From: Michael Hanke Date: Sun, 2 Jan 2011 19:14:04 +0000 (-0500) Subject: Draft for a project list and two proposals. X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=56fde2f99569b83e9b21c157793518e6ab6ba10d;p=neurodebian.git Draft for a project list and two proposals. --- diff --git a/artwork/workarea.svg b/artwork/workarea.svg new file mode 100644 index 0000000..a449ba2 --- /dev/null +++ b/artwork/workarea.svg @@ -0,0 +1,224 @@ + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/sphinx/_static/workarea.png b/sphinx/_static/workarea.png new file mode 100644 index 0000000..9112675 Binary files /dev/null and b/sphinx/_static/workarea.png differ diff --git a/sphinx/index.rst b/sphinx/index.rst index 862798c..47be627 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -13,7 +13,8 @@ or prospective packages which are not (yet) available from the main Debian_ archive, as well as backported or simply rebuilt packages also available elsewhere. Please see the :ref:`faq` for more information about the goals of this project, and :ref:`read what people say about it `. -If you appreciate this service, please |spread|. +Take a look at the :ref:`list of our current and planned projects ` if +you want to get involved. If you appreciate this service, please |spread|. .. note:: @@ -29,6 +30,7 @@ If you appreciate this service, please |spread|. +

.. _Ubuntu: http://www.ubuntu.com diff --git a/sphinx/proj_afni.rst b/sphinx/proj_afni.rst new file mode 100644 index 0000000..4a0d4e9 --- /dev/null +++ b/sphinx/proj_afni.rst @@ -0,0 +1,52 @@ +.. -*- mode: rst; fill-column: 78 -*- +.. ex: set sts=4 ts=4 sw=4 et tw=79: + +.. _project_afni: + +************** +Packaging AFNI +************** + +:ref:`AFNI ` is an environment for processing and displaying +functional MRI data. It provides a complete analysis toolchain, including 3D +cortical surface models, and mapping of volumetric data (SUMA). + +Packaging AFNI for Debian is part of our general efforts to provide +comprehensive neuro-imaging research support. + +Status +------ + +A fully functional package is available from the NeuroDebian repository. +Current work focuses on continuously tracking upstream development and making +the package fit for Debian proper. + +To ease development a `Git repository`_ has been created that contains the +history of AFNI development since 1998. Because upstream doesn't expose a +version control system the repository is populated with daily snapshots of the +sources. + +A new CMake-based build-system has been developed for AFNI. + +.. _Git repository: http://git.debian.org/?p=pkg-exppsy/afni.git + +.. todo:: AFNI packaging + + * Refurbish the afni-data package to meet Debian standards. + * Push remaining patches upstream. A first wave has been submitted, but not + yet adopted. It remains uncertain if the CMake buildsystem gets accepted. + * Perform a final license check. Lots of 3rd-party code has already been + removed from the package to allow for legal redistribution (e.g. edges3D + library). + * Develop a test suite for AFNI. We received a suitable dataset to implement + a test running a full retinotopic mapping analysis. + +References +---------- + +* `Debian ITP bug report `_ with information on + the packaging progress. +* `Git repository`_ with the full source code and the Debian packaging. +* `List of patches `_ + applied to the Debian package (i.e. the difference to the upstream AFNI + source code). diff --git a/sphinx/proj_matlab.rst b/sphinx/proj_matlab.rst new file mode 100644 index 0000000..11984e8 --- /dev/null +++ b/sphinx/proj_matlab.rst @@ -0,0 +1,67 @@ +.. -*- mode: rst; fill-column: 78 -*- +.. ex: set sts=4 ts=4 sw=4 et tw=79: + +.. _project_matlab: + +********************************* +Integrating Matlab-based software +********************************* + +There is a vast amount of Matlab-based software for neuro-imaging and +psychological research. For various reasons, such software has not been +considered for integration into Debian in the past. However, recent advances of +the Octave_ project allow running a significant number of Matlab tools without +a proprietary environment. + +To ease the transition to a completely open-source research environment, we are +following a two-fold approach. On one hand we start packaging all relevant +Octave-compatible software for Debian. On the other hand we work on a proper +integration of (still) Matlab-only software. + +The latter shall be achieved by establishing an adaptor Debian package that can +represent local Matlab installations to the Debian package management system. +Moreover, this package provides helper tools that ease building MEX extensions +from source during package installation with a local Matlab and therefor allow +for inclusion of such packages into Debian 'contrib' suite (given an appropriate +licence). + +The goal is to provide researchers with fully functional Matlab software, that +can be used with Matlab on Debian systems, while benefiting from all advantages +of Debian integration. However, at the same time researchers should have the +possibility to seamlessly switch to Octave_ whenever possible or necessary (e.g. +a laptop being out of reach of a university's license server), and eventually +completely migrate to Octave when full compatibility for a particular software +is achieved. + +This effort includes talking to upstream projects about the possibility to run +with Octave, as well as developing patches to achieve compatibility. + +.. _Octave: http://www.gnu.org/software/octave + +Status +------ + +A :ref:`Matlab-adaptor package ` draft is ready and available from +NeuroDebian. + +Packaging of individual Matlab-based software has started. This includes +:ref:`SPM ` and :ref:`Fieldtrip ` (see +references_ for more packages). Expanding the coverage is planned. + +.. todo:: Integrating Matlab-based software + + * Finish packaging of fieldtrip which is necessary to complete the packaging + of SPM. + * Adapt the packaging of `dynare `_ + in Debian to use the new adaptor package. Once this is done and reviewed by + its maintainers the adaptor package can be submitted for inclusion into + Debian proper. + +References +---------- + +* `SPM packaging progress `_ report. +* `Fieldtrip packaging progress `_ report. +* `EEGLab packaging progress `_ report. +* `PsychToolbox packaging progress `_ report. + diff --git a/sphinx/proj_template.txt b/sphinx/proj_template.txt new file mode 100644 index 0000000..5fb990d --- /dev/null +++ b/sphinx/proj_template.txt @@ -0,0 +1,23 @@ +.. -*- mode: rst; fill-column: 78 -*- +.. ex: set sts=4 ts=4 sw=4 et tw=79: + +.. _project_: + +************** + +************** + +<description> + +Status +------ + +<status report> + +.. todo:: <title> + + +References +---------- + +<references> diff --git a/sphinx/projects.rst b/sphinx/projects.rst new file mode 100644 index 0000000..f68aa10 --- /dev/null +++ b/sphinx/projects.rst @@ -0,0 +1,33 @@ +.. -*- mode: rst; fill-column: 78 -*- +.. ex: set sts=4 ts=4 sw=4 et tw=79: + +.. _projects: + +******************** +NeuroDebian Projects +******************** + +This page lists current and planned NeuroDebian projects. Each description +lists a couple of tasks the remain to be done to accomplish the goal of a +particular project. If you want to contribute, take a look at them and email the +neurodebian-devel_ mailing list with your intention to help. + + +Current projects +---------------- + +.. toctree:: + :maxdepth: 1 + + proj_afni + proj_matlab + + +.. + Planned projects + ---------------- + + Finished projects + ----------------- + +.. include:: link_names.txt