Merge pull request #255 from clamsproject/develop

releasing 1.3.2

Author: keighrim

Makefile

@@ -22,7 +22,7 @@ testcaches = .hypothesis .pytest_cache .pytype coverage.xml htmlcov .coverage
 
 all: version test build
 
-develop: devversion package
+develop: devversion package test
 	python3 setup.py develop --uninstall
 	python3 setup.py develop
 
@@ -32,7 +32,9 @@ publish: distclean version package test
 	@git push origin `cat VERSION`
 
 $(generatedcode): VERSION
-	python3 setup.py donothing
+    # this will generate the version subpackage inside clams package
+	python3 setup.py --help  2>/dev/null || echo "Ignore setuptools import error for now"
+	ls $(generatedcode)*
 
 # generating jsonschema depends on mmif-python and pydantic
 docs: mmif := $(shell grep mmif-python requirements.txt)
@@ -41,6 +43,7 @@ docs: VERSION $(generatedcode)
 	pip install --upgrade --no-input "$(mmif)" "$(pydantic)"
 	rm -rf docs
 	mkdir -p docs
+	ls clams/ver
 	python3 clams/appmetadata/__init__.py > documentation/appmetadata.jsonschema
 	sphinx-build -a -b html documentation/ docs
 	mv documentation/appmetadata.jsonschema docs/
@@ -96,5 +99,8 @@ distclean:
 	@rm -rf dist $(artifact) build/bdist*
 clean: distclean
 	@rm -rf VERSION VERSION.dev $(testcaches) $(buildcaches) $(generatedcode)
+	@rm -rf docs
+	@rm -rf .*cache
+	@rm -rf .hypothesis tests/.hypothesis
 cleandocs: 
 	@git checkout -- docs && git clean -fx docs

clams/__init__.py

@@ -1,10 +1,8 @@
+import argparse
 import sys
 
-from mmif import __specver__
-
+import mmif
 from clams import develop
-from clams.mmif_utils import source
-from clams.mmif_utils import rewind
 from clams.app import *
 from clams.app import __all__ as app_all
 from clams.appmetadata import AppMetadata
@@ -16,34 +14,41 @@
 
 
 def prep_argparser():
-    import argparse
     parser = argparse.ArgumentParser()
     parser.add_argument(
         '-v', '--version',
         action='version',
-        version=version_template.format(__version__, __specver__)
+        version=version_template.format(__version__, mmif.__specver__)
     )
     subparsers = parser.add_subparsers(title='sub-command', dest='subcmd')
-    for subcmd_module in [source, rewind, develop]:
-        subcmd_name = subcmd_module.__name__.rsplit('.')[-1]
-        subcmd_parser = subcmd_module.prep_argparser(add_help=False)
-        subparsers.add_parser(subcmd_name, parents=[subcmd_parser], 
-                              help=subcmd_module.describe_argparser()[0],
-                              description=subcmd_module.describe_argparser()[1],
-                              formatter_class=argparse.RawDescriptionHelpFormatter,
-                              )
-    return parser
+    return parser, subparsers
 
 
 def cli():
-    parser = prep_argparser()
+    parser, subparsers = prep_argparser()
+    cli_modules = {}
+    # thinly wrap all `mmif` subcommands
+    # this is primarily for backward compatibility for `souce` and `rewind` subcmds
+    to_register = list(mmif.find_all_modules('mmif.utils.cli'))
+    # then add my own subcommands
+    to_register.append(develop)
+    for cli_module in to_register:
+        cli_module_name = cli_module.__name__.rsplit('.')[-1]
+        cli_modules[cli_module_name] = cli_module
+        subcmd_parser = cli_module.prep_argparser(add_help=False)
+        subparsers.add_parser(cli_module_name, parents=[subcmd_parser],
+                              help=cli_module.describe_argparser()[0],
+                              description=cli_module.describe_argparser()[1],
+                              formatter_class=argparse.RawDescriptionHelpFormatter,
+                              )
     if len(sys.argv) == 1:
         parser.print_help(sys.stderr)
         sys.exit(1)
     args = parser.parse_args()
-    if args.subcmd == 'source':
-        source.main(args)
-    if args.subcmd == 'rewind':
-        rewind.main(args)
-    if args.subcmd == 'develop':
-        develop.main(args)
+    if args.subcmd not in cli_modules:
+        parser.print_help(sys.stderr)
+    else:
+        cli_modules[args.subcmd].main(args)
+
+if __name__ == '__main__':
+    cli()

clams/app/__init__.py

@@ -404,7 +404,13 @@ def cast(self, args: Dict[str, List[str]]) \
                             if valuetype == dict:
                                 casted.setdefault(k, {}).update(v)
                             else:
-                                casted.setdefault(k, []).append(v)
+                                # pytype will complain about the next line, but it is actually correct
+                                # casted.setdefault(k, []).append(v)
+                                # so doing it in a more explicit way
+                                if k in casted and isinstance(casted[k], list):
+                                    casted[k].append(v)
+                                else:
+                                    casted[k] = [v]
                         else: 
                             casted[k] = v
                 # when an empty value is passed (usually as a default value)