Write a traceback file

src/metatrain/__main__.py

@@ -1,22 +1,21 @@
 """The main entry point for the metatrain command line interface."""
 
 import argparse
-import importlib
 import logging
 import os
 import sys
 import traceback
 from datetime import datetime
 from pathlib import Path
 
-import metatensor.torch
-from omegaconf import OmegaConf
-
 from . import __version__
-from .cli.eval import _add_eval_model_parser, eval_model
-from .cli.export import _add_export_model_parser, export_model
-from .cli.train import _add_train_model_parser, train_model
-from .utils.architectures import check_architecture_name
+from .cli.eval import _add_eval_model_parser, _prepare_eval_model_args, eval_model
+from .cli.export import (
+    _add_export_model_parser,
+    _prepare_export_model_args,
+    export_model,
+)
+from .cli.train import _add_train_model_parser, _prepare_train_model_args, train_model
 from .utils.logging import setup_logging
 
 
@@ -71,62 +70,49 @@ def main():
     args = ap.parse_args()
     callable = args.__dict__.pop("callable")
     debug = args.__dict__.pop("debug")
-    logfile = None
+    log_file = None
+    error_file = Path("error.log")
 
     if debug:
         level = logging.DEBUG
     else:
         level = logging.INFO
 
-    if callable == "eval_model":
-        args.__dict__["model"] = metatensor.torch.atomistic.load_atomistic_model(
-            path=args.__dict__.pop("path"),
-            extensions_directory=args.__dict__.pop("extensions_directory"),
-        )
-    elif callable == "export_model":
-        architecture_name = args.__dict__.pop("architecture_name")
-        check_architecture_name(architecture_name)
-        architecture = importlib.import_module(f"metatrain.{architecture_name}")
-
-        args.__dict__["model"] = architecture.__model__.load_checkpoint(
-            args.__dict__.pop("path")
-        )
-    elif callable == "train_model":
-        # define and create `checkpoint_dir` based on current directory and date/time
+    if callable == "train_model":
+        # define and create `checkpoint_dir` based on current directory, date and time
         checkpoint_dir = _datetime_output_path(now=datetime.now())
         os.makedirs(checkpoint_dir)
-        args.__dict__["checkpoint_dir"] = checkpoint_dir
-
-        # save log to file
-        logfile = checkpoint_dir / "train.log"
-
-        # merge/override file options with command line options
-        override_options = args.__dict__.pop("override_options")
-        if override_options is None:
-            override_options = {}
+        args.checkpoint_dir = checkpoint_dir
 
-        args.options = OmegaConf.merge(args.options, override_options)
-    else:
-        raise ValueError("internal error when selecting a sub-command.")
+        log_file = checkpoint_dir / "train.log"
+        error_file = checkpoint_dir / error_file
 
-    with setup_logging(logger, logfile=logfile, level=level):
+    with setup_logging(logger, log_file=log_file, level=level):
         try:
             if callable == "eval_model":
+                _prepare_eval_model_args(args)
                 eval_model(**args.__dict__)
             elif callable == "export_model":
+                _prepare_export_model_args(args)
                 export_model(**args.__dict__)
             elif callable == "train_model":
+                _prepare_train_model_args(args)
                 train_model(**args.__dict__)
             else:
-                raise ValueError("internal error when selecting a sub-command.")
+                raise ValueError("internal error when selecting a sub-command")
         except Exception as err:
-            logging.error({traceback.format_exc()})
             logging.error(
                 "If the error message below is unclear, please help us improve it by "
                 "opening an issue at https://github.com/lab-cosmo/metatrain/issues. "
-                f"Thank you!\n\n{type(err).__name__}: {err}"
+                "When opening the issue, please include the full traceback log from "
+                f"{str(error_file.absolute().resolve())!r}. Thank you!\n\n{err}"
             )
 
+            with open(error_file, "w") as f:
+                f.write(traceback.format_exc())
+
+            sys.exit(1)
+
 
 if __name__ == "__main__":
     main()

src/metatrain/cli/eval.py

@@ -55,7 +55,7 @@ def _add_eval_model_parser(subparser: argparse._SubParsersAction) -> None:
     )
     parser.add_argument(
         "options",
-        type=OmegaConf.load,
+        type=str,
         help="Eval options file to define a dataset for evaluation.",
     )
     parser.add_argument(
@@ -81,6 +81,15 @@ def _add_eval_model_parser(subparser: argparse._SubParsersAction) -> None:
     )
 
 
+def _prepare_eval_model_args(args: argparse.Namespace) -> None:
+    """Prepare arguments for eval_model."""
+    args.options = OmegaConf.load(args.options)
+    args.model = metatensor.torch.atomistic.load_atomistic_model(
+        path=args.__dict__.pop("path"),
+        extensions_directory=args.__dict__.pop("extensions_directory"),
+    )
+
+
 def _concatenate_tensormaps(
     tensormap_dict_list: List[Dict[str, TensorMap]]
 ) -> Dict[str, TensorMap]:

src/metatrain/cli/export.py

@@ -1,11 +1,12 @@
 import argparse
+import importlib
 import logging
 from pathlib import Path
 from typing import Any, Union
 
 import torch
 
-from ..utils.architectures import find_all_architectures
+from ..utils.architectures import check_architecture_name, find_all_architectures
 from ..utils.export import is_exported
 from ..utils.io import check_suffix
 from .formatter import CustomHelpFormatter
@@ -53,6 +54,15 @@ def _add_export_model_parser(subparser: argparse._SubParsersAction) -> None:
     )
 
 
+def _prepare_export_model_args(args: argparse.Namespace) -> None:
+    """Prepare arguments for export_model."""
+    architecture_name = args.__dict__.pop("architecture_name")
+    check_architecture_name(architecture_name)
+    architecture = importlib.import_module(f"metatrain.{architecture_name}")
+
+    args.model = architecture.__model__.load_checkpoint(args.__dict__.pop("path"))
+
+
 def export_model(model: Any, output: Union[Path, str] = "exported-model.pt") -> None:
     """Export a trained model to allow it to make predictions.
 

src/metatrain/cli/train.py

@@ -56,7 +56,7 @@ def _add_train_model_parser(subparser: argparse._SubParsersAction) -> None:
 
     parser.add_argument(
         "options",
-        type=OmegaConf.load,
+        type=str,
         help="Options file",
     )
     parser.add_argument(
@@ -85,6 +85,17 @@ def _add_train_model_parser(subparser: argparse._SubParsersAction) -> None:
     )
 
 
+def _prepare_train_model_args(args: argparse.Namespace) -> None:
+    """Prepare arguments for train_model."""
+    args.options = OmegaConf.load(args.options)
+    # merge/override file options with command line options
+    override_options = args.__dict__.pop("override_options")
+    if override_options is None:
+        override_options = {}
+
+    args.options = OmegaConf.merge(args.options, override_options)
+
+
 def train_model(
     options: Union[DictConfig, Dict],
     output: str = "model.pt",

src/metatrain/utils/data/readers/readers.py

@@ -204,7 +204,7 @@ def read_targets(
                         fileformat=target["forces"]["file_format"],
                         dtype=dtype,
                     )
-                except KeyError:
+                except Exception:
                     logger.warning(
                         f"No Forces found in section {target_key!r}. "
                         "Continue without forces!"
@@ -232,7 +232,7 @@ def read_targets(
                         fileformat=target["stress"]["file_format"],
                         dtype=dtype,
                     )
-                except KeyError:
+                except Exception:
                     logger.warning(
                         f"No Stress found in section {target_key!r}. "
                         "Continue without stress!"
@@ -255,7 +255,7 @@ def read_targets(
                         fileformat=target["virial"]["file_format"],
                         dtype=dtype,
                     )
-                except KeyError:
+                except Exception:
                     logger.warning(
                         f"No Virial found in section {target_key!r}. "
                         "Continue without virial!"

src/metatrain/utils/data/readers/targets/ase.py

@@ -27,7 +27,7 @@ def read_energy_ase(
     blocks = []
     for i_system, atoms in enumerate(frames):
         if key not in atoms.info:
-            raise KeyError(
+            raise ValueError(
                 f"energy key {key!r} was not found in system {filename!r} at index "
                 f"{i_system}"
             )
@@ -70,7 +70,7 @@ def read_forces_ase(
     for i_system, atoms in enumerate(frames):
 
         if key not in atoms.arrays:
-            raise KeyError(
+            raise ValueError(
                 f"forces key {key!r} was not found in system {filename!r} at index "
                 f"{i_system}"
             )
@@ -150,8 +150,7 @@ def _read_virial_stress_ase(
     :param is_virial: if target values are stored as stress or virials.
     :param dtype: desired data type of returned tensor
 
-    :returns:
-        TensorMap containing the given information
+    :returns: TensorMap containing the given information
     """
     frames = ase.io.read(filename, ":")
 
@@ -170,7 +169,7 @@ def _read_virial_stress_ase(
             else:
                 target_name = "stress"
 
-            raise KeyError(
+            raise ValueError(
                 f"{target_name} key {key!r} was not found in system {filename!r} at "
                 f"index {i_system}"
             )

src/metatrain/utils/errors.py

@@ -12,7 +12,8 @@ class ArchitectureError(Exception):
 
     def __init__(self, exception):
         super().__init__(
-            f"{exception}\n\nThe error wbove most likely originates from an "
-            "architecture. If you think this is a bug, please contact its maintainer "
-            "(see the architecture's documentation)."
+            f"{exception}\n\nThe error above most likely originates from an "
+            "architecture.\n\nIf you think this is a bug, please contact its "
+            "maintainer (see the architecture's documentation) and include the full "
+            "traceback error.log."
         )

src/metatrain/utils/logging.py

@@ -137,17 +137,17 @@ def _get_digits(value: float) -> Tuple[int, int]:
 
 @contextlib.contextmanager
 def setup_logging(
-    logobj: logging.Logger,
-    logfile: Optional[Union[str, Path]] = None,
+    log_obj: logging.Logger,
+    log_file: Optional[Union[str, Path]] = None,
     level: int = logging.WARNING,
 ):
     """Create a logging environment for a given ``logobj``.
 
     Extracted and adjusted from
     github.com/MDAnalysis/mdacli/blob/main/src/mdacli/logger.py
 
-    :param logobj: A logging instance
-    :param logfile: Name of the log file
+    :param log_obj: A logging instance
+    :param log_file: Name of the log file
     :param level: Set the root logger level to the specified level. If for example set
         to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and function
         name are displayed. For :py:obj:`logging.INFO` only the message logged from
@@ -166,26 +166,27 @@ def setup_logging(
         stream_handler.setFormatter(formatter)
         handlers.append(stream_handler)
 
-        if logfile:
-            logfile = check_suffix(filename=logfile, suffix=".log")
-            file_handler = logging.FileHandler(filename=str(logfile), encoding="utf-8")
+        if log_file:
+            log_file = check_suffix(filename=log_file, suffix=".log")
+            file_handler = logging.FileHandler(filename=str(log_file), encoding="utf-8")
             file_handler.setFormatter(formatter)
             handlers.append(file_handler)
 
         logging.basicConfig(format=format, handlers=handlers, level=level, style="{")
 
-        if logfile:
-            logobj.info(f"This log is also available in {str(logfile)!r}.")
+        if log_file:
+            abs_path = str(Path(log_file).absolute().resolve())
+            log_obj.info(f"This log is also available at {abs_path!r}.")
         else:
-            logobj.info("Logging to file is disabled.")
+            log_obj.info("Logging to file is disabled.")
 
         for handler in handlers:
-            logobj.addHandler(handler)
+            log_obj.addHandler(handler)
 
         yield
 
     finally:
         for handler in handlers:
             handler.flush()
             handler.close()
-            logobj.removeHandler(handler)
+            log_obj.removeHandler(handler)

tests/cli/test_cli.py

@@ -1,8 +1,10 @@
 """Tests for argument parsing."""
 
+import glob
 import shutil
 import subprocess
 from pathlib import Path
+from subprocess import CalledProcessError
 from typing import List
 
 import pytest
@@ -103,3 +105,36 @@ def get_completion_suggestions(partial_word: str) -> List[str]:
 def test_subcommand_completion(partial_word, expected_completion):
     """Test that expected subcommand completion matches."""
     assert set(get_completion_suggestions(partial_word)) == set(expected_completion)
+
+
+@pytest.mark.parametrize("subcommand", ["train", "eval"])
+def test_error(subcommand, capfd, monkeypatch, tmp_path):
+    """Test expected display of errors to stdout and log files."""
+    monkeypatch.chdir(tmp_path)
+
+    command = ["mtt", subcommand]
+    if subcommand == "eval":
+        command += ["model.pt"]
+
+    command += ["foo.yaml"]
+
+    with pytest.raises(CalledProcessError):
+        subprocess.check_call(command)
+
+    stdout_log = capfd.readouterr().out
+
+    if subcommand == "train":
+        error_glob = glob.glob("outputs/*/*/error.log")
+        error_file = error_glob[0]
+    else:
+        error_file = "error.log"
+
+    error_file = str(Path(error_file).absolute().resolve())
+
+    with open(error_file) as f:
+        error_log = f.read()
+
+    print(error_file)
+    assert f"please include the full traceback log from {error_file!r}" in stdout_log
+    assert "No such file or directory" in stdout_log
+    assert "Traceback" in error_log