most of the cookiecutter, still need to check with Sven if it works

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mesh_CORE2_{{cookiecutter.mesh_name}}/polygons/polygon_pacific_45N_60N.txt~

+ 147.906826  45.012042 
+ -122.101815  45.087483 
+ -120.740927  49.811575 
+ -124.823589  54.333782 
+ -132.867944  58.290713 
+ -137.041331  59.865410 
+ -139.007056  59.946164 
+ 170.070565  60.551817 
+ 166.864919  62.974428 
+ 163.780242  60.390310 
+ 161.239919  58.694482 
+ 158.881048  55.787349 
+ 156.945565  51.749664 
+ 155.554435  50.296097 
+ 153.497984  48.196501 
+ 151.320565  46.581427 

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mesh_CORE2_{{cookiecutter.mesh_name}}/polygons/polygon_south_atlantic_20S_50N.txt

+-41.602823 -20.121131 
+-41.723790 -13.337820 
+-50.191532  -5.181696 
+-59.324597   2.247645 
+-65.675403   8.788694 
+-70.131048   8.304172 
+-72.671371   7.738896 
+-76.481855   6.689098 
+-77.147177   7.254374 
+ -77.631048   7.981157
+ -78.039315   8.707941
+ -78.674395   9.192463
+ -79.369960   9.313594
+ -79.763105   9.071332
+ -80.035282   8.748318
+ -80.549395   8.586810
+ -81.123992   8.384926
+ -81.910282   8.627187
+ -82.666331   8.869448
+ -83.513105   9.757739
+ -84.269153  10.807537
+ -84.662298  12.826380
+ -85.327621  14.360700
+ -87.232863  14.845222
+ -88.382056  15.168237
+ -89.924395  16.016151
+ -91.738911  17.429341
+ -94.526210  17.267833
+ -97.006048  18.963661
+ -98.578629  21.224764
+ -99.122984  25.666218
+ -98.699597  29.946164
+ -96.401210  31.884253
+ -90.110887  33.580081
+ -83.094758  36.083445
+ -77.409274  40.686406
+ -72.570565  43.674293
+ -72.066532  48.196501
+ -67.651210  50.376851
+ -57.459677  49.973082
+ -49.606855  49.650067
+ -43.558468  49.650067
+ -37.752016  49.892328
+ -31.340726  50.053836
+ -25.413306  49.892328
+ -19.364919  49.407806
+ -15.292339  49.569314
+  -9.788306  49.488560
+  -4.889113  48.842530
+  -1.743952  47.792732
+   2.852823  46.662180
+   6.905242  47.146703
+  11.864919  47.954240
+  16.159274  47.227456
+  20.393145  45.370121
+  23.256048  44.562584
+  25.493952  42.866756
+  27.671371  38.909825
+  30.272177  38.748318
+  33.840726  39.071332
+  36.622984  38.829071
+  38.195565  37.375505
+  37.953629  34.872140
+  37.288306  32.853297
+  36.199597  31.076716
+  34.868952  30.753701
+  32.510081  29.865410
+  28.881048  28.734859
+  23.558468  24.697174
+  11.643145  17.671602
+  10.836694   6.123822
+  15.252016  -5.827725
+  16.885081 -11.884253
+  14.203629 -19.475101
+  10.816532 -18.829071
+   4.284274 -19.071332
+  -2.913306 -19.475101
+  -9.445565 -19.636608
+ -19.153226 -20.040377
+ -29.637097 -20.040377
+ -41.602823 -20.121131

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mesh_CORE2_{{cookiecutter.mesh_name}}/priority_regions.txt

+59.       26.3
+55.2016   24.0
+72.7074   71.8275
+72.9378   70.3655
+41.6901   66.8202
+40.5012   66.1886

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mg_coastline.m

+ncFile='./raw_input_data/{{cookiecutter.input_fname}}';
+fldName='{{cookiecutter.input_varname}}';
+
+ncid=netcdf.open(ncFile,'nowrite');
+
+fld_id= netcdf.inqVarID(ncid,fldName);
+lon_id= netcdf.inqVarID(ncid,'lon');
+lat_id= netcdf.inqVarID(ncid,'lat');
+
+
+fld=netcdf.getVar(ncid,fld_id);
+fld=fld';
+
+lon=netcdf.getVar(ncid,lon_id);
+lat=netcdf.getVar(ncid,lat_id);
+%lon=-180:1/60:180; lon=lon';
+%lat=-90:1/60:90;   lat=lat';
+
+if min(size(lon))==2
+    lon=lon(1,:);
+    lat=lat(2,:);
+end
+
+netcdf.close(ncid)
+
+imagesc(lon,lat,fld)
+set(gca,'ydir','normal')
+
+[C h]=contour(lon,lat,fld,[0. 0.]);
+
+%cst=C';
+%for i=1:size(cst,1)
+%    if cst(i,1)==0
+%        ofs=cst(i,2);
+%        cst(i,:)=cst(i+ofs,:);
+%    end
+%end
+
+cst=C';
+CST=[];
+for i=1:size(cst,1)
+    if cst(i,1)==0 & cst(i,2)>180
+        ofs=cst(i,2)
+        CST=[CST; cst(i+1:i+ofs,:)];
+    end
+end
+
+save -ascii {{cookiecutter.mesh_name}}_cst.txt CST
+exit;

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mg_topo_prep_triangle_input.m

+%Set Input:
+%TopoDir='/work/ollie/sharig/data/topography/'
+TopoDir='./raw_input_data/'
+%TopoFile='herold_etal_eocene_topo_1x1.nc'
+TopoFile='{{cookiecutter.input_fname}}'
+
+% Set Output:
+SaveDir='./mg/topo/'
+suffix='{{cookiecutter.mesh_name}}';
+ncfile='{{cookiecutter.mesh_name}}_input_file_used_for_matlab_routine.nc'
+
+
+ncid=netcdf.open([TopoDir,TopoFile],'nowrite');
+
+
+if ~exist('{{cookiecutter.input_varname}}','var')
+  varid_z = netcdf.inqVarID(ncid,'{{cookiecutter.input_varname}}');
+  %lon/lat
+  varid_ln = netcdf.inqVarID(ncid,'lon'); % uncomment if file contains
+  varid_lt = netcdf.inqVarID(ncid,'lat');
+  t=netcdf.getVar(ncid,varid_z);
+  t=t';
+  ln=netcdf.getVar(ncid,varid_ln);
+  lt=netcdf.getVar(ncid,varid_lt);
+  %ln=-180:1/60:180; ln=ln'; %define lon/lat as file did not contain it
+  %lt=-90:1/60:90; lt=lt';
+end
+
+netcdf.close(ncid)
+
+lon=zeros(size(ln));
+lat=lt;
+
+topo=zeros(size(t));
+
+if min(ln)>=0
+    ind=find(ln>=180.0);
+    len=length(ind);
+    topo(:,1:len)=t(:,ind);
+    lon(1:len)=ln(ind)-360.0;
+    ind=find(ln<180.0);
+    topo(:,len+1:end)=t(:,ind);
+    lon(len+1:end)=ln(ind);
+else
+    lon=ln;
+    topo=t;
+end
+    
+meshType='global'
+
+% Options for meshType: global
+
+if strcmp(meshType,'global')
+    LonMin=-180.0
+    LonMax= 180.0
+    LatMin=-90.0
+    LatMax= 90.0
+end
+
+tp=topo;
+
+imagesc(lon,lat,tp)
+set(gca,'ydir','normal');
+title('This figure schould NOT be upside down')
+
+ix1=1;
+ix2=length(lon);
+iy1=1;
+iy2=length(lat);
+
+write_netcdf_output=1
+
+if write_netcdf_output
+  
+  disp('Writing netcdf output')
+    
+  ncid=netcdf.create([SaveDir,ncfile], 'clobber');
+  vid=netcdf.getConstant('NC_GLOBAL');
+  netcdf.putAtt(ncid,vid,'title','{{cookiecutter.mesh_name}} TOPOGRAPHY');
+  dimId_ax = netcdf.defDim(ncid,'nax',2);
+  dimId_lon = netcdf.defDim(ncid,'DimLon',ix2-ix1+1);
+  dimId_lat = netcdf.defDim(ncid,'DimLat',iy2-iy1+1);
+  
+  varId_lon = netcdf.defVar(ncid,'lon','NC_FLOAT',[dimId_ax dimId_lon]);
+  varId_lon360 = netcdf.defVar(ncid,'lon360','NC_FLOAT',[dimId_ax dimId_lon]);
+  varId_lat = netcdf.defVar(ncid,'lat','NC_FLOAT',[dimId_ax dimId_lat]);
+  varId_topo = netcdf.defVar(ncid,'topo','NC_FLOAT',[dimId_lon dimId_lat]);
+  
+  netcdf.putAtt(ncid,varId_topo,'field','topography value [m]');
+  netcdf.putAtt(ncid,varId_topo,'positions','lat, product; lon, product');
+  
+  netcdf.endDef(ncid)
+  
+  lon360 = lon;
+  ind=find(lon360<0);
+  lon360(ind)=lon360(ind)+360;
+  
+  netcdf.putVar(ncid,varId_lon,[lon'; zeros(1,length(lon))])
+  netcdf.putVar(ncid,varId_lon360,[lon360'; zeros(1,length(lon))])
+  netcdf.putVar(ncid,varId_lat,[zeros(1,length(lat)); lat'])
+  netcdf.putVar(ncid,varId_topo,tp')  
+  
+  netcdf.close(ncid)
+    
+end
+
+%disp('if you want to write TRIANGLE INPUT, please enter dbcont')
+%keyboard
+
+%disp('CAUTION: GRADIENT NOT COMPUTED')
+% calculate topography gradient
+[tpx tpy]=gradient(tp);
+tpxy=sqrt(tpx.^2+tpy.^2);  %  absolute value of the gradient
+tpxy=tpxy/max(max(tpxy));  %  normalise to 1
+
+fid=fopen([SaveDir,'lon_',suffix,'.bin32'],'w');
+count = fwrite(fid,lon,'float32')
+fclose(fid);
+
+fid=fopen([SaveDir,'lat_',suffix,'.bin32'],'w');
+count = fwrite(fid,lat,'float32')
+fclose(fid);
+
+%tp=tp'; % check orientation!
+tp=-tp'; % check orientation!
+fid=fopen([SaveDir,'topog_',suffix,'.bin32'],'w');
+count = fwrite(fid,tp,'float32')
+fclose(fid);
+
+tpxy=tpxy';
+fid=fopen([SaveDir,'topog_grad_',suffix,'.bin32'],'w');
+count = fwrite(fid,tpxy,'float32')
+fclose(fid);
+exit;

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mg_triangle_input_determine_array_sizes.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+This script determines array sizes to be used in ``triangle_refine_global.c``
+
+Dr. Paul Gierz, Jan 2020
+"""
+
+import argparse
+import pathlib
+
+# TODO: Add export functionality as module
+
+
+def parse_arguments():
+    parser = argparse.ArgumentParser(
+        description="Determines sizes to use in triangle_refine_global.c",
+        epilog="Dr. Paul Gierz, 2020",
+    )
+    parser.add_argument(
+        "input_dir",
+        help="The directory where lat, lon, topog, and topog_grad.bin32 files can be found",
+    )
+    return parser.parse_args()
+
+def print_topo_info(topo_path):
+    print(80*"=")
+    print("Determining sizes of all bin32 files in:", topo_path)
+    for f in topo_path.glob("*bin32"):
+        print("*   ", f)
+        with open(f, "rb") as fbin:
+            contents = fbin.read()
+            # Subtract 4 from the length...?
+            # TODO: Figure out why!
+            print("    ", len(contents)-4)
+    print(80*"=")
+
+def main():
+    args = parse_arguments()
+    topo_path = pathlib.Path(args.input_dir).resolve()
+    print_topo_info(topo_path)
+
+
+if __name__ == "__main__":
+    main()
+
+
+# -*- last line -*-

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/run_all.py

+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Bootstrap script to create a new mesh based on the CORE 2 Resolution.
+
+Dr. Paul Gierz, Jan 2020
+"""
+
+import os
+import shutil
+
+
+if __name__ == "__main__":
+    print(80*"=")
+    print("Starting generation of a mesh: {{cookiecutter.mesh_name}}.")
+    print(40*"- ")
+    print("Gathering input data:")
+    shutil.copyfile("{{cookiecutter.input_fpath}}", "./raw_input_data/{{cookiecutter.input_fname}}")
+    print(40*"- ")
+    print("* MATLAB Part:")
+    os.system("matlab.sh -s -S\"--mem=36000\" -M\"-nodisplay -r run('mg_topo_prep_triangle_input.m')\"")
+    os.system("matlab.sh -s -S\"--mem=36000\" -M\"-nodisplay -r run('mg_coastline.m')\"")
+    os.rename("{{cookiecutter.mesh_name}}_cst.txt", "mesh_CORE2_{{cookiecutter.mesh_name}}/{{cookiecutter.mesh_name}}_cst.txt")
+    # TODO: Get count from the other python script and write it somewhere
+    # TODO: C reads count from the file just written...
+    print(40*"- ")
+    print("* Triangle Part:")
+    os.system("sbatch -W run_triangle.sh")
+    print("Finished!")
+    print("You should now inspect your mesh!")
+    print(80*"=")

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/run_triangle.sh

+#!/bin/bash
+#SBATCH -c 18 --time=12:00:00 -p smp
+#Xsrun  I know what I am doing 
+
+cd {{cookiecutter.project_path}}/FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/mesh_CORE2_{{cookiecutter.mesh_name}}
+make clean
+make basic
+make refine
+module load intel.compiler
+make relax

cookiecutter.json

+{
+        "project_path": "/work/ollie/pgierz/PalModII/",
+        "mesh_name": "EXAMPLE",
+        "input_varname": "topo",
+        "input_fpath": "/work/ollie/pgierz/PalModII/FESOM2_MIS3_Mesh_Generation/raw_input_data/reconstruction_a1_0.25_degree_42.5kaBP.nc",
+        "input_fname": "{{ cookiecutter.input_fpath.split('/')[-1] }}"
+}