Merge pull request #98 from radionets-project/logging

Logging

Author: aknierim

docs/api-reference/utils/index.rst

@@ -22,6 +22,7 @@ Submodules
 
   config
   data
+  logging
 
 
 Reference/API

docs/api-reference/utils/logging.rst

@@ -0,0 +1,16 @@
+.. _utils_logging:
+
+***************************************
+Logging (:mod:`pyvisgen.utils.logging`)
+***************************************
+
+.. currentmodule:: pyvisgen.utils.logging
+
+Logging submodule of :mod:`pyvisgen.utils`.
+
+
+Reference/API
+=============
+
+.. automodapi:: pyvisgen.utils.logging
+    :inherited-members:

docs/changes/98.feature.rst

@@ -0,0 +1,4 @@
+- Added a new `setup_logger` function in {mod}`pyvisgen.utils`
+- Added logging throughout the codebase
+- Replaced bare prints with `LOGGER.info` or `LOGGER.warning` for better status messages
+- Added exception logging before raising an exception, providing better tracebacks and error context

docs/conf.py

@@ -185,6 +185,7 @@
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
     "pytest": ("https://docs.pytest.org/en/stable", None),
     "python": ("https://docs.python.org/3", None),
+    "rich": ("https://rich.readthedocs.io/en/stable", None),
     "scipy": ("https://docs.scipy.org/doc/scipy", None),
     "torch": ("https://pytorch.org/docs/stable/", None),
 }

src/pyvisgen/gridding/gridder.py

@@ -4,6 +4,9 @@
 from numpy.exceptions import AxisError
 
 from pyvisgen.gridding.alt_gridder import ms2dirty_python_fast
+from pyvisgen.utils.logging import setup_logger
+
+LOGGER = setup_logger()
 
 
 def ducc0_gridding(uv_data, freq_data):

src/pyvisgen/gridding/utils.py

@@ -9,8 +9,10 @@
 from pyvisgen.gridding import grid_data
 from pyvisgen.utils.config import read_data_set_conf
 from pyvisgen.utils.data import load_bundles, open_bundles
+from pyvisgen.utils.logging import setup_logger
 
 os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
+LOGGER = setup_logger()
 
 
 def create_gridded_data_set(config):

src/pyvisgen/layouts/layouts.py

@@ -6,6 +6,10 @@
 import torch
 from astropy.coordinates import EarthLocation
 
+from pyvisgen.utils.logging import setup_logger
+
+LOGGER = setup_logger()
+
 
 @dataclass
 class Stations:

src/pyvisgen/simulation/data_set.py

@@ -6,7 +6,7 @@
 from astropy import units as un
 from astropy.time import Time
 from joblib import Parallel, delayed
-from rich import print
+from rich.pretty import pretty_repr
 from tqdm.auto import tqdm
 
 import pyvisgen.fits.writer as writer
@@ -22,9 +22,11 @@
 from pyvisgen.simulation.visibility import vis_loop
 from pyvisgen.utils.config import read_data_set_conf
 from pyvisgen.utils.data import load_bundles, open_bundles
+from pyvisgen.utils.logging import setup_logger
 
 __all__ = ["SimulateDataSet"]
 
+LOGGER = setup_logger()
 
 DATEFMT = "%d-%m-%Y %H:%M:%S"
 
@@ -111,7 +113,8 @@ def from_config(
         else:
             raise ValueError("Expected config to be one of str, Path or dict!")
 
-        print("Simulation Config:\n", cls.conf)
+        LOGGER.info("Simulation Config:")
+        LOGGER.info(pretty_repr(cls.conf))
 
         cls.device = cls.conf["device"]
 
@@ -125,7 +128,7 @@ def from_config(
 
         cls.data_paths = load_bundles(cls.conf["in_path"])
 
-        if not cls.num_images:
+        if cls.num_images is None:
             data_bundles = tqdm(
                 range(len(cls.data_paths)),
                 position=0,
@@ -211,7 +214,7 @@ def _run(self) -> None:
                     truth_fft = convert_real_imag(truth_fft, sky_sim=True)
 
                 if sim_data.shape[1] != 2:
-                    raise ValueError("Expected sim_data axis 1 to be 2!")
+                    raise ValueError("Expected sim_data axis at index 1 to be 2!")
 
                 out = self.out_path / Path(
                     f"samp_{self.conf['file_prefix']}_" + str(i) + ".h5"
@@ -234,7 +237,7 @@ def _run(self) -> None:
                     f"samp_{self.conf['file_prefix']}_<id>.fits"
                 )
 
-        print(
+        LOGGER.info(
             f"Successfully simulated and saved {samp_opts_idx} images to '{path_msg}'!"
         )
 

src/pyvisgen/simulation/observation.py

@@ -11,8 +11,10 @@
 
 from pyvisgen.layouts import layouts
 from pyvisgen.simulation.array import Array
+from pyvisgen.utils.logging import setup_logger
 
 torch.set_default_dtype(torch.float64)
+LOGGER = setup_logger()
 
 __all__ = ["Baselines", "ValidBaselineSubset", "Observation"]
 
@@ -968,4 +970,5 @@ def calc_direction_cosines(
                 "Expected u, v, and w to have the same shapes "
                 f"but got {u.shape}, {v.shape}, and {w.shape}."
             )
+
         return u, v, w

src/pyvisgen/simulation/visibility.py

@@ -6,8 +6,10 @@
 from tqdm.auto import tqdm
 
 import pyvisgen.simulation.scan as scan
+from pyvisgen.utils.logging import setup_logger
 
 torch.set_default_dtype(torch.float64)
+LOGGER = setup_logger()
 
 __all__ = [
     "Visibilities",
@@ -500,8 +502,10 @@ def vis_loop(
     elif mode == "dense":
         if obs.device == torch.device("cpu"):
             raise ValueError("Only available for GPU calculations!")
-        obs.calc_dense_baselines()
-        bas = obs.dense_baselines_gpu
+
+        # We cannot test this at the moment
+        obs.calc_dense_baselines()  # pragma: no cover
+        bas = obs.dense_baselines_gpu  # pragma: nocover
     else:
         raise ValueError("Unsupported mode!")