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Merged
climbfuji merged 1 commit into from
Nov 20, 2025
Merged

Add unit tests for SDF reading #5

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7 changes: 5 additions & 2 deletions scripts/parse_tools/fortran_conditional.py
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Expand Up @@ -7,7 +7,10 @@

import re

FORTRAN_CONDITIONAL_REGEX_WORDS = [' ', '(', ')', '==', '/=', '<=', '>=', '<', '>', '.eqv.', '.neqv.',
fortran_conditional_regex_tokens = ['==', '/=', '<=', '>=', '<', '>', '.eqv.', '.neqv.',
'.true.', '.false.', '.lt.', '.le.', '.eq.', '.ge.', '.gt.', '.ne.',
'.not.', '.and.', '.or.', '.xor.']
FORTRAN_CONDITIONAL_REGEX = re.compile(r"[\w']+|" + "|".join([word.replace('(','\(').replace(')', '\)') for word in FORTRAN_CONDITIONAL_REGEX_WORDS]))

FORTRAN_CONDITIONAL_REGEX_WORDS = [' ', '[(]', '[)]'] + fortran_conditional_regex_tokens

FORTRAN_CONDITIONAL_REGEX = re.compile(r"[\w']+|[ ()]|" + "|".join([word for word in FORTRAN_CONDITIONAL_REGEX_WORDS]))
5 changes: 3 additions & 2 deletions scripts/parse_tools/parse_checkers.py
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Expand Up @@ -13,13 +13,14 @@
########################################################################

_UNITLESS_REGEX = "1"
_NON_LEADING_ZERO_NUM = "[1-9]\d*"
_NON_LEADING_ZERO_NUM = r"[1-9]\d*"
_CHAR_WITH_UNDERSCORE = "([a-zA-Z]+_[a-zA-Z]+)+"
_NEGATIVE_NON_LEADING_ZERO_NUM = f"[-]{_NON_LEADING_ZERO_NUM}"
_POSITIVE_NON_LEADING_ZERO_NUM = f"[+]{_NON_LEADING_ZERO_NUM}"
_UNIT_EXPONENT = f"({_NEGATIVE_NON_LEADING_ZERO_NUM}|{_POSITIVE_NON_LEADING_ZERO_NUM}|{_NON_LEADING_ZERO_NUM})"
_UNIT_REGEX = f"[a-zA-Z]+{_UNIT_EXPONENT}?"
_UNITS_REGEX = f"^({_CHAR_WITH_UNDERSCORE}|{_UNIT_REGEX}(\s{_UNIT_REGEX})*|{_UNITLESS_REGEX})$"
_UNIT_REGEXES = f"{_UNIT_REGEX}(" r"\s" f"{_UNIT_REGEX})"
_UNITS_REGEX = f"^({_CHAR_WITH_UNDERSCORE}|{_UNIT_REGEXES}*|{_UNITLESS_REGEX})$"
_UNITS_RE = re.compile(_UNITS_REGEX)
_MAX_MOLAR_MASS = 10000.0

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44 changes: 36 additions & 8 deletions scripts/parse_tools/xml_tools.py
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Expand Up @@ -38,10 +38,14 @@ def __init__(self, message):
super().__init__(message)

###############################################################################
def call_command(commands, logger, silent=False):
def call_command(commands, logger, silent=False, return_proc=False):
###############################################################################
"""
Try a command line and return the output on success (None on failure)
Try a command line and return True only for a zero return code
If silent==True, do not log output and simply return False on an exception
If return_proc==True, return the CompletedProcess instance instead of a boolean
If silent==True and return_proc==True, return None in the case of an exception

>>> _LOGGER = init_log('xml_tools')
>>> set_log_to_null(_LOGGER)
>>> call_command(['ls', 'really__improbable_fffilename.foo'], _LOGGER) #doctest: +IGNORE_EXCEPTION_DETAIL
Expand All @@ -50,6 +54,8 @@ def call_command(commands, logger, silent=False):
[Errno 2] No such file or directory
>>> call_command(['ls', 'really__improbable_fffilename.foo'], _LOGGER, silent=True)
False
>>> call_command(['ls'], _LOGGER, silent=True, return_proc=True).returncode
0
>>> call_command(['ls'], _LOGGER)
True
>>> try:
Expand All @@ -75,11 +81,22 @@ def call_command(commands, logger, silent=False):
capture_output=True)
if not silent:
logger.debug(cproc.stdout)
if cproc.stderr:
logger.warning(cproc.stderr)
# end if
# end if
if return_proc:
result = cproc
else:
result = cproc.returncode == 0
# end if
result = cproc.returncode == 0
except (OSError, CCPPError, subprocess.CalledProcessError) as err:
if silent:
result = False
if return_proc:
result = None
else:
result = False
# end if
else:
cmd = ' '.join(commands)
outstr = f"Execution of '{cmd}' failed with code: {err.returncode}\n"
Expand Down Expand Up @@ -213,7 +230,15 @@ def validate_xml_file(filename, schema_root, version, logger,
logger.debug("Checking file {} against schema {}".format(filename,
schema_file))
cmd = [_XMLLINT, '--noout', '--schema', schema_file, filename]
result = call_command(cmd, logger)
result = call_command(cmd, logger, return_proc=True)
if result.returncode == 0:
## We got a pass return code but some versions of xmllint do not
## correctly return an error code on non-validation so double check
## the result
result = b'validates' in result.stdout or b'validates' in result.stderr
else:
result = True
# end if
return result
# end if
lmsg = "xmllint not found, could not validate file {}"
Expand Down Expand Up @@ -411,11 +436,14 @@ def replace_nested_suite(element, nested_suite, default_path, logger):
suite_name = nested_suite.attrib.get("name")
group_name = nested_suite.attrib.get("group")
file = nested_suite.attrib.get("file")
if not file:
raise CCPPError("file attribute required for nested_suite tag")
# end if
if not os.path.isabs(file):
file = os.path.join(default_path, file)
referenced_suite = load_suite_by_name(suite_name, group_name, file,
logger=logger)
imported_content = [ET.fromstring(ET.tostring(child))
imported_content = [ET.fromstring(ET.tostring(child))
for child in referenced_suite]
# Swap nested suite with imported content
for item in imported_content:
Expand Down Expand Up @@ -581,7 +609,7 @@ def expand_nested_suites(suite, default_path, logger=None):
return
raise CCPPError("Exceeded number of iterations while expanding nested suites:" + \
"check for inifite recursion or adjust limit max_iterations")

###############################################################################
def write_xml_file(root, file_path, logger=None):
###############################################################################
Expand All @@ -598,7 +626,7 @@ def remove_whitespace_nodes(node):

# Convert ElementTree to a byte string
byte_string = ET.tostring(root, 'us-ascii')

# Parse string using minidom for pretty printing
reparsed = xml.dom.minidom.parseString(byte_string)

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10 changes: 10 additions & 0 deletions test/unit_tests/sample_suite_files/another_suite.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="another_suite" version="2.0">
<group name="another_group">
<subcycle loop="num_subcycles_for_ag">
<scheme>another_scheme</scheme>
</subcycle>
<scheme>more_scheme</scheme>
</group>
</suite>
16 changes: 16 additions & 0 deletions test/unit_tests/sample_suite_files/another_suite2.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="another_suite2" version="2.0">
<group name="another_group2">
<subcycle loop="num_subcycles_for_ag2">
<scheme>another_scheme</scheme>
</subcycle>
<scheme>more_scheme</scheme>
</group>
<group name="another_group3">
<subcycle loop="num_subcycles_for_ag3">
<scheme>another_scheme</scheme>
</subcycle>
<scheme>more_scheme</scheme>
</group>
</suite>
10 changes: 10 additions & 0 deletions test/unit_tests/sample_suite_files/nested_full_suite.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="nested_suite" version="2.0" >
<group name="nested_group1">
<scheme>g1_scheme1</scheme>
</group>
<group name="nested_group2">
<nested_suite name="subsuite_1" group="group1" file="subsuite1.xml"/>
</group>
</suite>
7 changes: 7 additions & 0 deletions test/unit_tests/sample_suite_files/subsuite1.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="subsuite_1" version="2.0">
<group name="group1">
<scheme>scheme_subsuite1</scheme>
</group>
</suite>
9 changes: 9 additions & 0 deletions test/unit_tests/sample_suite_files/subsuite_inline.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="subsuite_inline" version="1.0">
<group name="group2">
<scheme>scheme1i</scheme>
<scheme>scheme2i</scheme>
<scheme>scheme1i</scheme>
</group>
</suite>
16 changes: 16 additions & 0 deletions test/unit_tests/sample_suite_files/suite_bad_v2_duplicate_group.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="main_suite" version="2.0">
<group name="group1">
<subcycle loop="num_subcycles_for_scheme9">
<scheme>effr_pre</scheme>
<subcycle loop="2">
<subcycle loop="2">
<scheme>scheme9</scheme>
</subcycle>
</subcycle>
<scheme>scheme3</scheme>
</subcycle>
</group>
<nested_suite name="subsuite_1" file="subsuite1.xml"/>
</suite>
7 changes: 7 additions & 0 deletions test/unit_tests/sample_suite_files/suite_bad_v2_suite_tag.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="ver_test_suite" version="2.0">
<group name="group1">
<suite>subsuite_inline</suite>
</group>
</suite>
8 changes: 8 additions & 0 deletions test/unit_tests/sample_suite_files/suite_bad_version01.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="bad_suite_version" version="a">
<group name="group1">
<scheme>scheme1</scheme>
<scheme>scheme2</scheme>
</group>
</suite>
8 changes: 8 additions & 0 deletions test/unit_tests/sample_suite_files/suite_bad_version02.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="bad_suite_version" version="1.2.3">
<group name="group1">
<scheme>scheme1</scheme>
<scheme>scheme2</scheme>
</group>
</suite>
8 changes: 8 additions & 0 deletions test/unit_tests/sample_suite_files/suite_bad_version03.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="bad_suite_version" version="0.1">
<group name="group1">
<scheme>scheme1</scheme>
<scheme>scheme2</scheme>
</group>
</suite>
8 changes: 8 additions & 0 deletions test/unit_tests/sample_suite_files/suite_bad_version04.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="bad_suite_version" version="1.-1">
<group name="group1">
<scheme>scheme1</scheme>
<scheme>scheme2</scheme>
</group>
</suite>
8 changes: 8 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v1_test01.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="ver_test_suite" version="1.0">
<group name="group1">
<scheme>scheme1</scheme>
<scheme>scheme2</scheme>
</group>
</suite>
11 changes: 11 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v1_test02.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="good_suite" version="1.0">
<group name="physics">
<scheme>scheme1</scheme>
<scheme>scheme2</scheme>
<scheme>scheme3</scheme>
<scheme>scheme2</scheme>
<scheme>scheme1</scheme>
</group>
</suite>
9 changes: 9 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test01.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="ver_test_suite" version="2.0">
<group name="group1">
<scheme>scheme5</scheme>
<nested_suite name="subsuite_inline" group="group2" file="subsuite_inline.xml"/>
<scheme>scheme9</scheme>
</group>
</suite>
11 changes: 11 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test01_exp.xml
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<?xml version="1.0" ?>

<suite name="ver_test_suite" version="2.0">
<group name="group1">
<scheme>scheme5</scheme>
<scheme>scheme1i</scheme>
<scheme>scheme2i</scheme>
<scheme>scheme1i</scheme>
<scheme>scheme9</scheme>
</group>
</suite>
10 changes: 10 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test02.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="v2_suite" version="2.0">
<group name="main_group">
<subcycle loop="num_subcycles_for_scheme6">
<scheme>scheme6</scheme>
</subcycle>
<nested_suite name="another_suite2" group="another_group3" file="another_suite2.xml"/>
</group>
</suite>
13 changes: 13 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test02_exp.xml
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<?xml version="1.0" ?>

<suite name="v2_suite" version="2.0">
<group name="main_group">
<subcycle loop="num_subcycles_for_scheme6">
<scheme>scheme6</scheme>
</subcycle>
<subcycle loop="num_subcycles_for_ag3">
<scheme>another_scheme</scheme>
</subcycle>
<scheme>more_scheme</scheme>
</group>
</suite>
19 changes: 19 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test03.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="main_suite" version="2.0" >
<group name="groupp">
<scheme>scheme13</scheme>
<subcycle loop="num_subcycles_for_main1">
<scheme>effr_pre</scheme>
<subcycle loop="2">
<subcycle loop="2">
<scheme>main_calc</scheme>
</subcycle>
</subcycle>
<scheme>main_post</scheme>
</subcycle>
<nested_suite name="another_suite2" group="another_group3" file="another_suite2.xml"/>
<nested_suite name="another_suite" group="another_group" file="another_suite.xml"/>
</group>
<nested_suite name="nested_suite" file="nested_full_suite.xml"/>
</suite>
30 changes: 30 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test03_exp.xml
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<?xml version="1.0" ?>

<suite name="main_suite" version="2.0">
<group name="groupp">
<scheme>scheme13</scheme>
<subcycle loop="num_subcycles_for_main1">
<scheme>effr_pre</scheme>
<subcycle loop="2">
<subcycle loop="2">
<scheme>main_calc</scheme>
</subcycle>
</subcycle>
<scheme>main_post</scheme>
</subcycle>
<subcycle loop="num_subcycles_for_ag3">
<scheme>another_scheme</scheme>
</subcycle>
<scheme>more_scheme</scheme>
<subcycle loop="num_subcycles_for_ag">
<scheme>another_scheme</scheme>
</subcycle>
<scheme>more_scheme</scheme>
</group>
<group name="nested_group1">
<scheme>g1_scheme1</scheme>
</group>
<group name="nested_group2">
<scheme>scheme_subsuite1</scheme>
</group>
</suite>
18 changes: 18 additions & 0 deletions test/unit_tests/sample_suite_files/suite_good_v2_test04.xml
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<?xml version="1.0" encoding="UTF-8"?>

<suite name="ver_test_suite" version="2.0">
<group name="main11">
<subcycle loop="num_subcycles_for_main1">
<scheme>effr_pre</scheme>
<subcycle loop="2">
<subcycle loop="2">
<scheme>main_calc</scheme>
</subcycle>
</subcycle>
<scheme>main_post</scheme>
</subcycle>
<nested_suite name="another_suite2" group="another_group3" file="another_suite2.xml"/>
<nested_suite name="another_suite" group="another_group" file="another_suite.xml"/>
</group>
<nested_suite name="nested_suite" group="nested_group2" file="nested_full_suite.xml"/>
</suite>
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