eido 0.2.3__py3-none-any.whl → 0.2.5__py3-none-any.whl

eido/_version.py

@@ -1 +1 @@
-__version__ = "0.2.3"
+__version__ = "0.2.5"

eido/conversion.py

@@ -7,7 +7,6 @@ else:
 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)
 

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
@@ -42,8 +42,7 @@ def yaml_pep_filter(p, **kwargs) -> Dict[str, str]:
     """
     from yaml import dump
 
-    data = p.config.to_dict()
-    return {"project": dump(data, default_flow_style=False)}
+    return {"project": dump(p.config, default_flow_style=False)}
 
 
 def csv_pep_filter(p, **kwargs) -> Dict[str, str]:
@@ -70,7 +69,7 @@ def processed_pep_filter(p, **kwargs) -> Dict[str, str]:
     samples_as_objects = kwargs.get("samples_as_objects")
     subsamples_as_objects = kwargs.get("subsamples_as_objects")
 
-    prj_repr = p.config.to_dict()
+    prj_repr = p.config
 
     return {
         "project": str(prj_repr),

eido/exceptions.py

@@ -1,4 +1,4 @@
-""" Exceptions for specific eido issues. """
+"""Exceptions for specific eido issues."""
 
 from abc import ABCMeta
 

eido/output_formatters.py

@@ -110,7 +110,7 @@ class MultilineOutputFormatter(BaseOutputFormatter):
             ):
                 value = sample[attribute][sample_index]
             else:
-                value = sample[attribute]
+                value = sample.get(attribute)
 
             sample_row.append(value or "")
 

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
 
@@ -43,6 +43,10 @@ def _validate_object(obj: Mapping, schema: Union[str, dict], sample_name_colname
                 instance_name = error.instance[sample_name_colname]
             except KeyError:
                 instance_name = "project"
+            except TypeError:
+                instance_name = obj["samples"][error.absolute_path[1]][
+                    sample_name_colname
+                ]
             errors_by_type[error.message].append(
                 {
                     "type": error.message,
@@ -56,7 +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
 
@@ -64,7 +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
@@ -96,7 +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
 
@@ -119,7 +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
 

{eido-0.2.3.dist-info → eido-0.2.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: eido
-Version: 0.2.3
+Version: 0.2.5
 Summary: A project metadata validator
 Home-page: https://github.com/pepkit/eido/
 Author: Michal Stolarczyk, Nathan Sheffield
@@ -15,12 +15,22 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
+Requires-Dist: importlib-metadata; python_version < "3.10"
 Requires-Dist: jsonschema>=3.0.1
 Requires-Dist: logmuse>=0.2.5
-Requires-Dist: pandas
-Requires-Dist: peppy>=0.40.6
+Requires-Dist: pandas<3.0.0
+Requires-Dist: peppy>=0.40.7
 Requires-Dist: ubiquerg>=0.5.2
-Requires-Dist: importlib-metadata; python_version < "3.10"
+Dynamic: author
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
 
 # <img src="docs/img/eido.svg" alt="eido logo" height="70">
 

eido-0.2.5.dist-info/RECORD

@@ -0,0 +1,19 @@
+eido/__init__.py,sha256=D3CD9BefyY5Yckz-LswPca_VH_RIcZpr53_siXkbi14,612
+eido/__main__.py,sha256=L1wnnEreqYv27ZaaCwwImCIHZK0Mz5IxS80ZsNcS1zg,189
+eido/_version.py,sha256=Xsa3ayOMVkhUWm4t06YeyHE0apjpZefxLH4ylp0CDtU,22
+eido/argparser.py,sha256=vx59eO8CClaQpXehcW052y4HW5mttGTqM96PoJJwWkE,4806
+eido/cli.py,sha256=dXPaqF6uUYnGMlW2H9Mc628CfhCl3pEinxWYnQ94SVc,5814
+eido/const.py,sha256=Tb-fDKvneyZX3qLgLYVWtGGs4Hw4tRogB3OXIlwtpdY,1109
+eido/conversion.py,sha256=KARokqRn4gEh5ftstzSBDtpwwpAzIHOHXZnkkk2vZSo,3970
+eido/conversion_plugins.py,sha256=ad9XXxtlAbkhUOTkOF8yuwGz3D2tOB3acd-gktZCdcs,2491
+eido/exceptions.py,sha256=ZMrkp6OO-zgK_bdpu4DiI2-q_JzedEwKMLRt68QOiwc,1211
+eido/inspection.py,sha256=rfuXnAawGBWQFz_hbJA2VYP_sFvpYxztxOiXL6t610o,3223
+eido/output_formatters.py,sha256=gmS-UIRjRQ8Eg24UEyp2fmU046SDbIS7jh4zOLFHlcE,4485
+eido/schema.py,sha256=I75jlUlUdswkne6Xq2XLD8zm-f8p7VITQIj7J_x7aH8,2664
+eido/validation.py,sha256=eFc0YUbrnfANvJ_NzLPMZ-ApV0KUGls6V17MHyUwEJI,8661
+eido-0.2.5.dist-info/licenses/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
+eido-0.2.5.dist-info/METADATA,sha256=Fu8zDU6AmlNUfi5L_6g_A6EEGbaFHMDFE4iYj_tvtZk,1732
+eido-0.2.5.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+eido-0.2.5.dist-info/entry_points.txt,sha256=pu2Iw-IUjVa_bKRgt0xUtPT9iwfR0y2nfRYyaRlkLZU,263
+eido-0.2.5.dist-info/top_level.txt,sha256=oltuMelApqcnJZ09Rrg3lF7kmTkmU5bcA6oRvXhNu6A,5
+eido-0.2.5.dist-info/RECORD,,

{eido-0.2.3.dist-info → eido-0.2.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.1.2)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

eido-0.2.3.dist-info/RECORD

@@ -1,19 +0,0 @@
-eido/__init__.py,sha256=D3CD9BefyY5Yckz-LswPca_VH_RIcZpr53_siXkbi14,612
-eido/__main__.py,sha256=L1wnnEreqYv27ZaaCwwImCIHZK0Mz5IxS80ZsNcS1zg,189
-eido/_version.py,sha256=PNiDER4qM19h9zdsdfgKt2_dT4WgYK7EguJ8RU2qA_g,22
-eido/argparser.py,sha256=vx59eO8CClaQpXehcW052y4HW5mttGTqM96PoJJwWkE,4806
-eido/cli.py,sha256=dXPaqF6uUYnGMlW2H9Mc628CfhCl3pEinxWYnQ94SVc,5814
-eido/const.py,sha256=Tb-fDKvneyZX3qLgLYVWtGGs4Hw4tRogB3OXIlwtpdY,1109
-eido/conversion.py,sha256=MKuJWvLB10opq_noTiOSviiiJgMLY7n8B2stfCjEELE,4002
-eido/conversion_plugins.py,sha256=zqjJbUo1p3l50NddGcO2KccnK5fXvQPe-GFyABr5Pg4,2529
-eido/exceptions.py,sha256=C9gc_XnxYXT8uH7xXoh1NN7KUFXbRvLp4VN7H1DqF9w,1213
-eido/inspection.py,sha256=rfuXnAawGBWQFz_hbJA2VYP_sFvpYxztxOiXL6t610o,3223
-eido/output_formatters.py,sha256=bKqaashXRh-Vp6WbQzq8lQXbNHtvOR9IdXkn31rCmL8,4481
-eido/schema.py,sha256=I75jlUlUdswkne6Xq2XLD8zm-f8p7VITQIj7J_x7aH8,2664
-eido/validation.py,sha256=vmujhaDmNp2SFLhjBrh1SVGhM_NDf3ARVt91ZHaqrUA,8527
-eido-0.2.3.dist-info/LICENSE.txt,sha256=oB6ZGDa4kcznznJKJsLLFFcOZyi8Y6e2Jv0rJozgp-I,1269
-eido-0.2.3.dist-info/METADATA,sha256=kku0Ni4ZW43It53F7_xXQVVyKl7r9HIiBdRecT3USFM,1519
-eido-0.2.3.dist-info/WHEEL,sha256=cVxcB9AmuTcXqmwrtPhNK88dr7IR_b6qagTj0UvIEbY,91
-eido-0.2.3.dist-info/entry_points.txt,sha256=pu2Iw-IUjVa_bKRgt0xUtPT9iwfR0y2nfRYyaRlkLZU,263
-eido-0.2.3.dist-info/top_level.txt,sha256=oltuMelApqcnJZ09Rrg3lF7kmTkmU5bcA6oRvXhNu6A,5
-eido-0.2.3.dist-info/RECORD,,