diff --git a/Makefile b/Makefile index 6058bf46b1..d0f6e4a4ce 100644 --- a/Makefile +++ b/Makefile @@ -66,7 +66,7 @@ test: clean test-code html: @echo "building docs" - make -C doc clean html + make -C doc clean htmlonly specs: @echo "Checking specs and autogenerating spec tests" diff --git a/THANKS.rst b/THANKS.rst index 252512d2c0..4d8cdd47e7 100644 --- a/THANKS.rst +++ b/THANKS.rst @@ -1,102 +1,22 @@ .. -*- mode: rst -*- - Code contributors ----------------- -Contributors to Nipype include but are not limited to: - -.. hlist:: - * Aimi Watanabe - * Alexander Schaefer - * Alexandre Gramfort - * Alexandre Savio - * Anisha Keshavan - * Ariel Rokem - * Ben Acland - * Ben Cipollini - * Basile Pinsard - * Brendan Moloney - * Brian Cheung - * Charl Linssen - * Chris Filo Gorgolewski - * Chris Steele - * Christian Haselgrove - * Christopher Burns - * Cindee Madison - * Claire Tarbert - * Colin Buchanan - * Daniel Ginsburg - * Daniel Haehn - * Daniel Margulies - * Dav Clark - * David Welch - * Drew Erickson - * Erik Kastman - * Félix C. Morency - * Gael Varoquaux - * Hans Johnson - * Janosch Linkersdörfer - * Januzz - * Jarrod Millman - * Jeff Lai - * Jessica Forbes - * John Salvatore - * Lijie Huang - * Michael Hallquist - * Michael Hanke - * Michael Notter - * Michael Waskom - * Nolan Nichols - * Oliver Hinds - * Oscar Esteban - * Rosalia Tungaraza - * Satrajit Ghosh - * Sharad Sikka - * Stephan Gerhard - * Erik Ziegler - * Valentin Haenel - * Xiangzhen Kong - * Xu Wang - * Yannick Schwartz - * Yaroslav O. Halchenko +See `Github contributors list `__. -For full most up to date list see `Ohloh `__. +Funding +------- -Other contributors ------------------- +Nipype is currently supported by `1R01EB020740-01A1 Nipype: Dataflows for Reproducible Biomedical Research `__. -.. hlist:: +Satrajit Ghosh work on this project was partially funded by NIBIB `R03EB008673 `__ and by the `INCF `__ through a contract with TankThink Labs, LLC. +Chris Burns was supported by NIMH grant `5R01MH081909-02 Continued Development and Maintenance of the Neuroimaging in Python Project `__. Hans Jonson was supported by +`2 U54 EB005149 - 06 Core 2b Huntington's Disease - Driving Biological Project `__, +`S10 RR023392 Enterprise Storage In A Collaborative Neuroimaging Environment `__, +`R01 NS040068 Neurobiological Predictors of Huntington's Disease `__, +and `UL1 TR000442 University of Iowa Clinical and Translational Science Program `__. - * Matthew Brett - * Michael Castelle - * Philippe Ciuciu - * Yann Cointepas - * Mark D'Esposito - * Susan Gabrieli - * Brian Hawthorne - * Tim Leslie - * Fernando Perez - * Tyler Perrachione - * Jean-Baptiste Poline - * Alexis Roche - * Denis Riviere - * Gretchen Reynolds - * Jonathan Taylor - * Bertrand Thirion - * Bernjamin Thyreau - * Mike Trumpis - * Karl Young - * Tom Waite We would also like to thank `JetBrains `__ for providing `Pycharm `__ licenses. -Funding -------- -Satrajit Ghosh work on this project was partially funded by NIBIB R03 EB008673 (PI: Ghosh and Whitfield-Gabrieli) and by the `INCF `__ through a contract with TankThink Labs, LLC. -Chris Burns was supported by NIMH grant 5R01MH081909-02 (PI: Desposito). Hans Jonson was supported by -`2 U54 EB005149 - 06 Core 2b Huntington's Disease - Driving Biological Project `__, -`S10 RR023392 Enterprise Storage In A Collaborative Neuroimaging Environment `__, -`R01 NS040068 Neurobiological Predictors of Huntington's Disease `__, -and `UL1 TR000442 University of Iowa Clinical and Translational Science Program `__. - diff --git a/doc/_templates/indexsidebar.html b/doc/_templates/indexsidebar.html index a995843495..d2cb138923 100644 --- a/doc/_templates/indexsidebar.html +++ b/doc/_templates/indexsidebar.html @@ -5,7 +5,7 @@

{{ _('Links') }}

  • Docs: Stable · Nightly
  • Code: Github · Bugs-Requests
  • Forum: User · Developer
    • -
  • License · Funding
    • +
  • License · Funding
  • travis · Coverage Status
  • Downloads · Python Versions
    • diff --git a/doc/_templates/navbar.html b/doc/_templates/navbar.html index 7737d060ca..d0979f4e10 100644 --- a/doc/_templates/navbar.html +++ b/doc/_templates/navbar.html @@ -10,6 +10,6 @@ Home · Quickstart · Documentation · -Citation · -NiPy +About · +Nipy diff --git a/doc/_templates/sidebar_versions.html b/doc/_templates/sidebar_versions.html index 77e6b4bbe7..443e64d7f8 100644 --- a/doc/_templates/sidebar_versions.html +++ b/doc/_templates/sidebar_versions.html @@ -17,7 +17,7 @@

    {{ _('Versions') }}

    ReleaseDevel - 0.11.0{{ version }} + {{ release }}{{ version }} Download @@ -25,16 +25,6 @@

    {{ _('Versions') }}

    - -
    -
    - -
    - -
    -
    diff --git a/doc/about.rst b/doc/about.rst index 2d473d66df..b74736d857 100644 --- a/doc/about.rst +++ b/doc/about.rst @@ -14,7 +14,7 @@ Citation Ghosh SS. (2011). Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. Front. Neuroimform. 5:13. - `Download`__ + `Download Paper`__ __ paper_ diff --git a/doc/conf.py b/doc/conf.py index 6066689c44..1a0d7e9cca 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -14,12 +14,24 @@ import sys import os +from shutil import rmtree nipypepath = os.path.abspath('..') sys.path.insert(1, nipypepath) import nipype +if not os.path.exists('users/examples'): + os.mkdir('users/examples') +os.system('python ../tools/make_examples.py --no-exec') + +if os.path.exists('api/generated'): + rmtree('api/generated') +os.system('python ../tools/build_modref_templates.py') +if os.path.exists('interfaces/generated'): + rmtree('interfaces/generated') +os.system('python ../tools/build_interface_docs.py') + # 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. @@ -29,7 +41,8 @@ # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.todo', +extensions = ['readthedocs_ext.readthedocs', + 'sphinx.ext.todo', 'sphinx.ext.pngmath', 'sphinx.ext.inheritance_diagram', 'sphinx.ext.graphviz', @@ -40,8 +53,8 @@ 'numpy_ext.numpydoc', 'matplotlib.sphinxext.plot_directive', 'matplotlib.sphinxext.only_directives', - 'IPython.sphinxext.ipython_directive', - 'IPython.sphinxext.ipython_console_highlighting' + #'IPython.sphinxext.ipython_directive', + #'IPython.sphinxext.ipython_console_highlighting' ] # Add any paths that contain templates here, relative to this directory. @@ -58,7 +71,7 @@ # General information about the project. project = u'nipype' -copyright = u'2009-15, Neuroimaging in Python team' +copyright = u'2009-16, Neuroimaging in Python team' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the @@ -67,7 +80,7 @@ # The short X.Y version. version = nipype.__version__ # The full version, including alpha/beta/rc tags. -release = version +release = "0.11.0" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/examples/rsfmri_vol_surface_preprocessing_nipy.py b/examples/rsfmri_vol_surface_preprocessing_nipy.py index 477e1e377c..a59337b497 100644 --- a/examples/rsfmri_vol_surface_preprocessing_nipy.py +++ b/examples/rsfmri_vol_surface_preprocessing_nipy.py @@ -1,8 +1,8 @@ #!/usr/bin/env python """ -==================================== +===================================== rsfMRI: ANTS, FS, FSL, NiPy, aCompCor -==================================== +===================================== A preprocessing workflow for Siemens resting state data.