From 8e74a4e3b6d58cea6311a5fb7697762243e16d1d Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Tue, 3 Feb 2026 14:50:14 -0500 Subject: [PATCH 1/2] Removed NoReturn from functions --- .github/workflows/python-publish.yml | 4 ++-- .github/workflows/run-pytest.yml | 6 +++--- eido/_version.py | 2 +- eido/conversion.py | 3 +-- eido/conversion_plugins.py | 2 +- eido/exceptions.py | 2 +- eido/validation.py | 10 +++++----- 7 files changed, 14 insertions(+), 15 deletions(-) diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml index ddf9a38..cbcc87a 100644 --- a/.github/workflows/python-publish.yml +++ b/.github/workflows/python-publish.yml @@ -14,9 +14,9 @@ jobs: permissions: id-token: write steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@v6 with: python-version: '3.x' - name: Install dependencies diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml index 89ffd78..05037af 100644 --- a/.github/workflows/run-pytest.yml +++ b/.github/workflows/run-pytest.yml @@ -9,14 +9,14 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["3.8", "3.11"] + python-version: ["3.10", "3.11"] os: [ubuntu-latest] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v6 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v6 with: python-version: ${{ matrix.python-version }} diff --git a/eido/_version.py b/eido/_version.py index 788da1f..fe404ae 100644 --- a/eido/_version.py +++ b/eido/_version.py @@ -1 +1 @@ -__version__ = "0.2.4" +__version__ = "0.2.5" diff --git a/eido/conversion.py b/eido/conversion.py index 58cc85a..bf0652e 100644 --- a/eido/conversion.py +++ b/eido/conversion.py @@ -7,7 +7,6 @@ import inspect from logging import getLogger import os -from typing import NoReturn from .exceptions import * @@ -107,7 +106,7 @@ def run_filter(prj, filter_name, verbose=True, plugin_kwargs=None): 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) diff --git a/eido/conversion_plugins.py b/eido/conversion_plugins.py index fe45805..beb56cc 100644 --- a/eido/conversion_plugins.py +++ b/eido/conversion_plugins.py @@ -1,4 +1,4 @@ -""" built-in PEP filters """ +"""built-in PEP filters""" from typing import Dict from .output_formatters import MultilineOutputFormatter diff --git a/eido/exceptions.py b/eido/exceptions.py index ca40145..4ecff8d 100644 --- a/eido/exceptions.py +++ b/eido/exceptions.py @@ -1,4 +1,4 @@ -""" Exceptions for specific eido issues. """ +"""Exceptions for specific eido issues.""" from abc import ABCMeta diff --git a/eido/validation.py b/eido/validation.py index e75d7e6..e07d353 100644 --- a/eido/validation.py +++ b/eido/validation.py @@ -1,5 +1,5 @@ import os -from typing import NoReturn, Mapping, Union +from typing import Mapping, Union from copy import deepcopy as dpcpy from logging import getLogger @@ -60,7 +60,7 @@ def _validate_object(obj: Mapping, schema: Union[str, dict], sample_name_colname _LOGGER.debug("Validation was successful...") -def validate_project(project: peppy.Project, schema: Union[str, dict]) -> NoReturn: +def validate_project(project: peppy.Project, schema: Union[str, dict]) -> None: """ Validate a project object against a schema @@ -68,7 +68,7 @@ def validate_project(project: peppy.Project, schema: Union[str, dict]) -> NoRetu :param str | dict schema: schema dict to validate against or a path to one from the error. Useful when used ith large projects - :return: NoReturn + :return: None :raises EidoValidationError: if validation is unsuccessful """ sample_name_colname = project.sample_name_colname @@ -100,7 +100,7 @@ def _validate_sample_object(sample: peppy.Sample, schemas): def validate_sample( project: peppy.Project, sample_name: Union[str, int], schema: Union[str, dict] -) -> NoReturn: +) -> None: """ Validate the selected sample object against a schema @@ -123,7 +123,7 @@ def validate_sample( def validate_config( project: Union[peppy.Project, dict], schema: Union[str, dict] -) -> NoReturn: +) -> None: """ Validate the config part of the Project object against a schema From 6f21202cfcf4dedaf2f610da10efc06242a2bebf Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Tue, 3 Feb 2026 15:46:33 -0500 Subject: [PATCH 2/2] Fixed pandas version --- .github/workflows/run-pytest.yml | 2 +- requirements/requirements-all.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run-pytest.yml b/.github/workflows/run-pytest.yml index 05037af..9f10706 100644 --- a/.github/workflows/run-pytest.yml +++ b/.github/workflows/run-pytest.yml @@ -9,7 +9,7 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - python-version: ["3.10", "3.11"] + python-version: ["3.10", "3.13"] os: [ubuntu-latest] steps: diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt index 7c16b30..c4a845f 100644 --- a/requirements/requirements-all.txt +++ b/requirements/requirements-all.txt @@ -1,6 +1,6 @@ importlib-metadata; python_version < '3.10' jsonschema>=3.0.1 logmuse>=0.2.5 -pandas +pandas<3.0.0 peppy>=0.40.7 ubiquerg>=0.5.2