Merge pull request #423 from fchapoton/some_typos

fix a bunch of typos (found by codespell)

docs/source/tutorials/1_Introduction-to-the-API.ipynb

@@ -150,7 +150,7 @@
     "- A 2D array containing the values of the requested field.\n",
     "- An object containing metainformation about the extent of the grid (e.g `info_rho.z` and `info_rho.x` respectively return an array of the z and x positions).\n",
     "\n",
-    "These two objects can then be used in a Python environnement to perform numerical analysis."
+    "These two objects can then be used in a Python environment to perform numerical analysis."
    ]
   },
   {
@@ -208,7 +208,7 @@
    "source": [
     "### Additional documentation\n",
     "\n",
-    "Additional documentation on `get_field` can be obtained by reading its docstring. This can be done for instance by executing the following command in an IPython environnement."
+    "Additional documentation on `get_field` can be obtained by reading its docstring. This can be done for instance by executing the following command in an IPython environment."
    ]
   },
   {
@@ -351,7 +351,7 @@
    "source": [
     "### Missing or inconsistent arguments\n",
     "\n",
-    "As for the fieds, if an argument is missing or inconsistent, an exception will be raised and an helper message will be printed."
+    "As for the fields, if an argument is missing or inconsistent, an exception will be raised and an helper message will be printed."
    ]
   },
   {
@@ -361,7 +361,7 @@
    "source": [
     "### Additional documentation\n",
     "\n",
-    "As for the `get_field` method, the documentation on `get_particle` can be obtained by reading its docstring. This can be done for instance by executing the following command in an IPython environnement."
+    "As for the `get_field` method, the documentation on `get_particle` can be obtained by reading its docstring. This can be done for instance by executing the following command in an IPython environment."
    ]
   },
   {

docs/source/tutorials/5_Laser-plasma_tools.ipynb

@@ -355,7 +355,7 @@
    "metadata": {},
    "source": [
     "#### Laser $a_0$\n",
-    "A method to calculate the laser strenght a0 as given by $$a0 = E_{max} e / (m_e c \\omega)$$"
+    "A method to calculate the laser strength a0 as given by $$a0 = E_{max} e / (m_e c \\omega)$$"
    ]
   },
   {

openpmd_viewer/addons/pic/lpa_diagnostics.py

@@ -227,7 +227,7 @@ def get_sigma_gamma_slice(self, dz, t=None, iteration=None, species=None,
         plot : bool, optional
            Whether to plot the requested quantity
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's `plot` method
 
         Returns
@@ -270,7 +270,7 @@ def get_sigma_gamma_slice(self, dz, t=None, iteration=None, species=None,
 
     def get_charge( self, t=None, iteration=None, species=None, select=None ):
         """
-        Calculate the charge of the selcted particles.
+        Calculate the charge of the selected particles.
 
         Parameters
         ----------
@@ -411,7 +411,7 @@ def get_emittance(self, t=None, iteration=None, species=None,
             raise ValueError('Argument `kind` not recognized.')
         if description not in ['projected', 'slice-averaged', 'all-slices']:
             raise ValueError('Argument `description` not recognized.')
-        # Wheter to compute slice emittance
+        # Whether to compute slice emittance
         do_slice_emittance = ( description in ['slice-averaged',
                                                'all-slices'] )
         if do_slice_emittance and not nslices > 0:
@@ -496,11 +496,11 @@ def get_current( self, t=None, iteration=None, species=None, select=None,
         plot : bool, optional
            Whether to plot the requested quantity
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's `plot` method
         Returns
         -------
-        A tuple of arrays containig
+        A tuple of arrays containing
         - The current in each bin in Ampere
         - A FieldMetaInformation object
           (see object's docstring for more details)
@@ -511,7 +511,7 @@ def get_current( self, t=None, iteration=None, species=None, select=None,
             var_list=['z', 'uz', 'uy', 'ux', 'w', 'charge'],
             t=t, iteration=iteration,
             species=species, select=select )
-        # Length to be seperated in bins
+        # Length to be separated in bins
 
         if w.size > 0:
             min_z = np.min(z)
@@ -520,7 +520,7 @@ def get_current( self, t=None, iteration=None, species=None, select=None,
             gamma = np.sqrt(1 + ux ** 2 + uy ** 2 + uz ** 2)
             # Calculate particle velocities
             vz = uz / gamma * const.c
-            # Length to be seperated in bins
+            # Length to be separated in bins
             len_z = np.max(z) - np.min(z)
             vzq_sum, _ = np.histogram(z, bins=bins, weights=(vz * w * q))
             # Calculate the current in each bin
@@ -611,7 +611,7 @@ def get_laser_envelope( self, t=None, iteration=None, pol=None,
            along the 1st axis (first list) and 2nd axis (second list)
            Default: plots the full extent of the simulation box
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's `plot`(1D) or
            `imshow` (2D) method
 
@@ -757,7 +757,7 @@ def get_spectrum( self, t=None, iteration=None, pol=None,
         plot: bool, optional
            Whether to plot the data
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's `plot` method
 
         Returns
@@ -1016,7 +1016,7 @@ def get_spectrogram( self, t=None, iteration=None, pol=None,
         plot: bool, optional
             Whether to plot the spectrogram
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's `imshow` method
 
         Returns

openpmd_viewer/openpmd_timeseries/data_reader/data_reader.py

@@ -59,7 +59,7 @@ def __init__(self, backend):
     def list_iterations(self, path_to_dir):
         """
         Return a list of the iterations that correspond to the files
-        in this directory. (The correspondance between iterations and
+        in this directory. (The correspondence between iterations and
         files is stored internally.)
 
         Parameter
@@ -107,7 +107,8 @@ def list_iterations(self, path_to_dir):
                 file_path = path_to_dir
                 series_name = file_path
             else:
-                # match last occurance of integers and replace with %T wildcards
+                # match last occurrence of integers and replace
+                # with %T wildcards
                 # examples: data00000100.h5 diag4_00000500.h5 io12.0.bp
                 #           te42st.1234.yolo.json scan7_run14_data123.h5
                 file_path = re.sub(r'(\d+)(\.(?!\d).+$)', r'%T\2', first_file_name)

openpmd_viewer/openpmd_timeseries/main.py

@@ -200,7 +200,7 @@ def get_particle(self, var_list=None, species=None, t=None, iteration=None,
             particles affects neighboring bins.
             `cic` (which is the default) leads to smoother results than `ngp`.
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's
            hist or hist2d.
 
@@ -425,7 +425,7 @@ def get_field(self, field=None, coord=None, t=None, iteration=None,
            along the 1st axis (first list) and 2nd axis (second list)
            Default: plots the full extent of the simulation box
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's imshow.
 
         Returns
@@ -555,7 +555,7 @@ def iterate( self, called_method, *args, **kwargs ):
             Arguments that would normally be passed to `called_method` for
             a single iteration. Do not pass the argument `t` or `iteration`.
         """
-        # Add the iteration key in the keyword aguments
+        # Add the iteration key in the keyword arguments
         kwargs['iteration'] = self.iterations[0]
 
         # Check the shape of results

openpmd_viewer/openpmd_timeseries/particle_tracker.py

@@ -87,7 +87,8 @@ def __init__(self, ts, species=None, t=None,
             In this case, a NaN is returned at the index of this particle.
             When `preserve_particle_index=False`, no NaN is returned (the
             returned array is simply smaller when particles are absent) but
-            then it is not garanteed that a given particle keeps the same index
+            then it is not guaranteed that a given particle keeps the same
+            index
         """
 
         # Extract or load the particle id and sort them
@@ -220,7 +221,7 @@ def get_extraction_indices( self, pid ):
         sorted_pid = pid[ original_indices ]
 
         # Extract only the indices for which sorted_pid is one of pid
-        # in self.sselected_pid (i.e. which correpond to one
+        # in self.sselected_pid (i.e. which correspond to one
         # of the original particles)
         selected_indices = np.empty( self.N_selected, dtype=np.int64 )
         N_extracted = extract_indices(

openpmd_viewer/openpmd_timeseries/plotter.py

@@ -145,7 +145,7 @@ def hist1d(self, q1, w, quantity1, species, current_i, nbins, hist_range,
             particles affects neighboring bins.
             `cic` (which is the default) leads to smoother results than `ngp`.
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's bar function
         """
         # Check if matplotlib is available
@@ -222,7 +222,7 @@ def hist2d(self, q1, q2, w, quantity1, quantity2, species, current_i,
             particles affects neighboring bins.
             `cic` (which is the default) leads to smoother results than `ngp`.
 
-        **kw : dict, otional
+        **kw : dict, optional
            Additional options to be passed to matplotlib's imshow function
         """
         # Check if matplotlib is available
@@ -411,7 +411,7 @@ def print_cic_unavailable():
 
 def check_matplotlib():
     """Raise error messages or warnings when potential issues when
-    potenial issues with matplotlib are detected."""
+    potential issues with matplotlib are detected."""
 
     if not matplotlib_installed:
         raise RuntimeError( "Failed to import the openPMD-viewer plotter.\n"

openpmd_viewer/openpmd_timeseries/utilities.py

@@ -336,7 +336,7 @@ def construct_3d_from_circ( F3d, Fcirc, x_array, y_array, modes,
                 else:
                     raise Exception(order_error_msg)
 
-            # Loop over all modes and recontruct data
+            # Loop over all modes and reconstruct data
             if r == 0:
                 expItheta = 1. + 0.j
             else: