From 91c54c1a63221ced55165dbc602b2a2b7f85e678 Mon Sep 17 00:00:00 2001 From: khoroshevskyi Date: Thu, 6 Aug 2026 23:57:09 -0400 Subject: [PATCH] Moved eido and pephuclient to peppy package as modules --- looper/cli_pydantic.py | 4 ++-- looper/conductor.py | 4 ++-- looper/looper.py | 4 ++-- looper/pipeline_interface.py | 2 +- looper/plugins.py | 2 +- looper/processed_project.py | 4 ++-- looper/project.py | 2 +- looper/utils.py | 2 +- pyproject.toml | 4 +--- 9 files changed, 13 insertions(+), 15 deletions(-) diff --git a/looper/cli_pydantic.py b/looper/cli_pydantic.py index 5da08a66..274fc87d 100644 --- a/looper/cli_pydantic.py +++ b/looper/cli_pydantic.py @@ -86,8 +86,8 @@ def run_looper(args: Namespace, test_args=None): # Lazy imports - only load when actually running commands import logmuse import yaml - from eido import inspect_project - from pephubclient import PEPHubClient + from peppy.eido import inspect_project + from peppy.pephubclient import PEPHubClient from rich.console import Console from . import __version__ diff --git a/looper/conductor.py b/looper/conductor.py index 83756614..456e7bfa 100644 --- a/looper/conductor.py +++ b/looper/conductor.py @@ -15,10 +15,10 @@ import psutil import yaml -from eido import get_input_files_size, read_schema -from eido.const import INPUT_FILE_SIZE_KEY, MISSING_KEY from jinja2.exceptions import UndefinedError from peppy.const import CONFIG_KEY, SAMPLE_YAML_EXT +from peppy.eido import get_input_files_size, read_schema +from peppy.eido.const import INPUT_FILE_SIZE_KEY, MISSING_KEY from peppy.exceptions import RemoteYAMLError from pipestat import PipestatError from ubiquerg import expandpath diff --git a/looper/looper.py b/looper/looper.py index f4537d72..29c18e4a 100755 --- a/looper/looper.py +++ b/looper/looper.py @@ -21,8 +21,8 @@ from shutil import rmtree from colorama import Fore, Style -from eido import validate_config, validate_sample -from eido.exceptions import EidoValidationError +from peppy.eido import validate_config, validate_sample +from peppy.eido.exceptions import EidoValidationError from peppy.exceptions import RemoteYAMLError from pipestat.exceptions import PipestatSummarizeError from pipestat.reports import get_file_for_table diff --git a/looper/pipeline_interface.py b/looper/pipeline_interface.py index 87b45317..a3eec125 100644 --- a/looper/pipeline_interface.py +++ b/looper/pipeline_interface.py @@ -6,8 +6,8 @@ import jsonschema import pandas as pd -from eido import read_schema from peppy import utils as peputil +from peppy.eido import read_schema from ubiquerg import expandpath, is_url from yacman import YAMLConfigManager, load_yaml diff --git a/looper/plugins.py b/looper/plugins.py index 3d628038..552df6b5 100644 --- a/looper/plugins.py +++ b/looper/plugins.py @@ -87,7 +87,7 @@ def write_sample_yaml_cwl(namespaces: dict) -> dict: Returns: dict: Updated variable namespaces dict. """ - from eido import read_schema + from peppy.eido import read_schema from ubiquerg import is_url def _get_schema_source( diff --git a/looper/processed_project.py b/looper/processed_project.py index b863f10e..45586565 100644 --- a/looper/processed_project.py +++ b/looper/processed_project.py @@ -125,8 +125,8 @@ import os from logging import getLogger -from eido.const import PROP_KEY -from eido.exceptions import EidoSchemaInvalidError +from peppy.eido.const import PROP_KEY +from peppy.eido.exceptions import EidoSchemaInvalidError from peppy.project import Project from peppy.sample import Sample diff --git a/looper/project.py b/looper/project.py index 60262fd1..6b6e3905 100644 --- a/looper/project.py +++ b/looper/project.py @@ -11,11 +11,11 @@ # cached_property was introduced in python 3.8 cached_property = property -from eido import read_schema from jsonschema import ValidationError from pandas.core.common import flatten from peppy import Project as peppyProject from peppy.const import CONFIG_KEY +from peppy.eido import read_schema from peppy.utils import make_abs_via_cfg from pipestat import PipestatManager diff --git a/looper/utils.py b/looper/utils.py index 85b1c458..c4407866 100644 --- a/looper/utils.py +++ b/looper/utils.py @@ -11,9 +11,9 @@ import jinja2 import yaml -from pephubclient.constants import RegistryPath from peppy import Project as peppyProject from peppy.const import CONFIG_KEY, NAME_KEY, SAMPLE_MODS_KEY +from peppy.pephubclient.constants import RegistryPath from pydantic import ValidationError from rich.console import Console from rich.pretty import pprint diff --git a/pyproject.toml b/pyproject.toml index 22b17d8d..1bc3282a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,13 +26,11 @@ classifiers = [ ] dependencies = [ "colorama>=0.3.9", - "eido>=0.2.4", "jinja2", "logmuse>=0.2.0", "pandas>=2.0.2", - "pephubclient>=0.4.0", "pipestat>=0.12.0a1", - "peppy>=0.40.6", + "peppy>=0.50.0a4", "pyyaml>=3.12", "rich>=9.10.0", "ubiquerg>=0.8.1",