_arr, header_list, params_dict
 
@@ -894,8 +971,7 @@ class OpenFits:
         err_array = np.sqrt(1 / ivar_array)
 
         # Spectrum properties
-        params_dict = SPECTRUM_FITS_PARAMS['sdss']
-        params_dict['redshift'] = redshift
+        params_dict = {**SPECTRUM_FITS_PARAMS['sdss'], 'redshift': redshift}
 
         return wave_array, flux_array, err_array, header_list, params_dict
 
@@ -1124,6 +1200,7 @@ class OpenFits:
 
         return wave_array, flux_cube, err_cube, header_list, fits_params
 
+
     @staticmethod
     def desi(target_id, root_url='https://data.desi.lbl.gov/public/edr/spectro/redux', **kwargs):
 

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/archives/tables.py

@@ -25,7 +25,7 @@ def format_for_table(entry, rounddig=4, rounddig_er=2, scientific_notation=False
         rounddig_er = rounddig
 
     # Check None entry
-    if entry != None:
+    if entry is not None:
 
         # Check string entry
         if isinstance(entry, (str, bytes)):

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/changelog.txt

@@ -122,4 +122,34 @@ LiMe minor update - 2.0.4 - 12/05/2025
     - Further development for the functions involving redshift a line fitting using aspect
     - The spatial masking functions should not require the 'PARAM', 'PARAMIDX', 'PARAMVAL' and 'NUMSPAXE' in the .fits headers to plot the mask overlays
 
+LiMe medium update - 2.4.0 - 26/06/2026
+    - Added new ultraviolet and infrared lines to the database `lines_database_v2.0.6.txt`
+    - Major updates to `observations.py`: expanded spectrum observation handling
+    - Major updates to `workflow.py`: significant refactoring of the fitting workflow
+    - The Transition and Line classes are been update to have an `origin`, `redshift` and `atomic_data` as attributes. This will be documented in a future major update
+    - Changes to the matplotlib and bokeh plot functions to use common theme structure
+    - The `Spectrum.retrieve.lines_frame` has been update to include an origin as an input. This will be documented in a future major update
+    - The `Spectrum.retrieve.lines_frame` documentation added to the API.
+    - Added SDSS complete spectrum example script (`3_complete_spectrum_SDSS.py`)
+    - Added line groups prediction example script (`3_line_groups_prediction.py`)
+    - Updated `fitting/redshift.py` function to correct a bug issue with non-line measurements
+    - Updated `archives/read_fits.py`: FITS reading improvements
+    - Updated `pyproject.toml` updated dependencies to include ASPECT features
+    - The computation of the line continua now takes into account the covariance of the fitting. The nominal values remain constant but the uncertainty predicted is smaller
+    - Expanded the tests for the latex/pdf table making functions from the `test_tables.py` script
+    - Expanded the tests to compare the line measurements with synthetic lines for more profile parameters (including the line continuum levels)
+    - Improvement of the descriptions in the measurements documentation page and correction of wrong terms
+    - Updated plot baselines across multiple tests
+    - Added paper citation on the documentation
+    - Added more integration with aspect functions (next medium release will focus on documenting these updgrades)
+    - Adding releases on the github page to mark medium / major updates
+    - Bump minimum python to 3.12 version for uniform requirements with readthedocs compilation
+
+LiMe small update - 2.4.1 - 08/07/2026
+    - Now all instrument fits loading functions copy the configuration dictionary to avoid possible corruptions.
+    - Added lines to lines database.
+    - The lines database version now follows the current lime version.
+    - Renamed internal function "continuum_calculation" to "_cont_level_profile" in order to avoid confusion with external "Spectrum.fit.continuum"
+    - Bump the dependencies to the current versions. At the current state, LiMe should be compatible with Pandas 3.0.0 but more changes will be necessary to take full advantage of the library upgrades"
+
 

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/fitting/lines.py

@@ -1,5 +1,6 @@
 import logging
 
+import matplotlib.pyplot as plt
 import numpy as np
 from lmfit.models import Model
 from lmfit import fit_report
@@ -91,6 +92,7 @@ def const_cont_model(cont_array, prefix='cont_', allow_scale=False):
         # freeze at 1.0 -> truly constant
     return m, params
 
+
 def linear_model(x, m_cont, n_cont):
     """Linear line formulation"""
     return m_cont * x + n_cont
@@ -252,9 +254,9 @@ def power_area(line, idx, n_steps):
 def exp_area(line, idx, n_steps):
 
     amp = np.random.normal(line.amp[idx], line.amp_err[idx], n_steps)
-    alpha = np.random.normal(line.alpha[idx], line.alpha[idx], n_steps)
+    alpha = np.random.normal(line.alpha[idx], line.alpha_err[idx], n_steps)
 
-    return 2.5066282746 * amp * 1/alpha
+    return 2 * amp / alpha
 
 
 def pseudo_power_area(line, idx, n_steps):
@@ -938,9 +940,18 @@ class LineFitting:
         line.measurements.peak_wave = emis_wave[peakIdx]
         line.measurements.peak_flux = emis_flux[peakIdx]
         line.measurements.pixelWidth = np.diff(emis_wave).mean()
-        # line.measurements.cont = line.measurements.peak_wave * line.measurements.m_cont + line.measurements.n_cont
+
+        # Continuum level and uncertainty at peak
         line.measurements.cont = cont_arr[peakIdx]
-        line.measurements.cont_err = emis_err[peakIdx]
+
+        if self.cov_linear is None:
+            line.measurements.cont_err = np.sqrt(((emis_wave[-1] - emis_wave[peakIdx]) / (emis_wave[-1]-emis_wave[0]) * emis_err[0]) ** 2
+                                                 + ((emis_wave[peakIdx] - emis_wave[0]) / (emis_wave[-1]-emis_wave[0])  * emis_err[-1]) ** 2)
+        else:
+            line.measurements.cont_err = np.sqrt(self.cov_linear[0, 0] * emis_wave[peakIdx] ** 2 + self.cov_linear[1, 1]
+                                                 + 2 * self.cov_linear[0, 1] * emis_wave[peakIdx])
+
+        # y_val_err = np.sqrt(((emis_wave[-1] - emis_wave[peakIdx]) / (emis_wave[-1]-emis_wave[0]) * emis_err[0]) ** 2 + ((emis_wave[peakIdx] - emis_wave[0]) / (emis_wave[-1]-emis_wave[0])  * emis_err[-1]) ** 2)
 
         # Warning if continuum above or below line peak/through
         if emission_check and (cont_arr[peakIdx] > emis_flux[peakIdx]):
@@ -997,67 +1008,73 @@ class LineFitting:
 
         return
 
-    def continuum_calculation(self, idcs_emis, idcs_cont, user_cont_source, err_from_bands):
+    def _cont_level_profile(self, idcs_emis, idcs_cont, user_cont_source, err_from_bands):
 
         # Use the continuum bands for the calculation
         match user_cont_source:
 
             case 'adjacent':
-
-                # Check for zero err
                 err_cont = self._spec.err_flux[idcs_cont].compressed() if self._spec.err_flux is not None else None
-                err_cont = err_cont if np.any(err_cont) else None
+                # err_cont = err_cont if np.any(err_cont) else None
 
                 # Fit the model, including uncertainties
-                params, covariance = curve_fit(linear_model,
-                                               xdata=self._spec.wave[idcs_cont].compressed(),
-                                               ydata=self._spec.flux[idcs_cont].compressed(),
-                                               sigma=err_cont,
-                                               absolute_sigma=True, check_finite=False)
-
-                self.line.measurements.m_cont, self.line.measurements.n_cont = params
-                self.line.measurements.m_cont_err_intg, self.line.measurements.n_cont_err_intg = np.sqrt(np.diag(covariance))
+                params, self.cov_linear = curve_fit(linear_model, xdata=self._spec.wave[idcs_cont].compressed(),
+                                                    ydata=self._spec.flux[idcs_cont].compressed(), sigma=err_cont,
+                                                    absolute_sigma=True, check_finite=False)
+
+                self.line.measurements.m_cont = params[0]
+                self.line.measurements.n_cont = params[1]
+                self.line.measurements.m_cont_err_intg, self.line.measurements.n_cont_err_intg = np.sqrt(np.diag(self.cov_linear))
+
                 cont_arr = self._spec.wave * self.line.measurements.m_cont + self.line.measurements.n_cont
 
             case 'central':
-
                 x, y = self._spec.wave[idcs_emis].compressed(), self._spec.flux[idcs_emis].compressed()
                 err = self._spec.err_flux[idcs_emis].compressed() if self._spec.err_flux is not None else [0, 0]
 
-                self.line.measurements.m_cont = (y[-1] - y[0]) / (x[-1] - x[0])
+                dx = x[-1] - x[0]
+                self.line.measurements.m_cont = (y[-1] - y[0]) / dx
                 self.line.measurements.n_cont =  y[0] - self.line.measurements.m_cont * x[0]
 
-                self.line.measurements.m_cont_err_intg = np.sqrt((err[0] * (-1 / (x[-1] - x[0]))) ** 2 + (err[-1] * (1/(x[-1] - x[0]))) ** 2)
-                self.line.measurements.n_cont_err_intg = np.sqrt(err[0] ** 2 + (self.line.measurements.m_cont_err_intg * (-x[0])) ** 2)
+                self.line.measurements.m_cont_err_intg = np.sqrt((err[0] / dx) ** 2 + (err[-1] / dx) ** 2)
+                self.line.measurements.n_cont_err_intg = np.sqrt((err[0] * x[-1] / dx) ** 2 + (err[-1] * x[0] / dx) ** 2)
+
                 cont_arr = self._spec.wave * self.line.measurements.m_cont + self.line.measurements.n_cont
 
-            case 'fit':
 
+            case 'fit':
                 x, y = self._spec.wave[idcs_cont].compressed(), self._spec.cont[idcs_cont].compressed()
                 err = self._spec.err_flux[idcs_cont].compressed() if self._spec.err_flux is not None else [0, 0]
 
-                self.line.measurements.m_cont = (y[-1] - y[0]) / (x[-1] - x[0])
+                dx = x[-1] - x[0]
+                self.line.measurements.m_cont = (y[-1] - y[0]) / dx
                 self.line.measurements.n_cont =  y[0] - self.line.measurements.m_cont * x[0]
 
-                self.line.measurements.m_cont_err_intg = np.sqrt((err[0] * (-1 / (x[-1] - x[0]))) ** 2 + (err[-1] * (1/(x[-1] - x[0]))) ** 2)
-                self.line.measurements.n_cont_err_intg = np.sqrt(err[0] ** 2 + (self.line.measurements.m_cont_err_intg * (-x[0])) ** 2)
+                self.line.measurements.m_cont_err_intg = np.sqrt((err[0] / dx) ** 2 + (err[-1] / dx) ** 2)
+                self.line.measurements.n_cont_err_intg = np.sqrt((err[0] * x[-1] / dx) ** 2 + (err[-1] * x[0] / dx) ** 2)
+
+                # TODO here with the uncertainty from the spectrum fitted
                 cont_arr = self._spec.cont
 
             case _:
                 raise LiMe_Error(f'Continuum source "{user_cont_source}" is not recognized. '
                                  f'Please use "central", "adjacent" and "fit".')
 
-        # # Initial continuum level value
-        # self.line.measurements.cont = (self.line.measurements.m_cont * self._spec.wave[idcs_emis].compressed().mean() +
-        #                                self.line.measurements.n_cont)
+        # Bands constant pixel error
+        if err_from_bands:
+            err_arr = self._spec.wave * 0 + np.std(self._spec.flux[idcs_cont] - (self.line.measurements.m_cont * self._spec.wave[idcs_cont] + self.line.measurements.n_cont), ddof=2)
+
+        # Spectrum error
+        else:
+            err_arr = self._spec.err_flux
 
-        return cont_arr
+        return cont_arr, err_arr
 
     def pixel_error_calculation(self, idcs_continua, user_error_from_bands):
-
+        # TODO delete this one
         # Constant pixel error array from adjacent bands
         if user_error_from_bands:
-            return np.ma.array(np.full(self._spec.wave.shape, np.std(self._spec.flux[idcs_continua] - (self.line.measurements.m_cont * self._spec.wave[idcs_continua] + self.line.measurements.n_cont))), mask=np.zeros(self._spec.wave.shape, dtype=bool))
+            return np.ma.array(np.full(self._spec.wave.shape, np.std(self._spec.flux[idcs_continua] - (self.line.measurements.m_cont * self._spec.wave[idcs_continua] + self.line.measurements.n_cont), ddof=2)), mask=self._spec.wave.mask)
 
         # Pixel array
         else:

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/fitting/redshift.py

@@ -134,7 +134,6 @@ def redshift_key_method(spec, bands, z_min, z_max, delta_z, pred_arr, components
 
         # If there is only one line return nan
         if not (method_flux and not detection_only):
-            # match np.count_nonzero(np.diff(np.r_[False, idcs_lines])):
             match comp_counter(idcs_lines):
                 case 0:
                     return None # No components

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/io.py

@@ -205,7 +205,7 @@ def load_cfg(file_address, fit_cfg_suffix='_line_fitting'):
     return cfg_lime
 
 
-def save_cfg(output_file, param_dict, section_name=None, clear_section=False):
+def save_cfg(output_file, param_dict, section_name=None, clear_section=False, overwrite_file=False):
 
     """
     This function safes the input dictionary into a configuration file. If no section is provided the input dictionary
@@ -224,7 +224,7 @@ def save_cfg(output_file, param_dict, section_name=None, clear_section=False):
             output_data = param_dict if section_name is None else {section_name: param_dict}
 
             # If the file does not exist create a new file
-            if not output_path.is_file():
+            if not output_path.is_file() or overwrite_file:
                 with open(output_file, "w") as f:
                     toml.dump(output_data, f)
 

{lime_stable-2.2.dev6 → lime_stable-2.4.1}/src/lime/lime.toml

@@ -1,6 +1,7 @@
 [metadata]
 name = 'lime-stable'
-version = "2.2.dev6"
+version = "2.4.1"
+lines_database = 'lines_database_v2.4.1.txt'
 
 # =====================
 # Spectrum / Long-slit
@@ -42,6 +43,20 @@ cos.units_flux = "FLAM"
 cos.pixel_mask = "nan"
 cos.id_label = 'null'
 
+lzlcs_miri_merged.norm_flux = 'null'
+lzlcs_miri_merged.res_power = 'null'
+lzlcs_miri_merged.units_wave = "um"
+lzlcs_miri_merged.units_flux = "Jy"
+lzlcs_miri_merged.pixel_mask = "nan"
+lzlcs_miri_merged.id_label = 'null'
+
+lzlcs_miri_x1d.norm_flux = 'null'
+lzlcs_miri_x1d.res_power = 'null'
+lzlcs_miri_x1d.units_wave = "um"
+lzlcs_miri_x1d.units_flux = "Jy"
+lzlcs_miri_x1d.pixel_mask = "nan"
+lzlcs_miri_x1d.id_label = 'null'
+
 sdss.norm_flux = 'null'
 sdss.res_power = 'null'
 sdss.units_wave = "Angstrom"