relative imports

.gitignore

@@ -0,0 +1,11 @@
+# Ignore some symbolic links
+install
+
+# Ignore specific directories and files
+.ipynb_checkpoints/
+*/.ipynb_checkpoints/
+.vscode/
+*.pyc
+__pycache__/
+sbmy_control.egg-info/
+*.h5

sbmy_control.egg-info/PKG-INFO

@@ -1,35 +0,0 @@
-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

@@ -1,30 +0,0 @@
-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

@@ -1 +0,0 @@
-

sbmy_control.egg-info/entry_points.txt

@@ -1,8 +0,0 @@
-[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

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

sbmy_control.egg-info/top_level.txt

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

sbmy_control/.gitignore

@@ -1,30 +0,0 @@
-# Ignore feature_* directory (usually used as git worktree)
-feature_*/
-
-# Ignore extensions directory
-extensions/*
-!extensions/__init__.py
-
-# Ignore some symbolic links
-install
-
-# Ignore specific directories and files
-.ipynb_checkpoints/
-*/.ipynb_checkpoints/
-.vscode/
-*.pyc
-__pycache__/
-pysbmy.egg-info/
-*.h5
-*.rng
-*.gadget1
-*.gadget2
-*.gadget3
-log.txt
-testpdf.txt
-tests/
-params/
-results/
-slurm_logs/
-slurm_scripts/
-work/

sbmy_control/ICs.py

@@ -3,9 +3,9 @@ def main_ICs(parsed_args):
     """
     Main function for the initial conditions generator.
     """
-    from args_main import parse_arguments_main
-    from parameters_card import parse_arguments_card_for_ICs
-    from low_level import print_starting_module, print_message, print_ending_module
+    from .args_main import parse_arguments_main
+    from .parameters_card import parse_arguments_card_for_ICs
+    from .low_level import print_starting_module, print_message, print_ending_module
     from os.path import isfile
 
     main_dict = parse_arguments_main(parsed_args)
@@ -52,10 +52,10 @@ def main_ICs(parsed_args):
 
 
 def ICs_monofonic(parsed_args):
-    from monofonic import main_monofonic
+    from .monofonic import main_monofonic
     from os.path import isfile
-    from low_level import print_message
-    from parameters_monofonic import parse_arguments_monofonic
+    from .low_level import print_message
+    from .parameters_monofonic import parse_arguments_monofonic
 
     monofonic_dict = parse_arguments_monofonic(parsed_args)
 
@@ -67,9 +67,9 @@ def ICs_monofonic(parsed_args):
 
 
 def ICs_sbmy(parsed_args):
-    from low_level import print_starting_module, print_message
+    from .low_level import print_starting_module, print_message
     from os.path import isfile
-    from parameters_card import parse_arguments_card_for_ICs
+    from .parameters_card import parse_arguments_card_for_ICs
 
     print_starting_module("sbmy IC", verbose=parsed_args.verbose)
 
@@ -99,14 +99,14 @@ def ICs_sbmy(parsed_args):
 
 
 def create_sbmy_power_spectrum_file(parsed_args, card_dict, power_spectrum_file):
-    from cosmo_params import parse_arguments_cosmo
+    from .cosmo_params import parse_arguments_cosmo
     from pysbmy.power import PowerSpectrum
 
     cosmo_dict = parse_arguments_cosmo(parsed_args)
 
     if parsed_args.verbose < 2:
         from io import BytesIO
-        from low_level import stdout_redirector, stderr_redirector
+        from .low_level import stdout_redirector, stderr_redirector
         f = BytesIO()
         g = BytesIO()
         with stdout_redirector(f):
@@ -138,7 +138,7 @@ def create_sbmy_power_spectrum_file(parsed_args, card_dict, power_spectrum_file)
 def create_sbmy_white_noise_field(parsed_args, card_dict, white_noise_field_file):
     import numpy as np
     from gc import collect
-    from low_level import print_message
+    from .low_level import print_message
     from pysbmy.field import BaseField
 
     print_message(f"Seed: {parsed_args.seed}", 3, "sbmy IC", verbose=parsed_args.verbose)
@@ -161,7 +161,7 @@ def create_sbmy_white_noise_field(parsed_args, card_dict, white_noise_field_file
 
     if parsed_args.verbose < 2:
         from io import BytesIO
-        from low_level import stdout_redirector, stderr_redirector
+        from .low_level import stdout_redirector, stderr_redirector
         f = BytesIO()
         g = BytesIO()
         with stdout_redirector(f):
@@ -175,11 +175,11 @@ def create_sbmy_white_noise_field(parsed_args, card_dict, white_noise_field_file
 
 if __name__ == "__main__":
     from argparse import ArgumentParser
-    from args_main import register_arguments_main
-    from parameters_card import register_arguments_card_for_ICs
-    from cosmo_params import register_arguments_cosmo
-    from parameters_monofonic import register_arguments_monofonic
-    from slurm_submission import register_arguments_slurm
+    from .args_main import register_arguments_main
+    from .parameters_card import register_arguments_card_for_ICs
+    from .cosmo_params import register_arguments_cosmo
+    from .parameters_monofonic import register_arguments_monofonic
+    from .slurm_submission import register_arguments_slurm
 
     parser = ArgumentParser(description="Generate initial conditions for a Simbelmyne simulation.")
     # TODO: reduce the volume of arguments
@@ -190,4 +190,4 @@ if __name__ == "__main__":
     register_arguments_cosmo(parser)
     parsed_args = parser.parse_args()
 
-    main_ICs(parsed_args)
+    main_ICs(parsed_args)

sbmy_control/analysis/slices.py

@@ -2,7 +2,6 @@ import numpy as np
 
 import sys
 import os
-sys.path.append('/home/aubin/Simbelmyne/sbmy_control/')
 
 fs = 18
 fs_titles = fs - 4
@@ -40,7 +39,7 @@ def plot_imshow_with_reference( data_list,
     """
     import matplotlib.pyplot as plt
 
-    from colormaps import register_colormaps
+    from sbmy_control.analysis.colormaps import register_colormaps
     register_colormaps(plt.colormaps)
 
     if titles is None:
@@ -109,7 +108,7 @@ def plot_imshow_diff(data_list,
     
     import matplotlib.pyplot as plt
 
-    from colormaps import register_colormaps
+    from sbmy_control.analysis.colormapss import register_colormaps
     register_colormaps(plt.colormaps)
     
     if reference is None:

sbmy_control/main.py

@@ -1,9 +1,9 @@
 
 
 def main(parsed_args):
-    from low_level import print_starting_module, print_message, print_ending_module, wait_until_file_exists
+    from .low_level import print_starting_module, print_message, print_ending_module, wait_until_file_exists
     from os.path import isfile
-    from args_main import parse_arguments_main
+    from .args_main import parse_arguments_main
 
     print_starting_module("control", verbose=parsed_args.verbose)
     main_dict = parse_arguments_main(parsed_args)
@@ -12,22 +12,22 @@ def main(parsed_args):
 
         case "ICs" | "InitialConditions" | "InitialConditionsGenerator" | "ICsGenerator" | "ICsGen" | "ini":
             print_message("Running initial conditions generator.", 1, "control", verbose=parsed_args.verbose)
-            from ICs import main_ICs
+            from .ICs import main_ICs
             main_ICs(parsed_args)
             print_message("Initial conditions generator finished.", 1, "control", verbose=parsed_args.verbose)
         
 
         case "TS" | "timestepping":
             print_message("Running timestepping generator.", 1, "control", verbose=parsed_args.verbose)
-            from timestepping import main_timestepping
+            from .timestepping import main_timestepping
             main_timestepping(parsed_args)
             print_message("Timestepping generator finished.", 1, "control", verbose=parsed_args.verbose)
         
 
         case "PM" | "LPT" | "tCOLA" | "simbelmyne" | "sbmy":
             print_message(f"Running Simbelmyne in mode {main_dict["mode"]}.", 1, "control", verbose=parsed_args.verbose)
-            from simbelmyne import main_simbelmyne
-            from parameters_card import parse_arguments_card
+            from .simbelmyne import main_simbelmyne
+            from .parameters_card import parse_arguments_card
             from os.path import isfile
 
             card_dict = parse_arguments_card(parsed_args)
@@ -47,8 +47,8 @@ def main(parsed_args):
 
         case "pre_sCOLA":
             print_message("Running pre-sCOLA.", 1, "control", verbose=parsed_args.verbose)
-            from scola import main_pre_scola
-            from parameters_card import parse_arguments_card
+            from .scola import main_pre_scola
+            from .parameters_card import parse_arguments_card
 
             card_dict = parse_arguments_card(parsed_args)
 
@@ -60,8 +60,8 @@ def main(parsed_args):
 
         case "post_sCOLA":
             print_message("Running post-sCOLA.", 1, "control", verbose=parsed_args.verbose)
-            from scola import main_post_scola
-            from parameters_card import parse_arguments_card
+            from .scola import main_post_scola
+            from .parameters_card import parse_arguments_card
 
             card_dict = parse_arguments_card(parsed_args)
 
@@ -73,8 +73,8 @@ def main(parsed_args):
 
         case "sCOLA":        
             print_message("Running sCOLA.", 1, "control", verbose=parsed_args.verbose)
-            from scola import main_scola
-            from parameters_card import parse_arguments_card
+            from .scola import main_scola
+            from .parameters_card import parse_arguments_card
 
             card_dict = parse_arguments_card(parsed_args)
 
@@ -86,12 +86,12 @@ def main(parsed_args):
 
         case "alltCOLA" | "allPM":
             print_message(f"Running ICs and Simbelmyne in mode {main_dict["mode"]}.", 1, "control", verbose=parsed_args.verbose)
-            from parameters_card import parse_arguments_card, main_parameter_card
-            from timestepping import main_timestepping
-            from ICs import main_ICs
-            from simbelmyne import main_simbelmyne
+            from .parameters_card import parse_arguments_card, main_parameter_card
+            from .timestepping import main_timestepping
+            from .ICs import main_ICs
+            from .simbelmyne import main_simbelmyne
             from os.path import isfile
-            from low_level import wait_until_file_exists
+            from .low_level import wait_until_file_exists
 
             card_dict = main_parameter_card(parsed_args)
 
@@ -101,7 +101,7 @@ def main(parsed_args):
 
             ## Check consistency of ICs_gen and ICs
             if main_dict["ICs_gen"] == "monofonic":
-                from parameters_monofonic import parse_arguments_monofonic
+                from .parameters_monofonic import parse_arguments_monofonic
                 monofonic_dict = parse_arguments_monofonic(parsed_args)
                 if monofonic_dict["output"]+"DM_delta.h5" != card_dict["ICs"]:
                     raise ValueError(f"ICs {card_dict['ICs']} does not match monofonic output {monofonic_dict['output']+'DM_delta.h5'}")
@@ -133,10 +133,10 @@ def main(parsed_args):
 
         case "allsCOLA":
             print_message(f"Running ICs, pre_sCOLA, sCOLA and post_sCOLA.", 1, "control", verbose=parsed_args.verbose)
-            from parameters_card import parse_arguments_card, main_parameter_card
-            from timestepping import main_timestepping
-            from ICs import main_ICs
-            from scola import main_scola, main_pre_scola, main_post_scola, have_all_tiles
+            from .parameters_card import parse_arguments_card, main_parameter_card
+            from .timestepping import main_timestepping
+            from .ICs import main_ICs
+            from .scola import main_scola, main_pre_scola, main_post_scola, have_all_tiles
 
             card_dict = main_parameter_card(parsed_args)
 
@@ -146,7 +146,7 @@ def main(parsed_args):
 
             ## Check consistency of ICs_gen and OutputLPTPotential
             if main_dict["ICs_gen"] == "monofonic":
-                from parameters_monofonic import parse_arguments_monofonic
+                from .parameters_monofonic import parse_arguments_monofonic
                 monofonic_dict = parse_arguments_monofonic(parsed_args)
                 if monofonic_dict["output"]+"DM_phi.h5" != card_dict["OutputLPTPotential1"]:
                     raise ValueError(f"OutputLPTPotential1 {card_dict['OutputLPTPotential1']} does not match monofonic output {monofonic_dict['output']+'DM_phi.h5'}")
@@ -179,7 +179,7 @@ def main(parsed_args):
             main_scola(parsed_args)
             if parsed_args.execution == "slurm" and not have_all_tiles(parsed_args):
                 from tqdm import tqdm
-                from low_level import progress_bar_from_logfile
+                from .low_level import progress_bar_from_logfile
                 for b in tqdm(range(1,parsed_args.N_tiles**3+1), desc="sCOLA", unit="box", disable=(parsed_args.verbose==0)):
                     progress_bar_from_logfile(main_dict["logdir"]+main_dict["simname"]+".log_"+str(b), desc=f"Box {b}/{parsed_args.N_tiles**3}", verbose=parsed_args.verbose, leave=False)
             print_message("sCOLA finished.", 1, "control", verbose=parsed_args.verbose)
@@ -222,13 +222,13 @@ def check_consistency(card_dict, mode):
 
 def console_main():
     from argparse import ArgumentParser
-    from args_main import register_arguments_main
-    from timestepping import register_arguments_timestepping, main_timestepping
-    from parameters_card import register_arguments_card, main_parameter_card
-    from cosmo_params import register_arguments_cosmo
-    from parameters_monofonic import register_arguments_monofonic
-    from slurm_submission import register_arguments_slurm
-    from low_level import wait_until_file_exists
+    from .args_main import register_arguments_main
+    from .timestepping import register_arguments_timestepping, main_timestepping
+    from .parameters_card import register_arguments_card, main_parameter_card
+    from .cosmo_params import register_arguments_cosmo
+    from .parameters_monofonic import register_arguments_monofonic
+    from .slurm_submission import register_arguments_slurm
+    from .low_level import wait_until_file_exists
 
     parser = ArgumentParser(description="Run sCOLA.")
     register_arguments_main(parser)

sbmy_control/monofonic.py

@@ -2,8 +2,8 @@
 path_to_monofonic_binary = "/home/aubin/monofonic/build/monofonIC"
 
 def main_monofonic(parsed_args):
-    from parameters_monofonic import main_parameters_monofonic
-    from low_level import print_starting_module, print_message, print_ending_module
+    from .parameters_monofonic import main_parameters_monofonic
+    from .low_level import print_starting_module, print_message, print_ending_module
     from os.path import isfile
     import subprocess
     
@@ -27,8 +27,8 @@ def main_monofonic(parsed_args):
         print_message("Monofonic finished.", 1, "monofonic", verbose=parsed_args.verbose)
     
     elif parsed_args.execution == "slurm":
-        from slurm_submission import create_slurm_script, parse_arguments_slurm
-        from args_main import parse_arguments_main
+        from .slurm_submission import create_slurm_script, parse_arguments_slurm
+        from .args_main import parse_arguments_main
         print_message("Running monofonic in slurm mode.", 1, "monofonic", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
         main_dict=parse_arguments_main(parsed_args)
@@ -67,11 +67,11 @@ def main_monofonic(parsed_args):
 
 if __name__ == "__main__":
     from argparse import ArgumentParser
-    from parameters_monofonic import register_arguments_monofonic
-    from args_main import register_arguments_main
-    from parameters_card import register_arguments_card_for_ICs
-    from cosmo_params import register_arguments_cosmo
-    from slurm_submission import register_arguments_slurm
+    from .parameters_monofonic import register_arguments_monofonic
+    from .args_main import register_arguments_main
+    from .parameters_card import register_arguments_card_for_ICs
+    from .cosmo_params import register_arguments_cosmo
+    from .slurm_submission import register_arguments_slurm
 
     parser = ArgumentParser(description="Run monofonIC initial conditions generator for a Simbelmyne simulation.")
     # TODO: reduce the volume of arguments 
@@ -82,4 +82,4 @@ if __name__ == "__main__":
     register_arguments_cosmo(parser)
     parsed_args = parser.parse_args()
 
-    main_monofonic(parsed_args)
+    main_monofonic(parsed_args)

sbmy_control/parameters_card.py

@@ -73,8 +73,8 @@ def parse_arguments_card(parsed_args):
     """
     Parse the arguments for the parameter card.
     """
-    from args_main import parse_arguments_main
-    from cosmo_params import parse_arguments_cosmo
+    from .args_main import parse_arguments_main
+    from .cosmo_params import parse_arguments_cosmo
 
     cosmo_dict=parse_arguments_cosmo(parsed_args)
     card_dict=dict(
@@ -212,7 +212,7 @@ def parse_arguments_card_for_ICs(parsed_args):
     """
     Parse the arguments for the parameter card for ICs.
     """
-    from args_main import parse_arguments_main
+    from .args_main import parse_arguments_main
 
     main_dict = parse_arguments_main(parsed_args)
     card_dict = dict(
@@ -252,7 +252,7 @@ def parse_arguments_card_for_timestepping(parsed_args):
     """
     Parse the arguments for the parameter card for timestepping.
     """
-    from args_main import parse_arguments_main
+    from .args_main import parse_arguments_main
 
     main_dict = parse_arguments_main(parsed_args)
     card_dict = dict(
@@ -401,7 +401,7 @@ def write_parameter_card(parameter_card_dict:dict, filename:str, verbose:int = 1
 
     if verbose < 2:
         from io import BytesIO
-        from low_level import stdout_redirector, stderr_redirector
+        from .low_level import stdout_redirector, stderr_redirector
 
         f = BytesIO()
         g = BytesIO()
@@ -420,7 +420,7 @@ def main_parameter_card(parsed_args):
     """
     Main function for the parameter card.
     """
-    from low_level import print_message, print_starting_module, print_ending_module
+    from .low_level import print_message, print_starting_module, print_ending_module
     print_starting_module("card", verbose=parsed_args.verbose)
     print_message("Parsing arguments for the parameter card.", 1, "card", verbose=parsed_args.verbose)
     card_dict = parse_arguments_card(parsed_args)
@@ -436,8 +436,8 @@ def main_parameter_card(parsed_args):
     return card_dict
 
 if __name__ == "__main__":
-    from args_main import register_arguments_main
-    from cosmo_params import register_arguments_cosmo
+    from .args_main import register_arguments_main
+    from .cosmo_params import register_arguments_cosmo
 
     parser = ArgumentParser(description="Create sbmy parameter card.")
     register_arguments_main(parser)
@@ -445,4 +445,4 @@ if __name__ == "__main__":
     register_arguments_cosmo(parser)
     parsed_args = parser.parse_args()
 
-    main_parameter_card(parsed_args)
+    main_parameter_card(parsed_args)

sbmy_control/parameters_monofonic.py

@@ -16,9 +16,9 @@ def parse_arguments_monofonic(parsed_args):
     """
     Parse the arguments for the monofonIC parameters.
     """
-    from args_main import parse_arguments_main
-    from parameters_card import parse_arguments_card_for_ICs
-    from cosmo_params import parse_arguments_cosmo
+    from .args_main import parse_arguments_main
+    from .parameters_card import parse_arguments_card_for_ICs
+    from .cosmo_params import parse_arguments_cosmo
 
     main_dict = parse_arguments_main(parsed_args)
     card_dict = parse_arguments_card_for_ICs(parsed_args)
@@ -131,7 +131,7 @@ def get_config_from_dict(monofonic_dict):
 
 
 def main_parameters_monofonic(parsed_args):
-    from low_level import print_message
+    from .low_level import print_message
 
     print_message("Parsing arguments for the config file.", 1, "monofonic", verbose=parsed_args.verbose)
     monofonic_dict = parse_arguments_monofonic(parsed_args)
@@ -144,9 +144,9 @@ def main_parameters_monofonic(parsed_args):
     
 
 if __name__ == "__main__":
-    from args_main import register_arguments_main
-    from parameters_card import register_arguments_card_for_ICs
-    from cosmo_params import register_arguments_cosmo
+    from .args_main import register_arguments_main
+    from .parameters_card import register_arguments_card_for_ICs
+    from .cosmo_params import register_arguments_cosmo
 
     parser = ArgumentParser(description="Create monofonIC configuration file.")
     register_arguments_main(parser)
@@ -155,4 +155,4 @@ if __name__ == "__main__":
     register_arguments_cosmo(parser)
     parsed_args = parser.parse_args()
 
-    main_parameters_monofonic(parsed_args)
+    main_parameters_monofonic(parsed_args)

sbmy_control/progress_bar.py

@@ -1,7 +1,7 @@
 if __name__ == "__main__":
     from argparse import ArgumentParser
     from tqdm import tqdm
-    from low_level import progress_bar_from_logfile
+    from .low_level import progress_bar_from_logfile
 
     parser = ArgumentParser(description="Progress bar from log files.")
     parser.add_argument("-l","--logdir", type=str, help="Log directory.")
@@ -12,4 +12,4 @@ if __name__ == "__main__":
     parsed_args = parser.parse_args()
 
     for b in tqdm(range(1,parsed_args.N_tiles**3+1), desc="sCOLA", unit="box", disable=(parsed_args.verbose==0)):
-        progress_bar_from_logfile(parsed_args.logdir+parsed_args.simname+".log_"+str(b), desc=f"Box {b}/{parsed_args.N_tiles**3}", verbose=parsed_args.verbose, leave=False)
+        progress_bar_from_logfile(parsed_args.logdir+parsed_args.simname+".log_"+str(b), desc=f"Box {b}/{parsed_args.N_tiles**3}", verbose=parsed_args.verbose, leave=False)

sbmy_control/scola.py

@@ -1,8 +1,8 @@
 
 
 def main_scola(parsed_args):
-    from args_main import parse_arguments_main
-    from low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile, wait_until_file_exists
+    from .args_main import parse_arguments_main
+    from .low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile, wait_until_file_exists
     from os.path import isfile
     import subprocess
     
@@ -21,7 +21,7 @@ def main_scola(parsed_args):
         return
 
     if parsed_args.execution == "local":
-        from parameters_card import parse_arguments_card
+        from .parameters_card import parse_arguments_card
         from tqdm import tqdm
         card_dict = parse_arguments_card(parsed_args)
         print_message("Running sCOLA in local mode.", 1, "scola", verbose=parsed_args.verbose)
@@ -52,9 +52,9 @@ def main_scola(parsed_args):
         print_message("sCOLA finished.", 1, "scola", verbose=parsed_args.verbose)
     
     elif parsed_args.execution == "slurm":
-        from slurm_submission import create_slurm_script, parse_arguments_slurm, limit_slurm_arrays
-        from args_main import parse_arguments_main
-        from parameters_card import parse_arguments_card
+        from .slurm_submission import create_slurm_script, parse_arguments_slurm, limit_slurm_arrays
+        from .args_main import parse_arguments_main
+        from .parameters_card import parse_arguments_card
         import os
         print_message("Running scola in slurm mode.", 1, "scola", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
@@ -148,15 +148,15 @@ def main_pre_scola(parsed_args):
     If they already exist, it does nothing. If all tiles exist, raises error.
     """
     from os.path import isfile
-    from low_level import print_starting_module, print_message, print_ending_module
-    from parameters_card import parse_arguments_card
+    from .low_level import print_starting_module, print_message, print_ending_module
+    from .parameters_card import parse_arguments_card
     print_starting_module("pre-scola", verbose=parsed_args.verbose)
     card_dict = parse_arguments_card(parsed_args)
 
     if not isfile(card_dict["OutputLPTPotential1"]) or not isfile(card_dict["OutputLPTPotential2"]) or parsed_args.force:
         if not have_all_tiles(parsed_args):
             print_message("Running pre-scola.", 1, "pre-scola", verbose=parsed_args.verbose)
-            from simbelmyne import main_simbelmyne
+            from .simbelmyne import main_simbelmyne
             main_simbelmyne(parsed_args)
         else:
             raise NotImplementedError("All tiles exists, so calling simbelmyne would generate the final output instead of the LPT potentials.")
@@ -172,8 +172,8 @@ def main_post_scola(parsed_args):
     If the output already exists, it does nothing. If tiles are missing, print the missing tiles.
     """
     from os.path import isfile
-    from low_level import print_starting_module, print_message, print_ending_module
-    from parameters_card import parse_arguments_card
+    from .low_level import print_starting_module, print_message, print_ending_module
+    from .parameters_card import parse_arguments_card
     print_starting_module("post-scola", verbose=parsed_args.verbose)
     card_dict = parse_arguments_card(parsed_args)
 
@@ -186,7 +186,7 @@ def main_post_scola(parsed_args):
     if (card_dict["WriteFinalDensity"] and not isfile(card_dict["OutputFinalDensity"])) or (card_dict["WriteFinalSnapshot"] and not isfile(card_dict["OutputFinalSnapshot"])) or parsed_args.force:
         if have_all_tiles(parsed_args):
             print_message("Running post-scola.", 1, "post-scola", verbose=parsed_args.verbose)
-            from simbelmyne import main_simbelmyne
+            from .simbelmyne import main_simbelmyne
             main_simbelmyne(parsed_args)
         else:
             missing_tiles_arrays = get_missing_tiles_arrays(parsed_args)
@@ -203,7 +203,7 @@ def main_post_scola(parsed_args):
 
 def have_all_tiles(parsed_args):
     from os.path import isfile
-    from parameters_card import parse_arguments_card
+    from .parameters_card import parse_arguments_card
 
     card_dict = parse_arguments_card(parsed_args)
     nboxes_tot = int(parsed_args.N_tiles**3)
@@ -216,7 +216,7 @@ def have_all_tiles(parsed_args):
 
 def have_no_tiles(parsed_args):
     from os.path import isfile
-    from parameters_card import parse_arguments_card
+    from .parameters_card import parse_arguments_card
 
     card_dict = parse_arguments_card(parsed_args)
     nboxes_tot = int(parsed_args.N_tiles**3)
@@ -229,8 +229,8 @@ def have_no_tiles(parsed_args):
 
 def get_missing_tiles_arrays(parsed_args):
     from os.path import isfile
-    from parameters_card import parse_arguments_card
-    from slurm_submission import limit_slurm_arrays
+    from .parameters_card import parse_arguments_card
+    from .slurm_submission import limit_slurm_arrays
 
     card_dict = parse_arguments_card(parsed_args)
     nboxes_tot = int(parsed_args.N_tiles**3)
@@ -260,13 +260,13 @@ def get_missing_tiles_arrays(parsed_args):
 
 if __name__ == "__main__":
     from argparse import ArgumentParser
-    from args_main import register_arguments_main
-    from timestepping import register_arguments_timestepping, main_timestepping
-    from parameters_card import register_arguments_card, main_parameter_card
-    from cosmo_params import register_arguments_cosmo
-    from parameters_monofonic import register_arguments_monofonic
-    from slurm_submission import register_arguments_slurm
-    from low_level import wait_until_file_exists
+    from .args_main import register_arguments_main
+    from .timestepping import register_arguments_timestepping, main_timestepping
+    from .parameters_card import register_arguments_card, main_parameter_card
+    from .cosmo_params import register_arguments_cosmo
+    from .parameters_monofonic import register_arguments_monofonic
+    from .slurm_submission import register_arguments_slurm
+    from .low_level import wait_until_file_exists
 
     parser = ArgumentParser(description="Run sCOLA.")
     register_arguments_main(parser)

sbmy_control/simbelmyne.py

@@ -1,6 +1,6 @@
 def main_simbelmyne(parsed_args):
-    from args_main import parse_arguments_main
-    from low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile
+    from .args_main import parse_arguments_main
+    from .low_level import print_starting_module, print_message, print_ending_module, progress_bar_from_logfile
     from os.path import isfile
     import subprocess
     
@@ -30,8 +30,8 @@ def main_simbelmyne(parsed_args):
         print_message("Simbelyne finished.", 1, "simbelmyne", verbose=parsed_args.verbose)
     
     elif parsed_args.execution == "slurm":
-        from slurm_submission import create_slurm_script, parse_arguments_slurm
-        from args_main import parse_arguments_main
+        from .slurm_submission import create_slurm_script, parse_arguments_slurm
+        from .args_main import parse_arguments_main
         print_message("Running simbelmyne in slurm mode.", 1, "simbelmyne", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
         main_dict=parse_arguments_main(parsed_args)
@@ -76,12 +76,12 @@ def main_simbelmyne(parsed_args):
 
 if __name__ == "__main__":
     from argparse import ArgumentParser
-    from args_main import register_arguments_main
-    from timestepping import register_arguments_timestepping, main_timestepping
-    from parameters_card import register_arguments_card, main_parameter_card
-    from cosmo_params import register_arguments_cosmo
-    from parameters_simbelmyne import register_arguments_simbelmyne
-    from slurm_submission import register_arguments_slurm
+    from .args_main import register_arguments_main
+    from .timestepping import register_arguments_timestepping, main_timestepping
+    from .parameters_card import register_arguments_card, main_parameter_card
+    from .cosmo_params import register_arguments_cosmo
+    from .parameters_simbelmyne import register_arguments_simbelmyne
+    from .slurm_submission import register_arguments_slurm
 
     parser = ArgumentParser(description="Run Simbelmyne.")
     register_arguments_main(parser)
@@ -94,4 +94,4 @@ if __name__ == "__main__":
 
     main_parameter_card(parsed_args)
     main_timestepping(parsed_args)
-    main_simbelmyne(parsed_args)
+    main_simbelmyne(parsed_args)

sbmy_control/slurm_submission.py

@@ -1,5 +1,5 @@
 from argparse import ArgumentParser
-from args_main import parse_arguments_main
+from .args_main import parse_arguments_main
 
 path_to_monofonic_binary = "/home/aubin/monofonic/build/monofonIC"
 limit_slurm_arrays=799

sbmy_control/timestepping.py

@@ -18,8 +18,8 @@ def parse_arguments_timestepping(parsed_args):
     """
     Parse the arguments for the timestepping.
     """
-    from parameters_card import parse_arguments_card_for_timestepping
-    from cosmo_params import parse_arguments_cosmo, z2a
+    from .parameters_card import parse_arguments_card_for_timestepping
+    from .cosmo_params import parse_arguments_cosmo, z2a
 
     card_dict = parse_arguments_card_for_timestepping(parsed_args)
     cosmo_dict = parse_arguments_cosmo(parsed_args)
@@ -79,7 +79,7 @@ def create_timestepping(timestepping_dict, ts_filename:str, verbose:int=1):
     TS = StandardTimeStepping(**timestepping_dict)
     if verbose < 2:
         from io import BytesIO
-        from low_level import stdout_redirector, stderr_redirector
+        from .low_level import stdout_redirector, stderr_redirector
         f = BytesIO()
         g = BytesIO()
         with stdout_redirector(f):
@@ -95,7 +95,7 @@ def main_timestepping(parsed_args):
     """
     Main function for the timestepping.
     """
-    from low_level import print_message, print_ending_module, print_starting_module
+    from .low_level import print_message, print_ending_module, print_starting_module
 
     print_starting_module("timestepping", verbose=parsed_args.verbose)
     print_message("Parsing arguments for the timestepping file.", 1, "timestepping", verbose=parsed_args.verbose)
@@ -110,9 +110,9 @@ def main_timestepping(parsed_args):
     return timestepping_dict
 
 if __name__ == "__main__":
-    from args_main import register_arguments_main
-    from parameters_card import register_arguments_card_for_timestepping
-    from cosmo_params import register_arguments_cosmo
+    from .args_main import register_arguments_main
+    from .parameters_card import register_arguments_card_for_timestepping
+    from .cosmo_params import register_arguments_cosmo
 
     parser = ArgumentParser(description="Create timestepping file.")
     # TODO: reduce the volume of arguments
@@ -121,4 +121,4 @@ if __name__ == "__main__":
     register_arguments_card_for_timestepping(parser)
     register_arguments_cosmo(parser)
     parsed_args = parser.parse_args()
-    main_timestepping(parsed_args)
+    main_timestepping(parsed_args)