Merge pull request #1606 from effigies/doc/independent_doc_build

CI: Build docs outside of container

Author: oesteban

.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:
@@ -801,6 +790,9 @@ workflows:
     jobs:
       - build:
           filters:
+            branches:
+              ignore:
+                - /docs?\/.*/
             tags:
               only: /.*/
 
@@ -827,8 +819,6 @@ workflows:
               only: /.*/
 
       - build_docs:
-          requires:
-            - build
           filters:
             branches:
               ignore:

docs/environment.yml

@@ -28,6 +28,7 @@ dependencies:
     - svgutils
     - nitime
     - nilearn!=0.5.0,!=0.5.1
-    - niworkflows<0.9.0a0,>=0.8.1
-    - smriprep
     - tedana>=0.0.5
+    - git+https://github.com/effigies/niworkflows.git@e6a277ee5e47be5f8148b136b7201c9beb8e70a3#egg=niworkflows
+    - smriprep<0.3.0a0,>=0.2.0
+    - templateflow<0.2.0a0,>=0.1.3

docs/workflows.rst

@@ -20,9 +20,9 @@ is presented below:
 
     from fmriprep.workflows.base import init_single_subject_wf
     from collections import namedtuple
-    BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+    BIDSLayout = namedtuple('BIDSLayout', ['root'])
     wf = init_single_subject_wf(
-        layout=BIDSLayout(),
+        layout=BIDSLayout('.'),
         subject_id='test',
         name='single_subject_wf',
         task_id='',
@@ -273,7 +273,7 @@ BOLD preprocessing
     :simple_form: yes
 
     from collections import namedtuple
-    BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+    BIDSLayout = namedtuple('BIDSLayout', ['root'])
     from fmriprep.workflows.bold import init_func_preproc_wf
     wf = init_func_preproc_wf(
         '/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
@@ -287,7 +287,7 @@ BOLD preprocessing
         force_syn=True,
         freesurfer=True,
         ignore=[],
-        layout=BIDSLayout(),
+        layout=BIDSLayout('.'),
         low_mem=False,
         medial_surface_nan=False,
         omp_nthreads=1,

fmriprep/__about__.py

@@ -89,25 +89,24 @@
     'nilearn!=0.5.0,!=0.5.1',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows',
+    'niworkflows @ '
+    'git+https://github.com/effigies/niworkflows.git@5e9daf0b08fcad2b17350a71ecaf71fa9ce4eff7',
     'numpy',
     'pandas',
     'psutil>=5.4',
     'pybids<0.8.0a0,>=0.7.1',
     'pyyaml',
     'scikit-image',
-    'smriprep',
+    'smriprep<0.3.0a0,>=0.2.0',
     'statsmodels',
     'tedana>=0.0.5',
     'templateflow<0.2.0a0,>=0.1.3',
 ]
 
 
 LINKS_REQUIRES = [
-    'git+https://github.com/poldracklab/niworkflows.git@'
-    '076aed98962b10d107c83110c05e42466a89bbc4#egg=niworkflows',
-    'git+https://github.com/poldracklab/smriprep.git@'
-    'f1cfc37bcdc346549dbf1d037cdade3a3b32d5de#egg=smriprep-0.1.0',
+    'git+https://github.com/effigies/niworkflows.git@'
+    '5e9daf0b08fcad2b17350a71ecaf71fa9ce4eff7#egg=niworkflows',
 ]
 
 TESTS_REQUIRES = [

fmriprep/workflows/base.py

@@ -52,10 +52,10 @@ def init_fmriprep_wf(layout, subject_list, task_id, echo_idx, run_uuid, work_dir
 
         import os
         from collections import namedtuple
-        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(layout=BIDSLayout(),
+        wf = init_fmriprep_wf(layout=BIDSLayout('.'),
                               subject_list=['fmripreptest'],
                               task_id='',
                               echo_idx=None,
@@ -255,8 +255,8 @@ def init_single_subject_wf(layout, subject_id, task_id, echo_idx, name, reportle
 
         from fmriprep.workflows.base import init_single_subject_wf
         from collections import namedtuple
-        BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
-        wf = init_single_subject_wf(layout=BIDSLayout(),
+        BIDSLayout = namedtuple('BIDSLayout', ['root'])
+        wf = init_single_subject_wf(layout=BIDSLayout('.'),
                                     subject_id='test',
                                     task_id='',
                                     echo_idx=None,

fmriprep/workflows/bold/base.py

@@ -62,7 +62,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 
         from fmriprep.workflows.bold import init_func_preproc_wf
         from collections import namedtuple
-        BIDSLayout = namedtuple('BIDSLayout', ['root'], defaults='.')
+        BIDSLayout = namedtuple('BIDSLayout', ['root'])
         wf = init_func_preproc_wf('/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
                                   omp_nthreads=1,
                                   ignore=[],
@@ -88,7 +88,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                                   err_on_aroma_warn=False,
                                   aroma_melodic_dim=-200,
                                   num_bold=1,
-                                  layout=BIDSLayout())
+                                  layout=BIDSLayout('.'))
 
     **Parameters**
 

pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["pip>=18.1", "setuptools>=40.8", "wheel", "numpy"]

requirements.txt

@@ -1,4 +1,4 @@
 nilearn!=0.5.0,!=0.5.1
-git+https://github.com/poldracklab/niworkflows.git@076aed98962b10d107c83110c05e42466a89bbc4#egg=niworkflows
-git+https://github.com/poldracklab/smriprep.git@f1cfc37bcdc346549dbf1d037cdade3a3b32d5de#egg=smriprep-0.1.0
+git+https://github.com/effigies/niworkflows.git@5e9daf0b08fcad2b17350a71ecaf71fa9ce4eff7#egg=niworkflows
+smriprep<0.3.0a0,>=0.2.0
 templateflow<0.2.0a0,>=0.1.3