Merge branch 'typo_fixes'

.gitlab-ci.yml

@@ -2,7 +2,8 @@
     image: 'continuumio/miniconda3:latest'
 
 .before_script_linux: &before_script_linux
-  - apt-get -qq update && apt-get -qq install -y make
+  - apt-get update --fix-missing
+  - apt-get -qq install -y make
   - conda create -n gris_inv -c conda-forge mpi4py numpy scipy gfortran_linux-64 lapack matplotlib
   - conda init bash
   - source ~/.bashrc

grisinv/invert.py

@@ -193,7 +193,7 @@ def vfisv(
     inv_data : dict of numpy arrays
         The dict contains the following variables
         S0+S1,
-        vel_los, inclination, azimuth, field_strength and the corresponding uncertainities
+        vel_los, inclination, azimuth, field_strength and the corresponding uncertainties
         chi_square.
 
     stokes_data : dict of numpy arrays
@@ -306,22 +306,6 @@ class FitsCardGroup:
         self.cardlist = cardlist
         self.header = None
 
-    def add_card(self, card):
-        """
-
-        Parameters
-        ----------
-        card : str
-            a fits keyword
-
-        Returns
-        -------
-            empty fits card with the keyword
-        """
-
-        fitscard = fits.Card(card, None, "")
-
-        return fitscard
 
     def to_header(self):
         """
@@ -339,7 +323,7 @@ class FitsCardGroup:
 
         for card in self.cardlist:
             if card != "HISTORY":
-                self.header.append(self.add_card(card), end=True)
+                self.header.append(fits.Card(card, None, ""), end=True)
 
         return self.header
 
@@ -434,10 +418,6 @@ def get_stokes_fits(data, vfisv_params):
         array from vfisv containing all the data
     vfisv_params :
         the vfisvpackage class instance that holds all the params
-    index : int
-        the index of the desired variable based on VFISV manual
-    units :
-        the astropy.units that should be assigned to the data
 
     Returns
     -------
@@ -646,11 +626,11 @@ def write_fits(data, header, out, errors=None):
     out : str
         Output filename
     errors : str
-        Output filename for uncertainities
+        Output filename for uncertainties
 
     """
 
-    if errors == None:
+    if errors is None:
         print(termcolors.text + f"\nWriting results to {out}" + termcolors.end, end="")
 
     # header.comments['NAXIS1'] = 'Length of data axis 1'
@@ -675,7 +655,7 @@ def write_fits(data, header, out, errors=None):
         # adding the description
         hdu.header["BTYPE"] = vfisv_naming[iquant]["annotate"]
 
-        # adding the unit of the qauntity
+        # adding the unit of the quantity
         hdu.header["BUNIT"] = str(vfisv_naming[iquant]["unit"])
 
         # append the hdu in the list
@@ -689,10 +669,10 @@ def write_fits(data, header, out, errors=None):
         out, overwrite=True, output_verify="silentfix+exception", checksum=True
     )
 
-    if errors == None:
+    if errors is None:
         print(termcolors.text + ". " + termcolors.okay + "Done.\n" + termcolors.end)
 
-    if errors != None:
+    if errors is not None:
 
         hdu_list = []
         for iquant in vfisv_errors_naming:
@@ -710,7 +690,7 @@ def write_fits(data, header, out, errors=None):
             # adding the description
             hdu.header["BTYPE"] = vfisv_errors_naming[iquant]["annotate"]
 
-            # adding the unit of the qauntity
+            # adding the unit of the quantity
             hdu.header["BUNIT"] = str(vfisv_errors_naming[iquant]["unit"])
 
             # append the hdu in the list
@@ -1144,7 +1124,7 @@ def plot_image(
     ----------
     data : dict of numpy arrays
         The dict contains the following variables
-        Continnum_I, vel_los, inclination, azimuth, field_strength
+        Continuum_I, vel_los, inclination, azimuth, field_strength
     header : object
         Astropy fits header
     preview : str
@@ -1162,7 +1142,7 @@ def plot_image(
     cfmt :  str
         colorbar label format
     cticks : list
-        colobar ticks
+        colorbar ticks
 
     """
 
@@ -1261,7 +1241,7 @@ def correct_field(data, unit_data, unit_vmax, cticks, cfmt):
         # change the maximum if the max is less than the default
         unit_vmax = (
             np.max(unit_data.value)
-            if (unit_vmax != None) and (unit_vmax > np.max(unit_data.value))
+            if (unit_vmax is not None) and (unit_vmax > np.max(unit_data.value))
             else unit_vmax
         )
         # if the field strength is large then round the max and use matplotlib ticks
@@ -1284,7 +1264,7 @@ def correct_field(data, unit_data, unit_vmax, cticks, cfmt):
 def convert_units(data, vmin, vmax):
     """Convert the units of data based on vmin/vmax"""
 
-    if vmax == None:
+    if vmax is None:
         # if vmax is not provided with a unit
         unit_data = data
         unit_vmin = vmin
@@ -1320,7 +1300,7 @@ def merge_to_gif(filelist, outfile):
 def switch_coordinates(lon, lat, canvas):
     """in case the the labels are nor proper, switch the axis"""
 
-    # Check if the left or the bottom labels are drwan.
+    # Check if the left or the bottom labels are drawn.
     # If not, then this is possibly due to slit aligned horizontally.
     if ("l" not in lat.ticklabels.text) or ("b" not in lon.ticklabels.text):
         lon.set_ticks_position("l")
@@ -1423,7 +1403,7 @@ def create_preview(data, header, preview):
 
         # velocity calibration for preview images only
         if iquant == "vlos":
-            # setting a magnetic field mask of 1000 Guass.
+            # setting a magnetic field mask of 1000 Gauss.
             mag_mask = data["bmag"].value < 1000.0
             quant_data -= np.mean(quant_data[mag_mask])
 
@@ -1459,7 +1439,7 @@ def write_log_file(log, header, data, stokes, total_time, numproc):
     header : object
         Astropy header object
     data :  dict of numpy arrays
-        Array containing the inversion results and uncertainities
+        Array containing the inversion results and uncertainties
     stokes : dict of numpy arrays
         Array containing the stokes vector and fits
     total_time : float
@@ -1496,7 +1476,7 @@ def write_log_file(log, header, data, stokes, total_time, numproc):
     f.write(f"Number of processors     : {numproc}\n")
     f.write(f"Total profiles inverted  : {data['vlos'].size}\n\n")
 
-    # Some info about the uncertainities
+    # Some info about the uncertainties
     f.write(f"Mean  chi_sqr  : {data['chsq'].value.mean():5.2f}\n")
     f.write(f"Best  chi_sqr  : {data['chsq'].value.min():5.2f}\n")
     f.write(f"Worst chi_sqr  : {data['chsq'].value.max():5.2f}\n")
@@ -1597,7 +1577,8 @@ class VFISVpackage:
         self.LY = self.header["NAXIS2"]  # Length of the slit
         self.LZ = 16  # VFISV data structure
 
-    def get_line_list(self):
+    @staticmethod
+    def get_line_list():
         """Get the list of available lines"""
         line_list = (
             pkgutil.get_data("grisinv", os.path.join("data_files", "line_names.csv"))
@@ -1762,10 +1743,10 @@ class VFISVpackage:
                 ),
             )
 
-            # Set the pix continnum to pix_ini
+            # Set the pix continuum to pix_ini
             self.pix_cont = self.pix_ini
 
-            # Set the start of the wavelenght array for
+            # Set the start of the wavelength array for
             self.wave_start = wave_array[self.pix_ini]
 
         else:
@@ -1923,7 +1904,7 @@ class VFISVpackage:
 @click.option("-l", "--line", type=float, help="Wavelength of the line Angstrom")
 @click.option("-w", "--width", type=float, help="Wavelength range in Angstrom")
 @click.option("--preview", type=str, help="Filename to save the plot")
-@click.option("--errors", type=str, help="Filename to save the uncertainities")
+@click.option("--errors", type=str, help="Filename to save the uncertainties")
 @click.option("--diagnose", type=str, help="Filename to write the inversion fits")
 @click.option("--log", type=str, help="Filename to write the log file")
 def main(path, id, out, numproc, line, width, preview, errors, diagnose, log):