eido 0.2.3__tar.gz → 0.2.5__tar.gz

{eido-0.2.3/eido.egg-info → eido-0.2.5}/PKG-INFO

@@ -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
@@ -18,9 +18,19 @@ 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
+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/eido/_version.py

@@ -0,0 +1 @@
+__version__ = "0.2.5"

{eido-0.2.3 → eido-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-0.2.3 → eido-0.2.5}/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-0.2.3 → eido-0.2.5}/eido/exceptions.py

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

{eido-0.2.3 → eido-0.2.5}/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-0.2.3 → eido-0.2.5}/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 → eido-0.2.5/eido.egg-info}/PKG-INFO

@@ -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
@@ -18,9 +18,19 @@ 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
+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-0.2.3 → eido-0.2.5}/eido.egg-info/requires.txt

@@ -1,7 +1,7 @@
 jsonschema>=3.0.1
 logmuse>=0.2.5
-pandas
-peppy>=0.40.6
+pandas<3.0.0
+peppy>=0.40.7
 ubiquerg>=0.5.2
 
 [:python_version < "3.10"]

{eido-0.2.3 → eido-0.2.5}/requirements/requirements-all.txt

@@ -1,6 +1,6 @@
 importlib-metadata; python_version < '3.10'
 jsonschema>=3.0.1
 logmuse>=0.2.5
-pandas
-peppy>=0.40.6
+pandas<3.0.0
+peppy>=0.40.7
 ubiquerg>=0.5.2

{eido-0.2.3 → eido-0.2.5}/tests/test_conversions.py

@@ -1,4 +1,10 @@
-from eido.conversion import *
+from eido.conversion import (
+    run_filter,
+    get_available_pep_filters,
+    pep_conversion_plugins,
+    convert_project,
+)
+import peppy
 
 
 class TestConversionInfrastructure:
@@ -74,3 +80,27 @@ class TestConversionInfrastructure:
 
         assert save_result_mock.called
         assert conv_result == {"samples": output_pep_nextflow_taxprofiler}
+
+    def test_multiple_subsamples(self, test_multiple_subs):
+        project = peppy.Project(test_multiple_subs, sample_table_index="sample_id")
+
+        conversion = convert_project(
+            project,
+            "csv",
+        )
+        assert isinstance(conversion["samples"], str)
+        conversion = convert_project(
+            project,
+            "basic",
+        )
+        assert isinstance(conversion["project"], str)
+        conversion = convert_project(
+            project,
+            "yaml",
+        )
+        assert isinstance(conversion["project"], str)
+        conversion = convert_project(
+            project,
+            "yaml-samples",
+        )
+        assert isinstance(conversion["samples"], str)

{eido-0.2.3 → eido-0.2.5}/tests/test_validations.py

@@ -1,7 +1,6 @@
 import urllib
 
 import pytest
-from jsonschema.exceptions import ValidationError
 from peppy import Project
 from peppy.utils import load_yaml
 
@@ -140,9 +139,15 @@ class TestProjectWithoutConfigValidation:
             )
 
     def test_validate_file_existance(
-        self, test_file_existance_pep, test_file_existence_schema
+        self, test_file_existing_pep, test_file_existing_schema
     ):
-        schema_path = test_file_existence_schema
-        prj = Project(test_file_existance_pep)
+        schema_path = test_file_existing_schema
+        prj = Project(test_file_existing_pep)
         with pytest.raises(PathAttrNotFoundError):
             validate_input_files(prj, schema_path)
+
+    def test_validation_values(self, test_schema_value_check, test_file_value_check):
+        schema_path = test_schema_value_check
+        prj = Project(test_file_value_check)
+        with pytest.raises(EidoValidationError):
+            validate_project(project=prj, schema=schema_path)

eido-0.2.3/eido/_version.py

@@ -1 +0,0 @@
-__version__ = "0.2.3"