Merge pull request #382 from pepkit/381_eido_fix

v1.4.1
pepkit · Jun 27, 2023 · 5891017 · 5891017
2 parents e5191ef + 8cec618
commit 5891017
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Showing 5 changed files with 12 additions and 8 deletions.
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,6 +2,10 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [1.4.1] -- 2023-06-22
+
+### Fixed
+- Upgraded Eido version to 0.2.0 or higher.
 
 ## [1.4.0] -- 2023-04-24
 

diff --git a/looper/_version.py b/looper/_version.py
@@ -1 +1 @@
-__version__ = "1.4.0"
+__version__ = "1.4.1"
diff --git a/looper/conductor.py b/looper/conductor.py
@@ -7,10 +7,10 @@
 import time
 from copy import copy, deepcopy
 from json import loads
-from subprocess import CalledProcessError, check_output
+from subprocess import check_output
 from typing import *
 
-from eido import read_schema, validate_inputs
+from eido import read_schema, get_input_files_size
 from eido.const import INPUT_FILE_SIZE_KEY, MISSING_KEY
 from jinja2.exceptions import UndefinedError
 
@@ -454,7 +454,7 @@ def add_sample(self, sample, rerun=False):
         schema_source = self.pl_iface.get_pipeline_schemas()
         if schema_source and self.prj.file_checks:
             try:
-                validation = validate_inputs(sample, read_schema(schema_source))
+                validation = get_input_files_size(sample, read_schema(schema_source))
             except RemoteYAMLError:
                 _LOGGER.warn(
                     "Could not read remote schema. Skipping inputs validation."

diff --git a/looper/looper.py b/looper/looper.py
@@ -435,7 +435,7 @@ def __call__(self, args, rerun=False, **compute_kwargs):
         # for every pipeline matched for this project
         for schema_file in self.prj.get_schemas(self.prj.pipeline_interfaces):
             try:
-                validate_config(self.prj, schema_file, True)
+                validate_config(self.prj, schema_file)
             except RemoteYAMLError:
                 _LOGGER.warn(
                     "Could not read remote schema, skipping config validation."
@@ -476,7 +476,7 @@ def __call__(self, args, rerun=False, **compute_kwargs):
             # (from sample's piface)
             for schema_file in self.prj.get_schemas(sample_pifaces):
                 try:
-                    validate_sample(self.prj, sample.sample_name, schema_file, True)
+                    validate_sample(self.prj, sample.sample_name, schema_file)
                 except EidoValidationError as e:
                     _LOGGER.error(f"Short-circuiting due to validation error: {e}")
                     return False

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -1,11 +1,11 @@
 colorama>=0.3.9
 divvy>=0.5.0
-eido>=0.1.3
+eido>=0.2.0
 jinja2
 logmuse>=0.2.0
 pandas>=0.20.2
 pipestat>=0.1.0
-peppy>=0.35.4
+peppy>=0.35.5
 pyyaml>=3.12
 rich>=9.10.0
 ubiquerg>=0.5.2