Moved eido and pephuclient to peppy package as modules

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__

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

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

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
 

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(

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
 

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
 

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

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",