From: Yaroslav Halchenko Date: Mon, 4 Nov 2013 14:07:20 +0000 (-0500) Subject: Merge tag 'vm-7.2.0' X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=ef9c772594b08caa667db6faa7a7f1ef23e11479;hp=046f9378a760bea163e0a299b508e2b70b6c2c85;p=neurodebian.git Merge tag 'vm-7.2.0' uploaded 7.2.0 now * tag 'vm-7.2.0': Boost VM version to 7.2.0 --- diff --git a/Makefile b/Makefile index 33f54ba..4c06e30 100644 --- a/Makefile +++ b/Makefile @@ -26,7 +26,7 @@ pics: html: pics source rsync -rvlhpt sphinx/ build/src - cd artwork; cp button_w200.png logo_tuned/fmri_w200.png ../build/src/_static; cd .. + cd artwork; cp button_w200.png logo_tuned/fmri_w200.png *-logo_h50.png ../build/src/_static; cd .. cp 3rd/jquery.livetwitter/jquery.livetwitter.min.js build/src/_static cp neurodebian.cfg build/src/_static cd build/src && $(MAKE) html BUILDDIR=$(CURDIR)/build 2>&1 diff --git a/artwork/.gitignore b/artwork/.gitignore index 320616a..7d11a56 100644 --- a/artwork/.gitignore +++ b/artwork/.gitignore @@ -13,3 +13,7 @@ banner.pdf qrcode_sticker.pdf qrcode_sticker.png derivatives.png +ccn-logo_h50.png +uni-md-logo_h50.png +dartmouth-logo.png +dartmouth-logo_h50.png diff --git a/artwork/Makefile b/artwork/Makefile index c6b7713..7bcab85 100644 --- a/artwork/Makefile +++ b/artwork/Makefile @@ -1,12 +1,14 @@ all:: pics SVGIS=$(shell /bin/ls *.svgtune | sed -e 's/.svgtune/_tuned/g') +ICONSIZED=ccn-logo_h50.png uni-md-logo_h50.png dartmouth-logo_h50.png -pics: $(SVGIS) +pics: $(SVGIS) $(ICONSIZED) clean:: for p in *.svg; do rm -f $${p%*.svg}.{pdf,eps,png}; done rm -rf *_tuned + rm -f $(ICONSIZED) ignore-%: @grep -q "^$*$$" .gitignore || { \ @@ -28,6 +30,10 @@ ignore-%: @echo "Rendering $@" @inkscape -z -f "$<" -e "$@" -w 200 +# icon sized versions +%_h50.png: %.png ignore-%_h50.png + @echo "Generating downscaled $@" + @convert -geometry x50 "$<" "$@" # Some enforced conversions to overcome problems with transparency issues # in PDFs diff --git a/artwork/brochure/brochure_debian-neurodebian.tex b/artwork/brochure/brochure_debian-neurodebian.tex index 3817f00..d192799 100644 --- a/artwork/brochure/brochure_debian-neurodebian.tex +++ b/artwork/brochure/brochure_debian-neurodebian.tex @@ -144,7 +144,7 @@ Very (Special|Stable) Operating Platform requiring the most recent versions of software. %\item[Testing] \emph{Constantly changing future release candidate}\\ -\item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{wheezy})\\ +\item[``Always-ready-to-release'']\hfill\emph{Testing} (now \emph{jessie})\\ % What to become a next \emph{Stable} release candidate.\\ Software versions known to be secure and of good quality. % Software migrated from \emph{Unstable} which is known to be of good @@ -154,7 +154,7 @@ Very (Special|Stable) Operating Platform of software. %\item[Stable] \emph{Official release}\\ -\item[Official release]\hfill\emph{Stable} (now \emph{squeeze})\\ +\item[Official release]\hfill\emph{Stable} (now 7.2, \emph{wheezy})\\ % Software verified to be well tested and secure, % Very stable (hence the name) and secure % but might be lacking the most recent versions.\\% of the software.\\ @@ -163,7 +163,7 @@ Very (Special|Stable) Operating Platform \emph{Testing} is assured to be robust. %, on average bi-yearly. Complementary updates keep the system secure. \\ - \emph{Stable} is the best choice where stability and security are of + \emph{Stable} is the best choice where reliability and security are of primary importance. \end{description} @@ -171,13 +171,13 @@ Very (Special|Stable) Operating Platform \ndsubsection{It has names} The code names of Debian releases are names of characters from the Toy -Story animation, e.g. sid, squeeze, lenny. \emph{Unstable} +Story animation, \emph{e.g.} sid, jessie, wheezy. \emph{Unstable} flavor always called \emph{sid}, while a new name chosen for every upcoming release and assigned to \emph{Testing} to become a code name of the release when it becomes \emph{Stable}.\\ At the moment -\emph{squeeze} is \emph{Testing}, and \emph{lenny} is \emph{Stable}. -As soon as \emph{squeeze} gets released, \emph{Testing} will be given -a new name -- \emph{wheezy}. +\emph{jessie} is \emph{Testing}, and \emph{wheezy} is \emph{Stable}. +As soon as \emph{jessie} gets released, \emph{Testing} will be given +a new name.% -- \emph{jessie}. \end{comment} \ndsubsection{Three Debian components} @@ -233,6 +233,7 @@ teams, such as Debian-Science or Debian-Med. \item[Live CD/DVD] \url{http://www.debian.org/CD/live/} \item[Run in a Virtual Machine] \url{http://neuro.debian.net/vm.html} \item[Development version] \url{http://www.debian.org/devel/debian-installer} +\item[Use in a cloud] \url{https://wiki.debian.org/Cloud} \end{description} % \ndsubsection{Get \emph{Testing/Unstable} Debian} @@ -244,7 +245,11 @@ teams, such as Debian-Science or Debian-Med. \ndsubsection{How to install software} GUI (Synaptic): \textit{Select and click ``Apply''}\\ -\includegraphics[width=\columnwidth]{shots/synaptic-fslview} +\begin{center} +\vspace{-1.2em} +\includegraphics[width=0.95\columnwidth]{shots/synaptic-fslview} +\vspace{-0.7em} +\end{center} Command line: \texttt{apt-get install } @@ -261,9 +266,10 @@ Command line: \ndsubsection{How to get support} +\hspace{1em}\url{http://www.debian.org/support} + \begin{description}[nolistsep,leftmargin=1pc,style=nextline] -\item[Overview] -\url{http://www.debian.org/support} +%\item[Overview] %\item[GUI] % Use \emph{Synaptic Package Manager} @@ -422,11 +428,11 @@ efforts of thousands of Debian contributors. \vspace{-0.1em} \end{flushright} \textit{Distributed computing:} Condor, DMTCP, IPython, \ldots \\ -\textit{Electrophysiology:} BioSig, EEGLAB, Sigviewer, \ldots\\ +\textit{Electrophysiology:} BioSig, Neo, Sigviewer, \ldots\\ \textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\ -\textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT, \ldots\\ -\textit{Imaging:} AFNI, FSL, Mricron, NiPy, SPM, \ldots\\ -\textit{Psychophysics:} PsychoPy, Psychtoolbox, PyEPL, \ldots\\ +\textit{Neural Modeling:} Brian, CNrun, PyNN, XPPAUT \ldots\\ +\textit{Imaging:} AFNI, CMTK, FSL, Mricron, NiPy \ldots\\ +\textit{Psychophysics:} PsychoPy, Psychtoolbox-3, PyEPL \ldots\\ \vspace{-0.8em} % TODO: Environments... -- list avail cloud env using NeuroDebian @@ -502,17 +508,19 @@ buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dug \ndsubsection{Work-in-progress} \begin{description}[nolistsep,leftmargin=1pc,style=nextline] \item[Increased coverage] -\textit{Electrophysiology:} Fieldtrip, Spyke Viewer, \ldots \\ -\textit{Neural Modeling:} NEURON, (NEST), LFPy, \\ +\textit{Electrophysiology:} Fieldtrip \\ +\textit{Neural Modeling:} NEURON, (NEST), LFPy \\ \textit{Imaging:} DTI-TK, Freesurfer, XNAT, \ldots % \epigraph{Having FreeSurfer integrated into the Debian operating system by the NeuroDebian team would have enormous benefits for us, and for the thousands of users of FreeSurfer across the world.}{Prof. Bruce Fischl}{Director, Computational Core at Martinos Center at Massachusetts General Hospital, Charlestown, Massachusetts, USA} \item[Improved quality assurance] - Extended integration and regression testing + Extended integration and regression testing\\ + \url{http://testkraut.readthedocs.org} \item[Available snapshotting service] % Entire NeuroDebian repository for any given past moment All versions of packages readily available \item[Data as the 1st-class citizen] - \url{http://neuro.debian.net/datasets.html} + \url{http://neuro.debian.net/datasets.html}\\ + \url{http://github.com/neurodebian/datagit} % yoh: see TODO above -- we can say that it is available already %\item[Universal availability] % % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em] diff --git a/artwork/ccn-logo.png b/artwork/ccn-logo.png new file mode 100644 index 0000000..9289bd0 Binary files /dev/null and b/artwork/ccn-logo.png differ diff --git a/artwork/dartmouth-logo.svg b/artwork/dartmouth-logo.svg new file mode 100644 index 0000000..65bf213 --- /dev/null +++ b/artwork/dartmouth-logo.svg @@ -0,0 +1,75 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + diff --git a/artwork/openlogo.svg b/artwork/openlogo.svg index b38dc57..7869245 100644 --- a/artwork/openlogo.svg +++ b/artwork/openlogo.svg @@ -14,18 +14,21 @@ ]> - + - + - + diff --git a/artwork/uni-md-logo.png b/artwork/uni-md-logo.png new file mode 100644 index 0000000..b5f9058 Binary files /dev/null and b/artwork/uni-md-logo.png differ diff --git a/cmdsettings.sh b/cmdsettings.sh index 244189c..f8db565 100644 --- a/cmdsettings.sh +++ b/cmdsettings.sh @@ -7,8 +7,7 @@ buildplace="${cowbuilderroot}/build" # all currently supported dists allnddists="nd+debian-squeeze nd+debian-wheezy nd+debian-jessie nd+debian-sid \ - nd+ubuntu-lucid nd+ubuntu-oneiric nd+ubuntu-precise nd+ubuntu-quantal \ - nd+ubuntu-raring" + nd+ubuntu-lucid nd+ubuntu-precise nd+ubuntu-quantal nd+ubuntu-raring nd+ubuntu-saucy" alldists="$allnddists debian-squeeze debian-wheezy debian-jessie debian-sid" # default is debian diff --git a/debian/TODO b/debian/TODO index 0d57215..4e73550 100644 --- a/debian/TODO +++ b/debian/TODO @@ -1,2 +1,5 @@ * make ARCHS argument for cmdsettings.sh to be used by the tools so we could build on sparcs etc * add ipython-notebook/qtconsole (and probably ipython1x over ipython01x for >= wheezy) to welcomewizard + + would need to assure that mvpa2-tutorial is aware of ipython1x first + then... not now diff --git a/debian/changelog b/debian/changelog index 799d749..2f339f6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,9 +1,16 @@ -neurodebian (0.32) UNRELEASED; urgency=low +neurodebian (0.32) neurodebian; urgency=low + [ Michael Hanke ] + * complete redesign of the website, now based on modularized-away bigmess + + [ Yaroslav Halchenko ] * nd_* tools: - cmdsettings.sh: drop building for EOLed hardy, add raring + - vmsetupvizard: install all ipython frontends (notebook, qtconsole) + for recent versions of ipython + * bulk of other changes - -- + -- Yaroslav Halchenko Fri, 01 Nov 2013 16:30:46 -0400 neurodebian (0.31) neurodebian; urgency=low diff --git a/neurodebian.cfg b/neurodebian.cfg index b626a11..b49ddd3 100644 --- a/neurodebian.cfg +++ b/neurodebian.cfg @@ -58,6 +58,8 @@ precise = http://neuro.debian.net/debian/dists/precise/Release quantal = http://neuro.debian.net/debian/dists/quantal/Release # EOL: Jan 2014 raring = http://neuro.debian.net/debian/dists/raring/Release +# EOL: July 2014 +saucy = http://neuro.debian.net/debian/dists/saucy/Release # EOL: May 2014 squeeze = http://neuro.debian.net/debian/dists/squeeze/Release wheezy = http://neuro.debian.net/debian/dists/wheezy/Release @@ -205,3 +207,4 @@ oneiric = nd11.10 precise = nd12.04 quantal = nd12.10 raring = nd13.04 +saucy = nd13.10 diff --git a/sphinx/_static/neurodebian.css b/sphinx/_static/neurodebian.css index b0c0ebc..c389434 100644 --- a/sphinx/_static/neurodebian.css +++ b/sphinx/_static/neurodebian.css @@ -831,11 +831,18 @@ div.buttonbar ul { div.buttonbar li { display: inline; - float: left; margin: 5px; text-align: center; } +div.buttonbar.leftbar li { + float: left; +} + +div.buttonbar.rightbar li { + float: right; +} + div#randomquote { } diff --git a/sphinx/_templates/layout.html b/sphinx/_templates/layout.html index df859a9..989b92c 100644 --- a/sphinx/_templates/layout.html +++ b/sphinx/_templates/layout.html @@ -13,7 +13,7 @@ {% endblock %} {% block header %} -
+
-
+ +
+
    +
    • +
    • +
    • +
+
{% endblock %} {% block rootrellink %}{% endblock %} diff --git a/tools/nd-vmsetupwizard b/tools/nd-vmsetupwizard index 1ab3e4b..7afc313 100755 --- a/tools/nd-vmsetupwizard +++ b/tools/nd-vmsetupwizard @@ -108,7 +108,7 @@ fi # Figure out which version of IPython is available ipython_version=$(apt-cache policy ipython 2>/dev/null | sed -ne '/Version table:/ { n;s,^[ \*]*\(.*\) .*,\1,gp}') -dpkg --compare-versions $ipython_version lt 0.13.1 && ipython=ipython01x || ipython=ipython +dpkg --compare-versions $ipython_version lt 0.13.1 && ipython=ipython01x || ipython=ipython,ipython-notebook,ipython-qtconsole # TODO: add PyMVPA: # FALSE "PyMVPA" "python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorial-data" \ @@ -127,7 +127,7 @@ FALSE "OpenOffice.org" "openoffice.org" \ FALSE "PyMVPA Tutorial" "$ipython,python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorialdata,spyder" \ FALSE "Python: Electrophysiology & Modeling" "python-brian,python-pynn,python-pyentropy,stimfit" \ FALSE "Python: Neuroimaging" "$ipython,spyder,nipy-suite,python-mvpa2" \ -FALSE "Python: Scientific stack" "$ipython,spyder,python-matplotlib,python-pandas,python-sympy" \ +FALSE "Python: Scientific stack" "$ipython,spyder,python-matplotlib,python-pandas,python-sympy,python-statsmodels,python-skimage" \ FALSE "R" "r-recommended" \ FALSE "TeX Live" "texlive" \ FALSE "Adobe Flash browser plugin" "flashplugin-nonfree" \ diff --git a/tools/nd_build_testrdepends b/tools/nd_build_testrdepends index 307f69b..28a820d 100755 --- a/tools/nd_build_testrdepends +++ b/tools/nd_build_testrdepends @@ -28,9 +28,12 @@ srcdir=$testdir/srcs oldbuildsdir=$srcdir/old newbuildsdir=$srcdir/new -echo "I: Building the new package for $pkg" +echo "I: Updating target chroot $family $dist" +$CMD nd_updatedist $family $dist $arch mkdir -p $debdir $srcdir $bindir $secdir + +echo "I: Building the new package for $pkg" $CMD nd_build $family $dist $arch $dscfile --buildresult=$debdir echo "I: Initiating the repository" diff --git a/tools/nd_fetch_bdepends b/tools/nd_fetch_bdepends index 0a87390..f769de1 100755 --- a/tools/nd_fetch_bdepends +++ b/tools/nd_fetch_bdepends @@ -19,6 +19,7 @@ apt-get install -y devscripts dctrl-tools rm -f build-rdeps.output echo "D: querying rdepds for $@" +# D: interactive shell for debugging # /bin/bash < /dev/tty > /dev/tty 2> /dev/tty for pkg in "$@"; do diff --git a/tools/nd_rebuildarchive b/tools/nd_rebuildarchive index 0b8cafe..e41cfc7 100755 --- a/tools/nd_rebuildarchive +++ b/tools/nd_rebuildarchive @@ -92,7 +92,7 @@ mv `awk '{print $1,$2;}' up-to-date-list.txt | while read p v; do grep -l "${p}_ /home/neurodebian/reprepro/nd_processincoming.sh # locally now updated the cows -sudo nd_updatedist nd+ubuntu precise +sudo nd_updatedist nd+ubuntu $dist # And build which previously failed, most probably due to unsatisfied dependencies # and possibly failure with outdated versions of 3rd party modules