adding {file_handling}, {test_handling} and the respective {test_test_handling] from previous projects, docstring-adapted to brecal. Updating the environment yml to ensure, that pytest-cov is also present. Performing the first pytest incl. coverage, where the coverage_reports are gitignored

.gitignore

@@ -437,5 +437,6 @@ FodyWeavers.xsd
 
 # Local change logs
 change_log_metz.md
-
+src/notebooks_metz
+src/lib_brecal_utils/**.egg-info
 

src/lib_brecal_utils/brecal_utils/file_handling.py

@@ -0,0 +1,46 @@
+
+
+import os
+
+def get_project_root(root_base_name:str, root_dir:None=None):
+    """
+    given a {root_base_name}, this function searches the parent folders of {root_dir} until
+    the basename matches.
+
+    Example:
+        root_base_name = "brecal"
+        root_dir = "/home/arbitrary_user/brecal/_template/tests"
+
+        returns: "/home/arbitrary_user/brecal"
+
+    arguments:
+        root_base_name:str, base directory name that should be searched for
+        root_dir: defaults to 'None', whereas then the current working directory is selected. Can be an arbitrary path.
+
+    returns: root_dir
+    """
+    if root_dir is None:
+        root_dir = os.getcwd()
+
+    assert root_base_name in root_dir, f"the desired base name MUST be present within the root directory.\nRoot Directory: {root_dir}\nDesired Root Base Name: {root_base_name}"
+    assert root_dir.count(root_base_name)==1, f"found multiple matches for root_base_name" # do not change, as a pytest requires precise wording
+
+
+    while not os.path.basename(root_dir)==root_base_name:
+        root_dir = os.path.dirname(root_dir)
+
+    return root_dir
+
+def ensure_path(path, print_info=0):
+    """
+    Function ensures that a certain directory exists. If it does not exist, it will be created.
+    It further checks if the parent-directory of the file exists and also ensures that.
+    
+    options:
+    print_info: print additional information (debugging)
+    """
+    if not os.path.exists(path):
+        os.makedirs(path)
+        if print_info == 1:
+            print(f"Created directory and subdirectories: {path}")
+    return

src/lib_brecal_utils/brecal_utils/test_handling.py

@@ -0,0 +1,84 @@
+
+def execute_test_with_pytest(filepath):
+	"""
+	creates a subprocess to use 'pytest' on a script. Every function inside the filepath
+	will be tested individually. The function returns verbose information about the outcome.
+	
+	filepath:
+		can either be an individual .py file or a root directory, which contains multiple files
+	"""
+	import os
+	import pytest
+	from subprocess import Popen, PIPE
+	
+	assert os.path.exists(filepath), f"cannot find file {filepath}"
+
+	with Popen(['pytest',
+				'-v', 
+				'-W ignore::DeprecationWarning',
+				'-vv',
+				'--durations=0',
+				'--tb=short',  # shorter traceback format
+				str(filepath)], stdout=PIPE, bufsize=1, 
+			   universal_newlines=True) as p:
+		for line in p.stdout:
+			print(line, end='')
+	return
+	
+def execute_coverage_test(tests_path, coverage_path, cov_report_dst_dir=None, cov_fail_under_rate=80, is_test=0):
+	"""
+	creates a subprocess to use 'coverage' on a script. Every function inside the file
+	will be tested individually. The function returns verbose information about the outcome.
+	
+	this function needs two inputs:
+		tests_path, a path that locates each test that should be executed
+			e.g.: "/home/scope_sorting/brecal/src/lib_brecal_utils/tests"
+			
+		coverage_path, a path where the code is stored, which should be analyzed for coverage
+			e.g.: "/home/scope_sorting/brecal/src/lib_brecal_utils/brecal_utils"
+			
+	optional:
+		cov_report_dst_dir, which determines, where the coverage report will be stored. This function then
+		creates & stores an .html and .xml report in that folder. default: None
+		
+		cov_fail_under_rate, an integer which determines, when a coverage test should fail. Default: 80, meaning
+		that at least 80 % of the directory should be tested to pass the test.
+	"""
+	import os
+	import pytest
+	from subprocess import Popen, PIPE
+
+	assert os.path.exists(tests_path), f"cannot find root directory {tests_path}"
+	assert os.path.exists(coverage_path), f"cannot find root directory {coverage_path}"
+	
+	if cov_report_dst_dir is not None:
+		p_open_list_arguments = [
+			'pytest',
+			f"{str(tests_path)}", 
+			"-v",
+			"-vv",
+			"--durations=0",
+			"--cov-report=term",
+			f"--cov-report=html:{cov_report_dst_dir}",
+			f"--cov-report=xml:{cov_report_dst_dir}/coverage.xml",
+			f"--cov-fail-under={cov_fail_under_rate}",
+			f"--cov={str(coverage_path)}", 
+		]
+	else:
+		p_open_list_arguments = [
+			'pytest',
+			f"{str(tests_path)}", 
+			"-v",
+			"-vv",
+			"--durations=0",
+			"--cov-report=term",
+			f"--cov-fail-under={cov_fail_under_rate}",
+			f"--cov={str(coverage_path)}", 
+		]
+
+	with Popen(p_open_list_arguments, stdout=PIPE, bufsize=1,
+			universal_newlines=True) as p:
+		for line in p.stdout:
+			print(line, end='')
+			if is_test:
+				raise KeyboardInterrupt("is_test_interrupt")

src/lib_brecal_utils/environment.yml

@@ -16,7 +16,8 @@ dependencies:
   - conda-forge::matplotlib-base>=3.7.2=py311h54ef318_0
   - conda-forge::matplotlib>=3.7.2=py311h38be061_0
   - matplotlib-inline>=0.1.6=pyhd8ed1ab_0
-  - pytest>=7.4.0=pyhd8ed1ab_0
+  - conda-forge::pytest>=7.4.0=pyhd8ed1ab_0
+  - conda-forge::pytest-cov>=4.1.0=pyhd8ed1ab_0
   - python>=3.11.4=hab00c5b_0_cpython
   - pytz>=2023.3=pyhd8ed1ab_0
   - setuptools>=68.0.0=pyhd8ed1ab_0

src/lib_brecal_utils/tests/test_test_handling.py

@@ -0,0 +1,48 @@
+import unittest
+import pytest
+
+def test_execute_coverage_test():
+    """
+    executes {execute_coverage_test} to check, whether reporting works as expected
+    """
+    import os
+    import brecal_utils
+
+    from brecal_utils.file_handling import get_project_root
+    from brecal_utils.test_handling import execute_coverage_test
+
+    root_dir = brecal_utils.__file__
+    root_dir = get_project_root("lib_brecal_utils", root_dir=root_dir)
+
+    tests_path = os.path.join(root_dir, "tests")
+    coverage_path = os.path.join(root_dir, "brecal_utils")
+    report_path = os.path.join(root_dir, "coverage_reports")
+
+    with pytest.raises(KeyboardInterrupt, match="is_test_interrupt"):
+        execute_coverage_test(tests_path=tests_path, coverage_path=coverage_path, cov_report_dst_dir=report_path, cov_fail_under_rate=0, is_test=1)
+    return
+
+def test_execute_coverage_test_no_report():
+    """
+    executes {execute_coverage_test} to check, whether the function also works without reporting
+    """
+    import os
+    import brecal_utils
+
+    from brecal_utils.file_handling import get_project_root
+    from brecal_utils.test_handling import execute_coverage_test
+
+    root_dir = brecal_utils.__file__
+    root_dir = get_project_root("lib_brecal_utils", root_dir=root_dir)
+
+    tests_path = os.path.join(root_dir, "tests")
+    coverage_path = os.path.join(root_dir, "brecal_utils")
+    report_path = os.path.join(root_dir, "coverage_reports")
+
+    with pytest.raises(KeyboardInterrupt, match="is_test_interrupt"):
+        execute_coverage_test(tests_path=tests_path, coverage_path=coverage_path, cov_report_dst_dir=None, cov_fail_under_rate=0, is_test=1)
+    return
+
+
+if __name__=="__main__":
+    pass