minor help syntax edits, instruction fixes

bin/MarsCalendar.py

@@ -46,8 +46,9 @@
     formatter_class=argparse.RawTextHelpFormatter
 )
 
-group = parser.add_argument_group("Required Arguments",
-    "\n{Yellow}MarsCalendar requires either -ls or -sol.{Nclr}\n")
+group = parser.add_argument_group(
+    "Required Arguments:",
+    f"{Yellow}MarsCalendar requires either -ls or -sol.{Nclr}\n")
 exclusive_group = parser.add_mutually_exclusive_group(required=True)
 
 exclusive_group.add_argument('-sol', '--sol', nargs='+', type=float,

bin/MarsFiles.py

@@ -166,16 +166,18 @@ def parse_args(self, *args, **kwargs):
         f"> ls\n"
         f"00334.atmos_average.nc 00668.atmos_average.nc\n"
         f"> MarsFiles *.atmos_average.nc -c\n"
+        f"{Blue}Overwrites 00334.atmos_average.nc with concatenated "
+        f"files:\n"
         f"> ls\n"
         f"   00334.atmos_average.nc\n"
-        f"{Yellow}Overwrites 00334.atmos_average.nc with concatenated "
-        f"files. To override, use [-ext --extension]:{Green}\n"
+        f"{Blue}To preserve original files, use [-ext --extension]:"
+        f"{Green}\n"
         f"> MarsFiles *.atmos_average.nc -c -ext _concatenated\n"
+        f"{Blue}Produces 00334.atmos_average_concatenated.nc and "
+        f"preserves all other files:{Green}\n"
         f"> ls\n"
         f"   00334.atmos_average.nc 00668.atmos_average.nc "
         f"00334.atmos_average_concatenated.nc\n"
-        f"{Blue}(Produces 00334.atmos_average_concatenated.nc and "
-        f" preserves all other files)"
         f"{Nclr}\n\n"
     )
 )
@@ -358,8 +360,8 @@ def parse_args(self, *args, **kwargs):
         f"N = 1 diurnal tide, N = 2 semi-diurnal, etc.\n"
         f"{Yellow}Generates a new file ending in ``_tide_decomp.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 01336.atmos_diurn.nc -tide 2 -incl ps temp "
-        f"{Blue}(extracts semi-diurnal tide component of ps and temp "
+        f"> MarsFiles 01336.atmos_diurn.nc -tide 2 -incl ps temp\n"
+        f"{Blue}(extracts semi-diurnal tide component of ps and\ntemp "
         f"variables; 2 harmonics)"
         f"{Nclr}\n\n"
     )
@@ -376,10 +378,10 @@ def parse_args(self, *args, **kwargs):
         f"to the same standard grid [zstd, zagl, pstd, etc.].\n"
         f"{Yellow}Generates a new file ending in ``_regrid.nc``\n"
         f"{Green}Example:\n"
-        f"> MarsInterp 01336.atmos_average_pstd.nc -regrid "
-        f"01336.atmos_average_pstd_c48.nc"
-        f"{Yellow}NOTE: name of regridded file does not matter."
-        f"{Green}> MarsInterp sim1/01336.atmos_average_pstd.nc -regrid "
+        f"> MarsFiles 01336.atmos_average_pstd.nc -regrid "
+        f"01336.atmos_average_pstd_c48.nc\n"
+        f"{Yellow}NOTE: regridded file name does not matter:\n"
+        f"{Green}> MarsFiles sim1/01336.atmos_average_pstd.nc -regrid "
         f"sim2/01336.atmos_average_pstd.nc"
         f"{Nclr}\n\n"
     )
@@ -408,7 +410,7 @@ def parse_args(self, *args, **kwargs):
         f"dimension on which to trim the file.\nAcceptable values are "
         f"'areo', 'lev', 'lat', 'lon'. Default = 'areo'.\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 01336.atmos_average.nc --split 0 90 -dim areo"
+        f"> MarsFiles 01336.atmos_average.nc --split 0 90 -dim areo\n"
         f"> MarsFiles 01336.atmos_average.nc --split -70 -dim lat"
         f"{Nclr}\n\n"
     )
@@ -482,8 +484,8 @@ def parse_args(self, *args, **kwargs):
         f"CAP to create a new file with the extension name specified "
         f"here.\n"
         f"{Green}Example:\n"
-        f"> MarsFiles 00334.atmos_average.nc -c -ext _comb"
-        f"  {Blue}(produces 00334.atmos_average_comb.nc and "
+        f"> MarsFiles 00334.atmos_average.nc -c -ext _comb\n"
+        f"{Blue}(Produces 00334.atmos_average_comb.nc and "
         f"preserves all other files)"
         f"{Nclr}\n\n"
     )
@@ -710,7 +712,7 @@ def split_files(file_list, split_dim):
             # size areo = (time, tod, scalar_axis)
             reducing_dim = np.squeeze(fNcdf.variables['areo'][:, 0, :])
         else:
-            reducing_dim = np.squeeze(fNcdf.variables[split_dim][:])
+            reducing_dim = np.squeeze(fNcdf.variables[split_dim][:, 0])
     else:
         if split_dim == 'areo':
             # size areo = (time, scalar_axis)
@@ -719,22 +721,19 @@ def split_files(file_list, split_dim):
             reducing_dim = np.squeeze(fNcdf.variables[split_dim][:])
 
     print(f"\n{Yellow}All values in dimension:\n{reducing_dim}\n")
-
-    bounds_in=bounds.copy()
-    if split_dim == 'areo':
-        while (bounds[0] < reducing_dim[0]):
-            bounds += 360.
-        if len(np.atleast_1d(bounds)) == 2:
-            while (bounds[1] < bounds[0]):
-                bounds[1] += 360.
-
     if len(np.atleast_1d(bounds)) < 2:
         a=check_bounds(bounds[0],reducing_dim[0],reducing_dim[-1])
         indices = [(np.abs(reducing_dim - bounds[0])).argmin()]
         dim_out = reducing_dim[indices]
         print(f"Requested value = {bounds[0]}\n"
               f"Nearest value = {dim_out[0]}\n")
     else:
+        bounds_in=bounds.copy()
+        if split_dim == 'areo':
+            while (bounds[0] < reducing_dim[0]):
+                bounds += 360.
+            while (bounds[1] < bounds[0]):
+                bounds[1] += 360.
         a=check_bounds(bounds,reducing_dim[0],reducing_dim[-1])
         if ((split_dim == 'lon') & (bounds[1] < bounds[0])):
             indices = np.where((reducing_dim <= bounds[1]) | (reducing_dim >= bounds[0]))[0]

bin/MarsFormat.py

@@ -74,8 +74,8 @@
         f"Acceptable types include 'openmars', 'marswrf', 'emars', "
         f"and 'pcm' \n"
         f"{Green}Example:\n"
-        f"> MarsFormat openmars_file.nc -gcm openmars"
-        f"{Blue}Creates openmars_file_daily.nc"
+        f"> MarsFormat openmars_file.nc -gcm openmars\n"
+        f"{Blue}(Creates openmars_file_daily.nc)"
         f"{Nclr}\n\n"
     )
 )
@@ -86,11 +86,10 @@
         f"Calculate 5-day averages from instantaneous data. Generates "
         f"MGCM-like 'average' files.\n"
         f"{Green}Example:\n"
-        f"> MarsFormat openmars_file.nc -gcm openmars -ba "
-        f"{Blue}Creates openmars_file_average.nc"
-        f"{Blue}5-sol bin{Green}\n"
-        f"> MarsFormat openmars_file.nc -gcm openmars -ba 10 "
-        f"{Blue}10-sol bin"
+        f"> MarsFormat openmars_file.nc -gcm openmars -ba\n"
+        f"{Blue}(Creates openmars_file_average.nc; 5-sol bin){Green}\n"
+        f"> MarsFormat openmars_file.nc -gcm openmars -ba 10\n"
+        f"{Blue}(10-sol bin)"
         f"{Nclr}\n\n"
     )
 )
@@ -101,11 +100,10 @@
         f"Calculate 5-day averages binned by hour from instantaneous "
         f"data. Generates MGCM-like 'diurn' files.\n"
         f"{Green}Example:\n"
-        f"> MarsFormat openmars_file.nc -gcm openmars -bd "
-        f"{Blue}Creates openmars_file_daily.nc"
-        f"{Blue}uses a 5-sol bin{Green}\n"
-        f"> MarsFormat openmars_file.nc -gcm openmars -bd -ba 10 "
-        f"{Blue}uses a 10-sol bin"
+        f"> MarsFormat openmars_file.nc -gcm openmars -bd\n"
+        f"{Blue}(Creates openmars_file_daily.nc;  5-sol bin){Green}\n"
+        f"> MarsFormat openmars_file.nc -gcm openmars -bd -ba 10\n"
+        f"{Blue}(10-sol bin)"
         f"{Nclr}\n\n"
     )
 )
@@ -118,8 +116,8 @@
         f"Preserves the names of the variables and dimensions in the"
         f"original file.\n"
         f"{Green}Example:\n"
-        f"> MarsFormat openmars_file.nc -gcm openmars -rn"
-        f"{Blue}Creates openmars_file_daily.nc"
+        f"> MarsFormat openmars_file.nc -gcm openmars -rn\n"
+        f"{Blue}(Creates openmars_file_daily.nc)"
         f"{Nclr}\n\n"
     )
 )

bin/MarsInterp.py

@@ -88,7 +88,7 @@
 
 parser.add_argument('-v', '--vertical_grid', type=str, default=None,
     help=(
-        f"Layer IDs as defined in ``amescap_profile``. For first "
+        f"Layer IDs as defined in ``amescap_profile``.\nFor first "
         f"time use, copy ``amescap_profile`` to your home directory:\n"
         f"{Cyan}cp path/to/amesCAP/mars_templates/amescap_profile "
         f"~/.amescap_profile\n"
@@ -110,7 +110,7 @@
 
 parser.add_argument('-print', '--print_grid', action='store_true',
     help=(
-        f"Print the vertical grid to the screen. {Yellow}This does not "
+        f"Print the vertical grid to the screen.\n{Yellow}This does not "
         f"run the interpolation, it only prints grid information.\n"
         f"{Green}Example:\n"
         f"> MarsInterp 01336.atmos_average.nc -t pstd -v p44 -print"
@@ -128,8 +128,8 @@
         f"here.\n"
         f"{Green}Example:\n"
         f"> MarsInterp 00334.atmos_average.nc -t pstd -ext _dflt_levs\n"
-        f"  {Blue} produces 00334.atmos_average_dflt_levs.nc and "
-        f"preserves all other files."
+        f"{Blue}(Produces 00334.atmos_average_dflt_levs.nc and "
+        f"preserves all other files)"
         f"{Nclr}\n\n"
     )
 )

bin/MarsPlot.py

@@ -107,8 +107,8 @@
 parser.add_argument('-i', '--inspect_file', nargs='?',
     type=argparse.FileType('rb'),
     help=(
-        f"Print the content of a netCDF file to the screen. This is a "
-        f"ncdump-like feature. Variables are sorted by dimension.\n"
+        f"Print the content of a netCDF file to the screen.\nVariables "
+        f"are sorted by dimension.\n"
         f"{Green}Example:\n"
         f"> MarsPlot -i 01336.atmos_daily.nc"
         f"{Nclr}\n\n"
@@ -138,10 +138,10 @@
 parser.add_argument('-sy', '--stack_years', action='store_true',
     default=False,
     help=(
-        f"Stack consecutive years of data on the same axes (e.g., Ls ="
-        f"0-360) in 1D time series plots.\nThis only works if ADD LINE "
-        f"is used in the Custom.in template to overplot multiple years "
-        f"of data.\nDefault is to plot in monotonically increasing "
+        f"Plot consecutive years of data over the same axes range (e.g."
+        f"Ls=0–360). For 1D time series plots.\nRequires ADD LINE "
+        f"in the Custom.in template (see template for instructions)."
+        f"\nDefault is to plot in monotonically increasing "
         f"format.\n"
         f"{Green}Example:\n"
         f"> MarsPlot Custom.in -sy"
@@ -196,7 +196,7 @@
     default=False,
     help=(
         f"Generate a file called Custom.in that provides templates "
-        f"for making plots with CAP without the commented instructions "
+        f"for making plots\nwith CAP without the instructions "
         f"at top of the file.\n"
         f"{Green}Example:\n"
         f"> MarsPlot -template -trim\n"
@@ -208,7 +208,7 @@
 parser.add_argument('-values', '--print_values', nargs='+',
     default=None,
     help=(
-        f"For use with ``-i --inspect``: print the values of the "
+        f"For use with ``-i --inspect``:\nPrint the values of the "
         f"specified variable to the screen.\n"
         f"{Green}Example:\n"
         f"> MarsPlot -i 01336.atmos_daily.nc -values temp\n"
@@ -221,7 +221,7 @@
 # to be used jointly with --inspect
 parser.add_argument('-stats', '--statistics', nargs='+', default=None,
     help=(
-        f"For use with ``-i --inspect``: print the min, mean, and max "
+        f"For use with ``-i --inspect``:\nPrint the min, mean, and max "
         f"values of the specified variable to the screen.\n"
         f"{Green}Example:\n"
         f"> MarsPlot -i 01336.atmos_daily.nc -stats temp\n"
@@ -233,8 +233,8 @@
 
 parser.add_argument('--debug', action='store_true',
     help=(
-        f"Use with any other argument to pass all Python errors and\n"
-        f"status messages to the screen when running CAP.\n"
+        f"Use with any other argument to print all Python errors and "
+        f"status messages to the screen\n"
         f"{Green}Example:\n"
         f"> MarsPlot Custom.in --debug"
         f"{Nclr}\n\n"

bin/MarsPull.py

@@ -43,35 +43,25 @@
     prog=('MarsPull'),
     description=(
         f"{Yellow}Uility for downloading NASA Ames Mars Global Climate "
-        f"Model output files from the NAS Data Portal at:"
-        f"{Cyan}https://data.nas.nasa.gov/mcmcref/\n{Nclr}\n"
-        f"Requires the ``-id`` argument AND EITHER ``-f`` or ``-ls``."
+        f"Model output files from the NAS Data Portal at:\n"
+        f"{Cyan}https://data.nas.nasa.gov/mcmcref/\n{Nclr}"
+        f"Requires ``-f`` or ``-ls``."
         f"{Nclr}\n\n"
     ),
     formatter_class=argparse.RawTextHelpFormatter
 )
 
-parser.add_argument('-list', '--list_files', action='store_true',
-    help=(
-        f"Return a list of all the files available for download from:\n"
-        f"{Cyan}https://data.nas.nasa.gov/mcmcref/\n{Nclr}\n"
-        f"{Green}Example:\n"
-        f"> MarsPull -list"
-        f"{Nclr}\n\n"
-    )
-)
-
 parser.add_argument('directory_name', type=str, nargs='?',
     choices=[
         'FV3BETAOUT1', 'ACTIVECLDS', 'INERTCLDS', 'NEWBASE_ACTIVECLDS',
         'ACTIVECLDS_NCDF'],
     help=(
         f"Selects the simulation directory from the "
-        f"NAS data portal:\n"
-        f"{Cyan}https://data.nas.nasa.gov/mcmcref/\n{Nclr}\n"
-        f"Current options are:\n{Yellow}FV3BETAOUT1\nACTIVECLDS\n"
-        f"INERTCLDS\nNEWBASE_ACTIVECLDS\nACTIVECLDS_NCDF\n"
-        f"{Red}MUST be used with either ``-f`` or ``-ls``.\n"
+        f"NAS data portal ("
+        f"{Cyan}https://data.nas.nasa.gov/mcmcref/){Nclr}\n"
+        f"Current directory options are:\n{Yellow}FV3BETAOUT1, ACTIVECLDS, "
+        f"ACTIVECLDS, INERTCLDS, NEWBASE_ACTIVECLDS, ACTIVECLDS_NCDF\n"
+        f"{Red}MUST be used with either ``-f`` or ``-ls``\n"
         f"{Green}Example:\n"
         f"> MarsPull INERTCLDS -f fort.11_0690\n"
         f"{Blue}OR{Green}\n"
@@ -80,6 +70,16 @@
     )
 )
 
+parser.add_argument('-list', '--list_files', action='store_true',
+    help=(
+        f"Return a list of all the files available for download from "
+        f"{Cyan}https://data.nas.nasa.gov/mcmcref/{Nclr}\n"
+        f"{Green}Example:\n"
+        f"> MarsPull -list"
+        f"{Nclr}\n\n"
+    )
+)
+
 parser.add_argument('-f', '--filename', nargs='+', type=str,
     help=(
         f"The name(s) of the file(s) to download.\n"

bin/MarsVars.py

@@ -321,8 +321,8 @@ def add_help(var_list):
         f"A new variable (``var_col``) in [kg/m2] will be added to the "
         f"file.\n"
         f"{Green}Example:\n"
-        f"> MarsVars 01336.atmos_average.nc -col dst_mass_mom"
-        f"  {Blue}dst_mass_mom_col is derived and added to the file"
+        f"> MarsVars 01336.atmos_average.nc -col dst_mass_mom\n"
+        f"{Blue}(derive and add dst_mass_mom_col to the file)"
         f"{Nclr}\n\n"
     )
 )
@@ -333,8 +333,8 @@ def add_help(var_list):
         f"A new a variable (``var_p``) (for prime) will be added to the"
         f" file.\n"
         f"{Green}Example:\n"
-        f"> MarsVars 01336.atmos_average.nc -zd temp"
-        f"  {Blue}temp_p is derived and added to the file"
+        f"> MarsVars 01336.atmos_average.nc -zd temp\n"
+        f"{Blue}(temp_p is added to the file)"
         f"{Nclr}\n\n"
     )
 )
@@ -347,7 +347,7 @@ def add_help(var_list):
         f"file.\n"
         f"{Green}Example:\n"
         f"> MarsVars 01336.atmos_average.nc -to_dz temp\n"
-        f"  {Blue}temp_dp_to_dz is derived and added to the file"
+        f"{Blue}(temp_dp_to_dz is added to the file)"
         f"{Nclr}\n\n"
     )
 )
@@ -360,7 +360,7 @@ def add_help(var_list):
         f"file.\n"
         f"{Green}Example:\n"
         f"> MarsVars 01336.atmos_average.nc -to_dp temp\n"
-        f"  {Blue}temp_dz_to_dp is derived and added to the file"
+        f"{Blue}(temp_dz_to_dp is added to the file)"
         f"{Nclr}\n\n"
     )
 )
@@ -379,10 +379,10 @@ def add_help(var_list):
         f"Copy one or more variables from a file into a new file of "
         f"the same name with the appended extension: '_extract'.\n"
         f"{Green}Example:\n"
-        f"> MarsVars 01336.atmos_average.nc -extract ps temp"
-        f"  {Blue}Creates 01336.atmos_average_extract.nc containing ps "
-        f"and temp as well as their dimensional variables (e.g., lat, "
-        f"lon, lev, etc.)"
+        f"> MarsVars 01336.atmos_average.nc -extract ps temp\n"
+        f"{Blue}(Creates 01336.atmos_average_extract.nc containing ps "
+        f"and temp\nplus their dimensional variables [lat, "
+        f"lon, lev, etc.])"
         f"{Nclr}\n\n"
     )
 )

docs/source/installation.rst

@@ -81,7 +81,7 @@ Install CAP from the `NASA Planetary Science GitHub <https://github.com/NASA-Pla
 
    cp amescap/mars_templates/amescap_profile ~/.amescap_profile # For pip
    # OR
-   cp opt/anaconda3/envs/amescap/mars_templates/amescap-profile ~/.amescap-profile # For conda
+   cp /opt/anaconda3/envs/amescap/mars_templates/amescap-profile ~/.amescap-profile # For conda
 
 5. Test your installation
 ~~~~~~~~~~~~~~~~~~~~~~~~~