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
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+
+
+
+
diff --git a/sphinx/_static/workarea.png b/sphinx/_static/workarea.png
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diff --git a/sphinx/index.rst b/sphinx/index.rst
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--- 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
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+++ b/sphinx/proj_afni.rst
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+.. -*- 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
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--- /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_:
+
+**************
+
+**************
+
+
+
+Status
+------
+
+
+
+.. todo::
+
+
+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