Merge pull request #55 from MetaSys-LISBP/dev

Dev

physiofit/__init__.py

@@ -1,3 +1,6 @@
 import importlib.metadata
+import logging
 
-__version__ = importlib.metadata.version("physiofit")
+__version__ = importlib.metadata.version("physiofit")
+logger = logging.getLogger("physiofit")
+logger.setLevel(logging.DEBUG)

physiofit/base/fitter.py

@@ -11,8 +11,8 @@
 
 from physiofit.models.base_model import Model
 
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.INFO)
+logger = logging.getLogger(f"physiofit.{__name__}")
+
 
 
 # TODO: add estimate deg function (eq 6) with plot of best fit and measured values
@@ -320,15 +320,13 @@ def _run_optimization(
         """
 
         if method == "differential_evolution":
-            logger.debug(f"Optimization method = {method}")
             optimize_results = differential_evolution(
                 PhysioFitter._calculate_cost, bounds=bounds,
                 args=(
                 func, exp_data_matrix, time_vector, non_opt_params, sd_matrix),
                 polish=True, x0=np.array(params)
             )
         elif method == "L-BFGS-B":
-            logger.debug(f"Optimization method = {method}")
             optimize_results = minimize(
                 PhysioFitter._calculate_cost, x0=np.array(params),
                 args=(

physiofit/base/io.py

@@ -22,8 +22,7 @@
 # Switch matplotlib logger to higher level to not get debug logs in root logger
 logging.getLogger("matplotlib").setLevel(logging.WARNING)
 
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.DEBUG)
+logger = logging.getLogger(f"physiofit.{__name__}")
 
 
 class IoHandler:

physiofit/ui/cli.py

@@ -19,6 +19,8 @@
 
 from physiofit.base.io import IoHandler, StandardDevs, ConfigParser
 
+logger = logging.getLogger(f"physiofit")
+
 def args_parse():
     """
     Parse arguments from user input.
@@ -59,18 +61,18 @@ def args_parse():
     )
 
     # Parse selective output path arguments (for galaxy implementation mostly)
-    parser.add_argument(
-        "-op", "--output_pdf", type=str,
-        help="Path to output the pdf file containing plots"
-    )
-    parser.add_argument(
-        "-of", "--output_fluxes", type=str,
-        help="Path to output the flux results"
-    )
-    parser.add_argument(
-        "-os", "--output_stats", type=str,
-        help="Path to output the khi² test"
-    )
+    # parser.add_argument(
+    #     "-op", "--output_pdf", type=str,
+    #     help="Path to output the pdf file containing plots"
+    # )
+    # parser.add_argument(
+    #     "-of", "--output_fluxes", type=str,
+    #     help="Path to output the flux results"
+    # )
+    # parser.add_argument(
+    #     "-os", "--output_stats", type=str,
+    #     help="Path to output the khi² test"
+    # )
     parser.add_argument(
         "-oc", "--output_config", type=str,
         help="Path to output the yaml config file"
@@ -88,11 +90,11 @@ def args_parse():
 
 def run(data, args, logger, experiments):
 
+    io = IoHandler()
     for exp in experiments:
-        io = IoHandler()
         exp_data = data.loc[exp, :].sort_values("time").copy()
         logger.info(f"Input Data: \n{exp_data}")
-        if hasattr(args, 'galaxy'):
+        if args.galaxy:
             io.wkdir = Path('.')
         else:
             io.wkdir = Path(args.data).parent
@@ -129,10 +131,7 @@ def run(data, args, logger, experiments):
         if not io.multiple_experiments:
             io.multiple_experiments = []
         io.multiple_experiments.append(df)
-        if exp is not None:
-            res_path = io.wkdir / (io.wkdir.name + "_res") / exp
-        else:
-            res_path = io.wkdir / (io.wkdir.name + "_res")
+        res_path = io.wkdir / (io.wkdir.name + "_res") / exp
         logger.info(res_path)
         if not res_path.is_dir():
             res_path.mkdir(parents=True)
@@ -149,13 +148,17 @@ def run(data, args, logger, experiments):
         # for line in dir.rglob("*"):
         #     print(line)
         generate_zips(str(dir), args.output_zip, logger)
+    logger.debug(f"Dataframes to concatenate:\n{io.multiple_experiments}")
 
     # shutil.make_archive(
     #     args.output_zip,
     #     format='zip',
     #     root_dir=str(io.home_path / (io.home_path.name + "_res"))
     #     )
-    io.output_recap(export_path=args.output_recap, galaxy=True)
+    if args.galaxy:
+        io.output_recap(export_path=args.output_recap, galaxy=args.galaxy)
+    else:
+        io.output_recap(export_path=str(res_path.parent), galaxy=False)
 
 def generate_zips(path_to_data_folder, output_path, logger):
     """Generate output zip file containing results
@@ -221,16 +224,15 @@ def generate_config(args, data, logger):
 
 def process(args):
 
-    logger = logging.getLogger()
-    logger.setLevel(logging.DEBUG)
-    out_stream = logging.StreamHandler()
-    formatter = logging.Formatter()
-    out_stream.setFormatter(formatter)
+    cli_handle = logging.StreamHandler()
+    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+    cli_handle.setFormatter(formatter)
     if args.debug_mode:
-        out_stream.setLevel(logging.DEBUG)
+        cli_handle.setLevel(logging.DEBUG)
     else:
-        out_stream.setLevel(logging.INFO)
-    logger.addHandler(out_stream)
+        cli_handle.setLevel(logging.INFO)
+    logger.addHandler(cli_handle)
+
 
     if args.list:
         IoHandler.get_model_list()

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "physiofit"
-version = "3.3.4"
+version = "3.3.5"
 description = "Calculate extracellular fluxes from metabolite concentrations and biomass data"
 authors = ["llegregam <[email protected]>"]
 license = "GNU General Public License (GPL)"