From: Michael Hanke Date: Tue, 2 Oct 2012 12:17:35 +0000 (+0200) Subject: Merge branch 'master' into newdesign X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=dcb046162ac6009c0643c2a8d6e7b9cd42e010db;hp=caaa40935734bd63029d724d7ef93bcc9c216b96;p=neurodebian.git Merge branch 'master' into newdesign * master: changelog + nd-vmsetupwizard: Preparing 0.29 release of neurodebian for updated nd-vmsetupwizard Make ymax dynamic (5% above current max value), per each distribution + labels for every other month A slight overhaul of the brochure -- nothing radical but at least it is up to date now --- diff --git a/artwork/brochure/brochure_debian-neurodebian.tex b/artwork/brochure/brochure_debian-neurodebian.tex index ea0d7b1..ba19992 100644 --- a/artwork/brochure/brochure_debian-neurodebian.tex +++ b/artwork/brochure/brochure_debian-neurodebian.tex @@ -417,14 +417,18 @@ efforts of thousands of Debian contributors. \ndsubsection{Software at your fingertips} \begin{flushright} -\vspace{-0.5em} +\vspace{-1em} \url{http://neuro.debian.net/pkgs.html} \end{flushright} -\textit{Electrophysiology:} BioSig, Sigviewer, Brian, PyNN, \ldots\\ -\textit{Machine Learning:} PyMVPA, scikits.learn, \ldots\\ -\textit{Imaging:} AFNI, CV, FSL, Lipsia, Mricron, NiPy, \ldots\\ +\textit{Distributed computing:} Condor \\ +\textit{Electrophysiology:} BioSig, EEGLAB, Sigviewer, \ldots\\ +\textit{Machine Learning:} MDP, PyMVPA, sklearn, \ldots\\ +\textit{Neural Modeling:} Brian, PyNN, \ldots\\ +\textit{Imaging:} AFNI, FSL, Mricron, NiPy, SPM, \ldots\\ \textit{Psychophysics:} PsychoPy, Psychtoolbox, \ldots\\ -\vspace{-0.5em} +\vspace{-0.8em} + +% TODO: Environments... -- list avail cloud env using NeuroDebian \ndsubsection{Benefits from Debian integration} @@ -434,8 +438,8 @@ efforts of thousands of Debian contributors. \item Debian standards and policies guarantee quality and robustness. \item Debian's centralized bug tracking system provides a unified - single-point of entry for bug reporting and troubleshooting for any - software in Debian. + single-point of entry for bug reporting and troubleshooting + for any software in Debian. \item Debian makes software available through a world-wide distribution network, thus offloading bandwidth demands. @@ -455,9 +459,9 @@ efforts of thousands of Debian contributors. software for more than 60 languages. \end{description} -\item Neuroscience software becomes a 1st-class citizen within the Debian - project, which guarantees its availability, longevity, smooth - installation and upgrades. +\item Neuroscience software becomes a 1st-class citizen within the + Debian project, which guarantees its longevity, smooth installation + and upgrades. %\item Participation in the Debian community helps to assure Debian's % aptness for the neuroscientific software demands @@ -497,12 +501,10 @@ 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:} NEURON, Fieldtrip, \ldots \\ -\textit{Matlab/Octave toolboxes:} SPM, EEGLAB, \ldots \\ -\textit{Distributed computing:} Condor \\ -\textit{Imaging:} CMTK, Freesurfer, \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} +\textit{Electrophysiology:} Fieldtrip, \ldots \\ +\textit{Neural Modeling:} NEURON, (NEST) \\ +\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 \item[Available snapshotting service] @@ -510,13 +512,13 @@ buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dug All versions of packages readily available \item[Data as the 1st-class citizen] \url{http://neuro.debian.net/datasets.html} -\item[Universal availability] - % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em] - % \item Virtual Appliance enhancements - %\item - Cloud computing - %\end{itemize} - +% yoh: see TODO above -- we can say that it is available already +%\item[Universal availability] +% % \begin{itemize}[nolistsep,leftmargin=1pc,topsep=0em] +% % \item Virtual Appliance enhancements +% %\item +% Cloud computing +% %\end{itemize} \end{description} @@ -527,7 +529,8 @@ buga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dugabuga dug \vspace{-0.5em} \end{flushright} - +% TODO yoh: This one remains the best summary IMHO. But may be +% we would just kick this section out an place Testimonials into References \epigraph{The approach taken with NeuroDebian is plainly the most appropriate approach to software distribution for the dominant platform in brain image analysis, and I have great confidence that this project will be @@ -541,9 +544,21 @@ Pennsylvania, Philadelphia, USA} \ndsubsection{Acknowledgements} NeuroDebian is grateful to all Debian developers and contributors for -developing the Debian operating system, and to Prof. James V. Haxby (PBS Department, -Dartmouth College) for his continued support and endless supply of -Italian espresso (\url{http://neuro.debian.net/coffeeart.html}). +developing the Debian operating system, to +\href{http://www.incf.org}{INCF} for the support in community outreach +and technical collaborations, and to +Prof. \href{http://haxbylab.dartmouth.edu}{James V. Haxby} +(\href{http://www.dartmouth.edu/~psych}{PBS Department, Dartmouth + College}) for his continued support and endless supply of Italian +espresso (\url{http://neuro.debian.net/coffeeart.html}). + + +\ndsubsection{References} + +Halchenko, Y. O. \& Hanke, M. (2012). \href{http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full}{Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience}. Frontiers in Neuroinformatics, 6:22. + +% TODO: adjust for the new layout +\url{http://neuro.debian.net/#publications} %\columnbreak \end{multicols} diff --git a/debian/changelog b/debian/changelog index c37d292..ad929db 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,25 @@ +neurodebian (0.29) unstable; urgency=low + + [ Yaroslav Halchenko & Michael Hanke ] + * website: + - new mirror ([de-md]) + - dynamic ranges for the new distributions subscription stats plot + * VM (6.0.6): + - base on 6.0.6 Debian point release (finally version of NeuroDebian + VM is in sync with the Debian release) + - nd-vmsetupwizard: + - robustify check/linking of $HOME/host + - optional installations dialog: + - set height of the dialog to 450 for to fit all list items + - refactored "GIMP" section into "Graphics" which would install + also inkscape, vym and svgtune + - added sections for "PyMVPA tutorial", and different collections of + Python modules (Neuroimaging, Electrophysiology, etc) + - Python selections depend on ipython01x instead of older ipython + to provide IPython notebooks facilities out-of-the-box + + -- Yaroslav Halchenko Mon, 01 Oct 2012 12:26:37 -0400 + neurodebian (0.28) unstable; urgency=low [ Michael Hanke & Yaroslav Halchenko] diff --git a/tools/nd-vmsetupwizard b/tools/nd-vmsetupwizard index 8d69df4..496ccf1 100755 --- a/tools/nd-vmsetupwizard +++ b/tools/nd-vmsetupwizard @@ -102,12 +102,14 @@ Do you want to get those files, if available, sourced automatically for your env fi # create symlink to shared folder into homedir -[ ! -e $HOME/host ] && ln -s /media/sf_host $HOME/host +# note: -e check would exit 1 if link is broken +# ln -f is used for further robustness +[ ! -L $HOME/host ] && ln -sf /media/sf_host $HOME/host # TODO: add PyMVPA: # FALSE "PyMVPA" "python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorial-data" \ # needs -doc and -tutorial-data package -packages=$(zenity --list $icon_opt --checklist --column="Install" --column="Description" \ +packages=$(zenity --height 450 --list $icon_opt --checklist --column="Install" --column="Description" \ --column="Package Name" --print-column=3 --hide-column=3 --hide-header \ --separator=' ' --text="Please select any additional component that shall be installed. @@ -115,10 +117,14 @@ Please note that this selection will not affect packages already installed on the system. No installed packages will be reinstalled or removed, only additional components will be installed." \ FALSE "Emacs" "emacs" \ -FALSE "GNU Image Manipulation Program (Gimp)" "gimp" \ +FALSE "Graphics (e.g. GIMP, Inscape)" "gimp,inkscape,svgtune,xzgv,vym" \ FALSE "Octave" "octave,qtoctave" \ FALSE "OpenOffice.org" "openoffice.org" \ -FALSE "Scientific Python" "ipython,python-scipy,python-matplotlib" \ +FALSE "PyMVPA Tutorial" "ipython01x,python-mvpa2,python-mvpa2-doc,python-mvpa2-tutorialdata,spyder" \ +FALSE "Python: Electrophysiology & Modeling" "python-brian,python-pynn,python-pyentropy,stimfit" \ +FALSE "Python: Neuroimaging" "ipython01x,spyder,nipy-suite,python-mvpa2" \ +FALSE "Python: Scientific stack" "ipython01x,spyder,python-matplotlib,python-pandas,python-sympy" \ +FALSE "R" "r-recommended" \ FALSE "TeX Live" "texlive" \ FALSE "Adobe Flash browser plugin" "flashplugin-nonfree" \ FALSE "Sun Java browser plugin" "sun-java6-plugin" \ diff --git a/tools/nd_apachelogs2subscriptionstats b/tools/nd_apachelogs2subscriptionstats index c7c15d6..4de60c1 100755 --- a/tools/nd_apachelogs2subscriptionstats +++ b/tools/nd_apachelogs2subscriptionstats @@ -18,7 +18,7 @@ from matplotlib.dates import date2num, num2date from matplotlib.dates import YearLocator, MonthLocator, DateFormatter from matplotlib.font_manager import FontProperties from ConfigParser import SafeConfigParser - +from math import ceil dt = [('ip', '|S16'), ('loc', '|S3'), @@ -26,7 +26,7 @@ dt = [('ip', '|S16'), ('date', float)] -def make_figure(data, ymax): +def make_figure(data, ymax=None): fig = pl.figure(figsize=(14,3)) distros = ('Debian', 'Ubuntu') # Sorting is actually seems to be not needed on Python 2.7 @@ -75,7 +75,9 @@ def plot_datehist(ax, data, bins, suites, title=None, ymax=None): continue width = bin_edges[1] - bin_edges[0] # think lines - ax.plot(bin_edges[:-1]+(width/2), hist / width, + y = hist / width + global_y_max = max(max(y), global_y_max) + ax.plot(bin_edges[:-1]+(width/2), y, label=suite, color=colors[i%4], linestyle=linestyle[i//4], lw=2) # transparent curve shading ax.fill_between(bin_edges[:-1]+(width/2), 0, hist / width, alpha=0.2, @@ -83,8 +85,8 @@ def plot_datehist(ax, data, bins, suites, title=None, ymax=None): # figure out axis limits to avoid whitespace in plots x_max = bin_edges[-2] + width/2 x_min = bin_edges[0] + width/2 - if global_x_max is None or x_max > global_x_max: - global_x_max = x_max + + global_x_max = max(x_max, global_x_max) if global_x_min is None or x_min < global_x_min: global_x_min = x_min @@ -92,14 +94,16 @@ def plot_datehist(ax, data, bins, suites, title=None, ymax=None): ax.set_ylabel('New subscriptions [1/day]') if title: ax.set_title(title) - if ymax: - ax.set_ylim(0, ymax) + if not ymax: + # Always leave significant 5% for improvement ;-) + ymax = global_y_max * 1.05 + ax.set_ylim(0, ymax) # set x-ticks in date # see: http://matplotlib.sourceforge.net/examples/api/date_demo.html ax.xaxis.set_major_locator(YearLocator()) ax.xaxis.set_major_formatter(DateFormatter('\n\n%Y')) - ax.xaxis.set_minor_locator(MonthLocator()) + ax.xaxis.set_minor_locator(MonthLocator(interval=2)) ax.xaxis.set_minor_formatter(DateFormatter('%b')) # format the coords message box ax.format_xdata = DateFormatter('%Y-%m-%d') @@ -131,4 +135,4 @@ if __name__ == '__main__': date = datetime.strptime(date, "%d %b %Y") data.append((ip.strip(), loc, suite, date2num(date))) data = np.array(data, dtype=dt) - make_figure(data, ymax=21).savefig(sys.argv[1], bbox_inches='tight', dpi=60) + make_figure(data).savefig(sys.argv[1], bbox_inches='tight', dpi=60) diff --git a/vm/tools/nd_createappliance b/vm/tools/nd_createappliance index 6a4539b..fc76bcb 100755 --- a/vm/tools/nd_createappliance +++ b/vm/tools/nd_createappliance @@ -6,14 +6,14 @@ set -eu # TODO: arguments later on to become cmdline args #iso=debian-squeeze-di-beta1-amd64-businesscard.iso -iso=debian-6.0.3-${ARCH:=amd64}-businesscard.iso +iso=debian-6.0.6-${ARCH:=amd64}-businesscard.iso di_cd=$(readlink -f $PWD/../../../neurodebian-images/$iso) di_host=head1.hydra.dartmouth.edu # where to look for di preseed build_dir=$PWD/build dist_dir=$PWD/dist vendor="NeuroDebian" -vm_version="6.0.5" +vm_version="6.0.6" vm_ostype=Debian vendor_url="http://neuro.debian.net" product_url="${vendor_url}/vm.html"