Merge remote-tracking branch 'upstream/master' into maint/run-docker-as-user

Author: oesteban

docs/environment.yml

@@ -28,6 +28,6 @@ dependencies:
     - svgutils
     - nitime
     - nilearn
-    - niworkflows>=0.5.4,<0.6
+    - niworkflows>=0.7.2,<0.8.0a0
     - smriprep>=0.0.4,<0.1.0a0
     - tedana>=0.0.5

docs/installation.rst

@@ -26,20 +26,33 @@ In order to run fmriprep in a Docker container, Docker must be `installed
 <https://docs.docker.com/engine/installation/>`_.
 Once Docker is installed, the recommended way to run fmriprep is to use the
 fmriprep-docker_ wrapper, which requires Python and an Internet connection.
+``fmriprep-docker`` is a command that allows you to write your command line 
+as if you were running ``fmriprep`` directly, and converts it into a ``docker`` 
+command.
 
 To install::
 
     $ pip install --user --upgrade fmriprep-docker
 
-When run, ``fmriprep-docker`` will generate a Docker command line for you,
-print it out for reporting purposes, and then run the command, e.g.::
+When you run ``fmriprep-docker``, it will generate a Docker command line for you,
+print it out for reporting purposes, and then execute it without further action
+needed, e.g.::
 
     $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
     RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
         -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
         /data /out participant
     ...
 
+``fmriprep-docker`` accepts all of the typical options for ``fmriprep``,
+automatically translating directories into Docker mount points.
+
+We have published a `step-by-step tutorial
+<http://reproducibility.stanford.edu/fmriprep-tutorial-running-the-docker-image/>`_
+illustrating how to run ``fmriprep-docker``. 
+This tutorial also provides valuable troubleshooting insights and advice on 
+what to do after fmriprep has run.
+
 You may also invoke ``docker`` directly::
 
     $ docker run -ti --rm \
@@ -76,7 +89,7 @@ image directly on the HCP.
 This is as simple as: ::
 
     $ singularity build /my_images/fmriprep-<version>.simg docker://poldracklab/fmriprep:<version>
-    
+
 Where ``<version>`` should be replaced with the desired version of fMRIPrep that you want to download.
 
 

fmriprep/__about__.py

@@ -89,7 +89,7 @@
     'nilearn',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows',
+    'niworkflows>=0.7.2,<0.8.0a0',
     'numpy',
     'pandas',
     'psutil>=5.4',
@@ -104,8 +104,6 @@
 
 
 LINKS_REQUIRES = [
-    'git+https://github.com/poldracklab/niworkflows.git@'
-    'b97787ee2f1b93cafb104664b60fa0c4fd81253a#egg=niworkflows-0.7.1',
 ]
 
 TESTS_REQUIRES = [

fmriprep/__init__.py

@@ -28,3 +28,7 @@
 
 # cmp is not used by fmriprep, so ignore nipype-generated warnings
 warnings.filterwarnings('ignore', r'cmp not installed')
+warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
+warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
+warnings.simplefilter('ignore', DeprecationWarning)
+warnings.simplefilter('ignore', ResourceWarning)

requirements.txt

@@ -1,4 +1,4 @@
 pybids>=0.7.0,<0.8.0a0
-git+https://github.com/poldracklab/niworkflows.git@b97787ee2f1b93cafb104664b60fa0c4fd81253a#egg=niworkflows-0.7.1
+niworkflows>=0.7.2,<0.8.0a0
 smriprep>=0.0.5,<0.1.0a0
 templateflow>=0.0.4