Add logging of print statements

.github/workflows/test_pvade.yaml

@@ -25,10 +25,13 @@ jobs:
       - name: Build Conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:
+          # auto-update-conda: true
+          python-version: "3.10"
           environment-file: environment.yaml
+          activate-environment: pvade
       - name: Run pytest
         shell: bash -l {0}
-        run: pytest -sv pvade/tests/
+        run: PYTHONPATH=. pytest -sv pvade/tests/
 
   # Job 2 of 2 - enforce Black formatting
   formatting:

environment.yaml

@@ -1,7 +1,7 @@
 name: pvade
 channels:
   - conda-forge  
-  - defaults
+  - nodefaults
 dependencies:
   # Dependencies should be kept as loosely pinned to version numbers as possible
   - alive-progress

pvade/IO/DataStream.py

@@ -1,22 +1,64 @@
-# from dolfinx import *
-import numpy as np
-import time
-import os
-import shutil
-from dolfinx.io import XDMFFile, VTKFile
-from mpi4py import MPI
-from pathlib import Path
-import pytest
-import dolfinx
-from petsc4py import PETSc
-import json
+from dolfinx.io import XDMFFile
 
-# from dolfinx.fem import create_nonmatching_meshes_interpolation_data
+# import logging
+import sys
+from datetime import datetime
 
-# hello
+
+def start_print_and_log(rank, logfile_name):
+
+    class PrintAndLog:
+        """
+        A class to capture normal print statements in a log file
+        along with displaying them to the terminal as usual.
+        """
+
+        def __init__(self, logfile_name, rank, message_type):
+            self.logfile_name = logfile_name
+            self.rank = rank
+            self.message_type = message_type
+
+            if message_type == "INFO":
+                self.terminal = sys.__stdout__
+            elif message_type == "ERROR":
+                self.terminal = sys.__stdout__
+            else:
+                raise ValueError(f"Type {message_type} not recognized")
+
+        def write(self, message):
+            # Write to both the command line and save to the logfile
+            cleaned_message = message.rstrip()
+
+            # Can include a test like `len(message) > 0 and self.rank == 0`
+            # to limit this to only printing from rank 0, but for parallel
+            # debugging, it is often helpful to see messages from all ranks
+            # so we omit this check for now.
+            if len(cleaned_message) > 0:
+
+                cleaned_message += "\n"
+
+                self.terminal.write(f"{cleaned_message}")
+                timestamp = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
+
+                with open(self.logfile_name, "a") as fp:
+                    fp.write(f"{timestamp} [{self.message_type}] {cleaned_message}")
+
+        def flush(self):
+            # Dummy method
+            pass
+
+    with open(logfile_name, "w") as fp:
+        # Start with an empty file
+        pass
+
+    # Redirect stdout and stderr
+    sys.stdout = PrintAndLog(logfile_name, rank, message_type="INFO")
+    sys.stderr = PrintAndLog(logfile_name, rank, message_type="ERROR")
+
+    if rank == 0:
+        print("Starting PVade Run")
 
 
-# test actions
 class DataStream:
     """Input/Output and file writing class
 
@@ -50,11 +92,6 @@ def __init__(self, domain, flow, structure, params):
         self.ndim = domain.fluid.msh.topology.dim
         self.thermal_analysis = params.general.thermal_analysis
 
-        self.log_filename = f"{params.general.output_dir_sol}/log.txt"
-        if self.rank == 0:
-            with open(self.log_filename, "w") as fp:
-                fp.write("Run Started.\n")
-
         # If doing a fluid simulation, start a fluid solution file
         if params.general.fluid_analysis:
             self.results_filename_fluid = (
@@ -171,13 +208,6 @@ def save_XDMF_files(self, fsi_object, domain, tt):
                 f"Got found fsi object name = {fsi_object.name}, not recognized."
             )
 
-    def print_and_log(self, string_to_print):
-        if self.rank == 0:
-            print(string_to_print)
-
-            with open(self.log_filename, "a") as fp:
-                fp.write(f"{string_to_print}\n")
-
     # def fluid_struct(self, domain, flow, elasticity, params):
     #     # print("tst")
 

pvade/IO/Utilities.py

@@ -8,7 +8,7 @@ def get_input_file():
         "--input_file",
         metavar="",
         type=str,
-        help="The full path to the input file, e.g., 'intputs/my_params.yaml'",
+        help="The full path to the input file, e.g., 'inputs/my_params.yaml'",
     )
 
     command_line_inputs, unknown = parser.parse_known_args()

pvade_main.py

@@ -1,5 +1,5 @@
 from pvade.fluid.FlowManager import Flow
-from pvade.IO.DataStream import DataStream
+from pvade.IO.DataStream import DataStream, start_print_and_log
 from pvade.fsi.FSI import FSI
 from pvade.IO.Parameters import SimParams
 from pvade.IO.Utilities import get_input_file, write_metrics
@@ -25,6 +25,9 @@ def main(input_file=None):
     # Load the parameters object specified by the input file
     params = SimParams(input_file)
 
+    logfile_name = os.path.join(params.general.output_dir, "logfile.log")
+    start_print_and_log(params.rank, logfile_name)
+
     fluid_analysis = params.general.fluid_analysis
     structural_analysis = params.general.structural_analysis
     thermal_analysis = params.general.thermal_analysis