physioblocks 1.1.0__py3-none-any.whl → 1.1.1__py3-none-any.whl

physioblocks/__init__.py

@@ -26,7 +26,7 @@
 
 """Physioblocks package definition"""
 
-__version__ = "1.1.0"
+__version__ = "1.1.1"
 __copyright__ = "INRIA"
 __license__ = "LGPL-3.0-only"
 __authors__ = [

physioblocks/launcher/__main__.py

@@ -37,6 +37,7 @@ from pathlib import Path
 from typing import Any
 
 import pandas as pd
+from rich.logging import RichHandler
 
 import physioblocks.utils.exceptions_utils as exception_utils
 from physioblocks.configuration import Configuration, load, unwrap_aliases
@@ -64,8 +65,9 @@ from physioblocks.simulation import AbstractSimulation, SimulationError
 .. note:: When deleting a serie from the launcher folder, or a specific simulation from
   a serie, the launchers logs are updated the next time any simulation is launched.
 """
+FILE_LOG_FORMATTER = logging.Formatter(logging.BASIC_FORMAT)
+RICH_LOG_FORMATTER = logging.Formatter("%(message)s", "[%X]")
 
-SIMULATION_LOG_FORMATER = logging.Formatter(logging.BASIC_FORMAT)
 _root_logger = logging.getLogger()
 _root_logger.setLevel(logging.DEBUG)
 
@@ -90,8 +92,10 @@ def run_simulation(config: Configuration) -> pd.DataFrame:
     return pd.DataFrame(results)
 
 
-def add_log_handler(handler: logging.Handler, level: str | int) -> None:
-    handler.setFormatter(SIMULATION_LOG_FORMATER)
+def add_log_handler(
+    handler: logging.Handler, level: str | int, formatter: logging.Formatter
+) -> None:
+    handler.setFormatter(formatter)
     handler.setLevel(level)
     _root_logger.addHandler(handler)
 
@@ -132,7 +136,7 @@ def main(
     # configure the simulation log file (always in DEBUG)
     log_file_path = sim_folder / str.join(".", [sim_info.reference, "log"])
     file_handler = logging.FileHandler(log_file_path)
-    add_log_handler(file_handler, logging.DEBUG)
+    add_log_handler(file_handler, logging.DEBUG, FILE_LOG_FORMATTER)
 
     # log the current simulation infos
     _root_logger.info(str(sim_info))
@@ -260,8 +264,8 @@ if __name__ == "__main__":
 
     # setup logger when verbose
     if args.verbose is True:
-        stdout_handler = logging.StreamHandler(sys.stdout)
-        add_log_handler(stdout_handler, args.log_level)
+        # stdout_handler = logging.StreamHandler(sys.stdout)
+        add_log_handler(RichHandler(), args.log_level, RICH_LOG_FORMATTER)
 
     # create paths from arguments
     root_folder_path = Path(args.launcher_directory).absolute()

physioblocks/simulation/runtime.py

@@ -37,6 +37,7 @@ from typing import Any, TypeAlias
 
 import numpy as np
 from numpy.typing import NDArray
+from rich.progress import Progress
 
 from physioblocks.computing.assembling import EqSystem
 from physioblocks.computing.models import ModelComponent
@@ -359,77 +360,82 @@ class ForwardSimulation(AbstractSimulation):
         """
         # initialize the simulation and save the initial results
         results = self._initialize()
-
-        try:
-            while self.time_manager.ended is False:
-                next_step = self.time_manager.time.new
-
-                self._update_time()
-
-                while (
-                    np.abs(next_step - self.time_manager.time.current)
-                    > self.time_manager.min_step
-                ):
-                    self.state.reset_state_vector()
-
-                    sol = self.solver.solve(self.state, self.eq_system)
-
-                    if sol.converged is False:
-                        inter_time = 0.5 * self.time_manager.current_step_size
-                        if inter_time < self.time_manager.min_step:
-                            raise ConvergenceError(
-                                str.format(
-                                    "The solver did not converge at {0}s for minimal"
-                                    "time step {1}",
-                                    self.time_manager.time.current,
-                                    self.time_manager.min_step,
+        progress_step_update = (
+            100.0 * self.time_manager.step_size / self.time_manager.duration
+        )
+        with Progress() as progress:
+            try:
+                sim_task = progress.add_task("Simulation in progress...")
+                while self.time_manager.ended is False:
+                    next_step = self.time_manager.time.new
+
+                    self._update_time()
+
+                    while (
+                        np.abs(next_step - self.time_manager.time.current)
+                        > self.time_manager.min_step
+                    ):
+                        self.state.reset_state_vector()
+
+                        sol = self.solver.solve(self.state, self.eq_system)
+
+                        if sol.converged is False:
+                            inter_time = 0.5 * self.time_manager.current_step_size
+                            if inter_time < self.time_manager.min_step:
+                                raise ConvergenceError(
+                                    str.format(
+                                        "The solver did not converge at {0}s for "
+                                        "minimal time step {1}",
+                                        self.time_manager.time.current,
+                                        self.time_manager.min_step,
+                                    )
                                 )
-                            )
 
-                        self.time_manager.current_step_size = inter_time
-                        self.time_manager.time.update(
-                            self.time_manager.time.current
-                            + self.time_manager.current_step_size
-                        )
-                    else:
-                        self.state.set_state_vector(sol.x)
-
-                        self.time_manager.update_time()
-                        if (
-                            np.abs(next_step - self.time_manager.time.current)
-                            >= self.time_manager.min_step
-                        ):
-                            self.time_manager.current_step_size = (
-                                next_step - self.time_manager.time.current
-                            )
-                            self.time_manager.time.update(next_step)
-                        else:
-                            self.time_manager.time.initialize(next_step)
-                            self.time_manager.current_step_size = (
-                                self.time_manager.step_size
-                            )
+                            self.time_manager.current_step_size = inter_time
                             self.time_manager.time.update(
                                 self.time_manager.time.current
                                 + self.time_manager.current_step_size
                             )
+                        else:
+                            self.state.set_state_vector(sol.x)
+
+                            self.time_manager.update_time()
+                            if (
+                                np.abs(next_step - self.time_manager.time.current)
+                                >= self.time_manager.min_step
+                            ):
+                                self.time_manager.current_step_size = (
+                                    next_step - self.time_manager.time.current
+                                )
+                                self.time_manager.time.update(next_step)
+                            else:
+                                progress.update(sim_task, advance=progress_step_update)
+                                self.time_manager.time.initialize(next_step)
+                                self.time_manager.current_step_size = (
+                                    self.time_manager.step_size
+                                )
+                                self.time_manager.time.update(
+                                    self.time_manager.time.current
+                                    + self.time_manager.current_step_size
+                                )
 
-                self.state.set_state_vector(sol.x)
-                results.append(self._get_current_result())
-        except Exception as exception:
-            log_exception(
-                _logger,
-                type(exception),
-                exception,
-                exception.__traceback__,
-                logging.DEBUG,
-            )
-            raise SimulationError(
-                str.format(
-                    "An error caused the simulation to stop prematurely",
-                    intermediate_results=results,
-                ),
-                results,
-            ) from exception
+                    self.state.set_state_vector(sol.x)
+                    results.append(self._get_current_result())
+            except Exception as exception:
+                log_exception(
+                    _logger,
+                    type(exception),
+                    exception,
+                    exception.__traceback__,
+                    logging.DEBUG,
+                )
+                raise SimulationError(
+                    str.format(
+                        "An error caused the simulation to stop prematurely",
+                        intermediate_results=results,
+                    ),
+                    results,
+                ) from exception
 
         self._finalize()
         return results

{physioblocks-1.1.0.dist-info → physioblocks-1.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: physioblocks
-Version: 1.1.0
+Version: 1.1.1
 Dynamic: Author
 Dynamic: Author-email
 Dynamic: License
@@ -31,6 +31,7 @@ Requires-Dist: pandas
 Requires-Dist: plotly
 Requires-Dist: pyarrow
 Requires-Dist: regex
+Requires-Dist: rich
 Requires-Dist: scipy
 Provides-Extra: doc
 Requires-Dist: sphinx; extra == 'doc'

{physioblocks-1.1.0.dist-info → physioblocks-1.1.1.dist-info}/RECORD

@@ -1,4 +1,4 @@
-physioblocks/__init__.py,sha256=NGE_lMcYMiJkOlsYXaUITBFVAdwOmguluAly7DLiZ2k,1169
+physioblocks/__init__.py,sha256=NthjhG_G55GynSs5McIQOqRAVapELOh35oy3nf19u-E,1169
 physioblocks/base/__init__.py,sha256=2h6bk0fe8pwQvJ15Buytg4SZzYOH-Ep7WqoD6pd1eOQ,986
 physioblocks/base/operators.py,sha256=uUfswQZsaMNd2bd7wsaxSGFIYLAr1hQCQ6SQfYawdBc,5689
 physioblocks/base/registers.py,sha256=Cd0hmy1XqojjPQgb_jn4mGeAMTyWWgDkl3qJHCVjCRU,3119
@@ -25,7 +25,7 @@ physioblocks/description/nets.py,sha256=pKG2uB-4dABc-lvGswkybiho18bOkUwsVJYBdlX7
 physioblocks/io/__init__.py,sha256=bOGWA0hAifT9wHxD4kWFQuAXpAx0GzDmGfmcgNDUCGo,990
 physioblocks/io/aliases.py,sha256=d_Gqz0-8SVD6tA9N-T9xYL8SRhaSMmIOjqvOKHBb-Yo,2288
 physioblocks/io/configuration.py,sha256=UY8whA_7KcMwi_gXPIt5h8_gD7TKO2Co5cyf9MHO0yg,3578
-physioblocks/launcher/__main__.py,sha256=pLTJzaMZGN7elr8aAvgkjYOhnp6fbGouH5SWq_5bKIg,8811
+physioblocks/launcher/__main__.py,sha256=BMErik5JIbCKmjZecQHMUUq5_GQeRQg8zLwYvHFelxk,8968
 physioblocks/launcher/configuration.py,sha256=dqHCR_7PSDInA8NC3NFONqK3PPwSQYpLkZgYSyVU1vs,7959
 physioblocks/launcher/constants.py,sha256=FIBKde1vJrUzMk9dSl4q8f8jqN7bFxYF05EIG2-V0zw,3033
 physioblocks/launcher/files.py,sha256=zvif_8Woh3vEYCb_K3YnFFZYpgMhdlf4c2OSIVW4jC4,4950
@@ -72,7 +72,7 @@ physioblocks/registers/type_register.py,sha256=JUlrPfP-X_TjIOHewSTkzf7Ck3L0ivVoH
 physioblocks/simulation/__init__.py,sha256=wqKVI3OLLVWuQoUcWwKSs5ibdkTP3Da_5DOe36v1up4,1504
 physioblocks/simulation/constants.py,sha256=w9CsB4V7YtvcdW4N1p7Iu6MeV4i-kazcEPAygE7mSx0,1075
 physioblocks/simulation/functions.py,sha256=c6HFwXK8IAzH7gSkz9aMiXLqnWXn_4_9WsX4jrGN9pY,2307
-physioblocks/simulation/runtime.py,sha256=JDRBoN5lSDUmEKohXIWPadxjO6JcFHd7JYzUlkFrzxE,15498
+physioblocks/simulation/runtime.py,sha256=Moa6S1iR7oPuni8yvO7VwmBsubMcJMpIUeowk1BLaC0,16104
 physioblocks/simulation/saved_quantities.py,sha256=fKWr1wScqxHPhuCE7aDNs8lpm9oWfyLN8NZDus2knPM,4111
 physioblocks/simulation/setup.py,sha256=UmIklaHmfkxi_BIdYKOhorLoC9QT9D4oEXwC-Xfd6v0,18109
 physioblocks/simulation/solvers.py,sha256=xztL-QboEO2mgtws13QE0-wHJ22vjQQzAQahYfxXVBQ,7226
@@ -86,8 +86,8 @@ physioblocks/utils/math_utils.py,sha256=w5MDs4cP5WiTPHe8WofFuNZZ20WDNLT0XmFGlbis
 physioblocks/references/circulation_alone_sim.jsonc,sha256=qv27nzmK7jennhtCJ7wQ_f83mt9_YJSOTABjGCYMcZw,736
 physioblocks/references/spherical_heart_respiration_sim.jsonc,sha256=kKq5xf94r90O1KpkCHk1qwgy6DJ37ePo3-8buEtcu5Y,1397
 physioblocks/references/spherical_heart_sim.jsonc,sha256=kGGBqxY8dnmGKmpMv216kbneyJRGz_3VkcYn1OWavIA,1151
-physioblocks-1.1.0.dist-info/METADATA,sha256=d7JWdSGdkgL7dx9ExTNXLqB0O1LkIQ-qLpKeGoeHilU,4708
-physioblocks-1.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-physioblocks-1.1.0.dist-info/licenses/licenses/GPL-3.0-only.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-physioblocks-1.1.0.dist-info/licenses/licenses/LGPL-3.0-only.txt,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-physioblocks-1.1.0.dist-info/RECORD,,
+physioblocks-1.1.1.dist-info/METADATA,sha256=eDM0OMOHOexQxV_g4XMTCVcr9eJQYFoHVkqzSZ4O5Hk,4728
+physioblocks-1.1.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+physioblocks-1.1.1.dist-info/licenses/licenses/GPL-3.0-only.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+physioblocks-1.1.1.dist-info/licenses/licenses/LGPL-3.0-only.txt,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+physioblocks-1.1.1.dist-info/RECORD,,