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Merge 4e34abc into 1dbb91e
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@DarrinFong
DarrinFong committed Mar 27, 2020
2 parents 1dbb91e + 4e34abc commit 1ce1ebf
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5 changes: 3 additions & 2 deletions RELEASE.md
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Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,10 @@
python setup.py bdist_wheel --universal
twine upload dist/*
```
7. Generate Bosh API docs
7. Install [Sphinx](https://www.sphinx-doc.org/en/master/usage/installation.html) for python 3
8. Generate Bosh API docs
```
cd ./tools/sphinx/
pip install sphinx-rtd-theme
pip install sphinx-rtd-theme sphinx-argparse
python argparse_docs.py
```
74 changes: 40 additions & 34 deletions tools/python/boutiques/bosh.py
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Expand Up @@ -24,7 +24,8 @@


def parser_pprint():
parser = ArgumentParser("Boutiques pretty-print for generating help text")
parser = ArgumentParser(description="Boutiques pretty-print for"
"generating help text")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor.")
parser.add_argument("--sandbox", action="store_true",
Expand All @@ -47,7 +48,7 @@ def pprint(*params):


def parser_create():
parser = ArgumentParser("Boutiques descriptor creator")
parser = ArgumentParser(description="Boutiques descriptor creator")
parser.add_argument("descriptor", action="store",
help="Output file to store descriptor in.")
parser.add_argument("--docker-image", '-d', action="store",
Expand All @@ -74,7 +75,7 @@ def create(*params):


def parser_validate():
parser = ArgumentParser("Boutiques descriptor validator")
parser = ArgumentParser(description="Boutiques descriptor validator")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, JSON "
"string or Zenodo ID (prefixed by 'zenodo.').")
Expand Down Expand Up @@ -106,7 +107,8 @@ def validate(*params):


def parser_execute():
parser = ArgumentParser("Boutiques local executor", add_help=False)
parser = ArgumentParser(description="Boutiques local executor",
add_help=False)
parser.add_argument("mode", action="store",
help="Mode of operation to use. Launch: takes a "
"set of inputs compliant with invocation schema "
Expand All @@ -122,7 +124,7 @@ def parser_execute():


def parser_executeLaunch():
parser = ArgumentParser("Launches an invocation.")
parser = ArgumentParser(description="Launches an invocation.")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, "
"JSON string or Zenodo ID (prefixed by 'zenodo.').")
Expand Down Expand Up @@ -170,7 +172,7 @@ def parser_executeLaunch():


def parser_executeSimulate():
parser = ArgumentParser("Simulates an invocation.")
parser = ArgumentParser(description="Simulates an invocation.")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, "
"JSON string or Zenodo ID (prefixed by 'zenodo.').")
Expand All @@ -187,7 +189,7 @@ def parser_executeSimulate():


def parser_executePrepare():
parser = ArgumentParser("Pulls the container image for a given "
parser = ArgumentParser(description="Pulls the container image for a given "
"descriptor")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, "
Expand Down Expand Up @@ -330,8 +332,8 @@ def execute(*params):


def parser_importer():
parser = ArgumentParser("Imports old descriptor or BIDS app or CWL"
" descriptor or docopt script to spec.")
parser = ArgumentParser(description="Imports old descriptor or BIDS app or"
" CWL descriptor or docopt script to spec.")
parser.add_argument("type", help="Type of import we are performing."
" Allowed values: {" +
", ".join(["bids", "0.4", "cwl", "docopt"]) + "}",
Expand Down Expand Up @@ -375,7 +377,8 @@ def importer(*params):


def parser_exporter():
parser = ArgumentParser("Export Boutiques descriptor to other formats.")
parser = ArgumentParser(description="Export Boutiques descriptor to"
" other formats.")
parser.add_argument("type", help="Type of export we are performing.",
choices=["carmin"])
parser.add_argument("descriptor", help="Boutiques descriptor to export.")
Expand Down Expand Up @@ -463,9 +466,10 @@ def publish(*params):


def parser_invocation():
parser = ArgumentParser("Creates invocation schema and validates"
" invocations. Uses descriptor's invocation"
" schema if it exists, otherwise creates one.")
parser = ArgumentParser(description="Creates invocation schema and"
" validates invocations. Uses descriptor's"
" invocation schema if it exists, otherwise"
" creates one.")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, JSON "
"string or Zenodo ID (prefixed by 'zenodo.').")
Expand Down Expand Up @@ -510,8 +514,8 @@ def invocation(*params):


def parser_evaluate():
parser = ArgumentParser("Evaluates parameter values for a descriptor "
"and invocation")
parser = ArgumentParser(description="Evaluates parameter values for a"
" descriptor and invocation")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, JSON "
"string or Zenodo ID (prefixed by 'zenodo.').")
Expand Down Expand Up @@ -555,8 +559,8 @@ def evaluate(*params):


def parser_test():
parser = ArgumentParser("Perform all the tests defined within the"
" given descriptor")
parser = ArgumentParser(description="Perform all the tests defined within"
" the given descriptor")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, JSON "
"string or Zenodo ID (prefixed by 'zenodo.').")
Expand Down Expand Up @@ -603,9 +607,9 @@ def test(*params):


def parser_search():
parser = ArgumentParser("Search Zenodo for Boutiques descriptors. "
"When no term is supplied, will search for "
"all descriptors.")
parser = ArgumentParser(description="Search Zenodo for Boutiques"
" descriptors. When no term is supplied, will"
" search for all descriptors.")
parser.add_argument("query", nargs="?", default="boutiques",
action="store", help="Search query")
parser.add_argument("-v", "--verbose", action="store_true",
Expand Down Expand Up @@ -638,8 +642,8 @@ def search(*params):


def parser_example():
parser = ArgumentParser("Generates example invocation from a valid "
"descriptor")
parser = ArgumentParser(description="Generates example invocation from a"
" valid descriptor")
parser.add_argument("descriptor", action="store",
help="The Boutiques descriptor as a JSON file, "
"JSON string or Zenodo ID (prefixed by 'zenodo.').")
Expand Down Expand Up @@ -679,8 +683,8 @@ def example(*params):


def parser_pull():
parser = ArgumentParser("Ensures that Zenodo descriptors are locally "
"cached, downloading them if needed.")
parser = ArgumentParser(description="Ensures that Zenodo descriptors are"
" locally cached, downloading them if needed.")

parser.add_argument("zids", nargs="+", action="store", help="One or "
"more Zenodo IDs for the descriptor(s) to pull, "
Expand All @@ -707,7 +711,8 @@ def pull(*params):


def parser_data():
parser = ArgumentParser("Manage execution data collection.", add_help=False)
parser = ArgumentParser(description="Manage execution data collection.",
add_help=False)

parser.add_argument("action", action="store",
help="Manage execution data records. Inspect: displays "
Expand All @@ -723,14 +728,14 @@ def parser_data():


def parser_dataInspect():
parser = ArgumentParser("Displays contents of cache")
parser = ArgumentParser(description="Displays contents of cache")
parser.add_argument("-e", "--example", action="store_true",
help="Display example data file contents.")
return parser


def parser_dataPublish():
parser = ArgumentParser("Publishes record(s) to a data set.")
parser = ArgumentParser(description="Publishes record(s) to a data set.")
parser.add_argument("-a", "--author", action="store",
help="Set the author name for the data set "
"publication. Defaults to anonymous.")
Expand Down Expand Up @@ -766,7 +771,7 @@ def parser_dataPublish():


def parser_dataDelete():
parser = ArgumentParser("Delete data record(s) in cache.")
parser = ArgumentParser(description="Delete data record(s) in cache.")
parser.add_argument("-f", "--file", action="store",
help="Filename of record to delete.")
parser.add_argument("--no-int", '-y', action="store_true",
Expand Down Expand Up @@ -822,12 +827,13 @@ def data(*params):


def parser_deprecate():
parser = ArgumentParser("Deprecates a published descriptor by creating a"
" new version with the 'deprecated' tag on Zenodo."
" The descriptor remains available from its Zenodo"
"id, but it won't show in search results. This "
"works by creating a new version of the tool in "
"Zenodo, marked with keyword 'deprecated'.")
parser = ArgumentParser(description="Deprecates a published descriptor by"
" creating a new version with the 'deprecated' tag"
" on Zenodo. The descriptor remains available from"
" its Zenodo id, but it won't show in search"
" results. This works by creating a new version of"
" the tool in Zenodo, marked with keyword"
" 'deprecated'.")
parser.add_argument("zid", action="store", help="Zenodo id "
"of the descriptor to deprecate, "
"prefixed by 'zenodo.', e.g. zenodo.123456")
Expand Down

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