diff --git a/.cmake-format.py b/.cmake-format.py
index 94457f5b233fd324995fef4e7a2a39e6bef5ec42..06299106236de92c7574d3784ed289687c283e66 100644
--- a/.cmake-format.py
+++ b/.cmake-format.py
@@ -3,238 +3,242 @@
# ----------------------------------
with section("parse"):
- # Specify structure for custom cmake functions
- additional_commands = { 'foo': { 'flags': ['BAR', 'BAZ'],
- 'kwargs': {'DEPENDS': '*', 'HEADERS': '*', 'SOURCES': '*'}}}
+ # Specify structure for custom cmake functions
+ additional_commands = {
+ "foo": {
+ "flags": ["BAR", "BAZ"],
+ "kwargs": {"DEPENDS": "*", "HEADERS": "*", "SOURCES": "*"},
+ }
+ }
- # Override configurations per-command where available
- override_spec = {}
+ # Override configurations per-command where available
+ override_spec = {}
- # Specify variable tags.
- vartags = []
+ # Specify variable tags.
+ vartags = []
- # Specify property tags.
- proptags = []
+ # Specify property tags.
+ proptags = []
# -----------------------------
# Options affecting formatting.
# -----------------------------
with section("format"):
- # Disable formatting entirely, making cmake-format a no-op
- disable = False
+ # Disable formatting entirely, making cmake-format a no-op
+ disable = False
- # How wide to allow formatted cmake files
- line_width = 80
+ # How wide to allow formatted cmake files
+ line_width = 80
- # How many spaces to tab for indent
- tab_size = 2
+ # How many spaces to tab for indent
+ tab_size = 2
- # If true, lines are indented using tab characters (utf-8 0x09) instead of
- # <tab_size> space characters (utf-8 0x20). In cases where the layout would
- # require a fractional tab character, the behavior of the fractional
- # indentation is governed by <fractional_tab_policy>
- use_tabchars = False
+ # If true, lines are indented using tab characters (utf-8 0x09) instead of
+ # <tab_size> space characters (utf-8 0x20). In cases where the layout would
+ # require a fractional tab character, the behavior of the fractional
+ # indentation is governed by <fractional_tab_policy>
+ use_tabchars = False
- # If <use_tabchars> is True, then the value of this variable indicates how
- # fractional indentions are handled during whitespace replacement. If set to
- # 'use-space', fractional indentation is left as spaces (utf-8 0x20). If set
- # to `round-up` fractional indentation is replaced with a single tab character
- # (utf-8 0x09) effectively shifting the column to the next tabstop
- fractional_tab_policy = 'use-space'
+ # If <use_tabchars> is True, then the value of this variable indicates how
+ # fractional indentions are handled during whitespace replacement. If set to
+ # 'use-space', fractional indentation is left as spaces (utf-8 0x20). If set
+ # to `round-up` fractional indentation is replaced with a single tab character
+ # (utf-8 0x09) effectively shifting the column to the next tabstop
+ fractional_tab_policy = "use-space"
- # If an argument group contains more than this many sub-groups (parg or kwarg
- # groups) then force it to a vertical layout.
- max_subgroups_hwrap = 2
+ # If an argument group contains more than this many sub-groups (parg or kwarg
+ # groups) then force it to a vertical layout.
+ max_subgroups_hwrap = 2
- # If a positional argument group contains more than this many arguments, then
- # force it to a vertical layout.
- max_pargs_hwrap = 6
+ # If a positional argument group contains more than this many arguments, then
+ # force it to a vertical layout.
+ max_pargs_hwrap = 6
- # If a cmdline positional group consumes more than this many lines without
- # nesting, then invalidate the layout (and nest)
- max_rows_cmdline = 2
+ # If a cmdline positional group consumes more than this many lines without
+ # nesting, then invalidate the layout (and nest)
+ max_rows_cmdline = 2
- # If true, separate flow control names from their parentheses with a space
- separate_ctrl_name_with_space = False
+ # If true, separate flow control names from their parentheses with a space
+ separate_ctrl_name_with_space = False
- # If true, separate function names from parentheses with a space
- separate_fn_name_with_space = False
+ # If true, separate function names from parentheses with a space
+ separate_fn_name_with_space = False
- # If a statement is wrapped to more than one line, than dangle the closing
- # parenthesis on its own line.
- dangle_parens = False
+ # If a statement is wrapped to more than one line, than dangle the closing
+ # parenthesis on its own line.
+ dangle_parens = False
- # If the trailing parenthesis must be 'dangled' on its on line, then align it
- # to this reference: `prefix`: the start of the statement, `prefix-indent`:
- # the start of the statement, plus one indentation level, `child`: align to
- # the column of the arguments
- dangle_align = 'prefix'
+ # If the trailing parenthesis must be 'dangled' on its on line, then align it
+ # to this reference: `prefix`: the start of the statement, `prefix-indent`:
+ # the start of the statement, plus one indentation level, `child`: align to
+ # the column of the arguments
+ dangle_align = "prefix"
- # If the statement spelling length (including space and parenthesis) is
- # smaller than this amount, then force reject nested layouts.
- min_prefix_chars = 4
+ # If the statement spelling length (including space and parenthesis) is
+ # smaller than this amount, then force reject nested layouts.
+ min_prefix_chars = 4
- # If the statement spelling length (including space and parenthesis) is larger
- # than the tab width by more than this amount, then force reject un-nested
- # layouts.
- max_prefix_chars = 10
+ # If the statement spelling length (including space and parenthesis) is larger
+ # than the tab width by more than this amount, then force reject un-nested
+ # layouts.
+ max_prefix_chars = 10
- # If a candidate layout is wrapped horizontally but it exceeds this many
- # lines, then reject the layout.
- max_lines_hwrap = 2
+ # If a candidate layout is wrapped horizontally but it exceeds this many
+ # lines, then reject the layout.
+ max_lines_hwrap = 2
- # What style line endings to use in the output.
- line_ending = 'unix'
+ # What style line endings to use in the output.
+ line_ending = "unix"
- # Format command names consistently as 'lower' or 'upper' case
- command_case = 'canonical'
+ # Format command names consistently as 'lower' or 'upper' case
+ command_case = "canonical"
- # Format keywords consistently as 'lower' or 'upper' case
- keyword_case = 'unchanged'
+ # Format keywords consistently as 'lower' or 'upper' case
+ keyword_case = "unchanged"
- # A list of command names which should always be wrapped
- always_wrap = []
+ # A list of command names which should always be wrapped
+ always_wrap = []
- # If true, the argument lists which are known to be sortable will be sorted
- # lexicographicall
- enable_sort = True
+ # If true, the argument lists which are known to be sortable will be sorted
+ # lexicographicall
+ enable_sort = True
- # If true, the parsers may infer whether or not an argument list is sortable
- # (without annotation).
- autosort = False
+ # If true, the parsers may infer whether or not an argument list is sortable
+ # (without annotation).
+ autosort = False
- # By default, if cmake-format cannot successfully fit everything into the
- # desired linewidth it will apply the last, most agressive attempt that it
- # made. If this flag is True, however, cmake-format will print error, exit
- # with non-zero status code, and write-out nothing
- require_valid_layout = False
+ # By default, if cmake-format cannot successfully fit everything into the
+ # desired linewidth it will apply the last, most agressive attempt that it
+ # made. If this flag is True, however, cmake-format will print error, exit
+ # with non-zero status code, and write-out nothing
+ require_valid_layout = False
- # A dictionary mapping layout nodes to a list of wrap decisions. See the
- # documentation for more information.
- layout_passes = {}
+ # A dictionary mapping layout nodes to a list of wrap decisions. See the
+ # documentation for more information.
+ layout_passes = {}
# ------------------------------------------------
# Options affecting comment reflow and formatting.
# ------------------------------------------------
with section("markup"):
- # What character to use for bulleted lists
- bullet_char = '*'
+ # What character to use for bulleted lists
+ bullet_char = "*"
- # What character to use as punctuation after numerals in an enumerated list
- enum_char = '.'
+ # What character to use as punctuation after numerals in an enumerated list
+ enum_char = "."
- # If comment markup is enabled, don't reflow the first comment block in each
- # listfile. Use this to preserve formatting of your copyright/license
- # statements.
- first_comment_is_literal = False
+ # If comment markup is enabled, don't reflow the first comment block in each
+ # listfile. Use this to preserve formatting of your copyright/license
+ # statements.
+ first_comment_is_literal = False
- # If comment markup is enabled, don't reflow any comment block which matches
- # this (regex) pattern. Default is `None` (disabled).
- literal_comment_pattern = None
+ # If comment markup is enabled, don't reflow any comment block which matches
+ # this (regex) pattern. Default is `None` (disabled).
+ literal_comment_pattern = None
- # Regular expression to match preformat fences in comments default=
- # ``r'^\s*([`~]{3}[`~]*)(.*)$'``
- fence_pattern = '^\\s*([`~]{3}[`~]*)(.*)$'
+ # Regular expression to match preformat fences in comments default=
+ # ``r'^\s*([`~]{3}[`~]*)(.*)$'``
+ fence_pattern = "^\\s*([`~]{3}[`~]*)(.*)$"
- # Regular expression to match rulers in comments default=
- # ``r'^\s*[^\w\s]{3}.*[^\w\s]{3}$'``
- ruler_pattern = '^\\s*[^\\w\\s]{3}.*[^\\w\\s]{3}$'
+ # Regular expression to match rulers in comments default=
+ # ``r'^\s*[^\w\s]{3}.*[^\w\s]{3}$'``
+ ruler_pattern = "^\\s*[^\\w\\s]{3}.*[^\\w\\s]{3}$"
- # If a comment line matches starts with this pattern then it is explicitly a
- # trailing comment for the preceeding argument. Default is '#<'
- explicit_trailing_pattern = '#<'
+ # If a comment line matches starts with this pattern then it is explicitly a
+ # trailing comment for the preceeding argument. Default is '#<'
+ explicit_trailing_pattern = "#<"
- # If a comment line starts with at least this many consecutive hash
- # characters, then don't lstrip() them off. This allows for lazy hash rulers
- # where the first hash char is not separated by space
- hashruler_min_length = 10
+ # If a comment line starts with at least this many consecutive hash
+ # characters, then don't lstrip() them off. This allows for lazy hash rulers
+ # where the first hash char is not separated by space
+ hashruler_min_length = 10
- # If true, then insert a space between the first hash char and remaining hash
- # chars in a hash ruler, and normalize its length to fill the column
- canonicalize_hashrulers = True
+ # If true, then insert a space between the first hash char and remaining hash
+ # chars in a hash ruler, and normalize its length to fill the column
+ canonicalize_hashrulers = True
- # enable comment markup parsing and reflow
- enable_markup = False
+ # enable comment markup parsing and reflow
+ enable_markup = False
# ----------------------------
# Options affecting the linter
# ----------------------------
with section("lint"):
- # a list of lint codes to disable
- disabled_codes = []
+ # a list of lint codes to disable
+ disabled_codes = []
- # regular expression pattern describing valid function names
- function_pattern = '[0-9a-z_]+'
+ # regular expression pattern describing valid function names
+ function_pattern = "[0-9a-z_]+"
- # regular expression pattern describing valid macro names
- macro_pattern = '[0-9A-Z_]+'
+ # regular expression pattern describing valid macro names
+ macro_pattern = "[0-9A-Z_]+"
- # regular expression pattern describing valid names for variables with global
- # (cache) scope
- global_var_pattern = '[A-Z][0-9A-Z_]+'
+ # regular expression pattern describing valid names for variables with global
+ # (cache) scope
+ global_var_pattern = "[A-Z][0-9A-Z_]+"
- # regular expression pattern describing valid names for variables with global
- # scope (but internal semantic)
- internal_var_pattern = '_[A-Z][0-9A-Z_]+'
+ # regular expression pattern describing valid names for variables with global
+ # scope (but internal semantic)
+ internal_var_pattern = "_[A-Z][0-9A-Z_]+"
- # regular expression pattern describing valid names for variables with local
- # scope
- local_var_pattern = '[a-z][a-z0-9_]+'
+ # regular expression pattern describing valid names for variables with local
+ # scope
+ local_var_pattern = "[a-z][a-z0-9_]+"
- # regular expression pattern describing valid names for privatedirectory
- # variables
- private_var_pattern = '_[0-9a-z_]+'
+ # regular expression pattern describing valid names for privatedirectory
+ # variables
+ private_var_pattern = "_[0-9a-z_]+"
- # regular expression pattern describing valid names for public directory
- # variables
- public_var_pattern = '[A-Z][0-9A-Z_]+'
+ # regular expression pattern describing valid names for public directory
+ # variables
+ public_var_pattern = "[A-Z][0-9A-Z_]+"
- # regular expression pattern describing valid names for function/macro
- # arguments and loop variables.
- argument_var_pattern = '[a-z][a-z0-9_]+'
+ # regular expression pattern describing valid names for function/macro
+ # arguments and loop variables.
+ argument_var_pattern = "[a-z][a-z0-9_]+"
- # regular expression pattern describing valid names for keywords used in
- # functions or macros
- keyword_pattern = '[A-Z][0-9A-Z_]+'
+ # regular expression pattern describing valid names for keywords used in
+ # functions or macros
+ keyword_pattern = "[A-Z][0-9A-Z_]+"
- # In the heuristic for C0201, how many conditionals to match within a loop in
- # before considering the loop a parser.
- max_conditionals_custom_parser = 2
+ # In the heuristic for C0201, how many conditionals to match within a loop in
+ # before considering the loop a parser.
+ max_conditionals_custom_parser = 2
- # Require at least this many newlines between statements
- min_statement_spacing = 1
+ # Require at least this many newlines between statements
+ min_statement_spacing = 1
- # Require no more than this many newlines between statements
- max_statement_spacing = 2
- max_returns = 6
- max_branches = 12
- max_arguments = 5
- max_localvars = 15
- max_statements = 50
+ # Require no more than this many newlines between statements
+ max_statement_spacing = 2
+ max_returns = 6
+ max_branches = 12
+ max_arguments = 5
+ max_localvars = 15
+ max_statements = 50
# -------------------------------
# Options affecting file encoding
# -------------------------------
with section("encode"):
- # If true, emit the unicode byte-order mark (BOM) at the start of the file
- emit_byteorder_mark = False
+ # If true, emit the unicode byte-order mark (BOM) at the start of the file
+ emit_byteorder_mark = False
- # Specify the encoding of the input file. Defaults to utf-8
- input_encoding = 'utf-8'
+ # Specify the encoding of the input file. Defaults to utf-8
+ input_encoding = "utf-8"
- # Specify the encoding of the output file. Defaults to utf-8. Note that cmake
- # only claims to support utf-8 so be careful when using anything else
- output_encoding = 'utf-8'
+ # Specify the encoding of the output file. Defaults to utf-8. Note that cmake
+ # only claims to support utf-8 so be careful when using anything else
+ output_encoding = "utf-8"
# -------------------------------------
# Miscellaneous configurations options.
# -------------------------------------
with section("misc"):
- # A dictionary containing any per-command configuration overrides. Currently
- # only `command_case` is supported.
- per_command = {}
+ # A dictionary containing any per-command configuration overrides. Currently
+ # only `command_case` is supported.
+ per_command = {}
diff --git a/base/__init__.py b/base/__init__.py
index f4c23df5e9bf0af997bcfb288b8be0b9b5eadd44..939317c67c538fe8a3a85788567d09146553ab44 100644
--- a/base/__init__.py
+++ b/base/__init__.py
@@ -12,7 +12,8 @@ import pyrap.tables as pt
import numpy
import pylab
-def plotflags (tabnames):
+
+def plotflags(tabnames):
"""Plot NDPPP Count results
A flagging or count step in NDPPP can save the flagging percentages per
@@ -27,15 +28,17 @@ def plotflags (tabnames):
"""
t = pt.table(tabnames)
- if 'Frequency' in t.colnames():
- t1 = t.sort ('Frequency')
- pylab.plot (t1.getcol('Frequency'), t1.getcol('Percentage'))
- elif 'Station' in t.colnames():
+ if "Frequency" in t.colnames():
+ t1 = t.sort("Frequency")
+ pylab.plot(t1.getcol("Frequency"), t1.getcol("Percentage"))
+ elif "Station" in t.colnames():
percs = []
names = []
- for t1 in t.iter ('Station'):
- percs.append (t1.getcol('Percentage').mean())
- names.append (t1.getcell('Name', 0))
- pylab.plot (numpy.array(percs), '+')
+ for t1 in t.iter("Station"):
+ percs.append(t1.getcol("Percentage").mean())
+ names.append(t1.getcell("Name", 0))
+ pylab.plot(numpy.array(percs), "+")
else:
- raise RuntimeError('Table appears not to be a NDPPP Count result; it does not contain a Frequency or Station column')
+ raise RuntimeError(
+ "Table appears not to be a NDPPP Count result; it does not contain a Frequency or Station column"
+ )
diff --git a/ci/.produce-ci-metrics.py b/ci/.produce-ci-metrics.py
index 2039a52a69ca90c4ea6699ce4ca1a565d46bc281..cd8b68b422fd26428ebee82be02e709d173ddc38 100644
--- a/ci/.produce-ci-metrics.py
+++ b/ci/.produce-ci-metrics.py
@@ -11,79 +11,74 @@ import xml.dom.minidom
if sys.version_info[0] < 3:
b2s = lambda s: s
else:
- b2s = lambda s: s.decode('utf-8')
+ b2s = lambda s: s.decode("utf-8")
+
def _has_subelement(element, subelement_name):
return len(element.getElementsByTagName(subelement_name)) > 0
+
def _has_error(test_case):
- return _has_subelement(test_case, 'error')
+ return _has_subelement(test_case, "error")
+
def _has_failure(test_case):
- return _has_subelement(test_case, 'failure')
+ return _has_subelement(test_case, "failure")
+
def get_git_sha():
- if 'CI_COMMIT_SHA' in os.environ:
- return os.environ['CI_COMMIT_SHA']
- return b2s(subprocess.check_output(['git', 'rev-parse', 'HEAD']).strip())
+ if "CI_COMMIT_SHA" in os.environ:
+ return os.environ["CI_COMMIT_SHA"]
+ return b2s(subprocess.check_output(["git", "rev-parse", "HEAD"]).strip())
+
def get_coverage_metrics(cov_xml_file):
cov_dom = xml.dom.minidom.parse(cov_xml_file)
- coverage = cov_dom.getElementsByTagName('coverage')[0]
- coverage_line_rate = float(coverage.attributes['line-rate'].value)
- return {
- 'percentage': coverage_line_rate * 100
- }
+ coverage = cov_dom.getElementsByTagName("coverage")[0]
+ coverage_line_rate = float(coverage.attributes["line-rate"].value)
+ return {"percentage": coverage_line_rate * 100}
+
def get_tests_metrics(utests_xml_file):
utests_xml = xml.dom.minidom.parse(utests_xml_file)
- test_cases = utests_xml.getElementsByTagName('testcase')
+ test_cases = utests_xml.getElementsByTagName("testcase")
errors = len(list(filter(_has_error, test_cases)))
failures = len(list(filter(_has_failure, test_cases)))
- return {
- 'errors': errors,
- 'failed': failures,
- 'total': len(test_cases)
- }
+ return {"errors": errors, "failed": failures, "total": len(test_cases)}
+
def get_lint_metrics(lint_xml_file):
- return {
- 'errors': 0,
- 'failures': 0,
- 'tests': 0
- }
+ return {"errors": 0, "failures": 0, "tests": 0}
+
def get_build_status(ci_metrics):
now = time.time()
- test_metrics = ci_metrics['tests']
- if test_metrics['errors'] > 0 or test_metrics['failed'] > 0:
- last_build_status = 'failed'
+ test_metrics = ci_metrics["tests"]
+ if test_metrics["errors"] > 0 or test_metrics["failed"] > 0:
+ last_build_status = "failed"
else:
- last_build_status = 'passed'
+ last_build_status = "passed"
return {
- 'last': {
- 'status': last_build_status,
- 'timestamp': now
- },
- 'green': {
- 'timestamp': now
- }
+ "last": {"status": last_build_status, "timestamp": now},
+ "green": {"timestamp": now},
}
+
def produce_ci_metrics(build_dir):
- cov_xml_file = os.path.join(build_dir, 'code-coverage.xml')
- utests_xml_file = os.path.join(build_dir, 'unit-tests.xml')
- lint_xml_file = os.path.join(build_dir, 'linting.xml')
+ cov_xml_file = os.path.join(build_dir, "code-coverage.xml")
+ utests_xml_file = os.path.join(build_dir, "unit-tests.xml")
+ lint_xml_file = os.path.join(build_dir, "linting.xml")
ci_metrics = {
- 'commit_sha': get_git_sha(),
- 'coverage': get_coverage_metrics(cov_xml_file),
- 'tests': get_tests_metrics(utests_xml_file),
- 'lint': get_lint_metrics(lint_xml_file)
+ "commit_sha": get_git_sha(),
+ "coverage": get_coverage_metrics(cov_xml_file),
+ "tests": get_tests_metrics(utests_xml_file),
+ "lint": get_lint_metrics(lint_xml_file),
}
- ci_metrics['build-status'] = get_build_status(ci_metrics)
+ ci_metrics["build-status"] = get_build_status(ci_metrics)
print(json.dumps(ci_metrics, indent=2))
-if __name__ == '__main__':
- produce_ci_metrics(sys.argv[1])
\ No newline at end of file
+
+if __name__ == "__main__":
+ produce_ci_metrics(sys.argv[1])
diff --git a/ci/collect_metrics.py b/ci/collect_metrics.py
index ce6c27b63eaac076f4122e63c1507ac014bb92af..b584917974256a1436df9d6e747707f581177c3b 100644
--- a/ci/collect_metrics.py
+++ b/ci/collect_metrics.py
@@ -87,8 +87,8 @@ def count_junit_metrics(filename):
log = logging.getLogger(LOGGER_NAME)
try:
root_elem = etree.parse(filename).getroot()
- if root_elem.tag not in ['testsuites', 'testsuite']:
- raise ValueError('Invalid JUnit XML file.')
+ if root_elem.tag not in ["testsuites", "testsuite"]:
+ raise ValueError("Invalid JUnit XML file.")
stats = parse_junit_tree(root_elem)
result = dict(errors=0, failures=0, tests=0, skipped=0)
for key in result:
@@ -99,12 +99,16 @@ def count_junit_metrics(filename):
stats["testcase"][key],
)
else:
- result[key] = max(stats["testsuite"][key],
- stats["testcase"][key])
+ result[key] = max(
+ stats["testsuite"][key], stats["testcase"][key]
+ )
result["total"] = result["tests"]
del result["tests"]
except Exception as expt:
- log.exception("Exception caught parsing '%s', returning 0 since the CI does not allow any linting errors/warnings", filename)
+ log.exception(
+ "Exception caught parsing '%s', returning 0 since the CI does not allow any linting errors/warnings",
+ filename,
+ )
result = dict(errors=0, failures=0, total=0, skipped=0)
return result
@@ -174,8 +178,9 @@ def main():
# latest_pipeline_id = str(pipeline["id"])
latest_build_date = pipeline["created_at"]
latest_build_timestamp = datetime.timestamp(
- datetime.strptime(latest_build_date,
- "%Y-%m-%dT%H:%M:%S.%fZ")
+ datetime.strptime(
+ latest_build_date, "%Y-%m-%dT%H:%M:%S.%fZ"
+ )
)
break
except Exception as err:
@@ -216,4 +221,4 @@ def init_logging(name="", level=logging.DEBUG):
if __name__ == "__main__":
init_logging()
- main()
\ No newline at end of file
+ main()
diff --git a/ci/create_badges.py b/ci/create_badges.py
index d3953087a66e18058d42d1488cd0b40f14b1ea29..f4912e1520534ec8710a389164dc5bf26876bfc5 100644
--- a/ci/create_badges.py
+++ b/ci/create_badges.py
@@ -37,7 +37,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -65,7 +69,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -91,7 +99,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -117,7 +129,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -141,7 +157,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -214,7 +234,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -240,7 +264,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -264,7 +292,11 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
# Create badge
badge = anybadge.Badge(
- label=label, value=value, default_color=color, value_prefix=" ", value_suffix=" "
+ label=label,
+ value=value,
+ default_color=color,
+ value_prefix=" ",
+ value_suffix=" ",
)
# Write badge
@@ -272,4 +304,4 @@ def main(): # pylint: disable=too-many-branches,too-many-statements
if __name__ == "__main__":
- main()
\ No newline at end of file
+ main()
diff --git a/ddecal/test/integration/tBdaDdeCal.py b/ddecal/test/integration/tBdaDdeCal.py
index 149ba29707000ce0b35b88ed15c844fb828a3ce3..6c6136d68ee09ce153968b9840dd735c066cffda 100755
--- a/ddecal/test/integration/tBdaDdeCal.py
+++ b/ddecal/test/integration/tBdaDdeCal.py
@@ -53,9 +53,15 @@ def create_skymodel():
f.write(
"FORMAT = Name, Type, Ra, Dec, I, MajorAxis, MinorAxis, PositionAngle, ReferenceFrequency='134e6', SpectralIndex='[0.0]'\r\n"
)
- f.write("center, POINT, 16:38:28.205000, +63.44.34.314000, 1, , , , , \r\n")
- f.write("ra_off, POINT, 16:58:28.205000, +63.44.34.314000, 1, , , , , \r\n")
- f.write("radec_off, POINT, 16:38:28.205000, +65.44.34.314000, 1, , , , , \r\n")
+ f.write(
+ "center, POINT, 16:38:28.205000, +63.44.34.314000, 1, , , , , \r\n"
+ )
+ f.write(
+ "ra_off, POINT, 16:58:28.205000, +63.44.34.314000, 1, , , , , \r\n"
+ )
+ f.write(
+ "radec_off, POINT, 16:38:28.205000, +65.44.34.314000, 1, , , , , \r\n"
+ )
@pytest.fixture()
@@ -156,7 +162,11 @@ def test_only_predict(create_skymodel):
)
check_call(
- [tcf.DP3EXE, "msout=PREDICT_DIR_1.MS", "predict.sources=[center, dec_off]"]
+ [
+ tcf.DP3EXE,
+ "msout=PREDICT_DIR_1.MS",
+ "predict.sources=[center, dec_off]",
+ ]
+ common_args
+ predict_args
)
@@ -230,8 +240,14 @@ def test_uvwflagger(create_skymodel, create_corrupted_data_from_regular):
# When uvw flagging is disabled, the NaNs in the solution file are only 9
expected_flagged_solutions = 54
- assert np.count_nonzero(np.isnan(amplitude_solutions)) == expected_flagged_solutions
- assert np.count_nonzero(np.isnan(phase_solutions)) == expected_flagged_solutions
+ assert (
+ np.count_nonzero(np.isnan(amplitude_solutions))
+ == expected_flagged_solutions
+ )
+ assert (
+ np.count_nonzero(np.isnan(phase_solutions))
+ == expected_flagged_solutions
+ )
# Only test a limited set of caltype + nchannels combinations, since testing
@@ -256,7 +272,9 @@ def test_uvwflagger(create_skymodel, create_corrupted_data_from_regular):
# "rotation+diagonal", # part of fulljones -> not implemented
],
)
-def test_caltype(create_skymodel, create_corrupted_data_from_regular, caltype_nchan):
+def test_caltype(
+ create_skymodel, create_corrupted_data_from_regular, caltype_nchan
+):
"""Test calibration for different calibration types"""
caltype = caltype_nchan[:-1]
nchan = int(caltype_nchan[-1])
@@ -282,13 +300,20 @@ def test_caltype(create_skymodel, create_corrupted_data_from_regular, caltype_nc
h5 = h5py.File("solutions.h5", "r")
- if caltype in ["scalar", "diagonal", "scalaramplitude", "diagonalamplitude"]:
+ if caltype in [
+ "scalar",
+ "diagonal",
+ "scalaramplitude",
+ "diagonalamplitude",
+ ]:
amplitude_solutions = h5["sol000/amplitude000/val"]
if caltype.startswith("scalar"):
assert amplitude_solutions.attrs["AXES"] == b"time,freq,ant,dir"
else:
- assert amplitude_solutions.attrs["AXES"] == b"time,freq,ant,dir,pol"
+ assert (
+ amplitude_solutions.attrs["AXES"] == b"time,freq,ant,dir,pol"
+ )
if nchan == 0:
assert amplitude_solutions.shape[1] == 1
@@ -339,7 +364,12 @@ def test_subtract(create_skymodel, create_corrupted_data):
residual = float(
check_output(
- [tcf.TAQLEXE, "-nopr", "-noph", "select gmax(abs(DATA)) from out.MS"]
+ [
+ tcf.TAQLEXE,
+ "-nopr",
+ "-noph",
+ "select gmax(abs(DATA)) from out.MS",
+ ]
)
)
diff --git a/ddecal/test/integration/tDDECal.py b/ddecal/test/integration/tDDECal.py
index 12115a584fa67e66b07bc15abef768e8a438c20e..88a29cafdc10997509d91691658e24d4d0467ab8 100755
--- a/ddecal/test/integration/tDDECal.py
+++ b/ddecal/test/integration/tDDECal.py
@@ -114,12 +114,17 @@ def create_corrupted_visibilities():
@pytest.mark.parametrize(
- "caltype", ["complexgain", "scalarcomplexgain", "amplitudeonly", "scalaramplitude"]
+ "caltype",
+ ["complexgain", "scalarcomplexgain", "amplitudeonly", "scalaramplitude"],
)
@pytest.mark.parametrize("solint", [0, 1, 2, 4])
@pytest.mark.parametrize("nchan", [1, 2, 5])
def test(
- create_corrupted_visibilities, copy_data_to_model_data, caltype, solint, nchan
+ create_corrupted_visibilities,
+ copy_data_to_model_data,
+ caltype,
+ solint,
+ nchan,
):
# Subtract corrupted visibilities using multiple predict steps
check_call(
@@ -251,12 +256,13 @@ def test_calibration_with_dd_intervals(
>= reference_solutions["sol000/amplitude000/val"].shape[0]
):
corresponding_index = (
- reference_solutions["sol000/amplitude000/val"].shape[0] - 1
+ reference_solutions["sol000/amplitude000/val"].shape[0]
+ - 1
)
- values_reference = reference_solutions["sol000/amplitude000/val"][
- corresponding_index, :, :, direction_index, 0
- ]
+ values_reference = reference_solutions[
+ "sol000/amplitude000/val"
+ ][corresponding_index, :, :, direction_index, 0]
assert (abs(values_ddecal - values_reference) < 1.2).all()
@@ -331,12 +337,13 @@ def test_bug_ast_924(
>= reference_solutions["sol000/amplitude000/val"].shape[0]
):
corresponding_index = (
- reference_solutions["sol000/amplitude000/val"].shape[0] - 1
+ reference_solutions["sol000/amplitude000/val"].shape[0]
+ - 1
)
- values_reference = reference_solutions["sol000/amplitude000/val"][
- corresponding_index, :, :, direction_index, 0
- ]
+ values_reference = reference_solutions[
+ "sol000/amplitude000/val"
+ ][corresponding_index, :, :, direction_index, 0]
assert (abs(values_ddecal - values_reference) < 1.2).all()
@@ -347,7 +354,13 @@ def test_bug_ast_924(
)
@pytest.mark.parametrize(
"caltype",
- ["amplitudeonly", "scalaramplitude", "scalar", "diagonal", "diagonalamplitude"],
+ [
+ "amplitudeonly",
+ "scalaramplitude",
+ "scalar",
+ "diagonal",
+ "diagonalamplitude",
+ ],
)
def test_subtract_with_dd_intervals(
create_corrupted_visibilities,
@@ -739,7 +752,9 @@ def test_bda_constaints():
phase_bda = f_bda["sol000/phase000/val"]
phase_no_bda = f_no_bda["sol000/phase000/val"]
- np.testing.assert_allclose(ampl_bda, ampl_no_bda, rtol=0.05, atol=0, equal_nan=True)
+ np.testing.assert_allclose(
+ ampl_bda, ampl_no_bda, rtol=0.05, atol=0, equal_nan=True
+ )
np.testing.assert_allclose(
phase_bda, phase_no_bda, rtol=0.3, atol=0, equal_nan=True
)
diff --git a/ddecal/test/integration/tIDGPredict.py b/ddecal/test/integration/tIDGPredict.py
index 6bffac24444ad91b9d3edfa4958dfd666b289552..0299bc4bba134ec6fb2480e0beebe2d467769e81 100755
--- a/ddecal/test/integration/tIDGPredict.py
+++ b/ddecal/test/integration/tIDGPredict.py
@@ -101,7 +101,9 @@ def test_input_with_single_sources(source, offset):
except FileNotFoundError:
pytest.skip("WSClean not available")
- check_call(["wsclean", "-use-idg", "-predict", "-name", f"{source}", f"{MSIN}"])
+ check_call(
+ ["wsclean", "-use-idg", "-predict", "-name", f"{source}", f"{MSIN}"]
+ )
check_output(
[
tcf.TAQLEXE,
@@ -112,7 +114,10 @@ def test_input_with_single_sources(source, offset):
)
# Predict source: $source offset: $offset using IDG
- if "polygon" in open(f"{tcf.DDECAL_RESOURCEDIR}/{source}-{offset}.reg").read():
+ if (
+ "polygon"
+ in open(f"{tcf.DDECAL_RESOURCEDIR}/{source}-{offset}.reg").read()
+ ):
check_call(
[
tcf.DP3EXE,
diff --git a/ddecal/test/integration/tIDGPredict_ref.py b/ddecal/test/integration/tIDGPredict_ref.py
index 523b2be364247d5a34329647c05a063824e12e8d..6996d6ea65505dc656e3579539472e33294cca49 100755
--- a/ddecal/test/integration/tIDGPredict_ref.py
+++ b/ddecal/test/integration/tIDGPredict_ref.py
@@ -9,32 +9,31 @@ import os
os.system("rm dummy-image.fits dummy-dirty.fits")
# -channel-range 0 1 ensures the reference frequency is from the first channel.
-os.system("wsclean -size 512 512 -scale 0.01 -channel-range 0 1 -name dummy tDDECal.MS")
+os.system(
+ "wsclean -size 512 512 -scale 0.01 -channel-range 0 1 -name dummy tDDECal.MS"
+)
sources = {
- "radec": ( 400, 64 ),
- "ra": ( 400, 256 ),
- "dec": ( 256, 64 ),
- "center": ( 256, 256 )
- }
-brightness = {
- "radec": 10,
- "ra": 20,
- "dec": 20,
- "center": 10
- }
-term_brightness = { 0:10, 1:20000, 2:30000 }
-
-fits_files=[]
+ "radec": (400, 64),
+ "ra": (400, 256),
+ "dec": (256, 64),
+ "center": (256, 256),
+}
+brightness = {"radec": 10, "ra": 20, "dec": 20, "center": 10}
+term_brightness = {0: 10, 1: 20000, 2: 30000}
+
+fits_files = []
hdu = fits.open("dummy-image.fits")[0]
+
def write_fits(name):
filename = name + "-model.fits"
os.system("rm -rf " + filename)
hdu.writeto(filename)
fits_files.append(filename)
+
# Generate foursources.fits, which has all four sources.
hdu.data *= 0
diff --git a/docker/ubuntu_22_04_base b/docker/ubuntu_22_04_base
index fd26111764fb165746f9b1a671e32c24277e86e2..452ba8e0ab6f4260b433bd5783b7439c69cc5a77 100644
--- a/docker/ubuntu_22_04_base
+++ b/docker/ubuntu_22_04_base
@@ -80,6 +80,7 @@ RUN wget -nv -O /WSRT_Measures.ztar ftp://ftp.astron.nl/outgoing/Measures/WSRT_M
&& rm /WSRT_Measures.ztar
# Install pip dependencies
RUN pip3 install \
+ black \
cmake-format \
h5py \
sphinx \
diff --git a/external/aocommon b/external/aocommon
index b422a1bcc4a51d12ac4f8a3f08c5885c776f4a6d..c126d20b28c8557375e12bc3039bb6a64c05f8b0 160000
--- a/external/aocommon
+++ b/external/aocommon
@@ -1 +1 @@
-Subproject commit b422a1bcc4a51d12ac4f8a3f08c5885c776f4a6d
+Subproject commit c126d20b28c8557375e12bc3039bb6a64c05f8b0
diff --git a/parmdb/test/integration/tShowSourceDb.py b/parmdb/test/integration/tShowSourceDb.py
index 666ef7cae83dfaab52ced5f8b924b7029bb1b7ea..f1d856338229386346df3f6a1619dfb75fd823ea 100644
--- a/parmdb/test/integration/tShowSourceDb.py
+++ b/parmdb/test/integration/tShowSourceDb.py
@@ -24,6 +24,7 @@ Script can be invoked in two ways:
MSIN = "tDemix.in_MS"
CWD = os.getcwd()
+
@pytest.fixture(autouse=True)
def source_env():
os.chdir(CWD)
@@ -40,18 +41,35 @@ def source_env():
os.chdir(CWD)
shutil.rmtree(tmpdir)
+
def test_skymodel_sourcedb_roundtrip():
"""Check that skymodel in default format is reproduced after makesourcedb and showsourcedb"""
# sky.txt is not in the default format, create a skymodel in default format by going through sourcedb
check_call([tcf.MAKESOURCEDBEXE, "in=tDemix_tmp/sky.txt", "out=sourcedb"])
# The first line of showsourcedb is the application's announcement
- skymodel_defaultformat_input = check_output([tcf.SHOWSOURCEDBEXE, "in=sourcedb", "mode=skymodel"]).decode('utf-8').split('\n',1)[-1]
+ skymodel_defaultformat_input = (
+ check_output([tcf.SHOWSOURCEDBEXE, "in=sourcedb", "mode=skymodel"])
+ .decode("utf-8")
+ .split("\n", 1)[-1]
+ )
with open("tDemix_tmp/sky_defaultformat.txt", "w") as f:
f.write(skymodel_defaultformat_input)
# Now do the roundtrip test: make sourcedb and print the result in the default format
- check_call([tcf.MAKESOURCEDBEXE, "in=tDemix_tmp/sky_defaultformat.txt", "out=sourcedb_defaultformat"])
- skymodel_defaultformat_output = check_output([tcf.SHOWSOURCEDBEXE, "in=sourcedb_defaultformat", "mode=skymodel"]).decode('utf-8').split('\n',1)[-1]
+ check_call(
+ [
+ tcf.MAKESOURCEDBEXE,
+ "in=tDemix_tmp/sky_defaultformat.txt",
+ "out=sourcedb_defaultformat",
+ ]
+ )
+ skymodel_defaultformat_output = (
+ check_output(
+ [tcf.SHOWSOURCEDBEXE, "in=sourcedb_defaultformat", "mode=skymodel"]
+ )
+ .decode("utf-8")
+ .split("\n", 1)[-1]
+ )
assert skymodel_defaultformat_input == skymodel_defaultformat_output
diff --git a/scripts/run-format.sh b/scripts/run-format.sh
index 1bfd615db1202b30c55e909d886a6eb2eda2c0e2..0d915e53cfed4cc31454155968389da0be3e384b 100755
--- a/scripts/run-format.sh
+++ b/scripts/run-format.sh
@@ -12,12 +12,6 @@ SOURCE_DIR=$(dirname "$0")/..
#relative to SOURCE_DIR.
EXCLUDE_DIRS=(external build CMake)
-#The patterns of the C++ source files, which clang-format should format.
-CXX_SOURCES=(*.cc *.h)
-
-#The patterns of the CMake source files, which cmake-format should format.
-CMAKE_SOURCES=(CMakeLists.txt *.cmake)
-
#End script configuration.
#The common formatting script has further documentation.
diff --git a/steps/test/integration/tApplyBeam.py b/steps/test/integration/tApplyBeam.py
index 59bc18841aa73b63f1a62b2916913be2bae3c1e0..c06c34d62c1344bf03b5ada733be230d0bae120c 100644
--- a/steps/test/integration/tApplyBeam.py
+++ b/steps/test/integration/tApplyBeam.py
@@ -109,7 +109,5 @@ def test_with_updateweights():
f"applybeam.updateweights=true",
]
)
- taql_command = (
- f"select from {MSIN} where all(near(WEIGHT_SPECTRUM, NEW_WEIGHT_SPECTRUM))"
- )
+ taql_command = f"select from {MSIN} where all(near(WEIGHT_SPECTRUM, NEW_WEIGHT_SPECTRUM))"
assert_taql(taql_command)
diff --git a/steps/test/integration/tBdaExpander.py b/steps/test/integration/tBdaExpander.py
index 47e3f16a10350991484110acad9663988cd114cd..f115c997275a8d3ea20c40f40ae3fb06614702c1 100644
--- a/steps/test/integration/tBdaExpander.py
+++ b/steps/test/integration/tBdaExpander.py
@@ -54,9 +54,15 @@ def create_skymodel():
f.write(
"FORMAT = Name, Type, Ra, Dec, I, MajorAxis, MinorAxis, PositionAngle, ReferenceFrequency='134e6', SpectralIndex='[0.0]'\r\n"
)
- f.write("center, POINT, 16:38:28.205000, + 63.44.34.314000, 10, , , , , \r\n")
- f.write("ra_off, POINT, 16:38:28.205000, + 64.44.34.314000, 10, , , , , \r\n")
- f.write("radec_off, POINT, 16:38:28.205000, +65.44.34.314000, 10, , , , , \r\n")
+ f.write(
+ "center, POINT, 16:38:28.205000, + 63.44.34.314000, 10, , , , , \r\n"
+ )
+ f.write(
+ "ra_off, POINT, 16:38:28.205000, + 64.44.34.314000, 10, , , , , \r\n"
+ )
+ f.write(
+ "radec_off, POINT, 16:38:28.205000, +65.44.34.314000, 10, , , , , \r\n"
+ )
check_call([tcf.MAKESOURCEDBEXE, "in=test.skymodel", "out=test.sourcedb"])
@@ -143,6 +149,6 @@ def test_regular_buffer_writing():
"checkparset=true",
"msin=regular_buffer.MS",
"msout=out.MS",
- "steps=[]"
+ "steps=[]",
]
- )
\ No newline at end of file
+ )
diff --git a/steps/test/integration/tBdaPredict.py b/steps/test/integration/tBdaPredict.py
index f772277f515a9116f31ce6f1b8d4632e2a322ce2..6fce28d00d070f4adb492f931d51d2fed640987e 100755
--- a/steps/test/integration/tBdaPredict.py
+++ b/steps/test/integration/tBdaPredict.py
@@ -56,7 +56,12 @@ def create_skymodel():
)
check_call(
- [tcf.MAKESOURCEDBEXE, "in=test.skymodel", "out=test.sourcedb", "append=false"]
+ [
+ tcf.MAKESOURCEDBEXE,
+ "in=test.skymodel",
+ "out=test.sourcedb",
+ "append=false",
+ ]
)
@@ -66,10 +71,17 @@ def create_skymodel_in_phase_center():
f.write(
"FORMAT = Name, Type, Ra, Dec, I, MajorAxis, MinorAxis, PositionAngle, ReferenceFrequency='134e6', SpectralIndex='[0.0]'\r\n"
)
- f.write(f"center, POINT, 01:37:41.299000, +33.09.35.132000, 10, , , , , \r\n")
+ f.write(
+ f"center, POINT, 01:37:41.299000, +33.09.35.132000, 10, , , , , \r\n"
+ )
check_call(
- [tcf.MAKESOURCEDBEXE, "in=test.skymodel", "out=test.sourcedb", "append=false"]
+ [
+ tcf.MAKESOURCEDBEXE,
+ "in=test.skymodel",
+ "out=test.sourcedb",
+ "append=false",
+ ]
)
diff --git a/steps/test/integration/tDemix.py b/steps/test/integration/tDemix.py
index 8719699d722642e1778f68b57f65094b24ce938a..70bd7249e7628d479b0e6fe1a7832c954c630b43 100755
--- a/steps/test/integration/tDemix.py
+++ b/steps/test/integration/tDemix.py
@@ -40,7 +40,8 @@ common_args = [
"demix.subtractsources=[CasA]",
]
-skymodel_arg="demix.skymodel='tDemix_tmp/{}'"
+skymodel_arg = "demix.skymodel='tDemix_tmp/{}'"
+
@pytest.fixture(autouse=True)
def source_env():
@@ -50,7 +51,13 @@ def source_env():
os.chdir(tmpdir)
untar_ms(f"{tcf.RESOURCEDIR}/{MSIN}.tgz")
- check_call([tcf.MAKESOURCEDBEXE, "in=tDemix_tmp/sky.txt", "out=tDemix_tmp/sourcedb"])
+ check_call(
+ [
+ tcf.MAKESOURCEDBEXE,
+ "in=tDemix_tmp/sky.txt",
+ "out=tDemix_tmp/sourcedb",
+ ]
+ )
# Tests are executed here
yield
@@ -60,7 +67,7 @@ def source_env():
shutil.rmtree(tmpdir)
-@pytest.mark.parametrize("skymodel", ['sky.txt', 'sourcedb'])
+@pytest.mark.parametrize("skymodel", ["sky.txt", "sourcedb"])
def test_without_target(skymodel):
check_call(
[
@@ -73,13 +80,12 @@ def test_without_target(skymodel):
+ common_args
)
-
# Compare some columns of the output MS with the reference output.
taql_command = f"select from tDemix_out.MS t1, tDemix_tmp/tDemix_ref1.MS t2 where not all(near(t1.DATA,t2.DATA,1e-3) || (isnan(t1.DATA) && isnan(t2.DATA))) || not all(t1.FLAG = t2.FLAG) || not all(near(t1.WEIGHT_SPECTRUM, t2.WEIGHT_SPECTRUM)) || not all(t1.LOFAR_FULL_RES_FLAG = t2.LOFAR_FULL_RES_FLAG) || t1.ANTENNA1 != t2.ANTENNA1 || t1.ANTENNA2 != t2.ANTENNA2 || t1.TIME !~= t2.TIME"
assert_taql(taql_command)
-@pytest.mark.parametrize("skymodel", ['sky.txt', 'sourcedb'])
+@pytest.mark.parametrize("skymodel", ["sky.txt", "sourcedb"])
def test_with_target_projected_away(skymodel):
check_call(
[
@@ -92,13 +98,12 @@ def test_with_target_projected_away(skymodel):
+ common_args
)
-
# Compare some columns of the output MS with the reference output.
taql_command = f"select from tDemix_out.MS t1, tDemix_tmp/tDemix_ref2.MS t2 where not all(near(t1.DATA,t2.DATA,1e-3) || (isnan(t1.DATA) && isnan(t2.DATA))) || not all(t1.FLAG = t2.FLAG) || not all(near(t1.WEIGHT_SPECTRUM, t2.WEIGHT_SPECTRUM)) || not all(t1.LOFAR_FULL_RES_FLAG = t2.LOFAR_FULL_RES_FLAG) || t1.ANTENNA1 != t2.ANTENNA1 || t1.ANTENNA2 != t2.ANTENNA2 || t1.TIME !~= t2.TIME"
assert_taql(taql_command)
-@pytest.mark.parametrize("skymodel", ['sky.txt', 'sourcedb'])
+@pytest.mark.parametrize("skymodel", ["sky.txt", "sourcedb"])
def test_with_target(skymodel):
check_call(
[
@@ -131,7 +136,6 @@ def test_time_freq_resolution():
+ common_args
)
-
# Compare some columns of the output MS with the reference output.
taql_command = f"select from tDemix_out.MS t1, tDemix_tmp/tDemix_ref1.MS t2 where not all(near(t1.DATA,t2.DATA,1e-3) || (isnan(t1.DATA) && isnan(t2.DATA))) || not all(t1.FLAG = t2.FLAG) || not all(near(t1.WEIGHT_SPECTRUM, t2.WEIGHT_SPECTRUM)) || not all(t1.LOFAR_FULL_RES_FLAG = t2.LOFAR_FULL_RES_FLAG) || t1.ANTENNA1 != t2.ANTENNA1 || t1.ANTENNA2 != t2.ANTENNA2 || t1.TIME !~= t2.TIME"
assert_taql(taql_command)
diff --git a/steps/test/integration/tMsIn.py b/steps/test/integration/tMsIn.py
index ffdb541c535fc556a0af3847669e042cfcd18173..e70c8a81da4a12e67f4d877e25bac415ca06ddea 100644
--- a/steps/test/integration/tMsIn.py
+++ b/steps/test/integration/tMsIn.py
@@ -141,7 +141,8 @@ def test_write_thread_enabled():
assert re.search(b"use thread: *true", result)
assert re.search(
- b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Creating task\n", result
+ b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Creating task\n",
+ result,
)
assert re.search(
b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Writing \\(threaded\\)\n",
@@ -169,10 +170,12 @@ def test_write_thread_disabled():
assert re.search(b"use thread: *false", result)
assert (
re.search(
- b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Creating task\n", result
+ b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Creating task\n",
+ result,
)
== None
)
assert re.search(
- b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Writing\n", result
+ b"(1[0-9]| [ 0-9])[0-9]\\.[0-9]% \\([ 0-9]{5} [m ]s\\) Writing\n",
+ result,
)
diff --git a/steps/test/integration/tMsOut.py b/steps/test/integration/tMsOut.py
index 5c7a23eab58da83f9f9bbdcb21bc6843a55dd106..f2bc3a697c40d62e5ad4433855d17a528d0b76fb 100644
--- a/steps/test/integration/tMsOut.py
+++ b/steps/test/integration/tMsOut.py
@@ -19,6 +19,7 @@ from utils import untar_ms, get_taql_result, check_output
MSIN = "tNDPPP-generic.MS"
CWD = os.getcwd()
+
@pytest.fixture(autouse=True)
def source_env():
os.chdir(CWD)
@@ -52,16 +53,22 @@ def test_chunking():
assert os.path.exists("chunktest-000.ms")
assert os.path.exists("chunktest-001.ms")
assert os.path.exists("chunktest-002.ms")
-
+
# Each should have two timesteps:
taql_command = f"select unique TIME from chunktest-000.ms"
result = get_taql_result(taql_command)
- assert result == 'Unit: s\n29-Mar-2013/13:59:53.007\n29-Mar-2013/14:00:03.021'
-
+ assert (
+ result == "Unit: s\n29-Mar-2013/13:59:53.007\n29-Mar-2013/14:00:03.021"
+ )
+
taql_command = f"select unique TIME from chunktest-001.ms"
result = get_taql_result(taql_command)
- assert result == 'Unit: s\n29-Mar-2013/14:00:13.035\n29-Mar-2013/14:00:23.049'
+ assert (
+ result == "Unit: s\n29-Mar-2013/14:00:13.035\n29-Mar-2013/14:00:23.049"
+ )
taql_command = f"select unique TIME from chunktest-002.ms"
result = get_taql_result(taql_command)
- assert result == 'Unit: s\n29-Mar-2013/14:00:33.063\n29-Mar-2013/14:00:43.076'
+ assert (
+ result == "Unit: s\n29-Mar-2013/14:00:33.063\n29-Mar-2013/14:00:43.076"
+ )
diff --git a/steps/test/integration/tMultiApplyCal.py b/steps/test/integration/tMultiApplyCal.py
index 7e640374facfd742f04df3b97754513b0b733f44..5789a93c4ff4fd54b508129b80c122ee44ce36f5 100644
--- a/steps/test/integration/tMultiApplyCal.py
+++ b/steps/test/integration/tMultiApplyCal.py
@@ -23,7 +23,9 @@ Script can be invoked in two ways:
"""
MSIN = "tNDPPP-generic.MS"
-PARMDB_TGZ = "tApplyCal2.parmdb.tgz" # Note: This archive contains tApplyCal.parmdb.
+PARMDB_TGZ = (
+ "tApplyCal2.parmdb.tgz" # Note: This archive contains tApplyCal.parmdb.
+)
PARMDB = "tApplyCal.parmdb"
CWD = os.getcwd()
diff --git a/steps/test/integration/tNullStokes.py b/steps/test/integration/tNullStokes.py
index 8bfca87e9054b9ceb7323f05f04a6c8f00ed6bc9..cda2488b4fee18f4e97ac0b4ab2a263366960e36 100755
--- a/steps/test/integration/tNullStokes.py
+++ b/steps/test/integration/tNullStokes.py
@@ -71,15 +71,16 @@ def test_stokes_Qzero(create_model_data):
assert_taql(taql_command)
# Checking that Stokes I, U, V have not been changed
- taql_command = f"select from (select mscal.stokes(STOKES_QDATA, 'I') as a, mscal.stokes(DATA, 'I') as b from {MSOUT}) where not all(near(a, b))"
+ taql_command = f"select from (select mscal.stokes(STOKES_QDATA, 'I') as a, mscal.stokes(DATA, 'I') as b from {MSOUT}) where not all(near(a, b))"
assert_taql(taql_command)
- taql_command = f"select from (select mscal.stokes(STOKES_QDATA, 'U') as a, mscal.stokes(DATA, 'U') as b from {MSOUT}) where not all(near(a, b))"
+ taql_command = f"select from (select mscal.stokes(STOKES_QDATA, 'U') as a, mscal.stokes(DATA, 'U') as b from {MSOUT}) where not all(near(a, b))"
assert_taql(taql_command)
- taql_command = f"select from (select mscal.stokes(STOKES_QDATA, 'V') as a, mscal.stokes(DATA, 'V') as b from {MSOUT}) where not all(near(a, b))"
+ taql_command = f"select from (select mscal.stokes(STOKES_QDATA, 'V') as a, mscal.stokes(DATA, 'V') as b from {MSOUT}) where not all(near(a, b))"
assert_taql(taql_command)
+
def test_stokes_Uzero(create_model_data):
check_call(
[
@@ -97,11 +98,11 @@ def test_stokes_Uzero(create_model_data):
assert_taql(taql_command)
# Checking that Stokes I, Q, V have not been changed
- taql_command = f"select from (select mscal.stokes(STOKES_UDATA, 'I') as a, mscal.stokes(DATA, 'I') as b from {MSOUT}) where not all(near(a, b))"
+ taql_command = f"select from (select mscal.stokes(STOKES_UDATA, 'I') as a, mscal.stokes(DATA, 'I') as b from {MSOUT}) where not all(near(a, b))"
assert_taql(taql_command)
- taql_command = f"select from (select mscal.stokes(STOKES_UDATA, 'Q') as a, mscal.stokes(DATA, 'Q') as b from {MSOUT}) where not all(near(a, b))"
+ taql_command = f"select from (select mscal.stokes(STOKES_UDATA, 'Q') as a, mscal.stokes(DATA, 'Q') as b from {MSOUT}) where not all(near(a, b))"
assert_taql(taql_command)
- taql_command = f"select from (select mscal.stokes(STOKES_UDATA, 'V') as a, mscal.stokes(DATA, 'V') as b from {MSOUT}) where not all(near(a, b))"
+ taql_command = f"select from (select mscal.stokes(STOKES_UDATA, 'V') as a, mscal.stokes(DATA, 'V') as b from {MSOUT}) where not all(near(a, b))"
assert_taql(taql_command)
diff --git a/steps/test/integration/tPhaseshiftPredict.py b/steps/test/integration/tPhaseshiftPredict.py
index 1a4976495b49c9e0520e8cb7aa3851664c3ab82a..3fad33403ba6b632828913ae9817fe2abd4ceebb 100755
--- a/steps/test/integration/tPhaseshiftPredict.py
+++ b/steps/test/integration/tPhaseshiftPredict.py
@@ -22,6 +22,7 @@ Script can be invoked in two ways:
MSIN = "tNDPPP-generic.MS"
+
@pytest.fixture(autouse=True)
def source_env(tmpdir_factory):
tmpdir = str(tmpdir_factory.mktemp("data"))
@@ -36,7 +37,6 @@ def source_env(tmpdir_factory):
shutil.rmtree(tmpdir)
-
testdata = [
("POINT", 0, 0, 0, 2, 10),
("GAUSSIAN", 600, 60, 0, 2, 10),
@@ -44,12 +44,22 @@ testdata = [
("GAUSSIAN", 600, 60, 30, 2, 0),
("GAUSSIAN", 600, 60, 30, 0, 10),
("GAUSSIAN", 600, 60, 30, 2, 10),
- ("GAUSSIAN", 60, 60, 0, 2, 10)
+ ("GAUSSIAN", 60, 60, 0, 2, 10),
]
-@pytest.mark.parametrize("source_type,major_axis,minor_axis,orientation,offset_ra_hour,offset_dec_degree", testdata)
-def test_phaseshift_predict(source_type, major_axis, minor_axis, orientation, offset_ra_hour, offset_dec_degree):
+@pytest.mark.parametrize(
+ "source_type,major_axis,minor_axis,orientation,offset_ra_hour,offset_dec_degree",
+ testdata,
+)
+def test_phaseshift_predict(
+ source_type,
+ major_axis,
+ minor_axis,
+ orientation,
+ offset_ra_hour,
+ offset_dec_degree,
+):
"""
- Phaseshift MS to the position of a source
- Predict the source with the new phase center
@@ -60,14 +70,23 @@ def test_phaseshift_predict(source_type, major_axis, minor_axis, orientation, of
MS_PHASECENTER_RA = "01h37m41.299"
MS_PHASECENTER_DEC = "+033d09m35.132"
assert -1 < offset_ra_hour < 22 and int(offset_ra_hour) == offset_ra_hour
- assert -33 < offset_dec_degree < 56 and int(offset_dec_degree) == offset_dec_degree
- source_position_ra = MS_PHASECENTER_RA.replace("01", f"{1 + offset_ra_hour:02d}")
- source_position_dec = MS_PHASECENTER_DEC.replace("+033", f"{33 + offset_dec_degree:+04d}")
+ assert (
+ -33 < offset_dec_degree < 56
+ and int(offset_dec_degree) == offset_dec_degree
+ )
+ source_position_ra = MS_PHASECENTER_RA.replace(
+ "01", f"{1 + offset_ra_hour:02d}"
+ )
+ source_position_dec = MS_PHASECENTER_DEC.replace(
+ "+033", f"{33 + offset_dec_degree:+04d}"
+ )
with open("test.skymodel", "w") as f:
- f.write(f"""\
+ f.write(
+ f"""\
FORMAT = Name, Type, Ra, Dec, I, MajorAxis, MinorAxis, Orientation, OrientationIsAbsolute
dummysource, {source_type}, {source_position_ra}, {source_position_dec}, {major_axis}, {minor_axis}, 2, 112, True
-""")
+"""
+ )
check_call(
[
@@ -88,7 +107,9 @@ dummysource, {source_type}, {source_position_ra}, {source_position_dec}, {major_
]
)
- taql_command = f"select gmean(abs(DATA)) from out.MS WHERE ANTENNA1!=ANTENNA2"
+ taql_command = (
+ f"select gmean(abs(DATA)) from out.MS WHERE ANTENNA1!=ANTENNA2"
+ )
residual = float(get_taql_result(taql_command))
print("Residual:", residual)
assert residual < 0.001
diff --git a/steps/test/integration/tPredict.py b/steps/test/integration/tPredict.py
index 23ed4b0b578591315778e54c993aa5532423f1d5..b9511c36ec60b6f7caf1a2defc2fd30ef8865da1 100644
--- a/steps/test/integration/tPredict.py
+++ b/steps/test/integration/tPredict.py
@@ -139,7 +139,9 @@ def test_without_and_with_time_smearing(use_time_smearing):
)
shutil.rmtree(sourcedb, ignore_errors=True)
- check_call([tcf.MAKESOURCEDBEXE, "in=timesmearing.skymodel", f"out={sourcedb}"])
+ check_call(
+ [tcf.MAKESOURCEDBEXE, "in=timesmearing.skymodel", f"out={sourcedb}"]
+ )
check_call(
[
tcf.DP3EXE,
@@ -173,6 +175,7 @@ def test_without_and_with_time_smearing(use_time_smearing):
)
assert_taql(taql_command, 2)
+
@pytest.mark.parametrize("use_beam", [False, True])
def test_without_and_with_beam_parallelbaseline(use_beam):
predict_column = "PREDICT_beam" if use_beam else "PREDICT_nobeam"
diff --git a/steps/test/integration/tUVWFlagger.py b/steps/test/integration/tUVWFlagger.py
index 745494d1203980f197f16ecc26b8463c197f44d3..ec8e4de1830ccccec967ba0e078a2466d1f40275 100644
--- a/steps/test/integration/tUVWFlagger.py
+++ b/steps/test/integration/tUVWFlagger.py
@@ -85,7 +85,8 @@ def test_update_flags_inplace():
)
utils.assert_taql(count_flags_set, 168)
assert re.search(
- b"\nTotal flagged: 0.000% \\(0 out of 1344 visibilities\\)\n\n\n", result
+ b"\nTotal flagged: 0.000% \\(0 out of 1344 visibilities\\)\n\n\n",
+ result,
)
diff --git a/steps/test/unit/mock/mockpystep.py b/steps/test/unit/mock/mockpystep.py
index 0d2e9e9151c609a1f85a2023ffdde8d50b0b5b47..bb256477e31d9ec75362c724e863769b4e885aef 100644
--- a/steps/test/unit/mock/mockpystep.py
+++ b/steps/test/unit/mock/mockpystep.py
@@ -8,8 +8,10 @@ import parameterset
from pydp3 import Step
import numpy as np
+
class MockPyStep(Step):
"""Example python DPStep that multiplies DATA and WEIGHT_SPECTRUM"""
+
def __init__(self, parset, prefix):
"""
Set up the step (constructor). Read the parset here.