From 56fde2f99569b83e9b21c157793518e6ab6ba10d Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Sun, 2 Jan 2011 14:14:04 -0500 Subject: [PATCH] Draft for a project list and two proposals. --- artwork/workarea.svg | 224 ++++++++++++++++++++++++++++++++++++ sphinx/_static/workarea.png | Bin 0 -> 3685 bytes sphinx/index.rst | 4 +- sphinx/proj_afni.rst | 52 +++++++++ sphinx/proj_matlab.rst | 67 +++++++++++ sphinx/proj_template.txt | 23 ++++ sphinx/projects.rst | 33 ++++++ 7 files changed, 402 insertions(+), 1 deletion(-) create mode 100644 artwork/workarea.svg create mode 100644 sphinx/_static/workarea.png create mode 100644 sphinx/proj_afni.rst create mode 100644 sphinx/proj_matlab.rst create mode 100644 sphinx/proj_template.txt create mode 100644 sphinx/projects.rst 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 0000000000000000000000000000000000000000..911267598513b415ec0cd2cbdc4ff14261a9bf3d GIT binary patch literal 3685 zcmV-r4w~_aP)~qe(`?vSm`+VdPAp~3^gajF5|I8R0OerlS zg!u6VA|ZsqIlsa=@3SoHWg)~xw~e?!7-J2(uHVfX3<x^LC0RVCA=O>5M3 zT^k61D|{e)pI0fReW34PARRd8{NTZZZ_S!D>+Qb2zGIeU{Wk&N_xXHl)~s0*oH1iY zlPe&ZOeQVMvMHs1OnxRXqICSceR3Hf69mz9UDq_t2S5lR_~FBc-A)SKrSeBa5x;y05IPtei2% zOw%+LELgCCxI~I%e7Znwi5JE^K5)qp>Z|>13 zrG?ei)#Zc`*tTu;_V)H?T6`c6sIM7TC#>^gAn$vxTt|B2J^;WAuOa!}$sbxX$6r*& zt5YmP^ni|rVHl=i7zv-x7pSbPj8IDRG(w0!6bc0a5W_G`+qUf-f~EAUfpS66n8ETE zwT_k`9DDj-c)iLVQkby+_S!3%h7v;Lk}cnb5T4RBO~dc^2ZO<2h*Byv#gY(0aLcmn zfjsd?fXHg-C%+y>FGsW2AOZMSzcD;IVdM!g>MEaQ3|HBVceTH8=NqMz0D$It)|reh z5TXipz9X)}ljhVf{2>@2d3SIMahesvN; z2<|3`TtEot+y&uL(B&z>cm@dDwr$&gsH-S&{6d+kbfo3)5qWklSaDw3deNjFe0k4M z&bghbUs;Ei{`L_hd6=*W%fVuN0;w6GWb$FRS5yngU-xNMugkXmgRqVsX|pM^4tUX z@Z3jeX=%av^XGGdDP8(4u#$qbf>+`Qyu8QBo`Cd-;}t@v1B1YQB@lo}Lzd}R@d!6f z(-YiI3YOq3%i?yz5W{})ZoR5t-lXf1KXp8&PoIt@OP1h?C!WX&goX1_`h$BsJZcL7opv6NI6zzwTz%9)cc;~`U%p@M>xs)iAR0qtWh&h^HZ}qPwr<^u zqeqWo*REYyvSbOCEn9|;jt&4o_`%8Wj~H>2B!3E(M-!+6Q z$9do=N+_jSk9#HwUNHlezd1ifHA3+}+yQ@GYKygW=~BG;=9}o~=)kyf<2;sMv0?@4 z>+7+8{d&|sKOg76{%^94zSRl3_Z^5^N4x5RfI8YK08(4B)YKZlBksy6A2nv2^oZJR zr|VhLmg$z2O#tPJz!dDje=mMvQbLI^f&*nqrS#~}aC37&TSg4nSCHXleUs>X+m5vQ|qw9oR0yBMn3%1r>aZHv*r>iil+I^Fue zJQT(Mct@7P6DLl@?YG~a>f=uzP0pP=ht}3s?Ax~wufF;!^pQglUO3G&maX3da=G8* z6%~XFPzV7^6psLMQS_`AYOr(8Mb+_3)rH+rZ@OJM4@6@*t>4(#2wm5)bLUPEf7`Zg z9)P9)G80;)INc$d1byi>P(ncnoT-$WTEtn9Q@)U)?O700$5cuQV@#HsrcuTiEzT>B z)E>Tgv#L=3lyS&w@?>BS_4f8+?AWo`v13Qh_Q{hcr<5oRp>(--OGCFE0e$ylFiJrw zl_e#qGL_vjf?YX%!ByM=LUo_dcTLTx31iQg-_SqpO?yyhh&=befFJ;%r>6&uF|1m( zDrb8<9+&UMb0;D2)sg8&E+AUArIeQ-oM5LE?lMC%r%rkSo}Z2JKK$Gd=?CnON&dPYsf zxq{vGNXg*AL+bu!+}-8FhTY=x`9gy>wu45KvL7ogMCtdv2PKt`9Xp0Q@4OQyPo9*# z+itrJAAIlu^7GT#P17{bxX?{?D42PZhi5;(9W-e<>6bbwI2|X*@JK3=QL5KmH)hg^ zQD6Q>Fc^w3#^CR|h`iT2Ji-S*IR~^Tlm);vO+5Yd(>QhN6gF+zBo&=BX%e<=+Xh|N zF?4A9UP8@gE=8W13lh*}U3}65>nFR@aUx^HQ9LU~2=VFuKviKlT&*!iG{!(FMakMd zAUu7D@sAmf;(50t9*^UtmtI0!TN`4r7?v+zj$3ZI1`ER;97AQF9cOGBQ!XJab=*h?SKj{9@c-Wh zkI=H`=R*)+;lhP@_~C~!Wy%yxojMgwO-(p(-~j6C>SSMc9ofEpyX4K7F#`Z#r|toB z(x64n&?-vOUWpq>wrrIkC{ZFJ*A|5kk_srsz$}5HAMf>iprH9igl@hLD_5?>h7B7e zfB*jda=c1SO-%rRBS(&)zrP;cao|E!gj_q(S<1L|W$Jz4zYB+Me6Cjm3)>Bl8?RX3Q9rmzP5bfg?wb z00640(uYaIFaQA2Xfz8<;q03c9Pil)A@;AW&H_p0Hb3`XivW~T=$B#$y>i$iq~wvi zpbsy@;>C--Y15$t2M%EE+O-~@rfE2R`ZWB0zx3eHp+j-+z4ro0C5ML|dI;fgSb8;W zIfBR!=cgA60M^?d!Ps&Tl&YRjy=&?~>P)Ttb$dbLMp~gEVGLS411Cd@8Ih3@Wd?B2Z_GiT1k>eZ_O06TZ?#OtrW4gh%e*=MnC-8ulk?Afz%{P=N1 zA`vMsIKBo&_uP!$&HE&;|Cyg7c-I7wU{KvNf&>DAAD=vVvZ11~vZ}YQ-+#8P9mNYa z0m?KfU;iBx-FGY2uU{_}`csKg3ZKu1L?SU@pAjQQVAQD8tx`A~#^aAa4(pT4=={n; z@MwBm{v*>c_^JD#YZ~H-M6xUr+2{h9SW#Iy@=AZyf3dj*+L10fC@`)X!}mYuaq*v< zF12jIXHUK&>%^~P*y)$yFD;TlfPj@1!@jmG*SIef5uG8} zQ0LkHQXu``Mi2ty2h$-2LXxpbby|{1aRSiCdwj|J~zwzrL58&qn4RBhw9x`#*Jc*8%9=Mj8N0{@QuDk_D>{| zG0r*BIOkX1dFP#vYDSH!_33&b7!1N-8pJnmfB=!(0YcKpOnLNlp3J&DmLlB_<;dz9 z#dEpfDDN>uMm_T`SODnm{^VoMd6aU_f46$|>NBxuv`=tud}+uK1Oxt*5;R-E&jo^{ z?q@SWcmZ4uM8;)#+%Q9E2SkY$Nc0Ymh6OI>Oe9<>+)~q{pT@Qf}B$G+Q zNE)VkE(X%(A&Se>-&dxCGA5&+XUeNglA}rGYbny*fA;L(zrVe?x%pfokyz^aQO)w@ z%R_VK%$e->`+fKVlWCgfjvYJpJ^JXQ7vzs>+=S)+%&ES<{<8-ke6Xsfrl!20pdf@S zBmU(m7K_EtoH^6IY15|n+uPeKvVP{|68S6s;o1KKK<9qGMPT(l00000NkvXXu0mjf D*MJvb literal 0 HcmV?d00001 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 -- 2.39.2