Merge remote-tracking branch 'upstream/master'

.gitignore

@@ -3,3 +3,4 @@ aslprep/data/.DS_Store
 aslprep/.DS_Store
 .DS_Store
 .DS_Store
+.trash

docs/conf.py

@@ -17,21 +17,21 @@
 from datetime import datetime
 from sphinx import __version__ as sphinxversion
 from packaging import version as pver  # Avoid distutils.LooseVersion which is deprecated
+import sphinx
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.append(os.path.abspath("sphinxext")) 
 sys.path.insert(0, os.path.abspath("../wrapper"))
-sys.path.insert(0, os.path.abspath('../aslprep'))
 
 from github_link import make_linkcode_resolve
 
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = "1.5.3"
+#needs_sphinx = "2.4.4"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named "sphinx.ext.*") or your custom

docs/usage.rst

@@ -31,6 +31,7 @@ Example: ::
 
 Command-Line Arguments
 ----------------------
+
 .. argparse::
    :ref: aslprep.cli.run.get_parser
    :prog: aslprep

setup.cfg

@@ -24,6 +24,7 @@ install_requires =
     nibabel >= 3.0.1
     nipype >= 1.3.1
     nitime
+    sentry_sdk
     #niworkflows ~= 1.2.0
     numpy
     sphinx-argparse

wrapper/README.rst

@@ -0,0 +1,21 @@
+The fMRIPrep on Docker wrapper
+------------------------------
+
+fMRIprep is a functional magnetic resonance image pre-processing pipeline
+that is designed to provide an easily accessible, state-of-the-art interface
+that is robust to differences in scan acquisition protocols and that requires
+minimal user input, while providing easily interpretable and comprehensive
+error and output reporting.
+
+This is a lightweight Python wrapper to run fMRIPrep.
+It generates the appropriate Docker commands, providing an intuitive interface
+to running the fMRIPrep workflow in a Docker environment.
+Docker must be installed and running. This can be checked
+running ::
+
+  docker info
+
+Please report any feedback to our `GitHub repository
+<https://github.com/poldracklab/fmriprep>`_ and do not
+forget to `credit <https://fmriprep.readthedocs.io/en/latest/citing.html>`_ all
+the authors of software that fMRIPrep uses.