[skip ci] Merge remote-tracking branch 'upstream/master' into ref/multiple-output-spaces

oesteban · oesteban · commit 4afb89bca0c2 · 2019-05-03T14:33:19.000-07:00
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -294,47 +294,36 @@ jobs:
 
 
   build_docs:
-    machine:
-      image: circleci/classic:201711-01
-    working_directory: /home/circleci/out/docs
+    docker:
+        - image: python:latest
+    working_directory: /tmp/src/fmriprep
     steps:
-      - checkout:
-          path: /home/circleci/src/fmriprep
+      - checkout
       - run:
           name: Check whether build should be skipped
           command: |
-            cd /home/circleci/src/fmriprep
             if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?docs\]' )" != "" ]]; then
               echo "Skipping doc building job"
               circleci step halt
             fi
-
-      - attach_workspace:
-          at: /tmp
       - run:
-          name: Load Docker image layer cache
-          no_output_timeout: 30m
+          name: Check Python version and upgrade pip
           command: |
-            docker info
-            set +o pipefail
-            if [ -f /tmp/cache/docker.tar.gz ]; then
-              sudo apt update && sudo apt -y install pigz
-              pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
-              docker images
-            fi
+            python --version
+            python -m pip install -U pip
       - run:
-          name: Build fMRIPrep documentation
-          no_output_timeout: 2h
+          name: Install graphviz
           command: |
-            docker run -ti --rm=false -v $PWD:/_build_html \
-              --entrypoint=sphinx-build poldracklab/fmriprep:latest \
-              -T -E -b html -d _build/doctrees-readthedocs -W -D \
-              language=en /src/fmriprep/docs/ /_build_html 2>&1 \
-              | tee $PWD/builddocs.log
-            cat $PWD/builddocs.log
-            grep -qv "ERROR" $PWD/builddocs.log
+              apt-get update
+              apt-get install -y graphviz
+      - run:
+          name: Install fMRIPrep
+          command: python -m pip install ".[doc]"
+      - run:
+          name: Build documentation
+          command: make SPHINXOPTS="-W" -C docs html
       - store_artifacts:
-          path: /home/circleci/out/docs
+          path: /tmp/src/fmriprep/docs/_build/html
 
   ds005:
     machine:
@@ -802,6 +791,9 @@ workflows:
     jobs:
       - build:
           filters:
+            branches:
+              ignore:
+                - /docs?\/.*/
             tags:
               only: /.*/
 
@@ -828,8 +820,6 @@ workflows:
               only: /.*/
 
       - build_docs:
-          requires:
-            - build
           filters:
             branches:
               ignore:
diff --git a/docs/environment.yml b/docs/environment.yml
@@ -28,6 +28,7 @@ dependencies:
     - svgutils
     - nitime
     - nilearn!=0.5.0,!=0.5.1
-    - niworkflows<0.10.0a0,>=0.9.0
-    - smriprep<0.3.0a0,>=0.2.0
+    - git+https://github.com/poldracklab/niworkflows.git@e8f677a0407fc312b7f3d87a4c47726ceb8cd975#egg=niworkflows
     - tedana>=0.0.5
+    - smriprep<0.3.0a0,>=0.2.0
+    - templateflow<0.2.0a0,>=0.1.3
diff --git a/docs/workflows.rst b/docs/workflows.rst
@@ -20,7 +20,7 @@ is presented below:
 
     from fmriprep.workflows.base import init_single_subject_wf
     from collections import namedtuple, OrderedDict
-    BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+    BIDSLayout = namedtuple('BIDSLayout', ['root'])
     wf = init_single_subject_wf(
         anat_only=False,
         aroma_melodic_dim=-200,
@@ -35,7 +35,7 @@ is presented below:
         freesurfer=True,
         hires=True,
         ignore=[],
-        layout=BIDSLayout(),
+        layout=BIDSLayout('.'),
         longitudinal=False,
         low_mem=False,
         medial_surface_nan=False,
@@ -276,7 +276,7 @@ BOLD preprocessing
 
     from collections import namedtuple, OrderedDict
     from fmriprep.workflows.bold.base import init_func_preproc_wf
-    BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+    BIDSLayout = namedtuple('BIDSLayout', ['root'])
     wf = init_func_preproc_wf(
         aroma_melodic_dim=-200,
         bold2t1w_dof=9,
@@ -301,7 +301,7 @@ BOLD preprocessing
         use_aroma=False,
         use_bbr=True,
         use_syn=True,
-        layout=BIDSLayout(),
+        layout=BIDSLayout('.'),
         num_bold=1,
     )
 
diff --git a/fmriprep/__about__.py b/fmriprep/__about__.py
@@ -88,7 +88,8 @@
     'nilearn!=0.5.0,!=0.5.1',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows<0.10.0a0,>=0.9.0',
+    'niworkflows @ git+https://github.com/poldracklab/niworkflows.git@'
+    'e8f677a0407fc312b7f3d87a4c47726ceb8cd975',
     'numpy',
     'pandas',
     'psutil>=5.4',
@@ -103,6 +104,8 @@
 
 
 LINKS_REQUIRES = [
+    'git+https://github.com/poldracklab/niworkflows.git@'
+    'e8f677a0407fc312b7f3d87a4c47726ceb8cd975#egg=niworkflows',
 ]
 
 TESTS_REQUIRES = [
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
@@ -79,7 +79,7 @@ def init_fmriprep_wf(
 
         import os
         from collections import namedtuple, OrderedDict
-        BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+        BIDSLayout = namedtuple('BIDSLayout', ['root'])
         from fmriprep.workflows.base import init_fmriprep_wf
         os.environ['FREESURFER_HOME'] = os.getcwd()
         wf = init_fmriprep_wf(
@@ -96,7 +96,7 @@ def init_fmriprep_wf(
             freesurfer=True,
             hires=True,
             ignore=[],
-            layout=BIDSLayout(),
+            layout=BIDSLayout('.'),
             longitudinal=False,
             low_mem=False,
             medial_surface_nan=False,
@@ -300,7 +300,7 @@ def init_single_subject_wf(
 
         from fmriprep.workflows.base import init_single_subject_wf
         from collections import namedtuple, OrderedDict
-        BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+        BIDSLayout = namedtuple('BIDSLayout', ['root'])
         wf = init_single_subject_wf(
             anat_only=False,
             aroma_melodic_dim=-200,
@@ -315,7 +315,7 @@ def init_single_subject_wf(
             freesurfer=True,
             hires=True,
             ignore=[],
-            layout=BIDSLayout(),
+            layout=BIDSLayout('.'),
             longitudinal=False,
             low_mem=False,
             medial_surface_nan=False,
@@ -336,6 +336,7 @@ def init_single_subject_wf(
             use_syn=True,
         )
 
+
     Parameters
 
         anat_only : bool
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -86,7 +86,7 @@ def init_func_preproc_wf(
 
         from fmriprep.workflows.bold import init_func_preproc_wf
         from collections import namedtuple, OrderedDict
-        BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+        BIDSLayout = namedtuple('BIDSLayout', ['root'])
         wf = init_func_preproc_wf(
             aroma_melodic_dim=-200,
             bold2t1w_dof=9,
@@ -111,7 +111,7 @@ def init_func_preproc_wf(
             use_aroma=False,
             use_bbr=True,
             use_syn=True,
-            layout=BIDSLayout(),
+            layout=BIDSLayout('.'),
             num_bold=1,
         )
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,2 @@
+[build-system]
+requires = ["pip>=18.1", "setuptools>=40.8", "wheel", "numpy"]
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
 nilearn!=0.5.0,!=0.5.1
-niworkflows<0.10.0a0,>=0.9.0
+git+https://github.com/poldracklab/niworkflows.git@e8f677a0407fc312b7f3d87a4c47726ceb8cd975#egg=niworkflows
 smriprep<0.3.0a0,>=0.2.0
 templateflow<0.2.0a0,>=0.1.3

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+[build-system]`
	`2`	`+requires = ["pip>=18.1", "setuptools>=40.8", "wheel", "numpy"]`