bugfix: removed use of os library for exit codes (problem on Windows)

* fixed errors in documentation (`developing.rst`)
* version bump

Author: Paul K. Korir, PhD

.github/workflows/python-package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ 3.6, 3.7, 3.8, 3.9 ]
+        python-version: [ 3.6, 3.7, 3.8, 3.9, '3.10' ]
 
     steps:
       - uses: actions/checkout@v2

CHANGELOG.md

@@ -1,5 +1,18 @@
 #Changes by release
 
+## [0.7.2] - 2022-04-26
+
+add Python3.10 support
+
+* removed use of `os` package for exit codes (problems on Windows)
+* fixed errors in `developing` documentation
+
+## [0.7.1] - 2021-08-24
+
+bugfix: reading from HDF5 retains some ids as `numpy.int64`
+
+* tests added and pass
+
 ## [0.7.0] - 2021-06-17
 
 add Python3.9 support; dropped Python2.7

docs/_build/html/_sources/extending.rst.txt

@@ -305,7 +305,7 @@ In order to perform conversion using the command-line utility, we need to have t
         # ...
         sff_seg.export(args.output)
 
-        return os.EX_OK
+        return 0
 
 Once this is done the following should work:
 

docs/developing.rst

@@ -877,8 +877,8 @@ For each segment (voxel value) in the lattice create a 3D volume object that ref
     # segment one
     segment = sff.SFFSegment()
     vol1_value = 1
-    segment.volume = sff.SFFThreeDVolume(
-        latticeId=0,
+    segment.three_d_volume = sff.SFFThreeDVolume(
+        lattice_id=0,
         value=vol1_value,
     )
     segment.colour = sff.SFFRGBA(
@@ -892,8 +892,8 @@ For each segment (voxel value) in the lattice create a 3D volume object that ref
     # segment two
     segment = sff.SFFSegment()
     vol2_value = 37.1
-    segment.volume = sff.SFFThreeDVolume(
-        latticeId=2,
+    segment.three_d_volume = sff.SFFThreeDVolume(
+        lattice_id=2,
         value=vol2_value
     )
     segment.colour = sff.SFFRGBA(

setup.py

@@ -35,6 +35,7 @@
     u"Programming Language :: Python :: 3.7",
     u"Programming Language :: Python :: 3.8",
     u"Programming Language :: Python :: 3.9",
+    u"Programming Language :: Python :: 3.10",
     u"Topic :: Software Development :: Libraries :: Python Modules",
     u"Topic :: Terminals",
     u"Topic :: Text Processing",
@@ -62,26 +63,3 @@
         ]
     },
 )
-# if sys.version_info[0] > 2:
-# else:
-#     setup(
-#         name=SFFTKRW_NAME,
-#         version=SFFTKRW_VERSION,
-#         packages=find_packages(),
-#         author=SFFTKRW_AUTHOR,
-#         author_email=SFFTKRW_AUTHOR_EMAIL,
-#         description=SFFTKRW_DESCRIPTION,
-#         long_description=long_description,
-#         long_description_content_type=SFFTKRW_DESCRIPTION_CONTENT_TYPE,
-#         url=SFFTKRW_URL,
-#         license=SFFTKRW_LICENSE,
-#         keywords=SFFTKRW_KEYWORDS,
-#         setup_requires=SFFTKRW_SETUP_REQUIRES,
-#         install_requires=SFFTKRW_INSTALL_REQUIRES,
-#         classifiers=SFFTKRW_CLASSIFIERS,
-#         entry_points={
-#             'console_scripts': [
-#                 '{} = sfftkrw.sffrw:main'.format(SFFTKRW_ENTRY_POINT),
-#             ]
-#         },
-#     )

sfftkrw/conf.py

@@ -1,2 +1,2 @@
-SFFTKRW_VERSION = 'v0.7.1'
+SFFTKRW_VERSION = 'v0.7.2'
 SFFTKRW_ENTRY_POINT = 'sff'

sfftkrw/core/parser.py

@@ -234,13 +234,13 @@ def parse_args(_args, use_shlex=False):
         try:
             assert isinstance(_args, _basestring)
         except AssertionError:
-            return os.EX_USAGE
+            return 64
         import shlex
         _args = shlex.split(_args)
     # if we have no subcommands then show the available tools
     if len(_args) == 0:
         Parser.print_help()
-        return os.EX_OK
+        return 0
     # if we only have a subcommand then show that subcommand's help
     elif len(_args) == 1:
         # print(_args[0])
@@ -250,18 +250,18 @@ def parse_args(_args, use_shlex=False):
         if _args[0] == '-V' or _args[0] == '--version':
             print_date(
                 "sfftk-rw version: {} for EMDB-SFF {}".format(SFFTKRW_VERSION, ', '.join(SUPPORTED_EMDB_SFF_VERSIONS)))
-            return os.EX_OK
+            return 0
         # anytime a new argument is added to the base parser subparsers are bumped down in index
         elif _args[0] in _dict_iter_keys(Parser._actions[2].choices):
             exec('{}_parser.print_help()'.format(_args[0]))
-            return os.EX_OK
+            return 0
     # parse arguments
     args = Parser.parse_args(_args)
 
     # check values
     # view
     if args.subcommand == 'view':
-        pass # no view-specific checks yet
+        pass  # no view-specific checks yet
     # convert
     elif args.subcommand == 'convert':
         # we only use the first file in sfftk-rw; sfftk may use more than one file
@@ -281,7 +281,7 @@ def parse_args(_args, use_shlex=False):
                         invalid=args.format,
                         formats=", ".join(map(lambda x: x[0], FORMAT_LIST)))
                     )
-                    return os.EX_USAGE
+                    return 64
                 fn = ".".join(os.path.basename(from_file).split(
                     '.')[:-1]) + '.{}'.format(args.format)
                 args.__setattr__('output', os.path.join(dirname, fn))
@@ -311,8 +311,8 @@ def parse_args(_args, use_shlex=False):
                 ]
             except AssertionError:
                 print_date(
-                        "Invalid value for primary descriptor: {}".format(args.primary_descriptor))
-                return os.EX_USAGE
+                    "Invalid value for primary descriptor: {}".format(args.primary_descriptor))
+                return 64
             if args.verbose:
                 print_date(
                     "Trying to set primary descriptor to {}".format(args.primary_descriptor))
@@ -327,7 +327,7 @@ def parse_args(_args, use_shlex=False):
                 assert args.json_indent >= 0
             except AssertionError:
                 print_date("Invalid value for --json-indent: {}".format(args.json_indent))
-                return os.EX_USAGE
+                return 64
             if args.verbose:
                 print_date("Indenting JSON with indent={}".format(args.json_indent))
 
@@ -348,7 +348,7 @@ def parse_args(_args, use_shlex=False):
                 print_date(
                     "Unknown tool: {}; Available tools for test: {}".format(tool, ", ".join(tool_list))
                 )
-                return os.EX_USAGE
+                return 64
         if args.verbosity:
             try:
                 assert args.verbosity in range(4)
@@ -360,6 +360,6 @@ def parse_args(_args, use_shlex=False):
                         args.verbosity
                     )
                 )
-                return os.EX_USAGE
+                return 64
 
     return args

sfftkrw/schema/adapter_v0_7_0_dev0.py

@@ -1782,15 +1782,15 @@ def from_file(cls, fn, args=None):
                 seg._local = _sff.parse(fn, silence=True)
             except IOError:
                 print_date(_encode(u"File {} not found".format(fn), u'utf-8'))
-                sys.exit(os.EX_IOERR)
+                sys.exit(74)
         elif re.match(r'.*\.(hff|h5|hdf5)$', fn, re.IGNORECASE):
             with h5py.File(fn, u'r') as h:
                 seg._local = seg.from_hff(h, args=args)._local
         elif re.match(r'.*\.json$', fn, re.IGNORECASE):
             seg._local = seg.from_json(fn, args=args)._local
         else:
             print_date(_encode(u"Invalid EMDB-SFF file name: {}".format(fn), u'utf-8'))
-            sys.exit(os.EX_USAGE)
+            sys.exit(64)
         return seg
 
     @property
@@ -1813,7 +1813,7 @@ def as_hff(self, parent_group, name=None, args=None):
         group[u'version'] = self.version
         if self.primary_descriptor is None:
             print_date(_encode(u"Invalid segmentation: primary_descriptor required", u'utf-8'))
-            return os.EX_DATAERR
+            return 65
         group[u'primaryDescriptor'] = self.primary_descriptor
         # if we are adding another group then donu't set dict style; just return the populated group
         if self.software is None:
@@ -1872,7 +1872,7 @@ def from_hff(cls, hff_data, name=None, args=None):
             print_date(_encode(u'Segmentation name not found. Please check that {} is a valid EMDB-SFF file'.format(
                 hff_data.filename
             ), u'utf-8'))
-            sys.exit(os.EX_DATAERR)
+            sys.exit(65)
         obj.version = _decode(hff_data[u'version'][()], u'utf-8')
         obj.software = SFFSoftware.from_hff(hff_data[u'software'], args=args)
         obj.transforms = SFFTransformList.from_hff(hff_data[u'transforms'], args=args)
@@ -2068,7 +2068,7 @@ def merge_annotation(self, other_seg):
             assert isinstance(other_seg, SFFSegmentation)
         except AssertionError:
             print_date(_encode(u"Invalid type for other_seg: {}".format(type(other_seg)), u'utf-8'))
-            sys.exit(os.EX_DATAERR)
+            sys.exit(65)
         # global data
         self.name = other_seg.name
         self.software = other_seg.software

sfftkrw/schema/adapter_v0_8_0_dev1.py

@@ -2493,7 +2493,7 @@ def from_file(cls, fn, args=None):
         """
         if not os.path.exists(fn):
             print_date(_encode(u"File {} not found".format(fn), u'utf-8'))
-            sys.exit(os.EX_IOERR)
+            sys.exit(74)
         else:
             if re.match(r'.*\.(sff|xml)$', fn, re.IGNORECASE):
                 seg_local = _sff.parse(fn, silence=True)
@@ -2508,7 +2508,7 @@ def from_file(cls, fn, args=None):
                 seg_local = seg._local
             else:
                 print_date(_encode(u"Invalid EMDB-SFF file name: {}".format(fn), u'utf-8'))
-                sys.exit(os.EX_DATAERR)
+                sys.exit(65)
         # now create the output object
         obj = cls(new_obj=False)
         obj._local = seg_local

sfftkrw/schema/base.py

@@ -7,7 +7,6 @@
 import io
 import json
 import numbers
-import os
 import re
 
 import h5py
@@ -210,7 +209,7 @@ def export(self, fn, args=None, *_args, **_kwargs):
                         ", ".join(VALID_EXTENSIONS),
                         fn,
                     ), u'utf-8'))
-                    return os.EX_DATAERR
+                    return 65
                 if re.match(r"^(sff|xml)$", fn_ext, re.IGNORECASE):
                     with open(fn, u'w') as f:
                         # write version and encoding
@@ -238,7 +237,7 @@ def export(self, fn, args=None, *_args, **_kwargs):
                         # self.as_json(f, *_args, **_kwargs)
             elif issubclass(type(fn), io.IOBase):
                 self._local.export(fn, 0, *_args, **_kwargs)
-            return os.EX_OK
+            return 0
         else:
             raise SFFValueError("export failed due to validation error")
 
@@ -740,7 +739,7 @@ def _get_next_id(self):
         ids = list(self.get_ids())
         if len(ids) > 0:
             return max(ids) + 1
-        return 1 # to be on the safe side for segments (segment ids begin at 1)
+        return 1  # to be on the safe side for segments (segment ids begin at 1)
 
     def _add_to_dict(self, v):
         """Private method that adds to the convenience dictionary

sfftkrw/sffrw.py

@@ -9,7 +9,6 @@
 from __future__ import division, print_function
 
 import importlib
-import os
 import re
 import sys
 
@@ -68,7 +67,7 @@ def handle_convert(args):  # @UnusedVariable
     # perform actual export
     status = seg.export(args.output, args)
     if args.verbose:
-        if status == os.EX_OK:
+        if status == 0:
             print_date("Done")
         else:
             print_date("Error")
@@ -120,7 +119,7 @@ def handle_view(args):  # @UnusedVariable
         print(u"*" * 50)
     else:
         print(u"Not implemented view for files of type .{}".format(args.from_file.split('.')[-1]), file=sys.stderr)
-    return os.EX_OK
+    return 0
 
 
 def _module_test_runner(mod, args):
@@ -135,7 +134,7 @@ def _module_test_runner(mod, args):
     print_date(u"Found {} test cases in the suite...".format(suite.countTestCases()))
     if not args.dry_run:
         unittest.TextTestRunner(verbosity=args.verbosity).run(suite)
-    return os.EX_OK
+    return 0
 
 
 def _testcase_test_runner(tc, args):
@@ -150,7 +149,7 @@ def _testcase_test_runner(tc, args):
     print_date(u"Found {} test cases in the suite...".format(suite.countTestCases()))
     if not args.dry_run:
         unittest.TextTestRunner(verbosity=args.verbosity).run(suite)
-    return os.EX_OK
+    return 0
 
 
 def _discover_test_runner(path, args, top_level_dir=None):
@@ -165,7 +164,7 @@ def _discover_test_runner(path, args, top_level_dir=None):
     print_date(u"Found {} test cases in the suite...".format(suite.countTestCases()))
     if not args.dry_run:
         unittest.TextTestRunner(verbosity=args.verbosity).run(suite)
-    return os.EX_OK
+    return 0
 
 
 def handle_tests(args):
@@ -199,18 +198,18 @@ def handle_tests(args):
                 )
                 test_adapter = importlib.import_module(test_adapter_name)
                 _module_test_runner(test_adapter, args)
-    return os.EX_OK
+    return 0
 
 
 def main():
     try:
         from .core.parser import parse_args
         args = parse_args(sys.argv[1:])
         # missing args
-        if args == os.EX_USAGE:
-            return os.EX_USAGE
-        elif args == os.EX_OK:  # e.g. show version has no error but has no handler either
-            return os.EX_OK
+        if args == 64:
+            return 64
+        elif args == 0:  # e.g. show version has no error but has no handler either
+            return 0
         # subcommands
         if args.subcommand == 'convert':
             return handle_convert(args)
@@ -221,8 +220,8 @@ def main():
 
     except KeyboardInterrupt:
         ### handle keyboard interrupt ###
-        return os.EX_OK
-    return os.EX_OK
+        return 0
+    return 0
 
 
 if __name__ == "__main__":