From 6b99bca5d3083066abeaad769ec29b45c1da9db9 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Fri, 21 Sep 2012 20:54:51 +0200 Subject: [PATCH] First wave of the website redesign. --- artwork/config.svg | 192 + artwork/debian.svg | 278 + artwork/faq.svg | 432 ++ artwork/feedback.svg | 561 ++ artwork/neurodebian.svg | 335 ++ artwork/nitrc.svg | 6345 +++++++++++++++++++++++ neurodebian/templates/sources_lists.rst | 39 +- sphinx/_static/config.png | Bin 0 -> 4102 bytes sphinx/_static/debian.png | Bin 0 -> 4063 bytes sphinx/_static/faq.png | Bin 0 -> 3913 bytes sphinx/_static/feedback.png | Bin 0 -> 2866 bytes sphinx/_static/hotbrain_bg.jpg | Bin 0 -> 3382 bytes sphinx/_static/neurodebian.css | 78 +- sphinx/_static/neurodebian.png | Bin 0 -> 3909 bytes sphinx/_static/nitrc.png | Bin 0 -> 5235 bytes sphinx/_templates/layout.html | 70 +- sphinx/_templates/searchbox.html | 10 + sphinx/conf.py | 11 +- sphinx/faq.rst | 90 +- sphinx/index.rst | 310 +- 20 files changed, 8495 insertions(+), 256 deletions(-) create mode 100644 artwork/config.svg create mode 100644 artwork/debian.svg create mode 100644 artwork/faq.svg create mode 100644 artwork/feedback.svg create mode 100644 artwork/neurodebian.svg create mode 100644 artwork/nitrc.svg create mode 100644 sphinx/_static/config.png create mode 100644 sphinx/_static/debian.png create mode 100644 sphinx/_static/faq.png create mode 100644 sphinx/_static/feedback.png create mode 100644 sphinx/_static/hotbrain_bg.jpg create mode 100644 sphinx/_static/neurodebian.png create mode 100644 sphinx/_static/nitrc.png create mode 100644 sphinx/_templates/searchbox.html diff --git a/artwork/config.svg b/artwork/config.svg new file mode 100644 index 0000000..b8fe600 --- /dev/null +++ b/artwork/config.svg @@ -0,0 +1,192 @@ + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/debian.svg b/artwork/debian.svg new file mode 100644 index 0000000..d23a4b5 --- /dev/null +++ b/artwork/debian.svg @@ -0,0 +1,278 @@ + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/faq.svg b/artwork/faq.svg new file mode 100644 index 0000000..493b775 --- /dev/null +++ b/artwork/faq.svg @@ -0,0 +1,432 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/feedback.svg b/artwork/feedback.svg new file mode 100644 index 0000000..f7de496 --- /dev/null +++ b/artwork/feedback.svg @@ -0,0 +1,561 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/neurodebian.svg b/artwork/neurodebian.svg new file mode 100644 index 0000000..f877aae --- /dev/null +++ b/artwork/neurodebian.svg @@ -0,0 +1,335 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + diff --git a/artwork/nitrc.svg b/artwork/nitrc.svg new file mode 100644 index 0000000..7735073 --- /dev/null +++ b/artwork/nitrc.svg @@ -0,0 +1,6345 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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- 
- After selecting a release the setup code will be shown here.
-
-
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a/sphinx/_templates/layout.html b/sphinx/_templates/layout.html index 4e53265..d4b2839 100644 --- a/sphinx/_templates/layout.html +++ b/sphinx/_templates/layout.html @@ -4,62 +4,36 @@ {% endblock %} -{% block rootrellink %} -
  • Debian || 
    • -
  • Neuroscience : 
    • -
  • Software | 
    • -
  • Datasets | 
    • -
  • Virtual Machine | 
    • -
  • FAQ | 
    • -
  • Testimonials  
    • +{% block header %} +
    + +
    +
    {% endblock %} +{% block rootrellink %}{% endblock %} + {% block relbaritems %}
  • Comments |
    • -{% endblock %} - -{% block sidebar1 %}{% endblock %} - -{% block sidebar2 %} -{{ sidebar() }} -{% endblock %} - {% block sidebarsearch %} {{ super() }} - -

    -

    - - - -
    -

    - - - -

    Click to get yourself listed as a NeuroDebian user

    -

    NITRC-listed

    +{% endblock %} {% endblock %} +{% block sidebar1 %}{% endblock %} +{% block sidebar2 %}{% endblock %} {% block footer %} {{ super() }} diff --git a/sphinx/_templates/searchbox.html b/sphinx/_templates/searchbox.html new file mode 100644 index 0000000..67f7717 --- /dev/null +++ b/sphinx/_templates/searchbox.html @@ -0,0 +1,10 @@ +{%- if pagename != "search" %} + +{%- endif %} diff --git a/sphinx/conf.py b/sphinx/conf.py index 226e940..3ae121a 100644 --- a/sphinx/conf.py +++ b/sphinx/conf.py @@ -64,7 +64,7 @@ master_doc = 'index' # General information about the project. project = u'Debian Neuroscience Package Repository' -copyright = u'2009-2011, NeuroDebian Team' +copyright = u'2009-2012, NeuroDebian 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 @@ -118,6 +118,15 @@ pygments_style = 'sphinx' # given in html_static_path. html_style = 'neurodebian.css' +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +html_theme_options = {'nosidebar': True} + # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". html_title = project diff --git a/sphinx/faq.rst b/sphinx/faq.rst index 4757eca..2c736ae 100644 --- a/sphinx/faq.rst +++ b/sphinx/faq.rst @@ -9,8 +9,6 @@ Frequently Asked Questions ************************** Why NeuroDebian? ----------------- - In the course of our own research endeavors |we| have joined forces to develop `PyMVPA -- a Python framework for multivariate pattern analysis of neural data `_. To conveniently deploy PyMVPA for @@ -23,8 +21,6 @@ Why NeuroDebian? Why is NeuroDebian not a Pure Blend? ------------------------------------- - Because there is no need for it to become one, as the existing Debian Pure Blends already offer the desired functionality *within* Debian. Similar to Pure Blends, NeuroDebian's goal is to provide software for neuroscientists @@ -54,8 +50,6 @@ Why is NeuroDebian not a Pure Blend? I want to help. How do I get involved? --------------------------------------- - We always need people to help maintaining existing packages. If you need some additional software packaged and you want to try it on your own, we would be happy to mentor you. We also have a :ref:`list of ongoing and planned @@ -66,8 +60,6 @@ I want to help. How do I get involved? When does a package migrate from NeuroDebian into Debian proper? ----------------------------------------------------------------- - In short: When it is ready. The longer answer is that there is nothing special to packages in NeuroDebian in comparison to packages conducted elsewhere. Packaging efforts are announced to Debian via ITPs_ and the @@ -86,8 +78,6 @@ When does a package migrate from NeuroDebian into Debian proper? Debian, Debian, Debian -- What about Ubuntu? --------------------------------------------- - NeuroDebian offers backported binary packages for recent Ubuntu releases whenever possible. However, since Ubuntu (like many other derivatives) uses Debian as its foundation, it is more efficient to spend time maintaining @@ -103,32 +93,26 @@ Debian, Debian, Debian -- What about Ubuntu? How to create a mirror of the repository? ------------------------------------------ - The NeuroDebian repository can be mirrored with rsync. If you are interested in sponsoring storage space and bandwidth for another mirror, please `contact us `_. How do I get a new neuroscience-related FOSS into (Neuro)Debian? ----------------------------------------------------------------- - -The goal of NeuroDebian is to package neuroscience software for Debian. Hence -getting software into NeuroDebian means trying to get it into Debian. There are -at least two possibilities to achieve that: + The goal of NeuroDebian is to package neuroscience software for Debian. Hence + getting software into NeuroDebian means trying to get it into Debian. There are + at least two possibilities to achieve that: -* You can approach packaging it yourself. Start by filing an ITP_ (Intent to - package) bugreport) and `ask us `_ to mentor your - upload to Debian_, if you are not a Debian developer. + * You can approach packaging it yourself. Start by filing an ITP_ (Intent to + package) bugreport) and `ask us `_ to mentor your + upload to Debian_, if you are not a Debian developer. -* `Contact us `_ -- but then it might take a little - longer, depending on our current workload and interest in a particular - software. + * `Contact us `_ -- but then it might take a little + longer, depending on our current workload and interest in a particular + software. I have heard that some packages are non-free. Will you charge me for them? --------------------------------------------------------------------------- - No. The term :term:`non-free` refers to an archive section. NeuroDebian uses exactly the same `archive sections as Debian proper `_. The *non-free* @@ -142,42 +126,38 @@ I have heard that some packages are non-free. Will you charge me for them? .. _sec_pkg_authentication: What means "The following signatures couldn't be verified..."? --------------------------------------------------------------- - -When you start using this repository, you probably get warning messages -like this:: + When you start using this repository, you probably get warning messages + like this:: - The following signatures couldn't be verified because - the public key is not available. + The following signatures couldn't be verified because + the public key is not available. -Or you will be asked questions like this over and over:: + Or you will be asked questions like this over and over:: - WARNING: The following packages cannot be authenticated! - ... - Install these packages without verification [y/N]? + WARNING: The following packages cannot be authenticated! + ... + Install these packages without verification [y/N]? -This is because your APT installation initially does not know the GPG -key that is used to sign the release files of this repository. It is easy to -make APT happy again. The simplest way is to install the ``neurodebian-keyring`` -package that is available from the NeuroDebian repository. Alternatively: + This is because your APT installation initially does not know the GPG + key that is used to sign the release files of this repository. It is easy to + make APT happy again. The simplest way is to install the ``neurodebian-keyring`` + package that is available from the NeuroDebian repository. Alternatively: -1. Get the key. Either download the `repository key from here - <_static/neuro.debian.net.asc>`_ - or fetch it from http://wwwkeys.pgp.net (2649A5A9). + 1. Get the key. Either download the `repository key from here + <_static/neuro.debian.net.asc>`_ + or fetch it from http://wwwkeys.pgp.net (2649A5A9). -2. Now feed the key into APT by invoking:: + 2. Now feed the key into APT by invoking:: - apt-key add #file# + apt-key add #file# - Where `#file#` has to be replaced with the location of the key file you just - downloaded. You need to have superuser-privileges to do this (either do it - as root or use sudo). + Where `#file#` has to be replaced with the location of the key file you just + downloaded. You need to have superuser-privileges to do this (either do it + as root or use sudo). How can I cite NeuroDebian? ---------------------------- - -Please cite the following paper: + Please cite the following paper: Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience @@ -187,3 +167,13 @@ Please cite the following paper: .. include:: link_names.txt .. include:: substitutions.txt + +.. raw:: html + + + diff --git a/sphinx/index.rst b/sphinx/index.rst index 979c028..48871ed 100644 --- a/sphinx/index.rst +++ b/sphinx/index.rst @@ -1,28 +1,18 @@ .. _WELCOme: -*************************************************** - Welcome to the Ultimate Platform for Neuroscience -*************************************************** +************* + NeuroDebian +************* -.. quotes:: - :random: 1 +NeuroDebian provides a large collection of popular neuroscience research +software for the Debian_ operating system as well as Ubuntu_ and other +derivatives. Popular packages include FSL, Freesurfer, AFNI, PyMVPA and +:ref:`many others `. While we do strive to maintain a high level of +quality, we make no guarantee that a given package works as expected, so use +them at your own risk. If you do encounter problems or would just like to thank +us, simply `send us an email <#contacts>`_. -NeuroDebian provides a turnkey software platform for neuroscience -that is created by integrating research tools with the Debian_ operating -system. If you are using such software on Debian_ or its derivatives, -such as Ubuntu_, chances are that you are already using NeuroDebian. - -This website provides a :ref:`supplementary repository ` with -both unofficial or prospective packages which are not (yet) available from the -main Debian_ archive, as well as backported or simply rebuilt latest versions -of software. NeuroDebian serves as an "upstream" to some :ref:`derivative -` projects. Please see the :ref:`faq` for more information -about the goals of this project, and :ref:`read what people say about it -`. Take a look at the :ref:`list of our current and planned -projects ` if you want to get involved. This service is provided "as -is". There is no guarantee that a package works as expected, so use them at -your own risk. If you encounter problems, please `report <#contacts>`_ them. -Please help us |spread|: +Learn more about NeuroDebian, the goals of this project, and help us |spread|! Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience @@ -31,56 +21,37 @@ Please help us |spread|: .. raw:: html -

    - - - - - - - -

    - -.. _Ubuntu: http://www.ubuntu.com - -.. _news: + +
    +
    -News -==== +.. quotes:: + :random: 1 .. raw:: html - -
    - +
    -For more news and information see our :ref:`blog `. Older news items are -available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to -subscribe to the NeuroDebian news. - -.. _identi.ca: http://identi.ca/neurodebian -.. _twitter: http://twitter.com/NeuroDebian +.. _Ubuntu: http://www.ubuntu.com .. _repository_howto: +.. _chap_installation: +Get NeuroDebian +=============== +Make your selection to enable NeuroDebian on your computer: -How to use this repository -========================== +.. include:: sources_lists -To enable the NeuroDebian repository on your system, select your Debian or -Ubuntu release and a `repository mirror`_ from the lists below. Upon selection -a short command snippet will be displayed that can be copied and pasted into -a terminal session. These commands will configure the system package manager -with the NeuroDebian repository key and package source information. +.. raw:: html -.. include:: sources_lists + -Popularity Contest ------------------- - -We encourage you to participate in the `popularity -contest `_ (popcon), which anonymously -collects the list of packages you installed/use on your system. -Collecting such statistics is of particular importance for research -software projects as a prove of an existing user-base. If upon -installation of the system you rejected the invitation to participate -you can always change your decision by running:: - - sudo dpkg-reconfigure popularity-contest - -.. note:: - - If you are deploying multiple systems through cloning, to not have - all systems considered as one, it would be necessary to re-generate - the random MY_HOSTID. Following commands ran as root should do it - (as root) without any interactive dialog:: - - sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf - DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest - -In addition to popcon pages for your "core" distribution (e.g. `Debian -`__ or `Ubuntu -`__) you can see/get statistics for -submissions to `NeuroDebian `__ and -know that you are already contributing back to the community. - -.. _chap_installation: - -Ways to use NeuroDebian -======================= - -Virtual machine ---------------- + +.. _news: -The team -======== +News +==== + +.. raw:: html + + +
    + + +For more news and information see our :ref:`blog `. Older news items are +available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to +subscribe to the NeuroDebian news. + +.. _identi.ca: http://identi.ca/neurodebian +.. _twitter: http://twitter.com/NeuroDebian -`Michael Hanke `_ and `Yaroslav Halchenko -`_ originally started NeuroDebian (formerly the -`Experimental Psychology Debian packaging project -`_) and are the current project -leaders. However, the whole project would not be possible without the work of -over 3,000 Debian_ developers and contributors who are as enthusiastically -building the Debian operating system. -A number of packages that are available from the NeuroDebian repository have -been contributed by various individuals and other teams in Debian, such as -`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all -maintainers_ that help to make Debian_ the ultimate software platform for -neuroscience. -.. _maintainers: pkgs.html#by-maintainer .. _support: @@ -202,6 +146,27 @@ communication channels within the NeuroDebian community You are welcome also to join #neurodebian IRC room on OFTC network if you have quick questions or want to join a live discussion. +.. _chap_team: + +The team +======== + +`Michael Hanke `_ and `Yaroslav Halchenko +`_ originally started NeuroDebian (formerly the +`Experimental Psychology Debian packaging project +`_) and are the current project +leaders. However, the whole project would not be possible without the work of +over 3,000 Debian_ developers and contributors who are as enthusiastically +building the Debian operating system. +A number of packages that are available from the NeuroDebian repository have +been contributed by various individuals and other teams in Debian, such as +`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all +maintainers_ that help to make Debian_ the ultimate software platform for +neuroscience. + +.. _maintainers: pkgs.html#by-maintainer + + Acknowledgements ================ @@ -256,6 +221,11 @@ next step: An integrated, community-driven computing platform for neuroscience `_. *Frontiers in Neuroinformatics*, 6:22. +.. raw:: html + + +
    + Hanke, M. (2012). `The why and how of getting packaged <_files/Hanke_GetPackaged_CodeJam5_2012.pdf>`_. *Talk given at BrainScaleS CodeJam 5, Convergence in Computational Neuroscience*, @@ -323,9 +293,49 @@ efficient, more open, and more fun <_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at* `Dartmouth College`_, New Hampshire, USA. +.. raw:: html + +
    + .. _DebConf10: http://debconf10.debconf.org/ .. _Dartmouth College: http://www.dartmouth.edu/ +Popularity +========== + +.. raw:: html + +

    + +Popularity Contest +------------------ + +We encourage you to participate in the `popularity +contest `_ (popcon), which anonymously +collects the list of packages you installed/use on your system. +Collecting such statistics is of particular importance for research +software projects as a prove of an existing user-base. If upon +installation of the system you rejected the invitation to participate +you can always change your decision by running:: + + sudo dpkg-reconfigure popularity-contest + +.. note:: + + If you are deploying multiple systems through cloning, to not have + all systems considered as one, it would be necessary to re-generate + the random MY_HOSTID. Following commands ran as root should do it + (as root) without any interactive dialog:: + + sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf + DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest + +In addition to popcon pages for your "core" distribution (e.g. `Debian +`__ or `Ubuntu +`__) you can see/get statistics for +submissions to `NeuroDebian `__ and +know that you are already contributing back to the community. + .. toctree:: :hidden: @@ -355,3 +365,79 @@ efficient, more open, and more fun .. include:: link_names.txt .. include:: substitutions.txt + +.. raw:: html + + + + -- 2.39.2