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Import statements in examples are not working #51
Description
In the 'Dataset Exploration and Management in AtomWorks' example the first import statement:
from atomworks.ml.datasets.datasets import FileDataset
results in the following error when using AtomWorks installed from PyPI:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/datasets.py", line 18, in <module>
from atomworks.ml.datasets.parsers import MetadataRowParser, load_example_from_metadata_row
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/parsers/__init__.py", line 3, in <module>
from atomworks.ml.datasets.parsers.default_metadata_row_parsers import * # noqa: F403
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/parsers/default_metadata_row_parsers.py", line 86, in <module>
class PNUnitsDFParser(MetadataRowParser):
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/parsers/default_metadata_row_parsers.py", line 99, in PNUnitsDFParser
base_dir: Path | str | list[Path | str] | tuple[Path | str, ...] = Path(PDB_MIRROR_PATH),
^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/pathlib.py", line 1162, in __init__
super().__init__(*args)
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/pathlib.py", line 373, in __init__
raise TypeError(
TypeError: argument should be a str or an os.PathLike object where __fspath__ returns a str, not 'NoneType'
>>> from atomworks.ml.datasets.datasets import FileDataset
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/datasets.py", line 18, in <module>
from atomworks.ml.datasets.parsers import MetadataRowParser, load_example_from_metadata_row
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/parsers/__init__.py", line 3, in <module>
from atomworks.ml.datasets.parsers.default_metadata_row_parsers import * # noqa: F403
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/parsers/default_metadata_row_parsers.py", line 86, in <module>
class PNUnitsDFParser(MetadataRowParser):
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/site-packages/atomworks/ml/datasets/parsers/default_metadata_row_parsers.py", line 99, in PNUnitsDFParser
base_dir: Path | str | list[Path | str] | tuple[Path | str, ...] = Path(PDB_MIRROR_PATH),
^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/pathlib.py", line 1162, in __init__
super().__init__(*args)
File "/opt/miniconda3/envs/atomworks_env/lib/python3.12/pathlib.py", line 373, in __init__
raise TypeError(
TypeError: argument should be a str or an os.PathLike object where __fspath__ returns a str, not 'NoneType'
This error is not present if using AtomWorks installed locally from source.
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nscorley commentedon Oct 5, 2026
Addressed in production via #116. The example now imports FileDataset from atomworks.ml.datasets, and parser defaults no longer evaluate Path(None) at import time. Verified the import with both mirror environment variables unset.