Merge branch 'release/0.4.0'

Dockerfile

@@ -18,7 +18,7 @@ RUN apt-get -y update && apt-get install -y zip nodejs
 RUN npm install -g bids-validator
 RUN python3 -m pip install --upgrade pip
 RUN pip install --no-cache nipype pathvalidate
-RUN pip install --no-cache flywheel-sdk==11.*
+RUN pip install --no-cache flywheel-sdk~=14.6.5
 
 COPY . /src
 

docs/source/installation.rst

@@ -1,6 +1,13 @@
 Installation
 =============
 
+``fw-heudiconv`` can be run in the Flywheel GUI as a gear, or locally using the
+Command Line Interface distributed using `pip`. ``flaudit`` can `only` be run
+in the Flywheel GUI.
+
+.. note::
+    FlywheelTools are intended for use with a Flywheel site. At the University of
+    Pennsylvania, our site is available at `upenn.flywheel.io <https://upenn.flywheel.io>`_.
 
 To use locally, follow instructions below to set up your system for using ``fw-heudiconv`` on your machine:
 

docs/source/stepbystep.rst

@@ -223,6 +223,12 @@ uncheck it after this test run.
 When you're ready, hit "Run Gear"! Take note of the analysis' name to refer back
 to  later.
 
+To monitor progress of the gear, click on the session’s “Provenance” tab. A
+grey pause symbol indicates that the job is queued, a blue cog indicates that
+it is running, and a green check or red triangle indicates that the gear has
+finished, successfully or unsuccessfully, respectively; refresh the page to
+update the status of running gears.
+
 At the command line, this achieved with the following command:
 
 .. code-block:: python

fw_heudiconv/backend_funcs/convert.py

@@ -327,7 +327,7 @@ def confirm_bids_namespace(project_obj, dry_run):
             bids = {
                 'BIDS': {'Acknowledgements': '',
                 'Authors': [],
-                'BIDSVersion': '1.0.2',
+                'BIDSVersion': '1.6.0',
                 'DatasetDOI': '',
                 'Funding': [],
                 'HowToAcknowledge': '',

fw_heudiconv/backend_funcs/query.py

@@ -1,7 +1,10 @@
 import logging
 import collections
 import os
-from nibabel.nicom.dicomwrappers import wrapper_from_data
+import warnings
+with warnings.catch_warnings():
+    warnings.filterwarnings("ignore", category=UserWarning)
+    from nibabel.nicom.dicomwrappers import wrapper_from_data
 
 from heudiconv import utils
 

fw_heudiconv/cli/export.py

@@ -231,7 +231,7 @@ def download_bids(
     # Project's subject data
     for fi in to_download['project']:
 
-        if fi['BIDS'] is not None:
+        if fi['BIDS'] is not None and get_nested(fi, 'BIDS', 'Path') is not None:
             output_path = get_nested(fi, 'BIDS', 'Path')
             path = str(Path(output_path, fi['name']))
 
@@ -252,7 +252,7 @@ def download_bids(
             if fi['name'] not in attachments:
                 continue
 
-        if fi['BIDS'] is not None:
+        if fi['BIDS'] is not None and get_nested(fi, 'BIDS', 'Path') is not None:
 
             output_path = get_nested(fi, 'BIDS', 'Path')
             path = str(Path(output_path, fi['name']))
@@ -272,7 +272,7 @@ def download_bids(
             if not any([re.search(att, fi['name']) for att in attachments]):
                 continue
 
-        if fi['BIDS'] is not None:
+        if fi['BIDS'] is not None and get_nested(fi, 'BIDS', 'Path') is not None:
             output_path = Path(root_path, get_nested(fi, 'BIDS', 'Path'))
             path = str(Path(output_path, fi['name']))
 

manifest.json

@@ -2,7 +2,7 @@
 	"name": "fw-heudiconv",
 	"label": "Flywheel HeuDiConv",
 	"description": "HeuDiConv-style BIDS curation on Flywheel. Flywheel HeuDiConv (or fw-heudiconv, pronounced /fwuː di kɑː n(v)/) is a Python-based toolkit that leverages the flexibility and comprehensiveness of HeuDiConv to curate neuroimaging data on Flywheel into a BIDS-valid format.",
-	"version": "0.2.15_0.3.4",
+	"version": "0.2.15_0.4.0",
 	"inputs": {
 		"api_key": {
 			"base": "api-key"
@@ -24,11 +24,6 @@
 			"default": true,
 			"description": "Run without applying changes",
 			"type": "boolean"
-		},
-		"default_heuristic": {
-			"default": "",
-			"description": "Use a default heuristic from the HeuDiConv modules [DEPRECATED]",
-			"type": "string"
 		}
 	},
 	"command": "./fw_heudiconv_run.py",
@@ -41,7 +36,7 @@
 	"custom": {
 		"gear-builder": {
 			"category": "analysis",
-			"image": "pennbbl/fw-heudiconv:0.2.15_0.3.4"
+			"image": "pennbbl/fw-heudiconv:0.2.15_0.4.0"
 		},
 		"flywheel":{"suite": "PennBBL"}
 	}

release.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+if [ $# -eq 0 ]
+  then
+    echo "No version argument supplied"
+    exit
+fi
+
+echo Upgrading and uploading fw-heudiconv...
+
+VERSION=$1
+
+echo Building docker image:
+echo docker build -t pennbbl/fw-heudiconv:$VERSION .
+
+docker build -t pennbbl/fw-heudiconv:$VERSION .
+
+echo Testing local help call...
+
+fw gear local --help
+
+retVal=$?
+if [ $retVal -ne 0 ]; then
+    echo "Error with local test"
+    exit $retVal
+fi
+
+echo Uploading to pip...
+
+python setup.py sdist
+twine upload dist/*
+
+echo Uploading gear...
+
+fw gear upload

requirements.txt

@@ -1,4 +1,4 @@
-flywheel-sdk
+flywheel-sdk ~= 14.6.5
 heudiconv
 pandas
 bids-validator

setup.cfg

@@ -26,7 +26,7 @@ classifiers =
 
 [options]
 install_requires =
-    flywheel-sdk
+    flywheel-sdk ~= 14.6.5
     bids-validator
     nibabel >=3.0.0
     indexed_gzip >=0.8.8

setup.py

@@ -7,16 +7,16 @@
 
 setuptools.setup(
     name="fw_heudiconv",
-    version="0.3.4",
+    version="0.4.0",
     author="Tinashe M. Tapera, Matt Cieslak, Harsha Kethineni",
     author_email="[email protected]",
-    description="Use heudiconv heuristics for BIDS curation on flywheel",
+    description="Use heudiconv-like heuristics for BIDS curation on flywheel",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/PennBBL/fw_heudiconv",
     packages=setuptools.find_packages(),
     install_requires=[
-        "flywheel-sdk",
+        "flywheel-sdk~=14.6.5",
         "heudiconv",
         "pandas",
         "bids-validator",

testing/test_fwheudiconv.py

@@ -4,8 +4,15 @@
 
 import pytest
 import sys
+import flywheel
 
 def test_init():
     print(sys.version)
     assert 1
     return
+
+def test_client():
+
+    client = flywheel.Client()
+    assert client
+    return 1