diff --git a/Makefile b/Makefile index 79176270..6c366409 100644 --- a/Makefile +++ b/Makefile @@ -4,7 +4,7 @@ PYTHON ?= python NOSETESTS ?= nosetests -MODULE ?= datalad +MODULE ?= datalad_hirni all: clean test diff --git a/README.md b/README.md index c168ecf1..4c7f946b 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,4 @@ - ____ _ _ _ - | _ \ __ _ | |_ __ _ | | __ _ __| | - | | | | / _` || __| / _` || | / _` | / _` | - | |_| || (_| || |_ | (_| || |___ | (_| || (_| | - |____/ \__,_| \__| \__,_||_____| \__,_| \__,_| - Hirni +# Datalad-Hirni [![Travis tests status](https://secure.travis-ci.org/psychoinformatics-de/datalad-hirni.png?branch=master)](https://travis-ci.org/psychoinformatics-de/datalad-hirni) [![codecov.io](https://codecov.io/github/psychoinformatics-de/datalad-hirni/coverage.svg?branch=master)](https://codecov.io/github/psychoinformatics-de/datalad-hirni?branch=master) [![Documentation](https://readthedocs.org/projects/datalad-hirni/badge/?version=latest)](http://datalad-hirni.rtfd.org) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![GitHub release](https://img.shields.io/github/release/psychoinformatics-de/datalad-hirni.svg)](https://GitHub.com/psychoinformatics-de/datalad-hirni/releases/) [![PyPI version fury.io](https://badge.fury.io/py/datalad-hirni.svg)](https://pypi.python.org/pypi/datalad-hirni/) [![Average time to resolve an issue](http://isitmaintained.com/badge/resolution/psychoinformatics-de/datalad-hirni.svg)](http://isitmaintained.com/project/psychoinformatics-de/datalad-hirni "Average time to resolve an issue") [![Percentage of issues still open](http://isitmaintained.com/badge/open/psychoinformatics-de/datalad-hirni.svg)](http://isitmaintained.com/project/psychoinformatics-de/datalad-hirni "Percentage of issues still open") diff --git a/datalad_hirni/commands/dicom2spec.py b/datalad_hirni/commands/dicom2spec.py index c7fa09e2..e8283917 100644 --- a/datalad_hirni/commands/dicom2spec.py +++ b/datalad_hirni/commands/dicom2spec.py @@ -272,8 +272,8 @@ class Dicom2Spec(Interface): _params_ = dict( dataset=Parameter( args=("-d", "--dataset"), - doc="""specify a dataset containing the DICOM metadata to be - used. If no dataset is given, an attempt is made to identify + doc="""specify a dataset containing the DICOM metadata to be + used. If no dataset is given, an attempt is made to identify the dataset based on the current working directory""", constraints=EnsureDataset() | EnsureNone()), path=Parameter( @@ -290,7 +290,7 @@ class Dicom2Spec(Interface): subject=Parameter( args=("--subject",), metavar="SUBJECT", - doc="""subject identifier. If not specified, an attempt will be made + doc="""subject identifier. If not specified, an attempt will be made to derive SUBJECT from DICOM headers""", constraints=EnsureStr() | EnsureNone()), anon_subject=Parameter( @@ -301,7 +301,7 @@ class Dicom2Spec(Interface): acquisition=Parameter( args=("--acquisition",), metavar="ACQUISITION", - doc="""acquisition identifier. If not specified, an attempt + doc="""acquisition identifier. If not specified, an attempt will be made to derive an identifier from DICOM headers""", constraints=EnsureStr() | EnsureNone()), properties=Parameter( diff --git a/datalad_hirni/commands/import_dicoms.py b/datalad_hirni/commands/import_dicoms.py index 6e18b8c2..7d0f8140 100644 --- a/datalad_hirni/commands/import_dicoms.py +++ b/datalad_hirni/commands/import_dicoms.py @@ -185,21 +185,21 @@ class ImportDicoms(Interface): subject=Parameter( args=("--subject",), metavar="SUBJECT", - doc="""subject identifier. If not specified, an attempt will be made + doc="""subject identifier. If not specified, an attempt will be made to derive SUBJECT from DICOM headers. See hirni-dicom2spec for details.""", constraints=EnsureStr() | EnsureNone()), anon_subject=Parameter( args=("--anon-subject",), metavar="ANON_SUBJECT", - doc="""an anonymized subject identifier. This is needed for - anonymized conversion via spec2bids --anonymize and will be stored - in the specification snippet for the imported DICOMs. Hence it can + doc="""an anonymized subject identifier. This is needed for + anonymized conversion via spec2bids --anonymize and will be stored + in the specification snippet for the imported DICOMs. Hence it can be added later and isn't mandatory for the import.""", constraints=EnsureStr() | EnsureNone()), properties=Parameter( args=("--properties",), metavar="PATH or JSON string", - doc="""a JSON string or a path to a JSON file, to provide + doc="""a JSON string or a path to a JSON file, to provide overrides/additions to the to be created specification snippets for this acquisition. """, constraints=EnsureStr() | EnsureNone()), diff --git a/datalad_hirni/commands/spec2bids.py b/datalad_hirni/commands/spec2bids.py index ad021d3e..9720f84f 100644 --- a/datalad_hirni/commands/spec2bids.py +++ b/datalad_hirni/commands/spec2bids.py @@ -51,8 +51,8 @@ class Spec2Bids(Interface): args=("specfile",), metavar="SPEC_FILE", doc="""path(s) to the specification file(s) to use for conversion. - If a directory at the first level beneath the dataset's root is - given instead of a file, it's assumed to be an acqusition directory + If a directory at the first level beneath the dataset's root is + given instead of a file, it's assumed to be an acqusition directory that contains a specification file. By default this is a file named 'studyspec.json' in the acquisition directory. This default name can be configured via the @@ -64,8 +64,8 @@ class Spec2Bids(Interface): args=("--anonymize",), action="store_true", doc="""whether or not to anonymize for conversion. By now this means - to use 'anon_subject' instead of 'subject' from spec and to use - datalad-run with a sidecar file, to not leak potentially identifying + to use 'anon_subject' instead of 'subject' from spec and to use + datalad-run with a sidecar file, to not leak potentially identifying information into its record.""",), only_type=Parameter( args=("--only-type",), diff --git a/datalad_hirni/commands/spec4anything.py b/datalad_hirni/commands/spec4anything.py index 069604f2..e031b2a7 100644 --- a/datalad_hirni/commands/spec4anything.py +++ b/datalad_hirni/commands/spec4anything.py @@ -91,15 +91,15 @@ class Spec4Anything(Interface): dataset=Parameter( args=("-d", "--dataset"), metavar='PATH', - doc="""specify the dataset. If no dataset is given, an attempt is - made to identify the dataset based on the current working directory + doc="""specify the dataset. If no dataset is given, an attempt is + made to identify the dataset based on the current working directory and/or the `path` given""", constraints=EnsureDataset() | EnsureNone()), path=Parameter( args=("path",), metavar='PATH', doc="""path(s) of the data to create specification for. Each path - given will be treated as a data entity getting its own specification + given will be treated as a data entity getting its own specification snippet""", nargs="*", constraints=EnsureStr()), diff --git a/datalad_hirni/support/hirni_heuristic.py b/datalad_hirni/support/hirni_heuristic.py index 5fc1123b..fe8f1fc3 100644 --- a/datalad_hirni/support/hirni_heuristic.py +++ b/datalad_hirni/support/hirni_heuristic.py @@ -323,7 +323,7 @@ def infotodict(seqinfo): # pragma: no cover get_specval(series_spec, spec_key)) filename += "_GRE" - + if data_type == 'fmap': # Case 1: Phase difference image and at least one magnitude image # sub-/[ses-/] diff --git a/datalad_hirni/tests/test_dicom2spec.py b/datalad_hirni/tests/test_dicom2spec.py index a091204d..d18f361a 100644 --- a/datalad_hirni/tests/test_dicom2spec.py +++ b/datalad_hirni/tests/test_dicom2spec.py @@ -239,7 +239,7 @@ def test_custom_rules(path, toolbox_url): # older datalad version should return multiple values out of the box rule_files = ds.config.get("datalad.hirni.dicom2spec.rules") else: - raise + raise # ensure assumption about order (dicom2spec relies on it): diff --git a/datalad_hirni/version.py b/datalad_hirni/version.py index fa9c4ec2..27921526 100644 --- a/datalad_hirni/version.py +++ b/datalad_hirni/version.py @@ -1 +1 @@ -__version__ = '0.0.6' +__version__ = '0.0.7' diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 33873b67..73a2c6be 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -16,6 +16,13 @@ We would recommend to consult log of the `Git repository `__ for more details. +0.0.7 (October 7, 2020) +----------------------- + +- adapt for datalad 0.13 series and raise dependency to 0.13.4 +- raised dependency on datalad-neuroimaging +- several fixes for hirni’s tests and CI setup + 0.0.6 (April 6, 2020) ---------------------