Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Remove pkg_resources and go fully to pyproject.toml #1059

Closed
wants to merge 6 commits into from
Closed

Remove pkg_resources and go fully to pyproject.toml #1059

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
e382e4c
move to pyproject.toml
ocefpaf Apr 17, 2023
4f2af1a
add top 3 committers as maintainers
ocefpaf May 29, 2023
cf74a25
lint
ocefpaf Oct 4, 2023
e140e50
Merge branch 'develop' of https://github.com/ioos/compliance-checker …
ChrisBarker-NOAA Apr 8, 2024
9c4b0d2
put script in to pypacakge.toml, and removed pkg_resources
ChrisBarker-NOAA Apr 9, 2024
2f9c5ae
bring in pkg_resources removal
ChrisBarker-NOAA Apr 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
337 changes: 2 additions & 335 deletions cchecker.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,341 +1,8 @@
#!/usr/bin/env python

import argparse
import sys
import warnings
from collections import defaultdict
from textwrap import dedent

from compliance_checker import __version__
from compliance_checker.cf.util import download_cf_standard_name_table
from compliance_checker.runner import CheckSuite, ComplianceChecker


def _print_checker_name_header(checker_str):
"""
Helper function to prints a checker name surrounded by a border of "="
:param checker_suite: A check suite string name
:type checker: str
"""
print("{0}\n {1} \n{0}".format("=" * (len(checker_str) + 2), checker_str))


def parse_options(opts):
"""
Helper function to parse possible options. Splits option after the first
colon to split into key/value pairs.

:param opts: Iterable of strings with options
:rtype: dict
:return: Dictionary with keys as checker type (i.e. "cf", "acdd")
"""
options_dict = defaultdict(set)
for opt_str in opts:
try:
checker_type, checker_opt = opt_str.split(":", 1)
except ValueError:
warnings.warn(f"Could not split option {opt_str}, ignoring", stacklevel=2)
else:
options_dict[checker_type].add(checker_opt)
return options_dict


def main():
# Load all available checker classes
check_suite = CheckSuite()
check_suite.load_all_available_checkers()

parser = argparse.ArgumentParser()
parser.add_argument(
"--test",
"-t",
"--test=",
"-t=",
default=[],
action="append",
help=(
"Select the Checks you want to perform. Defaults to 'acdd'"
" if unspecified. Versions of standards can be specified via "
"`-t <test_standard>:<version>`. If `<version>` is omitted, or "
'is "latest", the latest version of the test standard is used.'
),
)

parser.add_argument(
"--criteria",
"-c",
help=(
"Define the criteria for the checks. "
"Either Strict, Normal, or Lenient. Defaults to Normal."
),
nargs="?",
default="normal",
choices=["lenient", "normal", "strict"],
)

parser.add_argument(
"--verbose",
"-v",
help="Increase output. May be specified up to three times.",
action="count",
default=0,
)

parser.add_argument(
"--describe-checks",
"-D",
help=(
"Describes checks for checkers specified using "
"`-t`. If `-t` is not specified, lists checks "
"from all available checkers."
),
action="store_true",
)

include_exclude = parser.add_mutually_exclusive_group()

include_exclude.add_argument(
"--skip-checks",
"-s",
help=dedent(
"""
Specifies tests to skip. Can take the form
of either `<check_name>` or
`<check_name>:<skip_level>`. The first
form skips any checks matching the name.
In the second form <skip_level> may be
specified as "A", "M", or "L". "A" skips
all checks and is equivalent to calling
the first form. "M" will only show high
priority output from the given check and
will skip medium and low. "L" will show
both high and medium priority issues, while
skipping low priority issues. Cannot be
used with `-i`/`--include-checks` option.
""",
),
action="append",
)

include_exclude.add_argument(
"--include-checks",
"-i",
help=dedent(
"""
Specifies checks to include. Can only take the form
of `<check_name>`. Cannot be specified along with
`-s`/`skip_checks`.
""",
),
action="append",
)

parser.add_argument(
"-f",
"--format",
default=[],
action="append",
help=(
"Output format(s). Options are 'text', 'html', 'json', 'json_new'."
" The difference between the 'json' and the 'json_new'"
" formats is that the 'json' format has the check as the top level"
" key, whereas the 'json_new' format has the dataset name(s) as the"
" main key in the output follow by any checks as subkeys. Also, "
"'json' format can be only be run against one input file, whereas "
"'json_new' can be run against multiple files."
),
choices=["text", "html", "json", "json_new"],
)

parser.add_argument(
"-o",
"--output",
default=[],
action="append",
help=(
"Output filename(s). If '-' is supplied, output to stdout."
" Can either be one or many files. If one file is supplied,"
" but the checker is run against many files, all the output"
" from the checks goes to that file (does not presently work "
"with 'json' format). If more than one output file is "
"supplied, the number of input datasets supplied must match "
"the number of output files."
),
)

parser.add_argument(
"-O",
"--option",
default=[],
action="append",
help=dedent(
"""
Additional options to be passed to the
checkers. Multiple options can be specified
via multiple invocations of this switch.
Options should be prefixed with a the
checker name followed by the option, e.g.
'<checker>:<option_name>'

Available options:
'cf:enable_appendix_a_checks' - Allow check
results against CF Appendix A for attribute
location and data types.
""",
),
)

parser.add_argument(
"-V",
"--version",
action="store_true",
help="Display the IOOS Compliance Checker version information.",
)

parser.add_argument(
"dataset_location",
nargs="*",
help=(
"Defines the location of the dataset to be checked. The location "
"can be a local netCDF file, a remote OPeNDAP endpoint, a remote "
"netCDF file which returns content-type header of "
"'application/x-netcdf', or an ERDDAP TableDAP endpoint. "
"Note that the ERDDAP TableDAP endpoint will currently attempt "
"to fetch the entire TableDAP dataset."
),
)

parser.add_argument(
"-l",
"--list-tests",
action="store_true",
help="List the available tests",
)

parser.add_argument(
"-d",
"--download-standard-names",
help=(
"Specify a version of the cf standard name table"
" to download as packaged version. Either specify"
' a version number (e.g. "72") to fetch a '
'specific version or "latest" to get the '
"latest CF standard name table."
),
)

# Add command line args from generator plugins
check_suite.add_plugin_args(parser)

args = parser.parse_args()

check_suite.load_generated_checkers(args)

if args.version:
print("IOOS compliance checker version %s" % __version__)
sys.exit(0)

options_dict = parse_options(args.option) if args.option else defaultdict(set)

if args.describe_checks:
error_stat = 0
if args.test:
checker_names = set(args.test)
else:
# skip "latest" meta-versions (":latest" or no explicit version
# specifier)
checker_names = [
c
for c in check_suite.checkers
if ":" in c and not c.endswith(":latest")
]

for checker_name in sorted(checker_names):
if checker_name not in check_suite.checkers:
print(
f"Cannot find checker '{checker_name}' with which to "
"describe checks",
file=sys.stderr,
)
error_stat = 1
else:
_print_checker_name_header(checker_name)
check_suite._print_checker(check_suite.checkers[checker_name])
sys.exit(error_stat)

if args.list_tests:
print("IOOS compliance checker available checker suites:")
check_suite._print_suites(args.verbose)
return 0

if args.download_standard_names:
download_cf_standard_name_table(args.download_standard_names)

if len(args.dataset_location) == 0:
parser.print_help()
sys.exit(1)

# Check the number of output files
if not args.output:
args.output = "-"
output_len = len(args.output)
if not (output_len == 1 or output_len == len(args.dataset_location)):
print(
"The number of output files must either be one or the same as the number of datasets",
file=sys.stderr,
)
sys.exit(2)

# Run the compliance checker
# 2 modes, concatenated output file or multiple output files
return_values = []
had_errors = []
if output_len == 1:
if args.format != "json":
print(
f"Running Compliance Checker on the datasets from: {args.dataset_location}",
file=sys.stderr,
)
return_value, errors = ComplianceChecker.run_checker(
args.dataset_location,
args.test or ["acdd"],
args.verbose,
args.criteria,
args.skip_checks,
args.include_checks,
args.output[0],
args.format or ["text"],
options=options_dict,
)
return_values.append(return_value)
had_errors.append(errors)
else:
for output, dataset in zip(args.output, args.dataset_location):
if args.format != "json":
print(
f"Running Compliance Checker on the dataset from: {dataset}",
file=sys.stderr,
)
return_value, errors = ComplianceChecker.run_checker(
[dataset],
args.test or ["acdd"],
args.verbose,
args.criteria,
args.skip_checks,
args.include_checks,
output,
args.format or ["text"],
options=options_dict,
)
return_values.append(return_value)
had_errors.append(errors)

if any(had_errors):
sys.exit(2)
if all(return_values):
sys.exit(0)
sys.exit(1)
from compliance_checker import cchecker

Check warning on line 4 in cchecker.py

View check run for this annotation

Codecov / codecov/patch

cchecker.py#L4 

Added line #L4 was not covered by tests


if __name__ == "__main__":
sys.exit(main())
sys.exit(cchecker.main())
7 changes: 4 additions & 3 deletions compliance_checker/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -191,9 +191,10 @@ def __del__(self):
are cleared before the next checker uses it. Some caches were
inadvertently mutated by other functions.
"""

cfutil.get_geophysical_variables.cache_clear()
cfutil.get_time_variables.cache_clear()
# odd errors -- module getting deleted before this object?
if cfutil is not None:
cfutil.get_geophysical_variables.cache_clear()
cfutil.get_time_variables.cache_clear()


class BaseNCCheck:
Expand Down
Loading