Update to match neurodatascience/nipoppy:main

.flake8

@@ -8,7 +8,7 @@ exclude =
 	venv,
 per-file-ignores =
     # - docstrings rules that should not be applied to tests
-	**/test_*: D100, D103, D104
+	**/test_*: D100, D101, D103, D104
     __init__.py:F401
     # allow "weird indentation"
 	tests/test_workflow_*.py: D100, D103, D104, E131, E127, E501

.github/workflows/run_tests_new.yml

@@ -18,6 +18,10 @@ jobs:
 
     runs-on: ubuntu-latest
 
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
     # only trigger on upstream repo
     if: github.repository_owner == 'neurodatascience' && github.event.repository.name == 'nipoppy'
 
@@ -29,7 +33,7 @@ jobs:
 
     - uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: ${{ matrix.python-version }}
 
     - name: Install package
       run: |

nipoppy_cli/docs/source/conf.py

@@ -86,6 +86,9 @@
     ("py:class", "argparse.HelpFormatter"),
     ("py:class", "argparse._SubParsersAction"),
     ("py:class", "argparse._ActionsContainer"),
+    ("py:class", "StrOrPathLike"),
+    ("py:class", "nipoppy.utils.StrOrPathLike"),
+    ("py:class", "typing_extensions.Self"),
 ]
 
 # -- Copybutton configuration -------------------------------------------------

nipoppy_cli/nipoppy/config/container.py

@@ -11,6 +11,7 @@
 from pydantic import BaseModel, ConfigDict, Field
 
 from nipoppy.logger import get_logger
+from nipoppy.utils import StrOrPathLike
 
 # Apptainer
 APPTAINER_BIND_FLAG = "--bind"
@@ -53,8 +54,8 @@ class ContainerConfig(BaseModel):
 
     def add_bind_path(
         self,
-        path_local: str | Path,
-        path_inside_container: Optional[str | Path] = None,
+        path_local: StrOrPathLike,
+        path_inside_container: Optional[StrOrPathLike] = None,
         mode: str = "rw",
     ):
         """Add a bind path."""
@@ -100,8 +101,8 @@ def get_container_config(self) -> ContainerConfig:
 
 def add_bind_path_to_args(
     args: list[str],
-    path_local: str | Path,
-    path_inside_container: Optional[str | Path] = None,
+    path_local: StrOrPathLike,
+    path_inside_container: Optional[StrOrPathLike] = None,
     mode: Optional[str] = "rw",
 ):
     """Add a bind path to the container arguments.
@@ -110,10 +111,10 @@ def add_bind_path_to_args(
     ----------
     args : list[str]
         Existing arguments
-    path_local : str | Path
+    path_local : nipoppy.utils.StrOrPathLike
         Path on disk. If this is a relative path or contains symlinks,
         it will be resolved
-    path_inside_container : Optional[str  |  Path], optional
+    path_inside_container : Optional[nipoppy.utils.StrOrPathLike], optional
         Path inside the container (if None, will be the same as the local path),
         by default None
     mode : str, optional

nipoppy_cli/nipoppy/config/main.py

@@ -1,13 +1,16 @@
 """Dataset configuration."""
 
+from __future__ import annotations
+
 from pathlib import Path
-from typing import Any, Optional, Self
+from typing import Any, Optional
 
 from pydantic import ConfigDict, Field, model_validator
+from typing_extensions import Self
 
 from nipoppy.config.container import ModelWithContainerConfig
 from nipoppy.config.pipeline import PipelineConfig
-from nipoppy.utils import check_session, load_json
+from nipoppy.utils import StrOrPathLike, check_session, load_json
 
 
 class Config(ModelWithContainerConfig):
@@ -106,12 +109,12 @@ def get_bids_pipeline_config(
                 f"{pipeline_name} {pipeline_version} {pipeline_step}"
             )
 
-    def save(self, fpath: str | Path, **kwargs):
+    def save(self, fpath: StrOrPathLike, **kwargs):
         """Save the config to a JSON file.
 
         Parameters
         ----------
-        fpath : str | Path
+        fpath : nipoppy.utils.StrOrPathLike
             Path to the JSON file to write
         """
         fpath = Path(fpath)
@@ -122,6 +125,6 @@ def save(self, fpath: str | Path, **kwargs):
             file.write(self.model_dump_json(**kwargs))
 
     @classmethod
-    def load(cls, path: str | Path) -> Self:
+    def load(cls, path: StrOrPathLike) -> Self:
         """Load a dataset configuration."""
         return cls(**load_json(path))

nipoppy_cli/nipoppy/config/pipeline.py

@@ -1,5 +1,7 @@
 """Pipeline configuration."""
 
+from __future__ import annotations
+
 import re
 from pathlib import Path
 from typing import Optional, Sequence

nipoppy_cli/nipoppy/layout.py

@@ -7,7 +7,12 @@
 from pydantic import BaseModel, ConfigDict, Field
 
 from nipoppy.base import Base
-from nipoppy.utils import FPATH_DEFAULT_LAYOUT, get_pipeline_tag, load_json
+from nipoppy.utils import (
+    FPATH_DEFAULT_LAYOUT,
+    StrOrPathLike,
+    get_pipeline_tag,
+    load_json,
+)
 
 
 class PathInfo(BaseModel):
@@ -129,17 +134,24 @@ class DatasetLayout(Base):
     """File/directory structure for a specific dataset."""
 
     def __init__(
-        self, dpath_root: Path | str, fpath_config: Optional[Path | str] = None
+        self,
+        dpath_root: StrOrPathLike,
+        fpath_config: Optional[StrOrPathLike] = None,
     ):
         """Initialize the object.
 
         Parameters
         ----------
-        dataset_root: Path | str
+        dpath_root : nipoppy.utils.StrOrPathLike
             Path to the root directory of the dataset.
-        fpath_config: Path | str | None
-            Path to layout config to use, by default None.
+        fpath_config : Optional[nipoppy.utils.StrOrPathLike], optional
+            Path to the layout config to use, by default None.
             If None, the default layout will be used.
+
+        Raises
+        ------
+        FileNotFoundError
+            If ``fpath_config`` does not exist.
         """
         # use the default layout if none is specified
         if fpath_config is None:
@@ -187,7 +199,7 @@ def __init__(
         self.dname_pipeline_work = "work"
         self.dname_pipeline_output = "output"
 
-    def get_full_path(self, path: str | Path) -> Path:
+    def get_full_path(self, path: StrOrPathLike) -> Path:
         """Build a full path from a relative path."""
         return self.dpath_root / path
 

nipoppy_cli/nipoppy/logger.py

@@ -6,6 +6,8 @@
 
 from rich.logging import RichHandler
 
+from nipoppy.utils import StrOrPathLike
+
 DATE_FORMAT = "[%Y-%m-%d %X]"
 FORMAT_RICH = "%(message)s"
 FORMAT_FILE = "%(asctime)s %(levelname)-7s %(message)s"
@@ -23,7 +25,7 @@ def get_logger(name: Optional[str] = None, level: int = logging.INFO) -> logging
     return logging.getLogger(name=name)
 
 
-def add_logfile(logger: logging.Logger, fpath_log: Path | str) -> None:
+def add_logfile(logger: logging.Logger, fpath_log: StrOrPathLike) -> None:
     """Add a file handler to the logger."""
     fpath_log = Path(fpath_log)
 

nipoppy_cli/nipoppy/tabular/base.py

@@ -1,14 +1,17 @@
 """Generic class for tabular data."""
 
+from __future__ import annotations
+
 import contextlib
 from abc import ABC, abstractmethod
 from pathlib import Path
-from typing import Any, Optional, Self, Sequence
+from typing import Any, Optional, Sequence
 
 import pandas as pd
 from pydantic import BaseModel, ValidationError, model_validator
+from typing_extensions import Self
 
-from nipoppy.utils import save_df_with_backup
+from nipoppy.utils import StrOrPathLike, save_df_with_backup
 
 
 class BaseTabularModel(BaseModel):
@@ -77,7 +80,7 @@ def model(self) -> type[BaseTabularModel]:
         raise NotImplementedError("model must be assigned in subclass")
 
     @classmethod
-    def load(cls, fpath: str | Path, validate=True, **kwargs) -> Self:
+    def load(cls, fpath: StrOrPathLike, validate=True, **kwargs) -> Self:
         """Load (and optionally validate) a tabular data file."""
         if "dtype" in kwargs:
             raise ValueError(
@@ -190,7 +193,7 @@ def concatenate(self, other: Self, validate=True) -> Self:
 
     def save_with_backup(
         self,
-        fpath_symlink: str | Path,
+        fpath_symlink: StrOrPathLike,
         dname_backups: Optional[str] = None,
         use_relative_path=True,
         sort=True,

nipoppy_cli/nipoppy/tabular/doughnut.py

@@ -1,15 +1,19 @@
 """Class for the doughnut file."""
 
+from __future__ import annotations
+
 import logging
 from pathlib import Path
-from typing import Optional, Self
+from typing import Optional
 
 from pydantic import Field
+from typing_extensions import Self
 
 from nipoppy.logger import get_logger
 from nipoppy.tabular.manifest import Manifest, ManifestModel
 from nipoppy.utils import (
     FIELD_DESCRIPTION_MAP,
+    StrOrPathLike,
     participant_id_to_bids_id,
     participant_id_to_dicom_id,
 )
@@ -145,17 +149,17 @@ def get_bidsified_participants_sessions(
 
 def generate_doughnut(
     manifest: Manifest,
-    dpath_downloaded: Optional[str | Path] = None,
-    dpath_organized: Optional[str | Path] = None,
-    dpath_bidsified: Optional[str | Path] = None,
+    dpath_downloaded: Optional[StrOrPathLike] = None,
+    dpath_organized: Optional[StrOrPathLike] = None,
+    dpath_bidsified: Optional[StrOrPathLike] = None,
     empty=False,
     logger: Optional[logging.Logger] = None,
     # TODO allow custom map from participant_id to participant_dicom_dir
 ) -> Doughnut:
     """Generate a doughnut object."""
 
     def check_status(
-        dpath: Optional[str | Path],
+        dpath: Optional[StrOrPathLike],
         participant_dname: str,
         session: str,
         session_first=False,
@@ -242,9 +246,9 @@ def check_status(
 def update_doughnut(
     doughnut: Doughnut,
     manifest: Manifest,
-    dpath_downloaded: Optional[str | Path] = None,
-    dpath_organized: Optional[str | Path] = None,
-    dpath_bidsified: Optional[str | Path] = None,
+    dpath_downloaded: Optional[StrOrPathLike] = None,
+    dpath_organized: Optional[StrOrPathLike] = None,
+    dpath_bidsified: Optional[StrOrPathLike] = None,
     empty=False,
     logger: Optional[logging.Logger] = None,
 ) -> Doughnut:

nipoppy_cli/nipoppy/tabular/manifest.py

@@ -1,9 +1,12 @@
 """Class for the dataset manifest."""
 
-from typing import Optional, Self
+from __future__ import annotations
+
+from typing import Optional
 
 import pandas as pd
 from pydantic import ConfigDict, Field
+from typing_extensions import Self
 
 from nipoppy.tabular.base import BaseTabular, BaseTabularModel
 from nipoppy.utils import FIELD_DESCRIPTION_MAP