adding patch (see: https://github.com/nipy/nipype/issues/3223) and check function

3 files changed, 68 insertions, 4 deletions

diff --git a/.SRCINFO b/.SRCINFO
index b01dd735cbcc..1e6a173bd051 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = python-nipype
 	pkgdesc = Neuroimaging in python pipelines and interfaces
 	pkgver = 1.5.0
-	pkgrel = 1
+	pkgrel = 2
 	url = https://github.com/nipy/nipype
 	arch = any
 	license = Apache
@@ -37,7 +37,9 @@ pkgbase = python-nipype
 	optdepends = fsl
 	optdepends = spm12
 	source = nipype-1.5.0.tar.gz::https://github.com/nipy/nipype/archive/1.5.0.tar.gz
+	source = 0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch
 	sha256sums = dbbe74ac99740da749350a6957326bd78d6ba388694b0c09cd92575f111576af
+	sha256sums = 50dd1c4093399d05fdf0f6558f5d31ef6fdfd30771c23c54314e190e18a217d2
 
 pkgname = python-nipype
 
diff --git a/0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch b/0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch
new file mode 100644
index 000000000000..5755cc762750
--- /dev/null
+++ b/0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch
@@ -0,0 +1,44 @@
+From dc230ef7c9e6261164d66124f82918807473a81d Mon Sep 17 00:00:00 2001
+From: Chris Markiewicz <markiewicz@stanford.edu>
+Date: Thu, 4 Jun 2020 13:30:11 -0400
+Subject: [PATCH] DOC: Skip BIDSDataGrabber doctest if pybids is missing
+
+---
+ nipype/conftest.py      | 1 +
+ nipype/interfaces/io.py | 8 ++++++++
+ 2 files changed, 9 insertions(+)
+
+diff --git a/nipype/conftest.py b/nipype/conftest.py
+index b099fd007..7323e7284 100644
+--- a/nipype/conftest.py
++++ b/nipype/conftest.py
+@@ -17,6 +17,7 @@ shutil.copytree(NIPYPE_DATADIR, data_dir)
+ def add_np(doctest_namespace):
+     doctest_namespace["np"] = numpy
+     doctest_namespace["os"] = os
++    doctest_namespace["pytest"] = pytest
+     doctest_namespace["datadir"] = data_dir
+ 
+ 
+diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
+index d9b578caa..2b2510f16 100644
+--- a/nipype/interfaces/io.py
++++ b/nipype/interfaces/io.py
+@@ -2895,6 +2895,14 @@ class BIDSDataGrabber(LibraryBaseInterface, IOBase):
+ 
+     Examples
+     --------
++
++    .. setup::
++
++        >>> try:
++        ...     import bids
++        ... except ImportError:
++        ...     pytest.skip()
++
+     By default, the BIDSDataGrabber fetches anatomical and functional images
+     from a project, and makes BIDS entities (e.g. subject) available for
+     filtering outputs.
+-- 
+2.27.0
+
diff --git a/PKGBUILD b/PKGBUILD
index dc77654c210e..df255fd24e41 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -10,7 +10,7 @@
 pkgname=python-nipype
 _name=${pkgname/python-/}
 pkgver=1.5.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Neuroimaging in python pipelines and interfaces'
 arch=('any')
 url='https://github.com/nipy/nipype'
@@ -18,8 +18,9 @@ license=('Apache')
 depends=('python-click' 'python-networkx' 'python-nibabel' 'python-numpy' 'python-packaging' 'python-prov' 'python-pydot' 'python-pydotplus' 'python-dateutil' 'python-rdflib>=5.0.0' 'python-scipy' 'python-simplejson' 'python-traits' 'python-filelock' 'python-matplotlib' 'python-numpydoc' 'python-future' 'python-funcsigs' 'python-pytest' 'python-mock' 'python-etelemetry>=0.2.0')
 makedepends=('python-sphinx' 'python-sphinxcontrib-napoleon')
 optdepends=('python-pybids' 'python-dipy' 'ants-git' '3dslicer' 'afni' 'freesurfer' 'fsl' 'spm12')
-source=("${_name}-${pkgver}.tar.gz::https://github.com/nipy/${_name}/archive/${pkgver}.tar.gz")
-sha256sums=('dbbe74ac99740da749350a6957326bd78d6ba388694b0c09cd92575f111576af')
+source=("${_name}-${pkgver}.tar.gz::https://github.com/nipy/${_name}/archive/${pkgver}.tar.gz" "0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch")
+sha256sums=('dbbe74ac99740da749350a6957326bd78d6ba388694b0c09cd92575f111576af'
+            '50dd1c4093399d05fdf0f6558f5d31ef6fdfd30771c23c54314e190e18a217d2')
 
 _setpaths(){
 
@@ -44,6 +45,14 @@ _setpaths(){
 
 }
 
+prepare() {
+
+    mv 0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch ${srcdir}/${_name}-${pkgver}
+    cd ${srcdir}/${_name}-${pkgver}
+
+    patch --forward --strip=1 --input=0001-DOC-Skip-BIDSDataGrabber-doctest-if-pybids-is-missin.patch
+}
+
 
 build() {
 
@@ -55,6 +64,15 @@ build() {
 
 }
 
+check() {
+
+    cd ${srcdir}/${_name}-${pkgver}
+
+    _setpaths
+    echo "MATLABCMD: ${MATLABCMD}"
+
+    pytest -v --doctest-modules nipype
+}
 
 package() {