modernized phase 4

Author: khoroshevskyi

peppy/eido/cli.py

@@ -1,6 +1,5 @@
 import sys
 from logging import CRITICAL, DEBUG, ERROR, INFO, WARN, Logger
-from typing import Dict, List, Optional
 
 import typer
 from logmuse import init_logger
@@ -23,8 +22,8 @@
 
 
 def _configure_logging(
-    verbosity: Optional[int],
-    logging_level: Optional[str],
+    verbosity: int | None,
+    logging_level: str | None,
     dbg: bool,
 ) -> str:
     """Mimic old verbosity / logging-level behavior."""
@@ -38,7 +37,7 @@ def _configure_logging(
     return level
 
 
-def _parse_filter_args_str(input: Optional[List[str]]) -> Dict[str, str]:
+def _parse_filter_args_str(input: list[str] | None) -> dict[str, str]:
     """
     Parse user input specification.
 
@@ -57,7 +56,7 @@ def _parse_filter_args_str(input: Optional[List[str]]) -> Dict[str, str]:
 
 
 def print_error_summary(
-    errors_by_type: Dict[str, List[Dict[str, str]]], _LOGGER: Logger
+    errors_by_type: dict[str, list[dict[str, str]]], _LOGGER: Logger
 ):
     """Print a summary of errors, organized by error type"""
     n_error_types = len(errors_by_type)
@@ -80,14 +79,14 @@ def print_error_summary(
 @app.callback()
 def common(
     ctx: typer.Context,
-    verbosity: Optional[int] = typer.Option(
+    verbosity: int | None = typer.Option(
         None,
         "--verbosity",
         min=0,
         max=len(LEVEL_BY_VERBOSITY) - 1,
         help=f"Choose level of verbosity (default: {None})",
     ),
-    logging_level: Optional[str] = typer.Option(
+    logging_level: str | None = typer.Option(
         None,
         "--logging-level",
         help="logging level",
@@ -114,18 +113,18 @@ def common(
 @app.command(name=CONVERT_CMD, help=SUBPARSER_MSGS[CONVERT_CMD])
 def convert(
     ctx: typer.Context,
-    pep: Optional[str] = typer.Argument(
+    pep: str | None = typer.Argument(
         None,
         metavar="PEP",
         help="Path to a PEP configuration file in yaml format.",
     ),
-    st_index: Optional[str] = typer.Option(
+    st_index: str | None = typer.Option(
         None, "--st-index", help="Sample table index to use"
     ),
-    sst_index: Optional[str] = typer.Option(
+    sst_index: str | None = typer.Option(
         None, "--sst-index", help="Subsample table index to use"
     ),
-    amendments: Optional[List[str]] = typer.Option(
+    amendments: list[str] | None = typer.Option(
         None,
         "--amendments",
         help="Names of the amendments to activate.",
@@ -136,13 +135,13 @@ def convert(
         "--format",
         help="Output format (name of filter; use -l to see available).",
     ),
-    sample_name: Optional[List[str]] = typer.Option(
+    sample_name: list[str] | None = typer.Option(
         None,
         "-n",
         "--sample-name",
         help="Name of the samples to inspect.",
     ),
-    args: Optional[List[str]] = typer.Option(
+    args: list[str] | None = typer.Option(
         None,
         "-a",
         "--args",
@@ -162,7 +161,7 @@ def convert(
         "--describe",
         help="Show description for a given filter.",
     ),
-    paths_: Optional[List[str]] = typer.Option(
+    paths_: list[str] | None = typer.Option(
         None,
         "-p",
         "--paths",
@@ -226,28 +225,28 @@ def validate(
         metavar="S",
         help="Path to a PEP schema file in yaml format.",
     ),
-    st_index: Optional[str] = typer.Option(
+    st_index: str | None = typer.Option(
         None,
         "--st-index",
         help=(
             f"Sample table index to use; samples are identified by "
             f"'{SAMPLE_NAME_ATTR}' by default."
         ),
     ),
-    sst_index: Optional[str] = typer.Option(
+    sst_index: str | None = typer.Option(
         None,
         "--sst-index",
         help=(
             f"Subsample table index to use; samples are identified by "
             f"'{SAMPLE_NAME_ATTR}' by default."
         ),
     ),
-    amendments: Optional[List[str]] = typer.Option(
+    amendments: list[str] | None = typer.Option(
         None,
         "--amendments",
         help="Names of the amendments to activate.",
     ),
-    sample_name: Optional[str] = typer.Option(
+    sample_name: str | None = typer.Option(
         None,
         "-n",
         "--sample-name",
@@ -311,28 +310,28 @@ def inspect(
         metavar="PEP",
         help="Path to a PEP configuration file in yaml format.",
     ),
-    st_index: Optional[str] = typer.Option(
+    st_index: str | None = typer.Option(
         None,
         "--st-index",
         help=(
             f"Sample table index to use; samples are identified by "
             f"'{SAMPLE_NAME_ATTR}' by default."
         ),
     ),
-    sst_index: Optional[str] = typer.Option(
+    sst_index: str | None = typer.Option(
         None,
         "--sst-index",
         help=(
             f"Subsample table index to use; samples are identified by "
             f"'{SAMPLE_NAME_ATTR}' by default."
         ),
     ),
-    amendments: Optional[List[str]] = typer.Option(
+    amendments: list[str] | None = typer.Option(
         None,
         "--amendments",
         help="Names of the amendments to activate.",
     ),
-    sample_name: Optional[List[str]] = typer.Option(
+    sample_name: list[str] | None = typer.Option(
         None,
         "-n",
         "--sample-name",

peppy/eido/conversion.py

@@ -4,15 +4,15 @@
 import os
 import sys
 from logging import getLogger
-from typing import Callable, Dict, List, NoReturn, Optional
+from collections.abc import Callable
 
 from ..project import Project
 from .exceptions import EidoFilterError
 
 _LOGGER = getLogger(__name__)
 
 
-def pep_conversion_plugins() -> Dict[str, Callable]:
+def pep_conversion_plugins() -> dict[str, Callable]:
     """Plugins registered by entry points in the current Python env.
 
     Returns:
@@ -35,8 +35,8 @@ def pep_conversion_plugins() -> Dict[str, Callable]:
 
 
 def convert_project(
-    prj: Project, target_format: str, plugin_kwargs: Optional[Dict] = None
-) -> Dict[str, str]:
+    prj: Project, target_format: str, plugin_kwargs: dict | None = None
+) -> dict[str, str]:
     """Convert a `peppy.Project` object to a selected format.
 
     Args:
@@ -57,8 +57,8 @@ def run_filter(
     prj: Project,
     filter_name: str,
     verbose: bool = True,
-    plugin_kwargs: Optional[Dict] = None,
-) -> Dict[str, str]:
+    plugin_kwargs: dict | None = None,
+) -> dict[str, str]:
     """Run a selected filter on a peppy.Project object.
 
     Args:
@@ -124,12 +124,12 @@ def run_filter(
     return conv_result
 
 
-def save_result(result_path: str, content: str) -> NoReturn:
+def save_result(result_path: str, content: str) -> None:
     with open(result_path, "w") as f:
         f.write(content)
 
 
-def get_available_pep_filters() -> List[str]:
+def get_available_pep_filters() -> list[str]:
     """Get a list of available target formats.
 
     Returns:

peppy/eido/conversion_plugins.py

@@ -1,11 +1,10 @@
 """built-in PEP filters"""
 
-from typing import Dict
 
 from .output_formatters import MultilineOutputFormatter
 
 
-def basic_pep_filter(p, **kwargs) -> Dict[str, str]:
+def basic_pep_filter(p, **kwargs) -> dict[str, str]:
     """
     Basic PEP filter, that does not convert the Project object.
 
@@ -16,7 +15,7 @@ def basic_pep_filter(p, **kwargs) -> Dict[str, str]:
     return {"project": str(p)}
 
 
-def yaml_samples_pep_filter(p, **kwargs) -> Dict[str, str]:
+def yaml_samples_pep_filter(p, **kwargs) -> dict[str, str]:
     """
     YAML samples PEP filter, that returns only Sample object representations.
 
@@ -33,7 +32,7 @@ def yaml_samples_pep_filter(p, **kwargs) -> Dict[str, str]:
     return {"samples": dump(samples_yaml, default_flow_style=False)}
 
 
-def yaml_pep_filter(p, **kwargs) -> Dict[str, str]:
+def yaml_pep_filter(p, **kwargs) -> dict[str, str]:
     """
     YAML PEP filter, that returns Project object representation.
 
@@ -46,7 +45,7 @@ def yaml_pep_filter(p, **kwargs) -> Dict[str, str]:
     return {"project": dump(p.config, default_flow_style=False)}
 
 
-def csv_pep_filter(p, **kwargs) -> Dict[str, str]:
+def csv_pep_filter(p, **kwargs) -> dict[str, str]:
     """
     CSV PEP filter, that returns Sample object representations
 
@@ -58,7 +57,7 @@ def csv_pep_filter(p, **kwargs) -> Dict[str, str]:
     return {"samples": MultilineOutputFormatter.format(p.samples)}
 
 
-def processed_pep_filter(p, **kwargs) -> Dict[str, str]:
+def processed_pep_filter(p, **kwargs) -> dict[str, str]:
     """
     Processed PEP filter, that returns the converted sample and subsample tables.
     This filter can return the tables as a table or a document.

peppy/eido/exceptions.py

@@ -1,7 +1,6 @@
 """Exceptions for specific eido issues."""
 
 from abc import ABCMeta
-from typing import Dict, List
 
 __all__ = [
     "EidoFilterError",
@@ -41,7 +40,7 @@ def __init__(self, key):
 class EidoValidationError(EidoException):
     """Object was not validated successfully according to schema."""
 
-    def __init__(self, message: str, errors_by_type: Dict[str, List[Dict[str, str]]]):
+    def __init__(self, message: str, errors_by_type: dict[str, list[dict[str, str]]]):
         super().__init__(message)
         self.errors_by_type = errors_by_type
         self.message = message

peppy/eido/inspection.py

@@ -1,6 +1,6 @@
 import os
 from logging import getLogger
-from typing import Dict, Iterable, List, Set, Union
+from collections.abc import Iterable
 from warnings import catch_warnings
 
 from ubiquerg import size
@@ -23,7 +23,7 @@
 
 
 def inspect_project(
-    p: Project, sample_names: Union[None, List[str]] = None, max_attr: int = 10
+    p: Project, sample_names: list[str] | None = None, max_attr: int = 10
 ) -> None:
     """Print inspection info: Project or, if sample_names argument is provided, matched samples.
 
@@ -46,8 +46,8 @@ def inspect_project(
 
 
 def get_input_files_size(
-    sample: Sample, schema: Union[str, List[Dict]]
-) -> Dict[str, Union[List[str], Set[str], float]]:
+    sample: Sample, schema: str | list[dict]
+) -> dict[str, list[str] | set[str] | float]:
     """Determine which of this Sample's required attributes/files are missing and calculate sizes.
 
     The names of the attributes that are required and/or deemed as inputs

peppy/eido/output_formatters.py

@@ -1,13 +1,13 @@
 from abc import ABC, abstractmethod
-from typing import Iterable, List, Union
+from collections.abc import Iterable
 
 from ..sample import Sample
 
 
 class BaseOutputFormatter(ABC):
     @staticmethod
     @abstractmethod
-    def format(samples: List[Sample]) -> str:
+    def format(samples: list[Sample]) -> str:
         """
         Convert the samples to correct format.
         """
@@ -16,7 +16,7 @@ def format(samples: List[Sample]) -> str:
 
 class MultilineOutputFormatter(BaseOutputFormatter):
     @staticmethod
-    def format(samples: List[Sample]) -> str:
+    def format(samples: list[Sample]) -> str:
         output_rows = []
         sample_attributes = [
             attribute
@@ -43,20 +43,20 @@ def format(samples: List[Sample]) -> str:
         return "\n".join(header + output_rows) + "\n"
 
     @staticmethod
-    def _get_header(header_column_names: List[str]) -> List[str]:
+    def _get_header(header_column_names: list[str]) -> list[str]:
         return [",".join(header_column_names)]
 
     @staticmethod
     def _get_the_name_of_the_first_attribute_with_multiple_properties(
-        sample: Sample, sample_attributes: List[str]
-    ) -> Union[str, None]:
+        sample: Sample, sample_attributes: list[str]
+    ) -> str | None:
         for attribute in sample_attributes:
             if MultilineOutputFormatter._sample_attribute_is_list(sample, attribute):
                 return attribute
 
     @staticmethod
     def _split_sample_to_multiple_rows(
-        sample: Sample, sample_attributes: List, attribute_with_multiple_properties: str
+        sample: Sample, sample_attributes: list, attribute_with_multiple_properties: str
     ) -> Iterable[str]:
         """
         If one sample object contains array properties instead of single value, then it will be converted
@@ -84,7 +84,7 @@ def _split_sample_to_multiple_rows(
 
     @staticmethod
     def _convert_sample_to_row(
-        sample: Sample, sample_attributes: List, sample_index: int = 0
+        sample: Sample, sample_attributes: list, sample_index: int = 0
     ) -> str:
         """
         Converts single sample object to CSV row.
@@ -122,5 +122,5 @@ def _sample_attribute_is_list(sample: Sample, attribute: str) -> bool:
 
 
 class SampleSubsampleOutputFormatter(BaseOutputFormatter):
-    def format(self, samples: List[Sample]) -> str:
+    def format(self, samples: list[Sample]) -> str:
         pass