reorganising all files as a pip installable package

sbmy_control.egg-info/PKG-INFO

@@ -0,0 +1,35 @@
+Metadata-Version: 2.4
+Name: sbmy_control
+Version: 0.1.0
+Summary: Simbelmyne control package
+Home-page: https://git.aquila-consortium.org/maubin/sbmy_control
+Author: Mayeul Aubin
+Author-email: mayeul.aubin@iap.fr
+License: GPL-3.0
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: pysbmy
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: h5py
+Requires-Dist: tqdm
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+This package provides control functionalities for Simbelmyne. It allows to create automatically all the required files and scripts to run a N-body simulation with Simbelmyne, using monofonIC for initial conditions. The subpackage `analysis` provides tools to analyze the results of the simulation (slices and power spectra), while the subpackage `scripts` includes tools to handle snapshots, tiles and density fields.

sbmy_control.egg-info/SOURCES.txt

@@ -0,0 +1,30 @@
+setup.py
+sbmy_control/ICs.py
+sbmy_control/__init__.py
+sbmy_control/args_main.py
+sbmy_control/cosmo_params.py
+sbmy_control/low_level.py
+sbmy_control/main.py
+sbmy_control/monofonic.py
+sbmy_control/parameters_card.py
+sbmy_control/parameters_monofonic.py
+sbmy_control/progress_bar.py
+sbmy_control/scola.py
+sbmy_control/simbelmyne.py
+sbmy_control/slurm_submission.py
+sbmy_control/timestepping.py
+sbmy_control.egg-info/PKG-INFO
+sbmy_control.egg-info/SOURCES.txt
+sbmy_control.egg-info/dependency_links.txt
+sbmy_control.egg-info/entry_points.txt
+sbmy_control.egg-info/requires.txt
+sbmy_control.egg-info/top_level.txt
+sbmy_control/analysis/__init__.py
+sbmy_control/analysis/colormaps.py
+sbmy_control/analysis/power_spectrum.py
+sbmy_control/analysis/slices.py
+sbmy_control/scripts/__init__.py
+sbmy_control/scripts/convert_snapshot_to_density.py
+sbmy_control/scripts/field_to_field.py
+sbmy_control/scripts/gather_tiles.py
+sbmy_control/scripts/scola_submit.py

sbmy_control.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

sbmy_control.egg-info/entry_points.txt

@@ -0,0 +1,8 @@
+[console_scripts]
+convert_snapshot_to_density = sbmy_control.scripts.convert_snapshot_to_density:console_main
+field_to_field = sbmy_control.scripts.field_to_field:console_main
+gather_tiles = sbmy_control.scripts.gather_tiles:console_main
+power_spectrum = sbmy_control.analysis.power_spectrum:console_main
+sbmy_control = sbmy_control.main:console_main
+scola_submit = sbmy_control.scripts.scola_submit:console_main
+slices = sbmy_control.analysis.slices:console_main

sbmy_control.egg-info/requires.txt

@@ -0,0 +1,5 @@
+pysbmy
+numpy
+matplotlib
+h5py
+tqdm

sbmy_control.egg-info/top_level.txt

@@ -0,0 +1 @@
+sbmy_control

sbmy_control/analysis/power_spectrum.py

@@ -1,4 +1,5 @@
 import numpy as np
+import os
 
 kmin = 1e-1
 kmax = 2e0
@@ -262,7 +263,9 @@ def get_ylims_and_yticks(ylims):
     return ylims, yticks
 
 
-if __name__ == "__main__":
+
+
+def console_main():
     from argparse import ArgumentParser
     parser = ArgumentParser(description='Plot power spectra of fields')
 
@@ -286,6 +289,10 @@ if __name__ == "__main__":
     if not args.power_spectrum and not args.cross_correlation:
         print('You must choose between power_spectrum and cross_correlation.')
         exit()
+    
+    for _k,f in enumerate(args.filenames):
+        if not os.path.exists(args.directory+f):
+            raise FileNotFoundError(f"File {args.directory+f} does not exist.")
 
     if args.reference is not None:
         from pysbmy.field import read_field
@@ -398,5 +405,8 @@ if __name__ == "__main__":
         fig.savefig(args.output)
     else:
         fig.savefig(args.directory+'power_spectrum.png')
-    
 
+
+if __name__ == "__main__":
+    console_main()
+    

sbmy_control/analysis/slices.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 import sys
+import os
 sys.path.append('/home/aubin/Simbelmyne/sbmy_control/')
 
 fs = 18
@@ -10,11 +11,11 @@ def add_ax_ticks(ax, ticks, tick_labels):
     from matplotlib import ticker
     ax.set_xticks(ticks)
     ax.set_yticks(ticks)
-    ax.set_xticklabels(tick_labels)
-    ax.set_yticklabels(tick_labels)
+    ax.set_xticklabels([int(t) for t in tick_labels])
+    ax.set_yticklabels([int(t) for t in tick_labels])
     ax.set_xlabel('Mpc/h')
-    ax.xaxis.set_major_formatter(ticker.FormatStrFormatter('%d'))
-    ax.yaxis.set_major_formatter(ticker.FormatStrFormatter('%d'))
+    # ax.xaxis.set_major_formatter(ticker.FormatStrFormatter('%d')) # Does not work
+    # ax.yaxis.set_major_formatter(ticker.FormatStrFormatter('%d'))
 
 
 
@@ -53,7 +54,7 @@ def plot_imshow_with_reference( data_list,
     sep = 10 if L[0] < 50 else 20 if L[0] < 100 else 50 if L[0]<250 else 100 if L[0] < 500 else 200 if L[0] < 1000 else 500 if L[0] < 2500 else 1000
     ticks = [np.arange(0, l+1, sep)*len(dat)/l for l, dat in zip(L,data_list)]
     tick_labels = [np.arange(0, l+1, sep) for l in L]
-
+    
     def score(data, reference):
         return np.linalg.norm(data-reference)/np.linalg.norm(reference)
 
@@ -148,8 +149,7 @@ def plot_imshow_diff(data_list,
     return fig, axes
 
 
-
-if __name__ == "__main__":
+def console_main():
     from argparse import ArgumentParser
     parser = ArgumentParser(description='Comparisons of fields slices.')
 
@@ -177,6 +177,8 @@ if __name__ == "__main__":
     ref_field = read_field(args.directory+args.reference) if args.reference is not None else None
     fields = []
     for k,f in enumerate(args.filenames):
+        if not os.path.exists(args.directory+f):
+            raise FileNotFoundError(f"File {args.directory+f} does not exist.")
         if args.reference is not None and f == args.reference:
             fields.append(ref_field) # Simply copy the reference field instead of reading it again
             if args.labels is not None:
@@ -220,3 +222,8 @@ if __name__ == "__main__":
         fig.savefig(args.output,bbox_inches='tight')
     else:
         fig.savefig(args.directory+'slices.jpg',bbox_inches='tight')
+
+
+
+if __name__ == "__main__":
+    console_main()

sbmy_control/main.py

@@ -220,7 +220,7 @@ def check_consistency(card_dict, mode):
             raise ValueError(f"ModulePMCOLA is not 1: ModulePMCOLA={card_dict["ModulePMCOLA"]}")
 
 
-if __name__ == "__main__":
+def console_main():
     from argparse import ArgumentParser
     from args_main import register_arguments_main
     from timestepping import register_arguments_timestepping, main_timestepping
@@ -238,4 +238,9 @@ if __name__ == "__main__":
     register_arguments_card(parser)
     register_arguments_cosmo(parser)
     parsed_args = parser.parse_args()
-    main(parsed_args)
+    main(parsed_args)
+
+
+if __name__ == "__main__":
+    console_main()
+    

sbmy_control/scripts/convert_snapshot_to_density.py

@@ -36,8 +36,7 @@ def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0,
     print("Done.")
 
 
-
-if __name__ == "__main__":
+def console_main():
     parser = argparse.ArgumentParser(description="Convert snapshot to density.")
     parser.add_argument(
         "-S",
@@ -76,4 +75,8 @@ if __name__ == "__main__":
         output_path=args.output,
         N=args.N,
         corner=args.corner,
-    )
+    )
+
+
+if __name__ == "__main__":
+    console_main()

sbmy_control/scripts/field_to_field.py

@@ -1,5 +1,5 @@
 from pysbmy.density import mesh_to_mesh
-from pysbmy.Field import Field, read_field
+from pysbmy.field import Field, read_field
 import numpy as np
 import os
 
@@ -8,23 +8,43 @@ def field_to_field(
         input_file:str,
         output_file:str,
         output_size:int|tuple[int,int,int]|list[int],
+        output_L:float|tuple[float,float,float]|list[float],
         output_dpm:float|tuple[float,float,float]|list[float],
         output_corner:tuple[float,float,float]|list[float],
         boundary_conditions:int,
         ):
     
 
+    ### Make sure all inputs are valid
+    if output_L is not None and output_dpm is not None:
+        raise ValueError("Either output_L or output_dpm can be specified, not both.")
+
     if isinstance(output_size, int):
         output_size = (output_size, output_size, output_size) # N0, N1, N2
+    elif len(output_size) == 1:
+        output_size = (output_size[0], output_size[0], output_size[0])
+
+    if output_L is not None:
+        if isinstance(output_L, float):
+            output_L = (output_L, output_L, output_L)
+        elif len(output_L) == 1:
+            output_L = (output_L[0], output_L[0], output_L[0])
     
-    if isinstance(output_dpm, float):
+    if output_dpm is None:
+        if output_L is None:
+            output_dpm = (-1, -1, -1)
+        else:
+            output_dpm = (output_L[0] / output_size[0], output_L[1] / output_size[1], output_L[2] / output_size[2])
+    elif isinstance(output_dpm, float):
         output_dpm = (output_dpm, output_dpm, output_dpm) # d0, d1, d2
-    elif output_dpm is None:
-        output_dpm = (-1, -1, -1)
+    elif len(output_dpm) == 1:
+        output_dpm = (output_dpm[0], output_dpm[0], output_dpm[0])
 
     if not os.path.exists(input_file):
         raise FileNotFoundError(f"Input file {input_file} does not exist.")
     
+
+    
     # Read the input field
     print(f"Reading input field from {input_file}")
     input_field = read_field(input_file)
@@ -59,9 +79,9 @@ def field_to_field(
     print(f"Output field size:   {output_size[0]} x {output_size[1]} x {output_size[2]}")
     print(f"Input field dpm:     {d0_in:.3f} x {d1_in:.3f} x {d2_in:.3f}")
     print(f"Output field dpm:    {d0_out:.3f} x {d1_out:.3f} x {d2_out:.3f}")
-    print(f"Input field corner:  {corner0:.1f} x {corner1:.1f} x {corner2:.1f}")
-    print(f"Output field corner: {output_corner[0]:.1f} x {output_corner[1]:.1f} x {output_corner[2]:.1f}")
-    print(f"Boundary conditions: {boundary_conditions}")
+    print(f"Input field corner:  ({corner0:.1f}, {corner1:.1f}, {corner2:.1f})")
+    print(f"Output field corner: ({output_corner[0]:.1f}, {output_corner[1]:.1f}, {output_corner[2]:.1f})")
+    print(f"Boundary conditions: {'periodic' if boundary_conditions == 1 else 'non-periodic'}")
     print("-----------------------------------------")
 
     input_grid = input_field.data
@@ -95,16 +115,20 @@ def field_to_field(
     print("Done.")
 
 
-
-if __name__ == "__main__":
+def console_main():
     import argparse
     parser = argparse.ArgumentParser(description="Convert a field from one size to another.")
     parser.add_argument("-i","--input_file", type=str, help="Input field file")
     parser.add_argument("-o","--output_file", type=str, help="Output field file")
-    parser.add_argument("-N","--output_size", type=int, nargs=3, help="Output field size (N0, N1, N2)")
-    parser.add_argument("-dpm","--output_dpm", type=float, nargs=3, default=None, help="Output field dpm (d0, d1, d2)")
+    parser.add_argument("-N","--output_size", type=int, nargs="+", help="Output field size (N0, N1, N2)")
+    parser.add_argument("-L","--output_L", type=float, nargs="+", default=None, help="Output field size (L0, L1, L2)")
+    parser.add_argument("-dpm","--output_dpm", type=float, nargs="+", default=None, help="Output field dpm (d0, d1, d2)")
     parser.add_argument("-corner","--output_corner", type=float, nargs=3, default=(0.,0.,0.), help="Output field corner (corner0, corner1, corner2)")
-    parser.add_argument("-BC","--boundary_conditions", type=int, default=1, help="Boundary conditions (0: periodic, 1: non-periodic)")
+    parser.add_argument("-BC","--boundary_conditions", type=int, default=1, help="Boundary conditions (1: periodic, 3: non-periodic)")
     args = parser.parse_args()
 
-    field_to_field(args.input_file, args.output_file, args.output_size, args.output_dpm, args.output_corner, args.boundary_conditions)
+    field_to_field(args.input_file, args.output_file, args.output_size, args.output_L, args.output_dpm, args.output_corner, args.boundary_conditions)
+
+
+if __name__ == "__main__":
+    console_main()

sbmy_control/scripts/gather_tiles.py

@@ -99,8 +99,7 @@ def gather_tiles(folder, tile_base, L, Np, N_TILES, buffer):
 
 
 
-
-if __name__ == "__main__":
+def console_main():
     parser = argparse.ArgumentParser(description="Gather density from tiles.")
     parser.add_argument("-d","--folder", type=str, default="./", help="Folder containing the tiles")
     parser.add_argument("--tile_base", type=str, default="sCOLA_tile", help="Base name of the tiles")
@@ -121,4 +120,9 @@ if __name__ == "__main__":
     Np_tile = Np//N_TILES
     dpm = L/Np_tile
 
-    gather_tiles(folder, tile_base, L, Np, N_TILES, buffer)
+    gather_tiles(folder, tile_base, L, Np, N_TILES, buffer)
+
+
+
+if __name__ == "__main__":
+    console_main()

sbmy_control/scripts/scola_submit.py

@@ -255,7 +255,7 @@ def check_previous_jobs(workdir,slurmdir,slurmfile,tilefile,sleeptime,job_ids_ar
             if os.path.exists(workdir+f"{tilefile}{prev_box}.h5"):
                 job_status_categories['CP'].append(prev_box) # Classify as completed
             else:
-                resubmit_job(slurmdir,slurmfile,job_ids_array,prev_box,resubmit_count,error_count,MAX_RESUBMIT,MAX_ERRORS)
+                resubmit_count, error_count = resubmit_job(slurmdir,slurmfile,job_ids_array,prev_box,resubmit_count,error_count,MAX_RESUBMIT,MAX_ERRORS)
                 job_status_categories[status].append(prev_box) # Classify as failed
                 # Sleep for a while before resubmitting the next job
                 time.sleep(sleeptime)
@@ -445,6 +445,7 @@ def scola_submit(directory,
 
 
     job_status_categories, resubmit_count, error_count = check_previous_jobs(workdir,slurmdir,slurmfile,tilefile,sleep,job_ids_array,N_tiles**3+1,resubmit_count,error_count,MAX_RESUBMIT,MAX_ERRORS)
+    print_summary_job_status(job_status_categories, box, resubmit_count, error_count)
     # Now wait for all jobs to finish
     while len(job_status_categories['CP'])<N_tiles**3:
         time.sleep(10*sleep)
@@ -461,9 +462,7 @@ def scola_submit(directory,
 
 
 
-
-
-if __name__ == "__main__":
+def console_main():
     parser = argparse.ArgumentParser(description="Submit slurm jobs for sCOLA tiles.")
 
     parser.add_argument("-d", "--directory", type=str, default="./", help="Main directory where the output will be saved (if other dir and filenames are not specified).")
@@ -495,4 +494,9 @@ if __name__ == "__main__":
 
 
 
+if __name__ == "__main__":
+    console_main()
+
+
+
             

setup.py

@@ -0,0 +1,42 @@
+from setuptools import setup, find_packages
+setup(
+    name='sbmy_control',
+    version='0.1.0',
+    author='Mayeul Aubin',
+    author_email='mayeul.aubin@iap.fr',
+    description='Simbelmyne control package',
+    long_description='This package provides control functionalities for Simbelmyne. It allows to create automatically all the required files and scripts to run a N-body simulation with Simbelmyne, using monofonIC for initial conditions. The subpackage `analysis` provides tools to analyze the results of the simulation (slices and power spectra), while the subpackage `scripts` includes tools to handle snapshots, tiles and density fields.',
+    long_description_content_type='text/markdown',
+    url='https://git.aquila-consortium.org/maubin/sbmy_control',
+    packages=find_packages(),
+    install_requires=[
+        'pysbmy',
+        'numpy',
+        'matplotlib',
+        'h5py',
+        'tqdm',
+    ],
+    license='GPL-3.0',
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+    ],
+    python_requires='>=3.8',
+    entry_points={
+        'console_scripts': [
+            'sbmy_control=sbmy_control.main:console_main',
+            'slices=sbmy_control.analysis.slices:console_main',
+            'power_spectrum=sbmy_control.analysis.power_spectrum:console_main',
+            'field_to_field=sbmy_control.scripts.field_to_field:console_main',
+            'gather_tiles=sbmy_control.scripts.gather_tiles:console_main',
+            'convert_snapshot_to_density=sbmy_control.scripts.convert_snapshot_to_density:console_main',
+            'scola_submit=sbmy_control.scripts.scola_submit:console_main',
+        ],
+    },
+)