Merge pull request #234 from databio/dev

donaldcampbelljr · web-flow · commit a7ca5ef30de5 · 2025-09-22T12:22:48.000-06:00
v 0.14.5 release
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,5 +1,10 @@
 # Changelog
 
+
+## [0.14.5] -- 2025-09-22
+### Changed
+- Remove veracitools dependency [#233](https://github.com/databio/pypiper/issues/233)
+
 ## [0.14.4] -- 2025-02-25
 ### Changed
 - Fixed warnings for Python >3.12
diff --git a/init_interactive.py b/init_interactive.py
@@ -1,4 +1,4 @@
-""" Create dummy PipelineManager and NGSTk instance for interactive session. """
+"""Create dummy PipelineManager and NGSTk instance for interactive session."""
 
 import os
 
diff --git a/pypiper/_version.py b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.14.4"
+__version__ = "0.14.5"
diff --git a/pypiper/const.py b/pypiper/const.py
@@ -1,4 +1,4 @@
-""" Pypiper constants. """
+"""Pypiper constants."""
 
 CHECKPOINT_EXTENSION = ".checkpoint"
 DEFAULT_SAMPLE_NAME = "DEFAULT_SAMPLE_NAME"
diff --git a/pypiper/exceptions.py b/pypiper/exceptions.py
@@ -1,4 +1,4 @@
-""" Custom pypiper exceptions """
+"""Custom pypiper exceptions"""
 
 __author__ = "Vince Reuter"
 __email__ = "vreuter@virginia.edu"
diff --git a/pypiper/flags.py b/pypiper/flags.py
@@ -1,4 +1,4 @@
-""" Status flags """
+"""Status flags"""
 
 # TODO: ultimately, these should migrate to pep.
 RUN_FLAG = "running"
diff --git a/pypiper/folder_context.py b/pypiper/folder_context.py
@@ -1,4 +1,4 @@
-""" Context manager for temporarily changing folder. """
+"""Context manager for temporarily changing folder."""
 
 import os
 
diff --git a/pypiper/ngstk.py b/pypiper/ngstk.py
@@ -1,4 +1,4 @@
-""" Broadly applicable NGS processing/analysis functionality """
+"""Broadly applicable NGS processing/analysis functionality"""
 
 import errno
 import os
diff --git a/pypiper/pipeline.py b/pypiper/pipeline.py
@@ -1,4 +1,4 @@
-""" Pipeline base class """
+"""Pipeline base class"""
 
 import abc
 import glob
diff --git a/pypiper/stage.py b/pypiper/stage.py
@@ -1,4 +1,4 @@
-""" Conceptualize a pipeline processing phase/stage. """
+"""Conceptualize a pipeline processing phase/stage."""
 
 import copy
 
diff --git a/pypiper/utils.py b/pypiper/utils.py
@@ -1,4 +1,4 @@
-""" Shared utilities """
+"""Shared utilities"""
 
 import os
 import re
diff --git a/requirements/requirements-test.txt b/requirements/requirements-test.txt
@@ -3,5 +3,4 @@ pytest>=4.6.9
 pytest-cov>=2.8.1
 hypothesis==4.38.0
 coveralls
-veracitools
 pytest-remotedata
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,4 +1,4 @@
-""" Fixtures and configuration visible to all tests """
+"""Fixtures and configuration visible to all tests"""
 
 import copy
 import os
diff --git a/tests/helpers.py b/tests/helpers.py
@@ -1,4 +1,4 @@
-""" Helpers for tests """
+"""Helpers for tests"""
 
 import glob
 import os
@@ -67,3 +67,33 @@ def __init__(self, *args, **kwargs):
         kwd_args = {"multi": True}  # Like interactive mode.
         kwd_args.update(kwargs)
         super(SafeTestPipeline, self).__init__(*args, **kwd_args)
+
+
+# originally imported from veracitools v0.1.4 (now deprecated)
+class ExpectContext(object):
+    """Pytest validation context, a framework for varied kinds of expectations."""
+
+    def __init__(self, expected, test_func):
+        """
+        Create the test context by specifying expectation and function.
+
+        :param object | type expected: expected result or exception
+        :param callable test_func: the callable object to test
+        """
+        self._f = test_func
+        self._exp = expected
+
+    def __enter__(self):
+        """Return the instance for use as a callable."""
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        pass
+
+    def __call__(self, *args, **kwargs):
+        """Execute the instance's function, passing given args/kwargs."""
+        if isinstance(self._exp, type) and issubclass(self._exp, Exception):
+            with pytest.raises(self._exp):
+                self._f(*args, **kwargs)
+        else:
+            assert self._exp == self._f(*args, **kwargs)
diff --git a/tests/pipeline/conftest.py b/tests/pipeline/conftest.py
@@ -1,4 +1,4 @@
-""" Test configuration for Pipeline tests. """
+"""Test configuration for Pipeline tests."""
 
 import os
 
diff --git a/tests/pipeline/test_multi_pipeline_sample.py b/tests/pipeline/test_multi_pipeline_sample.py
@@ -1,4 +1,4 @@
-""" Tests for case in which multiple pipelines process a single sample. """
+"""Tests for case in which multiple pipelines process a single sample."""
 
 import os
 
diff --git a/tests/pipeline/test_pipeline.py b/tests/pipeline/test_pipeline.py
@@ -1,4 +1,4 @@
-""" Tests for the Pipeline data type """
+"""Tests for the Pipeline data type"""
 
 import glob
 import os
diff --git a/tests/pipeline/test_pipeline_checkpoint.py b/tests/pipeline/test_pipeline_checkpoint.py
@@ -1,4 +1,4 @@
-""" Tests for a pipeline's ability to checkpoint its stages. """
+"""Tests for a pipeline's ability to checkpoint its stages."""
 
 import os
 import time
diff --git a/tests/pipeline/test_pipeline_constructor.py b/tests/pipeline/test_pipeline_constructor.py
@@ -1,4 +1,4 @@
-""" Tests for construction of a Pipeline """
+"""Tests for construction of a Pipeline"""
 
 import pytest
 
diff --git a/tests/pipeline_manager/test_halt.py b/tests/pipeline_manager/test_halt.py
@@ -1,4 +1,4 @@
-""" Tests for effects of pipeline manager's halt() function. """
+"""Tests for effects of pipeline manager's halt() function."""
 
 import os
 
diff --git a/tests/pipeline_manager/test_manager_constructor.py b/tests/pipeline_manager/test_manager_constructor.py
@@ -1,4 +1,4 @@
-""" Test effects of construction of a pipeline manager. """
+"""Test effects of construction of a pipeline manager."""
 
 import argparse
 import os
diff --git a/tests/pipeline_manager/test_manager_state.py b/tests/pipeline_manager/test_manager_state.py
@@ -1,4 +1,4 @@
-""" Tests related to pipeline manager state. """
+"""Tests related to pipeline manager state."""
 
 import os
 
diff --git a/tests/pipeline_manager/test_pipeline_manager.py b/tests/pipeline_manager/test_pipeline_manager.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-""" PipelineManager tests. """
+"""PipelineManager tests."""
 
 import glob
 import os
diff --git a/tests/pipeline_manager/test_pipeline_manager_timestamp.py b/tests/pipeline_manager/test_pipeline_manager_timestamp.py
@@ -1,4 +1,4 @@
-""" Tests for the timestamp functionality of a PipelineManager. """
+"""Tests for the timestamp functionality of a PipelineManager."""
 
 import os
 import sys
diff --git a/tests/pipeline_manager/test_pipeline_manager_timestamp_checkpoint_filepath.py b/tests/pipeline_manager/test_pipeline_manager_timestamp_checkpoint_filepath.py
@@ -1,4 +1,4 @@
-""" Tests for construction of checkpoint filepath """
+"""Tests for construction of checkpoint filepath"""
 
 import glob
 import os
diff --git a/tests/pipeline_manager/test_set_status_flag.py b/tests/pipeline_manager/test_set_status_flag.py
@@ -1,4 +1,4 @@
-""" Tests for changes to pipepline manager's status flag. """
+"""Tests for changes to pipepline manager's status flag."""
 
 import pytest
 
diff --git a/tests/test_packaging.py b/tests/test_packaging.py
@@ -1,4 +1,4 @@
-""" Validate what's available directly on the top-level import. """
+"""Validate what's available directly on the top-level import."""
 
 from inspect import isfunction
 
diff --git a/tests/test_pipeline_filepath.py b/tests/test_pipeline_filepath.py
@@ -1,4 +1,4 @@
-""" Tests for utility functions """
+"""Tests for utility functions"""
 
 import os
 
diff --git a/tests/utils_tests/test_check_command_callability.py b/tests/utils_tests/test_check_command_callability.py
@@ -1,11 +1,11 @@
-""" Tests for checking a collection of commands for callability """
+"""Tests for checking a collection of commands for callability"""
 
 import os
 
 import mock
 import pytest
 from ubiquerg import powerset
-from veracitools import ExpectContext
+from tests.helpers import ExpectContext
 
 from pypiper import utils as piper_utils
 
diff --git a/tests/utils_tests/test_head_util.py b/tests/utils_tests/test_head_util.py
@@ -1,4 +1,4 @@
-""" Tests for the head() utility function """
+"""Tests for the head() utility function"""
 
 import random
 import string

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Create dummy PipelineManager and NGSTk instance for interactive session. """`
	`1`	`+"""Create dummy PipelineManager and NGSTk instance for interactive session."""`
`2`	`2`
`3`	`3`	`import os`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-__version__ = "0.14.4"`
	`1`	`+__version__ = "0.14.5"`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Pypiper constants. """`
	`1`	`+"""Pypiper constants."""`
`2`	`2`
`3`	`3`	`CHECKPOINT_EXTENSION = ".checkpoint"`
`4`	`4`	`DEFAULT_SAMPLE_NAME = "DEFAULT_SAMPLE_NAME"`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Custom pypiper exceptions """`
	`1`	`+"""Custom pypiper exceptions"""`
`2`	`2`
`3`	`3`	`__author__ = "Vince Reuter"`
`4`	`4`	`__email__ = "vreuter@virginia.edu"`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Status flags """`
	`1`	`+"""Status flags"""`
`2`	`2`
`3`	`3`	`# TODO: ultimately, these should migrate to pep.`
`4`	`4`	`RUN_FLAG = "running"`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Context manager for temporarily changing folder. """`
	`1`	`+"""Context manager for temporarily changing folder."""`
`2`	`2`
`3`	`3`	`import os`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Broadly applicable NGS processing/analysis functionality """`
	`1`	`+"""Broadly applicable NGS processing/analysis functionality"""`
`2`	`2`
`3`	`3`	`import errno`
`4`	`4`	`import os`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Pipeline base class """`
	`1`	`+"""Pipeline base class"""`
`2`	`2`
`3`	`3`	`import abc`
`4`	`4`	`import glob`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-""" Conceptualize a pipeline processing phase/stage. """`
	`1`	`+"""Conceptualize a pipeline processing phase/stage."""`
`2`	`2`
`3`	`3`	`import copy`
`4`	`4`