-#WWW_UPLOAD_URI = neuro.debian.net:/home/www/neuro.debian.net/www
-WWW_UPLOAD_URI = ../www
+WWW_UPLOAD_URI = neurodebian@neurodebian.ovgu.de:/home/neurodebian/www
+#WWW_UPLOAD_URI = ../www
WWW_DIR = build/html/
WWW_UPLOAD_URI_STATIC=$(WWW_UPLOAD_URI)/_static
+BIGMESS_OPTS = -c neurodebian_repo.cfg
+BIGMESS_CMD = PYTHONPATH=.:../bigmess:$(PYTHONPATH) ../bigmess/bin/bigmess
+BIGMESS = $(BIGMESS_CMD) $(BIGMESS_OPTS)
+
# Lentghy one due to updatedb
all: updatedb upload-website mirmon
# Quick one -- just rebuilds html if new changes and adjusts the status of the mirrors
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
+ ln -fs /usr/share/javascript build/html/
mv $(WWW_DIR)/_static/robots.txt $(WWW_DIR)/
cp -r build/src/lists $(WWW_DIR)/
cp -r sphinx/survey/2011/figures/* $(WWW_DIR)/_images/
source: source-stamp
-source-stamp: build/db.db
- PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
- --cfg neurodebian.cfg \
- --db build/db.db \
- --outdir build/src \
- --pkgaddenum pkgs \
- --extracts /home/www/neuro.debian.net/www/debian/extracts \
- commandisirrelevant
- rm -f html-stamp
+source-stamp:
+ mkdir -p build/src/pkgs/
+ mkdir -p build/src/lists/
+ mkdir -p build/src/pkglists/
+ $(BIGMESS) mkpkgs -d build/src/pkgs/
+ $(BIGMESS) mkaptcfgs -d build/src/lists/
+ $(BIGMESS) mkrepocfg > build/src/sources_lists
+ $(BIGMESS) mkpkgtocs -d build/src/pkglists > build/src/pkgs.rst
touch $@
-removecache:
- -rm -rf build/cache
-
-removedb:
- -rm -f build/db.db
-
-
-updatedb: removedb removecache build/db.db
-
-
-build/db.db:
- mkdir -p build
- PYTHONPATH=.:$(PYTHONPATH) python neurodebian/dde.py \
- --cfg neurodebian.cfg \
- --db build/db.db \
- updatedb
- -rm -f source-stamp
-
+updatedb:
+ $(BIGMESS) cachefiles
+ $(BIGMESS) updatedb
upload-website: html
rsync -rvzlhp --delete \
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+++ /dev/null
-#!/usr/bin/env python
-"""Tell me who you are!
-"""
-
-import pysvn
-import json
-import numpy as np
-
-from ConfigParser import SafeConfigParser
-from optparse import OptionParser, OptionGroup, OptionConflictError
-
-# Lets first assure no guarding (but annoying) warnings
-import warnings
-warnings.simplefilter('ignore', FutureWarning)
-warnings.filterwarnings('ignore',
- 'Module debian_bundle was already imported.*', UserWarning)
-
-from debian import deb822
-import apt # initializes the "_system" ;)
-from apt_pkg import version_compare
-
-import sys
-import os
-import copy
-import shutil
-import urllib2
-import urllib
-import codecs
-import subprocess
-import time
-import re
-
-# templating
-from jinja2 import Environment, PackageLoader
-
-from pprint import PrettyPrinter
-
-
-class AptListsCache(object):
- def __init__(self, cachedir='build/cache',
- ro_cachedirs=None,
- init_db=None):
- self.cachedir = cachedir
-
- if not ro_cachedirs is None:
- self.ro_cachedirs = ro_cachedirs
- else:
- self.ro_cachedirs = []
-
- # create cachedir
- create_dir(self.cachedir)
-
- def get(self, url, update=False):
- """Looks in the cache if the file is there and takes the cached one.
- Otherwise it is downloaded first.
-
- Knows how to deal with http:// and svn:// URLs.
-
- :Return:
- file handler
- """
- # look whether it is compressed
- cext = url.split('.')[-1]
- if cext in ['gz', 'bz2']:
- target_url = url[:-1 * len(cext) -1]
- else:
- # assume not compressed
- target_url = url
- cext = None
-
- # turn url into a filename -- mimik what APT does for
- # /var/lib/apt/lists/
- tfilename = '_'.join(target_url.split('/')[2:])
-
- # if we need to download anyway do not search
- if update:
- cfilename = os.path.join(self.cachedir, tfilename)
- else:
- # look for the uncompressed file anywhere in the cache
- cfilename = None
- for cp in [self.cachedir] + self.ro_cachedirs:
- if os.path.exists(os.path.join(cp, tfilename)):
- cfilename = os.path.join(cp, tfilename)
-
- # nothing found?
- if cfilename is None:
- # add cache item
- cfilename = os.path.join(self.cachedir, tfilename)
- update = True
-
- # if updated needed -- download
- if update:
- #print 'Caching file from %s' % url
-
- if url.startswith('svn://'):
- # export from SVN
- pysvn.Client().export(url, cfilename)
- if url.startswith('http://'):
- # download
- tempfile, ignored = urllib.urlretrieve(url)
-
- # decompress
- decompressor = None
- if cext == 'gz':
- decompressor = 'gzip'
- elif cext == 'bz2':
- decompressor = 'bzip2'
- elif cext == None:
- decompressor = None
- else:
- raise ValueError, \
- "Don't know how to decompress %s files" \
- % cext
-
- if not decompressor is None:
- if subprocess.call([decompressor, '-d', '-q', '-f',
- tempfile]) == 1:
- raise RuntimeError, \
- "Something went wrong while decompressing '%s'" \
- % tempfile
-
- # move decompressed file into cache
- shutil.move(os.path.splitext(tempfile)[0], cfilename)
-
- # XXX do we need that if explicit filename is provided?
- urllib.urlcleanup()
-
- # open cached file
- fh = codecs.open(cfilename, 'r', 'utf-8')
-
- return fh
-
-
-def add_pkgfromtaskfile(db, urls):
- cache = AptListsCache()
- pkgs = []
-
- for task in urls:
- fh = cache.get(task)
-
- # loop over all stanzas
- for stanza in deb822.Packages.iter_paragraphs(fh):
- if stanza.has_key('Depends'):
- pkg = stanza['Depends']
- elif stanza.has_key('Recommends'):
- pkg = stanza['Recommends']
- elif stanza.has_key('Suggests'):
- pkg = stanza['Suggests']
- else:
- continue
-
- # account for multiple packages per line
- if pkg.count(','):
- pkgs += [p.strip() for p in pkg.split(',')]
- else:
- pkgs.append(pkg.strip())
-
- for p in pkgs:
- if not db.has_key(p):
- db[p] = get_emptydbentry()
-
- return db
-
-def get_emptydbentry():
- return {'main': {}}
-
-def import_blendstask(cfg, db, url):
- cache = AptListsCache()
- fh = cache.get(url)
- task_name = None
-
- # figure out blend's task page URL, since they differ from blend to blend
- urlsec = url.split('/')
- blendname = urlsec[-3]
- if blendname == 'debian-med':
- taskpage_url = 'http://debian-med.alioth.debian.org/tasks/'
- elif blendname == 'debian-science':
- taskpage_url = 'http://blends.alioth.debian.org/science/tasks/'
- else:
- raise ValueError('Unknown blend "%s"' % blendname)
- taskpage_url += urlsec[-1]
-
- for st in deb822.Packages.iter_paragraphs(fh):
- if st.has_key('Task'):
- task_name = st['Task']
- task = (blendname, task_name, taskpage_url)
-
- if st.has_key('Depends'):
- pkg = st['Depends']
- elif st.has_key('Recommends'):
- pkg = st['Recommends']
- elif st.has_key('Suggests'):
- pkg = st['Suggests']
- else:
-# print 'Warning: Cannot determine name of prospective package ' \
-# '... ignoring. Dump follows:'
-# print st
- continue
-
- # take care of pkg lists
- for p in pkg.split(', '):
- if not db.has_key(p):
- print 'Ignoring blend package "%s"' % p
- continue
-
- info = {}
-
- # blends info
- info['tasks'] = [task]
- if st.has_key('License'):
- info['license'] = st['License']
- if st.has_key('Responsible'):
- info['responsible'] = st['Responsible']
-
- # pkg description
- if st.has_key('Pkg-Description'):
- descr = st['Pkg-Description'].split('\n')
- info['description'] = descr[0].strip()
- info['long_description'] = \
- u'\n'.join(descr[1:])
-
- # charge the basic property set
- db[p]['main']['description'] = info['description']
- db[p]['main']['long_description'] = info['long_description']
- if st.has_key('WNPP'):
- db[p]['main']['debian_itp'] = st['WNPP']
- if st.has_key('Pkg-URL'):
- db[p]['main']['other_pkg'] = st['Pkg-URL']
- if st.has_key('Homepage'):
- db[p]['main']['homepage'] = st['Homepage']
-
- # Publications
- if st.has_key('Published-Title'):
- title = st['Published-Title']
- if title[-1] == '.':
- # trip trailing dot -- added later
- pub = {'title': title[:-1]}
- else:
- pub = {'title': title}
- if st.has_key('Published-Authors'):
- pub['authors'] = st['Published-Authors']
- if st.has_key('Published-Year'):
- pub['year'] = st['Published-Year']
- if st.has_key('Published-In'):
- pub['in'] = st['Published-In']
- if st.has_key('Published-URL'):
- pub['url'] = st['Published-URL']
- if st.has_key('Published-DOI'):
- pub['doi'] = st['Published-DOI']
- # need at least one URL
- if not pub.has_key('url'):
- pub['url'] = "http://dx.doi.org/%s" % st['Published-DOI']
-
- db[p]['main']['publication'] = pub
-
- # Registration
- if st.has_key('Registration'):
- db[p]['main']['registration'] = st['Registration']
-
- # Remarks
- if st.has_key('Remark'):
- # prepend a single space to make it look like a long description
- info['remark'] = convert_longdescr(' ' + st['Remark'])
-
- # only store if there isn't something already
- if not db[p].has_key('blends'):
- db[p]['blends'] = info
- else:
- # just add this tasks name and id
- db[p]['blends']['tasks'].append(task)
-
- # handle pkg name aliases
- if p in cfg.options('blend package aliases'):
- src_entry = db[p].copy()
- # remove original entry
- del db[p]
- # copy the entry into all aliases
- for alias in cfg.get('blend package aliases', p).split():
- print "Aliasing %s to %s" % (p, alias)
- db[alias] = copy.deepcopy(src_entry)
-
- return db
-
-
-def get_releaseinfo(rurl):
- cache = AptListsCache()
- # root URL of the repository
- baseurl = '/'.join(rurl.split('/')[:-1])
- # get the release file from the cache
- release_file = cache.get(rurl)
-
- # create parser instance
- rp = deb822.Release(release_file)
-
- # architectures on this dist
- archs = rp['Architectures'].split()
- components = rp['Components'].split()
- # compile a new codename that also considers the repository label
- # to distinguish between official and unofficial repos.
- label = rp['Label']
- origin = rp['Origin']
- codename = rp['Codename']
- labelcode = '_'.join([rp['Label'], rp['Codename']])
-
- # cleanup
- release_file.close()
-
- return {'baseurl': baseurl, 'archs': archs, 'components': components,
- 'codename': codename, 'label': label, 'labelcode': labelcode,
- 'origin': origin}
-
-
-def build_pkgsurl(baseurl, component, arch):
- return '/'.join([baseurl, component, 'binary-' + arch, 'Packages.bz2'])
-
-
-def import_release(cfg, db, rurl):
- cache = AptListsCache()
-
- ri = get_releaseinfo(rurl)
-
- # compile the list of Packages files to parse and parse them
- for c in ri['components']:
- for a in ri['archs']:
- # compile packages URL
- pkgsurl = build_pkgsurl(ri['baseurl'], c, a)
-
- # retrieve from cache
- packages_file = cache.get(pkgsurl)
-
- # parse
- for stanza in deb822.Packages.iter_paragraphs(packages_file):
- db = _store_pkg(cfg, db, stanza, ri['origin'], ri['codename'], c, ri['baseurl'])
-
- # cleanup
- packages_file.close()
-
- return db
-
-def _store_pkg(cfg, db, st, origin, codename, component, baseurl):
- """
- :Parameter:
- st: Package section
- """
- pkg = st['Package']
-
- # only care for known packages
- if not db.has_key(pkg):
-# print 'Ignoring NeuroDebian package "%s"' % pkg
- return db
-
- distkey = (trans_codename(codename, cfg), 'neurodebian-' + codename)
-
- if db[pkg].has_key(distkey):
- info = db[pkg][distkey]
- else:
- info = {'architecture': []}
-
- # fill in data
- if not st['Architecture'] in info['architecture']:
- info['architecture'].append(st['Architecture'])
- info['maintainer'] = st['Maintainer']
- if st.has_key('Homepage'):
- info['homepage'] = st['Homepage']
- info['version'] = st['Version']
-
- # origin
- info['distribution'] = origin
- info['release'] = codename
- info['component'] = component
-
- # pool url
- info['poolurl'] = '/'.join([os.path.dirname(st['Filename'])])
-
- # pkg description
- descr = st['Description'].replace('%', '%%').split('\n')
- info['description'] = descr[0].strip()
- info['long_description'] = u'\n'.join(descr[1:])
-
- db[pkg][distkey] = info
-
- # charge the basic property set
- db[pkg]['main']['description'] = info['description']
- db[pkg]['main']['long_description'] = info['long_description']
- if st.has_key('Source'):
- db[pkg]['main']['sv'] = "%s %s" % (st['Source'], st['Version'])
- else:
- db[pkg]['main']['sv'] = "%s %s" % (st['Package'], st['Version'])
- if st.has_key('Homepage'):
- db[pkg]['main']['homepage'] = st['Homepage']
- if st.has_key('Recommends'):
- db[pkg]['main']['recommends'] = st['Recommends']
-
- return db
-
-
-def trans_codename(codename, cfg):
- """Translate a known codename into a release description.
-
- Unknown codenames will simply be returned as is.
- """
- # if we know something, tell
- if codename in cfg.options('release codenames'):
- return cfg.get('release codenames', codename)
- else:
- return codename
-
-
-def create_dir(path):
- if os.path.exists(path):
- return
-
- ps = path.split(os.path.sep)
-
- for i in range(1,len(ps) + 1):
- p = os.path.sep.join(ps[:i])
-
- if not os.path.exists(p):
- os.mkdir(p)
-
-
-def dde_get(url, fail=False):
- # enforce delay to be friendly to DDE
- time.sleep(3)
- try:
- data = json.load(urllib2.urlopen(url+"?t=json"))['r']
- print "SUCCESS:", url
- return data
- except urllib2.HTTPError, e:
- print "NOINFO:", url, type(e)
- return False
- except urllib2.URLError, e:
- print "URLERROR:", url, type(e)
- if fail:
- print "Permanant failure"
- return False
- print "Try again after 30 seconds..."
- time.sleep(30)
- return dde_get(url, fail=True)
- except (StopIteration):
- print "NOINFO:", url
- return False
- except Exception, e:
- print "UDD-DOWN?:", url, type(e)
- return False
-
-
-def nitrc_get(spec, fail=False):
- nitrc_url = 'http://www.nitrc.org/export/site/projects.json.php'
- try:
- # change into this from python 2.6 on
- #data = json.loads(urllib2.urlopen(nitrc_url + '?spec=%s' % spec).read())
- data = json.load(urllib2.urlopen(nitrc_url + '?spec=%s' % spec))
- print "NITRC-SUCCESS:", spec
- except urllib2.HTTPError, e:
- print "NITRC-NOINFO:", spec, type(e)
- return False
- except urllib2.URLError, e:
- print "NITRC-URLERROR:", spec, type(e)
- if fail:
- print "Permanant failure"
- return False
- print "Try again after 30 seconds..."
- time.sleep(30)
- return nitrc_get(spec, fail=True)
- return data
-
-
-def parse_nitrc(data):
- if data is False:
- return None
- # simplify -- there is only one project in the data
- project = data['projects'][0]
- nitrc_filtered = {'downloads': 0,
- 'id': project['id']}
- for pkg in project['packages']:
- for release in pkg['releases']:
- for file in release['files']:
- nitrc_filtered['downloads'] += file['download_count']
- return nitrc_filtered
-
-
-def import_nitrc(cfg, db):
- for p in db.keys():
- if not cfg.has_option("nitrc ids", p):
- continue
- nitrc_spec = cfg.get("nitrc ids", p)
- nitrc_data = nitrc_get(nitrc_spec)
- nitrc_excerpt = parse_nitrc(nitrc_data)
- if not nitrc_excerpt is None:
- db[p]['nitrc'] = nitrc_excerpt
- return db
-
-
-def import_dde(cfg, db):
- query_url = cfg.get('dde', 'pkgquery_url')
- for p in db.keys():
- # get freshest
- q = dde_get(query_url + "/packages/all/%s" % p)
- if q:
- # copy all stuff, while preserving non-overlapping information
- for k, v in q.iteritems():
- db[p]['main'][k] = v
- # get latest popcon info for debian and ubuntu
- # cannot use origin field itself, since it is none for few packages
- # i.e. python-nifti
- origin = q['drc'].split()[0]
- if origin == 'ubuntu':
- if q.has_key('popcon'):
- db[p]['main']['ubuntu_popcon'] = q['popcon']
- # if we have ubuntu, need to get debian
- q = dde_get(query_url + "/packages/prio-debian-sid/%s" % p)
- if q and q.has_key('popcon'):
- db[p]['main']['debian_popcon'] = q['popcon']
- elif origin == 'debian':
- if q.has_key('popcon'):
- db[p]['main']['debian_popcon'] = q['popcon']
- # if we have debian, need to get ubuntu
- q = dde_get(query_url + "/packages/prio-ubuntu-precise/%s" % p)
- if q and q.has_key('popcon'):
- db[p]['main']['ubuntu_popcon'] = q['popcon']
- else:
- print("Ignoring unkown origin '%s' for package '%s'." \
- % (origin, p))
-
- # now get info for package from all releases in UDD
- q = dde_get(query_url + "/dist/p:%s" % p)
- if not q:
- continue
- # hold all info about this package per distribution release
- info = {}
- for cp in q:
- distkey = (trans_codename(cp['release'], cfg),
- "%s-%s" % (cp['distribution'], cp['release']))
- if not info.has_key(distkey):
- info[distkey] = cp
- # turn into a list to append others later
- info[distkey]['architecture'] = [info[distkey]['architecture']]
- # accumulate data for multiple over archs
- else:
- comp = version_compare(cp['version'],
- info[distkey]['version'])
- # found another arch for the same version
- if comp == 0:
- info[distkey]['architecture'].append(cp['architecture'])
- # found newer version, dump the old ones
- elif comp > 0:
- info[distkey] = cp
- # turn into a list to append others later
- info[distkey]['architecture'] = [info[distkey]['architecture']]
- # simply ignore older versions
- else:
- pass
-
- # finally assign the new package data
- for k, v in info.iteritems():
- db[p][k] = v
-
- return db
-
-def assure_unicode(s):
- """Assure that argument is unicode
-
- Necessary if strings are not carrying out Pythonish 'u' prefix to
- signal UTF8 strings, but are in fact UTF8
- """
- if type(s) is unicode:
- return s
- elif type(s) is str:
- # attempt regular unicode call and if fails -- just decode it
- # into utf8
- try:
- return unicode(s)
- except UnicodeDecodeError, e:
- return s.decode('utf8')
- else:
- return assure_unicode(str(s))
-
-
-def convert_longdescr(ld):
- """
-
- yoh: I think all this long description conversion will keep giving
- us problems since per se there is no strict regulations,
- especially in blends files
- """
- descr = u''
- ld = ld.replace('% ', '%% ')
- ld = ld.replace(r'\t', ' ') # just in case assuming tab 4
- ld = ld.split('\n')
- re_leadblanks = re.compile("^ *")
- re_itemized = re.compile("^[o*-+] +")
- re_itemized_gr = re.compile("^( *)([-o*+] +)?(.*?)$")
- re_description_gr = re.compile("^( *[^-]+ - )(.*?)$")
-
- def unwrap_lines(lines):
- out = []
- indent_levels = [-1]
- for l in lines:
- match = re_itemized_gr.search(l).groups()
- if ((len(match[0]) in indent_levels and match[1] is None)
- or (len(match[0]) > max(indent_levels)+4)) \
- and match[2].strip() != '.':
- # append to previous
- if not out[-1].endswith(" "):
- out[-1] += " "
- out[-1] += match[2]
- else:
- out.append(l)
-
- indent_levels = [len(match[0])]
- if match[1] is not None:
- indent_levels += [len(match[0]) + len(match[1])]
- if match[2].strip() == '.':
- # reset though if '.'
- indent_levels = [-1]
- return out
-
- def dedent_withlevel(lines):
- """Dedent `lines` given in a list provide dedented lines and how much was dedented
- """
- nleading = min([re_leadblanks.search(l).span()[1]
- for l in lines])
- return [l[nleading:] for l in lines], nleading
-
- def block_lines(ld, level=0):
- # so we got list of lines
- # dedent all of them first
- ld, level = dedent_withlevel(ld)
-
- # lets collect them in blocks/paragraphs
- # 1. into paragraphs split by '.'
- blocks, block = [], None
-
- # next block can begin if
- # 1. . line
- # 2. it was an itemized list and all items begin with
- # the same symbol or get further indented accordingly
- # so let's first check if it is an itemized list
- itemized_match = re_itemized.search(ld[0])
- if itemized_match:
- allow_indents = " "*itemized_match.span()[1]
- else:
- allow_indents = None
- for l in ld:
- if block is None or l.strip() == '.' \
- or (len(l) and ( len(block) and (
- (l.startswith(' ') and not block[-1].startswith(' '))
- or
- (not l.startswith(' ') and block[-1].startswith(' '))))):
- block = []
- blocks.append(block)
- if l.strip() != '.':
- block.append(l)
- if len(blocks) == 1:
- return blocks[0]
- else:
- return [block_lines(b, level+1) for b in blocks if len(b)]
-
- def blocks_to_rst(bls, level=0):
- # check if this block is an itemized beast
- #itemized_match = re_itemized_gr.search(bls[0][0])
- #if itemized_match:
- # res += ' 'allow_indents = " "*itemized_match.span()[1]
- out = ''
- for b in bls:
- if isinstance(b, list):
- if len(b) == 1:
- out += " "*level + b[0] + '\n\n'
- else:
- out += blocks_to_rst(b, level+1)
- else:
- e = " "*level + b + '\n'
- if not re_itemized.search(b):
- pass
- #e += '\n'
- elif len(e) and e[0] == ' ':
- # strip 1 leading blank
- e = e[1:]
- out += e
- out += '\n'
- return out
-
- ld = unwrap_lines(ld)
- bls = block_lines(ld)
- return blocks_to_rst(bls)
-
-
-def underline_text(text, symbol):
- underline = symbol * len(text)
- return '%s\n%s\n' % (text, underline)
-
-
-def generate_pkgpage(pkg, cfg, db, template, addenum_dir, extracts_dir):
- # local binding for ease of use
- pkgdb = db[pkg]
- # do nothing if there is not at least the very basic stuff
- if not pkgdb['main'].has_key('description'):
- return
- title = '**%s** -- %s' % (pkg, pkgdb['main']['description'])
- title = underline_text(title, '*')
-
- ex_dir = None
- if 'sv' in pkgdb['main']:
- ex_dir = os.path.join(extracts_dir, pkgdb['main']['sv'].split()[0])
- if not os.path.exists(ex_dir):
- ex_dir = None
- long_description = 'Description missing'
- if 'long_description' in pkgdb['main']:
- long_description=convert_longdescr(
- assure_unicode(pkgdb['main']['long_description']))
- page = template.render(
- pkg=pkg,
- title=title,
- long_description=long_description,
- cfg=cfg,
- db=pkgdb,
- fulldb=db,
- extracts_dir=ex_dir,
- op=os.path)
- # the following can be replaced by something like
- # {% include "sidebar.html" ignore missing %}
- # in the template whenever jinja 2.2 becomes available
- addenum = os.path.join(os.path.abspath(addenum_dir), '%s.rst' % pkg)
- if os.path.exists(addenum):
- page += '\n\n.. include:: %s\n' % addenum
- return page
-
-
-def store_db(db, filename):
- pp = PrettyPrinter(indent=2)
- f = codecs.open(filename, 'w', 'utf-8')
- f.write(pp.pformat(db))
- f.close()
-
-
-def read_db(filename):
- f = codecs.open(filename, 'r', 'utf-8')
- db = eval(f.read())
- return db
-
-def write_sourceslist(jinja_env, cfg, outdir):
- create_dir(outdir)
- create_dir(os.path.join(outdir, 'lists'))
-
- repos = {}
- for release in cfg.options('release codenames'):
- if release == 'data':
- # no seperate list for the data archive
- continue
- transrel = trans_codename(release, cfg)
- repos[transrel] = []
- for mirror in cfg.options('mirrors'):
- listname = '%s.%s' % (release, mirror)
- repos[transrel].append((mirror, listname))
- lf = open(os.path.join(outdir, 'lists', listname), 'w')
- for rel in ('data', release):
- aptcfg = '%s %s main contrib non-free\n' % (cfg.get('mirrors', mirror),
- rel)
- lf.write('deb %s' % aptcfg)
- lf.write('#deb-src %s' % aptcfg)
- lf.close()
-
- id2codename = dict([(cfg.get('release backport ids', r), r)
- for r in cfg.options('release codenames')])
- id2relname = dict([(cfg.get('release backport ids', r), trans_codename(r, cfg))
- for r in cfg.options('release codenames')])
- mirror2name = dict([(m, cfg.get('mirror names', m))
- for m in cfg.options('mirrors')])
- mirror2url = dict([(m, cfg.get('mirrors', m))
- for m in cfg.options('mirrors')])
- srclist_template = jinja_env.get_template('sources_lists.rst')
- sl = open(os.path.join(outdir, 'sources_lists'), 'w')
- sl.write(srclist_template.render(id2codename=id2codename,
- id2relname=id2relname,
- mirror2name=mirror2name,
- mirror2url=mirror2url))
- sl.close()
-
-
-def write_mirmonlists(cfg, outdir):
- """Write list of mirrors in the format suitable for mirmon
-
- It will reuse the same 'lists' directory
- """
- print "I: Composing mirmon lists"
- outdir = os.path.join(outdir, 'lists')
- create_dir(outdir)
-
- for sec, sep in (('mirrors', ' '),
- ('mirror names', ' - ')):
- entries = ['%s%s%s' % (mirror, sep, cfg.get(sec, mirror))
- for mirror in cfg.options('mirrors')]
- f = open(os.path.join(outdir, 'mirmon-%s.txt' % sec.replace(' ', '-')),
- 'w')
- f.write('\n'.join(entries + ['']))
- f.close()
-
-
-def sort_by_tasks(db):
- tasks = {}
- for pkg in db.keys():
- if not 'blends' in db[pkg]:
- # no blend info
- continue
- blendinfo = db[pkg]['blends']
- if not 'tasks' in blendinfo:
- # no task info in blend data
- continue
- taskinfo = blendinfo['tasks']
- for task in taskinfo:
- taskname = task[1]
- if not taskname in tasks:
- tasks[taskname] = []
- else:
- tasks[taskname].append(pkg)
- return tasks
-
-
-def sort_by_maintainer(db):
- maints = {}
- maint_ids = {}
- for pkg in db.keys():
- maint = None
- pkginfo = db[pkg]
- # start with the blends info
- if 'blends' in pkginfo and 'responsible' in pkginfo['blends']:
- maint = pkginfo['blends']['responsible']
- if not 'main' in db[pkg] and maint is None:
- # no info
- continue
- info = db[pkg]['main']
- if not 'maintainer' in info and maint is None:
- # no maintainer info
- continue
- if 'original_maintainer' in info and not info['original_maintainer'] is None:
- maint = info['original_maintainer']
- elif 'maintainer' in info and not info['maintainer'] is None:
- maint = info['maintainer']
- if maint is None:
- # no sane maintainer info
- continue
- # safeguard: <> confuses sphinx and we don't care about different emails
- maint = maint[:maint.find('<')].strip()
- # kick out non-ascii ones (should not be, but too tired to find the bug)
- try:
- codecs.ascii_decode(maint)
- except UnicodeEncodeError:
- continue
- if not maint.lower() in maints:
- maints[maint.lower()] = []
- maint_ids[maint.lower()] = [maint]
- else:
- maint_ids[maint.lower()].append(maint)
- maints[maint.lower()].append(pkg)
- # remove duplicates
- out = {}
- for m in maints:
- out[maint_ids[m][0]] = np.unique(maints[m])
- return out
-
-
-def sort_by_release(db):
- rels = {}
- for pkg in db.keys():
- pkginfo = db[pkg]
- for sec in pkginfo:
- if not isinstance(sec, tuple):
- # only releases are of interest
- continue
- relname = sec[0]
- if not relname in rels:
- rels[relname] = []
- else:
- rels[relname].append(pkg)
- # remove duplicates
- for r in rels:
- rels[r] = np.unique(rels[r])
- return rels
-
-
-def write_pkgpages(jinja_env, cfg, db, outdir, addenum_dir, extracts_dir):
- create_dir(outdir)
- create_dir(os.path.join(outdir, 'pkgs'))
- create_dir(os.path.join(outdir, 'pkglists'))
- # template for individual package listings
- toc_template = jinja_env.get_template('pkgs_toc.rst')
- # the high-level package list overview
- hltoc = codecs.open(os.path.join(outdir, 'pkgs.rst'), 'w', 'utf-8')
- hltoc.write('.. _pkglists:\n\n')
- hltoc.write(underline_text('Software packages', '='))
- defs = [(sort_by_tasks(db), 'By purpose', 'Packages for %s'),
- (sort_by_release(db), 'By release', 'Packages for %s'),
- (sort_by_maintainer(db), 'By maintainer', 'Packages by %s')]
- for def_ in defs:
- # TOC for each thingie
- pkgsdict, sectitle, title_tmpl = def_
- hltoc.write(underline_text(sectitle, '-'))
- ids = pkgsdict.keys()
- ids.sort()
- for id_ in ids:
- label = ('pkgs-%s-%s' % (sectitle, id_)).lower().replace(' ', '_').replace('/', '_')
- # filter out crap
- filtered_pkgs = [p for p in pkgsdict[id_] if p in db]
- if not len(filtered_pkgs):
- continue
- plist = toc_template.render(
- label=label,
- title=underline_text(title_tmpl % id_, '='),
- pkgs=filtered_pkgs,
- db=db)
- toc = codecs.open(os.path.join(outdir,
- 'pkglists',
- '%s.rst' % label),
- 'w', 'utf-8')
- toc.write(plist)
- toc.close()
- hltoc.write('* :ref:`%s`\n' % label)
- hltoc.write('\n\n')
-
-
- # now a complete list of all packages
- hltoc.write(underline_text('Complete list', '-'))
- toc = codecs.open(os.path.join(outdir, 'pkglists', 'pkgs-all.rst'),
- 'w', 'utf-8')
- toc.write(toc_template.render(label='full_pkg_list',
- title=underline_text('Complete package list', '='),
- pkgs=db.keys(), db=db))
- toc.close()
- hltoc.write('* :ref:`full_pkg_list`\n')
- hltoc.close()
-
- # and now each individual package page
- pkg_template = jinja_env.get_template('pkg.rst')
- for p in db.keys():
- page = generate_pkgpage(p, cfg, db, pkg_template, addenum_dir, extracts_dir)
- # when no page is available skip this package
- if page is None:
- continue
- pf = codecs.open(os.path.join(outdir, 'pkgs', p + '.rst'), 'w', 'utf-8')
- pf.write(page)
- pf.close()
-
-
-def prepOptParser(op):
- # use module docstring for help output
- op.usage = "%s [OPTIONS]\n\n" % sys.argv[0] + __doc__
-
- op.add_option("--db",
- action="store", type="string", dest="db",
- default=None,
- help="Database file to read. Default: None")
-
- op.add_option("--cfg",
- action="store", type="string", dest="cfg",
- default=None,
- help="Repository config file.")
-
- op.add_option("-o", "--outdir",
- action="store", type="string", dest="outdir",
- default=None,
- help="Target directory for ReST output. Default: None")
-
- op.add_option("-r", "--release-url",
- action="append", dest="release_urls",
- help="None")
-
- op.add_option("--pkgaddenum", action="store", dest="addenum_dir",
- type="string", default=None, help="None")
-
- op.add_option("--extracts", action="store", dest="extracts_dir",
- type="string", default=None, help="None")
-
-
-def main():
- op = OptionParser(version="%prog 0.0.2")
- prepOptParser(op)
-
- (opts, args) = op.parse_args()
-
- if len(args) != 1:
- print('There needs to be exactly one command')
- sys.exit(1)
-
- cmd = args[0]
-
- if opts.cfg is None:
- print("'--cfg' option is mandatory.")
- sys.exit(1)
- if opts.db is None:
- print("'--db' option is mandatory.")
- sys.exit(1)
-
-
- cfg = SafeConfigParser()
- cfg.read(opts.cfg)
-
- if cmd == 'debug_ld':
- # load the db from file
- db = read_db(opts.db)
-
- for p in db.keys():
- #for p in ['dtitk', 'psychopy', 'psytoolkit', 'ginkgo-cadx', 'gridengine-master', 'cctools']:
- if not 'long_description' in db[p]['main']:
- continue
- ld = db[p]['main']['long_description']
-
- print ">>>>>>>>> ", p
- #print ld
- print "----"
- print convert_longdescr(ld)
- raise SystemExit
- # load existing db, unless renew is requested
- if cmd == 'updatedb':
- db = {}
- if cfg.has_option('packages', 'select taskfiles'):
- db = add_pkgfromtaskfile(db, cfg.get('packages',
- 'select taskfiles').split())
-
- # add additional package names from config file
- if cfg.has_option('packages', 'select names'):
- for p in cfg.get('packages', 'select names').split():
- if not db.has_key(p):
- db[p] = get_emptydbentry()
-
- # get info from task files
- if cfg.has_option('packages', 'prospective'):
- for url in cfg.get('packages', 'prospective').split():
- db = import_blendstask(cfg, db, url)
-
- # parse NeuroDebian repository
- if cfg.has_option('neurodebian', 'releases'):
- for rurl in cfg.get('neurodebian', 'releases').split():
- db = import_release(cfg, db, rurl)
-
- # collect package information from DDE
- db = import_dde(cfg, db)
- # get info from NITRC
- db = import_nitrc(cfg, db)
- # store the new DB
- store_db(db, opts.db)
- # and be done
- return
-
- # load the db from file
- db = read_db(opts.db)
-
- # fire up jinja
- jinja_env = Environment(loader=PackageLoader('neurodebian', 'templates'))
-
- # generate package pages and TOC and write them to files
- write_pkgpages(jinja_env, cfg, db, opts.outdir, opts.addenum_dir, opts.extracts_dir)
-
- write_sourceslist(jinja_env, cfg, opts.outdir)
-
- write_mirmonlists(cfg, opts.outdir)
-
-if __name__ == "__main__":
- main()
+++ /dev/null
-
-.. _pkg_{{ pkg }}:
-
-
-{{ title }}
-
-{{ long_description }}
-
-External links:
-
-.. raw:: html
-
- <p><a href="{{ db.main.homepage }}">
- <img border="0" src="../_static/go-home.png" title="Go to {{ pkg }} homepage" /></a>
- {%- if extracts_dir -%}
- {%- if op.exists(op.join(extracts_dir, 'copyright')) -%}
- <a href="../debian/extracts/{{ db.main.sv.split()[0] }}/copyright">
- <img border="0" src="../_static/legal.png" title="Copyright information for this package" /></a>
- {%- endif -%}
- {%- if op.exists(op.join(extracts_dir, 'changelog')) -%}
- <a href="../debian/extracts/{{ db.main.sv.split()[0] }}/changelog">
- <img border="0" src="../_static/debian-changelog.png" title="Debian changelog of this software" /></a>
- {%- endif -%}
- {%- if op.exists(op.join(extracts_dir, 'README.Debian')) -%}
- <a href="../debian/extracts/{{ db.main.sv.split()[0] }}/README.Debian">
- <img border="0" src="../_static/info.png" title="Information on Debian-specific aspects of this software" /></a>
- {%- endif -%}
- {%- endif -%}
- {%- if cfg.has_option("nitrc ids", pkg) -%}
- <a href="http://www.nitrc.org/project?group_id={{ cfg.get("nitrc ids", pkg) }}">
- <img border="0" src="../_static/nitrc_listed.png" title="See the entry on nitrc.org" /></a>
- {%- endif -%}
- {% if db.blends %}{% for blend, name, url in db.blends.tasks -%}
- {%- if blend == 'debian-med' -%}
- <a href="{{ url }}#{{ pkg }}">
- <img border="0" src="../_static/debianmed.png" title="Part of Debian Med {{ name }} task" /></a>
- {%- endif -%}
- {%- if blend == 'debian-science' -%}
- <a href="{{ url }}#{{ pkg }}">
- <img border="0" src="../_static/debianscience.png" title="Part of Debian Science {{ name }} task" /></a>
- {%- endif -%}
- {%- endfor -%}
- {%- endif -%}
- </p>
-
-{% if db.main.publication %}
-Citable reference:
- *{{ db.main.publication.authors }}* ({{ db.main.publication.year }}).
- {%- if db.main.publication.url %} `{{ db.main.publication.title }} <{{ db.main.publication.url }}>`_.
- {%- else %} {{ db.main.publication.title }}.
- {%- endif %} {{ db.main.publication.in }}.
- {%- if db.main.publication.doi %} (`DOI <http://dx.doi.org/{{ db.main.publication.doi }}>`_)
- {%- endif %}
-{% endif %}
-
-{% if db.main.registration -%}
-.. note::
- The software authors ask users to
- `register <{{ db.main.registration }}>`_. Available user statistics might be
- helpful to acquire funding for this project and therefore foster continued
- development in the future.
-
-{% endif -%}
-{% if db.blends and db.blends.remark %}
-.. note::
-{{ db.blends.remark | indent(width=2, indentfirst=true) }}
-
-{% endif -%}
-
-{% if db.nitrc or db.main.debian_popcon or db.main.ubuntu_popcon or
- db.main.recommends or db.main.suggests -%}
-Package Details
-===============
-
-{% if db.nitrc or db.main.debian_popcon or db.main.ubuntu_popcon %}
-Package popularity
-------------------
-{% if db.main.debian_popcon -%}
-- Debian [1]_: {{ db.main.debian_popcon.insts }} (`more info <http://qa.debian.org/popcon.php?package={{ db.main.sv.split()[0] }}>`__)
-{% endif -%}
-{% if db.main.ubuntu_popcon -%}
-- Ubuntu [1]_: {{ db.main.ubuntu_popcon.insts }} (`more info <http://popcon2.net/package/{{ db.main.sv.split()[0] }}.html#graph-1>`__)
-{% endif %}
-{% if db.nitrc and db.nitrc.downloads -%}
-- NITRC [2]_: {{ db.nitrc.downloads }}
-{% endif %}
-
-.. [1] Due to the nature of this data, the reported number can only be
- considered a conservative estimate of the lower bound of the true
- number of installations.
-
-.. [2] This is the total number of downloads from NITRC for this software,
- comprising all releases for all platforms -- typically not Debian
- packages.
-{% endif -%}
-{% endif -%}
-
-{% if db.main.recommends or db.main.suggests %}
-Related packages
-----------------
-{% if db.main.recommends %}
-{%- for pkg in db.main.recommends.split(',') %}
-{%- if pkg.split('|')[0].strip() in fulldb %}
-* :ref:`pkg_{{ pkg.strip() }}`
-{%- else %}
-* {{ pkg }}
-{% endif -%}{% endfor %}{% endif %}
-{%- if db.main.suggests %}
-{%- for pkg in db.main.suggests.split(',') %}
-{%- if pkg.split('|')[0].strip() in fulldb %}
-* :ref:`pkg_{{ pkg.strip() }}`
-{%- else %}
-* {{ pkg.strip() }}
-{% endif -%}{% endfor %}{% endif %}
-{% endif %}
-
-Binary packages
-===============
-
-NeuroDebian
------------
-
-{% for dist, distpkg in db|dictsort if dist[1].startswith('neurodebian') -%}
-{% if loop.first -%}
-The repository contains binary packages for the following distribution
-releases and system architectures. The corresponding source packages
-are available too.
-
-.. note::
-
- Do not download this package manually if you plan to use it
- regularly. Instead configure your package manager to use this
- repository by following the instructions on the :ref:`front page
- <repository_howto>`.
-{% endif %}
-{{ dist[0] }} [{{ distpkg.component}}]:
- `{{distpkg.version}} <../../debian/{{ distpkg.poolurl }}>`__ [{{ ', '.join(distpkg.architecture) }}]
-
-{% if loop.last %}
-.. seealso::
-
-{% if "neuro.debian.net" in distpkg.maintainer %}
- - Maintainer: {{ distpkg.maintainer }}
- - Bug reports: neurodebian-users_
-{% else %}
- - Original Maintainer: {{ distpkg.maintainer }}
-
- (if there is any chance that some problem is specific to the package
- distributed through the NeuroDebian repository, please email
- neurodebian-users_ instead of the original
- maintainer)
-{% endif %}
-{% endif %}
-{% else %}
-*There are no packages in the NeuroDebian repository.*
-{% endfor %}
-
-
-Debian
-------
-
-{% for dist, distpkg in db|dictsort if dist[1].startswith('debian') %}
-{% if loop.first %}
-{% endif %}
-{{ dist[0] }} [{{ distpkg.component}}]:
- `{{distpkg.version}} <http://packages.debian.org/search?suite={{ distpkg.release}}&keywords={{ pkg }}>`__ [{{ ', '.join(distpkg.architecture) }}]
-
-{% if loop.last %}
-.. seealso::
-
- - Maintainer: {{ distpkg.maintainer }}
- - Bug reports: `Debian bugtracking system <http://bugs.debian.org/src:{{ distpkg.source }}>`__
-{% endif %}
-{% else %}
-*There are no official Debian packages available.*
-
-{% if db.main.debian_itp %}
-However, a Debian packaging effort has been officially announced.
-Please see the corresponding
-`intent-to-package bug report <http://bugs.debian.org/{{ db.main.debian_itp }}>`__
-for more information about its current status.
-{% endif %}
-{% endfor %}
-
-
-Ubuntu
-------
-
-{% for dist, distpkg in db|dictsort if dist[1].startswith('ubuntu') %}
-{% if loop.first %}
-{% endif %}
-{{ dist[0] }} [{{ distpkg.component }}]:
- `{{distpkg.version}} <http://packages.ubuntu.com/search?suite={{ distpkg.release }}&keywords={{ pkg }}>`__ [{{ ', '.join(distpkg.architecture) }}]
-
-{% if loop.last %}
-.. seealso::
-
- - Maintainer: {{ distpkg.maintainer }}
- - Bug reports: `Ubuntu Launchpad <https://bugs.launchpad.net/ubuntu/+source/{{ distpkg.source }}>`__
-{% endif %}
-{% else %}
-*There are no official Ubuntu packages available.*
-{% endfor %}
-
-{% if db.main.other_pkg and not "neuro.debian" in db.main.other_pkg -%}
-
-Other Debian/Ubuntu Packages
-----------------------------
-
-- {{ db.main.other_pkg }}
-
-{% endif %}
-
-
-.. include:: ../link_names.txt
+++ /dev/null
-.. _{{ label }}:
-
-{{ title }}
-
-{% for p in pkgs|sort %}
-* :ref:`{{ p }} <pkg_{{ p }}>` ({{ db[p].main.description }})
-{%- endfor %}
-
+++ /dev/null
-.. raw:: html
-
- <select id="release" name="release">
- <option value="">Select a release</option>
-{%- for id, relname in id2relname|dictsort(true, 'value') %}
- <option value="{{ id }}">{{ relname }}</option>
-{%- endfor %}
- </select>
- <select id="mirror" name="mirror">
-{%- for id, mirrorname in mirror2name|dictsort %}
-{%- if id == 'us-nh' %}
- <option selected value="{{ id }}">{{ mirrorname }}</option>
-{%- else %}
- <option value="{{ id }}">{{ mirrorname }}</option>
-{%- endif %}
-{%- endfor %}
- </select>
-
- <div class="highlight-python" id="reposetup">
- <pre id="code">
- After selecting a release the setup code will be shown here.
- </pre>
- </div>
- <script>
- <!--
-
- var rel2name = {
-{%- for id, codename in id2codename|dictsort %}
- "{{ id }}" : "{{ codename }}",
-{%- endfor %}
- };
-
- var mirrors = {
-{%- for id, url in mirror2url|dictsort %}
- "{{ id }}" : "{{ url }}",
-{%- endfor %}
- };
-
- function createrepourl(rel, mir) {
- if(rel in rel2name && mir in mirrors) {
-
- var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel2name[rel] + "."
- + mir + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
- + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
- return retrepo;
- }
-
- };
- function updateout(rel, mir) {
- $('#code').text(createrepourl(rel, mir));
- };
- $('#release').change(function() {
- var singleValues = $("#release").val();
- var mirrorVal = $("#mirror").val();
- updateout(singleValues, mirrorVal);
- });
- $('#mirror').change(function() {
- var singleValues = $("#release").val();
- var mirrorVal = $("#mirror").val();
- updateout(singleValues, mirrorVal);
- });
-
- //-->
- </script>
-
--- /dev/null
+[mirrors]
+au = http://mirror.aarnet.edu.au/pub/neurodebian
+de-m = http://neurodebian.g-node.org
+de-md = http://apsy.gse.uni-magdeburg.de/debian
+de-v = http://nd.zetatech.org
+gr = http://neurobot.bio.auth.gr/neurodebian
+jp = http://neuroimaging.sakura.ne.jp/neurodebian
+ua = http://www.neuro.webdisk.com.ua
+us-ca = http://neurodeb.pirsquared.org
+us-nh = http://neuro.debian.net/debian
+us-tn = http://masi.vuse.vanderbilt.edu/neurodebian
+
+[mirror names]
+au = Australia (AARNET)
+de-m = Germany (Ludwig-Maximilians-Universität, München)
+de-md = Germany (University of Magdeburg)
+de-v = Germany (Nikolaus Valentin Haenel, Vogtland)
+gr = Greece (Aristotle University of Thessaloniki)
+jp = Japan (Kiyotaka Nemoto)
+ua = Ukraine (Iaroslav Iurchenko)
+us-ca = USA-CA (Paul Ivanov, California)
+us-nh = USA-NH (Dartmouth College)
+us-tn = USA-TN (Vanderbilt)
+
+[release files]
+# Release files of all repositories to be contained in the website
+# Package info files for all these releases will be downloaded.
+data = http://neuro.debian.net/debian/dists/data/Release
+hardy = http://neuro.debian.net/debian/dists/hardy/Release
+karmic = http://neuro.debian.net/debian/dists/karmic/Release
+lucid = http://neuro.debian.net/debian/dists/lucid/Release
+maverick = http://neuro.debian.net/debian/dists/maverick/Release
+natty = http://neuro.debian.net/debian/dists/natty/Release
+oneiric = http://neuro.debian.net/debian/dists/oneiric/Release
+precise = http://neuro.debian.net/debian/dists/precise/Release
+squeeze = http://neuro.debian.net/debian/dists/squeeze/Release
+wheezy = http://neuro.debian.net/debian/dists/wheezy/Release
+sid = http://neuro.debian.net/debian/dists/sid/Release
+
+[release names]
+# each item here will result in the respective release being advertised
+# on the website, i.e. sources.list being available and config form contains
+# a corresponding item -- please prune an entry when a release is no longer
+# supported
+# the 'data' entry should not be changed, as this exact setting also serves as
+# a test condition in the DDE code
+data = Datasets (data)
+#etch = Debian GNU/Linux 4.0 (etch)
+lenny = Debian GNU/Linux 5.0 (lenny)
+squeeze = Debian GNU/Linux 6.0 (squeeze)
+wheezy = Debian testing (wheezy)
+sid = Debian unstable (sid)
+# EOL: May 12 2011 (Desktop) April 2013 (Server)
+hardy = Ubuntu 08.04 LTS "Hardy Heron" (hardy)
+# EOL: Oct 23 2010
+#jaunty = Ubuntu 09.04 "Jaunty Jackalope" (jaunty)
+# EOL: April 2011
+karmic = Ubuntu 09.10 "Karmic Koala" (karmic)
+# EOL: April 2013 (Desktop) April 2015 (Server)
+lucid = Ubuntu 10.04 LTS "Lucid Lynx" (lucid)
+# EOL: April 2012
+maverick = Ubuntu 10.10 "Maverick Meerkat" (maverick)
+# EOL: October 2012
+natty = Ubuntu 11.04 "Natty Narwhal" (natty)
+# EOL: April 2013
+oneiric = Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
+# EOL: April 2017 (LTS)
+precise = Ubuntu 12.04 LTS "Precise Pangolin" (precise)
+
+[metadata]
+# base url: <url>/<src_pkg-name>/<file>
+source extracts baseurl = http://neuro.debian.net/debian/extracts
+# files to query
+source extracts filenames = upstream README.Debian copyright
--- /dev/null
+.package-info-links {
+ float: right;
+ margin-left: 1em;
+ padding-left: 1em;
+ border-left: 1px solid #ccc;
+}
+
+.package-info-links dd {
+ margin-left: 0px;
+}
+
+.package-info-links dd {
+ margin-left: 0px;
+}
+
+.package-info-links ul {
+ margin-left: 0;
+ padding-left: 0;
+ list-style-type: none;
+}
+
+.package-info-links a {
+ display: block;
+ padding: 3px;
+}
+
+.pkg-install-link,
+.pkg-bugreport-link{
+ width: 100%;
+ text-align: center;
+ display: inline;
+}
+
+.pkg-install-link a,
+.pkg-bugreport-link a {
+ color: #444;
+ font-weight: bold;
+ padding: 0.5em;
+}
+
+.pkg-bugreport-link a {
+ background-color: #ffe7e7;
+ border-top: 1px solid #d70751;
+ border-bottom: 1px solid #d70751;
+}
+
+.pkg-install-link a {
+ background-color: #e7e7ff;
+ border-top: 1px solid #20435C;
+ border-bottom: 1px solid #20435C;
+}
+
+.pkg-install-link a:hover {
+ background-color: #20435C;
+}
+
+.pkg-bugreport-link a:hover {
+ background-color: #d70751;
+}
+
+.pkg-install-link a:hover,
+.pkg-bugreport-link a:hover {
+ text-decoration: none;
+ color: white;
+}
+
+.license-reminder {
+ color: #d70751;
+ font-weight: bold;
+}
+
+.package-availability {
+ padding-top: 2em;
+}
+
+.package-availability caption {
+ font-style: italic;
+ text-align: left;
+ margin-bottom: .5em;
+}
* Sphinx Doc Design
*/
+@import "bigmess.css";
+
body {
font-family: sans-serif;
font-size: 100%;
- background-color: #444;
+ background-color: #fff;
color: #000;
margin: 0;
padding: 0;
/* :::: LAYOUT :::: */
div.document {
- background-color: #afafaf;
+ background-color: #fff;
}
div.documentwrapper {
div.body {
background-color: white;
+ background-image: url(hotbrain_bg.jpg);
+ background-repeat:no-repeat;
+ background-position:100% 100%;
+ background-attachment:fixed;
padding: 0 20px 30px 20px;
}
}
div.footer {
- color: #fff;
+ color: #000;
width: 100%;
padding: 9px 0 9px 0;
text-align: center;
font-size: 75%;
}
-div.footer a {
- color: #fff;
- text-decoration: underline;
-}
-
div.related {
background-color: #2c3c3d;
- color: #fff;
+ color: #888;
width: 100%;
line-height: 30px;
font-size: 90%;
+ float: right;
}
div.related h3 {
}
div.related a {
- color: white;
+ color: #fff;
}
/* ::: TOC :::: */
text-align: left;
}
+ul.simple {
+ margin-bottom: 1em;
+}
+
ul.keywordmatches li.goodmatch a {
font-weight: bold;
}
div.body h5,
div.body h6 {
font-family: 'Trebuchet MS', sans-serif;
- background-color: #f2f2f2;
+ background-color: rgba(242, 242, 242, 0.5);
font-weight: normal;
color: #20435c;
border-bottom: 1px solid #ccc;
padding: 3px 0 3px 10px;
}
-div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h1 { margin-top: 0em; font-size: 180%; padding-top: 1em;}
div.body h2 { font-size: 160%; }
div.body h3 { font-size: 140%; }
div.body h4 { font-size: 120%; }
}
div.note {
- background-color: #eaf2f9;
+ background-color: rgba(234, 242, 249, 0.6);
border: 1px solid #3d7aa5;
border-left: none;
border-right: none;
color: #060;
}
+dt {
+ font-weight: bold;
+ margin-top: 1em;
+}
+
dt:target,
.highlight {
background-color: #fbe54e;
pre {
padding: 5px;
- background-color: #efc;
+ background-color: rgba(238, 255, 204, 0.6);
color: #333;
border: 1px solid #ac9;
border-left: none;
text-align: left;
}
+.button {
+ background-color: transparent;
+ font-weight: normal;
+ color: #20435c;
+ border: 1px solid #ccc;
+ padding: 3px;
+ text-align: center;
+ cursor: pointer;
+}
+
+div.buttonbar {
+ background-color: #fff;
+ font-size: 70%;
+}
+
+div.buttonbar a:hover {
+ text-decoration: none;
+}
+
+div.buttonbar a:hover img {
+ background-color: #ffc7da;
+}
+
+div.buttonbar ul {
+ list-style: none;
+ padding: 0px;
+}
+
+div.buttonbar li {
+ display: inline;
+ float: left;
+ margin: 5px;
+ text-align: center;
+}
+
+div#randomquote {
+}
+
+div#randomquote blockquote.epigraph {
+ padding: 0 2em 2em 2em;
+ background-color: transparent;
+ font-style: italic;
+ font-size: 80%;
+ border: 0px
+}
+
+#troubleshooting dt,
+div#frequently-asked-questions dt {
+ font-weight: bold;
+ margin-top: 1em;
+ margin-left: 1em;
+ cursor: pointer;
+ display: list-item;
+ list-style-image:url(neurodebian_bullet.png);
+}
+
+div#frequently-asked-questions dt:after {
+ content: "\203A\203A";
+ padding-left: .25em;
+}
+div#sitemap ul {
+ float: left;
+ list-style: none;
+}
+.linkmore {
+ margin-top: -2em;
+ float: right;
+ font-size: 70%;
+}
+
+.nojavascriptinstructions {
+ font-size: 70%;
+}
+
+.expandinstructions {
+ font-size: 70%;
+ display: none;
+}
+
+.linkmore:before,
+.nojavascriptinstructions:before,
+.expandinstructions:before {
+ content: "["
+}
+
+.linkmore:after,
+.nojavascriptinstructions:after,
+.expandinstructions:after {
+ content: "]"
+}
+
+
+.highlighted {
+ background-color: yellow;
+}
+
+#searchbox p {
+ display: inline;
+}
+
+.inlineimage {
+ vertical-align: baseline;
+}
+
+a img.inlineimage:hover {
+ background-color: #820430;
+}
{% block extrahead %}
<meta name="keywords" content="debian, neuroscience">
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-mousewheel/jquery.mousewheel.min.js"></script>
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-tablesorter/jquery.tablesorter.min.js"></script>
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-easing/jquery.easing.min.js"></script>
+ <script language="javascript" type="text/javascript"
+ src="/javascript/jquery-fancybox/jquery.fancybox.min.js"></script>
+ <link rel="stylesheet" href="/javascript/jquery-fancybox/jquery.fancybox.css"
+ type="text/css" media="screen" />
{% endblock %}
-{% block rootrellink %}
- <li><a href="http://www.debian.org" target="_blank">Debian</a> || </li>
- <li><a href="{{ pathto('index') }}">Neuroscience</a> : </li>
- <li><a href="{{ pathto('pkgs') }}">Software</a> | </li>
- <li><a href="{{ pathto('pkglists/pkgs-by_release-datasets_(data)') }}">Datasets</a> | </li>
- <li><a href="{{ pathto('vm') }}">Virtual Machine</a> | </li>
- <li><a href="{{ pathto('faq') }}">FAQ</a> | </li>
- <li><a href="{{ pathto('testimonials') }}">Testimonials</a> </li>
+{% block header %}
+ <div class="buttonbar">
+ <ul>
+ <li><a href="http://www.debian.org" target="_blank"><img border="0" src="/_static/debian.png" title="Visit debian.org" /><br />Debian</a></li>
+ <li><a href="{{ pathto('index') }}"><img border="0" src="/_static/neurodebian.png" title="Go to the home page" /><br />Home</a></li>
+ <li><a href="{{ pathto('pkgs') }}"><img border="0" src="/_static/package.png" title="List of available software" /><br />Software</a></li>
+ <li><a href="{{ pathto('pkglists/toc_pkgs_for_suite_data') }}"><img border="0" src="/_static/datasets.png" title="List of available datasets" /><br />Data</a></li>
+ <li><a href="{{ pathto('vm') }}"><img border="0" src="/_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /><br />VM</a></li>
+ <li><a href="{{ pathto('projects') }}"><img border="0" src="/_static/workarea.png" title="Current and planned projects: Get involved!" /><br />Contribute</a></li>
+ <li><a href="{{ pathto('derivatives') }}"><img border="0" src="/_static/derivatives.png" title="Projects that use NeuroDebian as a foundation" /><br />Derived</a></li>
+ <li><a href="/blog/index.html"><img border="0" src="/_static/rssfeeds.png" title="Read news, and how-to's in the NeuroDebian Insider Blog. Subscribe!" /><br />Blog</a></li>
+ <li><a href="{{ pathto('faq') }}"><img border="0" src="/_static/faq.png" title="Frequently asked questions" /><br />FAQ</a></li>
+ </ul>
+ </div>
+ <div class="clearer"></div>
{% endblock %}
+{% block rootrellink %}{% endblock %}
+
{% block relbaritems %}
<li class="right"><a href="#disqus_thread">Comments</a> |</li>
-{% endblock %}
-
-{% block sidebar1 %}{% endblock %}
-
-{% block sidebar2 %}
-{{ sidebar() }}
-{% endblock %}
-
{% block sidebarsearch %}
{{ super() }}
-
-<p>
-<form method="POST" action="https://openhatch.org/+do/project.views.wanna_help_do">
- <input type="hidden" name="from_offsite" value="True" />
- <input type="hidden" value="7781" name="project"/>
- <input type="submit" value="I want to help" rel="tipsy-south" id="openhatch-wannahelp-button" original-title="Click to add yourself to the list of people who want to contribute. People of all levels are welcome!"/>
-</form>
-</p>
-<style>
- @import url('https://openhatch.org/static/css/tipsy.css');
-</style>
-<style type="text/css">
-#openhatch-wannahelp-button:hover, #openhatch-wannahelp-button:focus {
- background-image:url('https://openhatch.org/static/images/wannahelp-button-bg-hover.png');
- color:#222; text-decoration:none; }
-#openhatch-wannahelp-button { width: 90%; height: 3em; margin-bottom: 1em; background: #C8E29D
- url('https://openhatch.org/static/images/wannahelp-button-bg.png') repeat-x
- scroll center top; border:3px solid #fff; cursor:pointer; cursor: hand;
- font-family: Helvetica, sans-serif; font-size:13pt; font-weight:normal;
- text-align:center; text-shadow:0 1px 0 #fff; white-space:normal; }
-#openhatch-wannahelp-button { -moz-border-radius: 8px; color: #444; float:left;
- padding:10px 20px; display:block; padding:0px 8px; }
-#openhatch-wannahelp-button:focus { outline-color:-moz-use-text-color;
- outline-style:none; outline-width:medium; }
-</style>
-<!-- Disabling openhatche's copy of jquery, even though loosing cool tipsy functionality for now
-<script type="text/javascript" src="https://openhatch.org/static/packed/selections_for_widget.js?1271800811"></script>
--->
-<p><a href="https://www.ohloh.net/stack_entries/new?project_id=neurodebian&ref=sample"><img
-src="{{ pathto('_static/ohloh_iuseit.png', 1) }}" border="0" alt="Click to get yourself listed as a NeuroDebian user" /></a></p>
-<p><a href="http://www.nitrc.org/projects/neurodebian"><img
-src="{{ pathto('_static/nitrc_listed.png', 1) }}" border="0" alt="NITRC-listed" /></a></p>
+{% endblock %}
+<li class="right" style="position:relative;top:3px"><div class="g-plusone"></div></li>
+<li class="right" style="position:relative;top:1px"><a href="https://twitter.com/share" class="twitter-share-button" data-size="large" data-hashtags="neurodebian" data-dnt="true"></a></li?
{% endblock %}
+{% block sidebar1 %}{% endblock %}
+{% block sidebar2 %}{% endblock %}
{% block footer %}
+<div class="clearer"></div>
{{ super() }}
-<div class="footer">
+<div class="footer" style="padding-top:0px">
The source code for this portal is licensed under the
<a href="http://www.gnu.org/licenses/gpl-3.0.html"
title="Text of the GPL-3 license">GPL-3</a> and is available on
title="Browse or clone the Git repository">
git.debian.org</a>.
</div>
+<!-- G+ button logic -->
+<script type="text/javascript" src="https://apis.google.com/js/plusone.js">
+ {parsetags: 'explicit'}
+</script>
+<script type="text/javascript">gapi.plusone.go();</script>
+<!-- Twitter -->
+<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0];if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src="//platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>
+<!-- trigger convenience setup with javascript enabled -->
+<script type="text/javascript">
+ $('.foldup dt').click(function(e){
+ Â Â Â $(this).nextUntil('dt').toggle();
+ });
+ $('.foldup dd').hide();
+ $('.expandinstructions').show();
+ $('.nojavascriptinstructions').hide();
+</script>
+<!-- turn all [youtube] links into buttons and open them in fancy player-->
+<script type="text/javascript">
+$(document).ready(function(){
+ $('a[href^="http://www.youtube.com/watch"]').click(function() {
+ $.fancybox({
+ 'title': this.title,
+ 'href': this.href.replace(new RegExp("watch\\?v=", "i"), 'v/'),
+ 'type': 'swf',
+ 'swf': {'wmode': 'transparent', 'allowfullscreen': 'true'}
+ });
+ return false;
+ });
+ $('a[href^="http://www.youtube.com/watch"]').each(function() {
+ var content = $(this).html();
+ if (content.charAt(0) == '[' && content.charAt(content.length-1) == ']') {
+ $(this).html('<img class="inlineimage" src="/_static/video_button.png" alt="video link button" title="' + content + '" />');
+ } else {
+ return content;
+ };
+ });
+});
+</script>
{% endblock %}
<!-- HEADNOTES -->
{{ super() }}
+<script type="text/javascript">
+$(document).ready(function()
+ {
+ $(".package-availability table").tablesorter();
+ }
+);
+</script>
<h2>Comments</h2>
<div id="disqus_thread"></div>
(document.getElementsByTagName('HEAD')[0] || document.getElementsByTagName('BODY')[0]).appendChild(s);
}());
</script>
+
{% endblock %}
--- /dev/null
+{%- if pagename != "search" %}
+<li id="searchbox">
+ <form class="search" style="display:inline" action="{{ pathto('search') }}" method="get">
+ <input type="search" size="15" maxlength="1000" value="search for..." name="q" onfocus="this.value=''" />
+ <input type="submit" value="{{ _('Go') }}" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</li>
+{%- endif %}
-2010
-====
+Blog posts in 2010
+==================
.. toctree::
:maxdepth: 1
-2011
-====
+Blog posts in 2011
+==================
.. toctree::
:maxdepth: 1
-2012
-====
+Blog posts in 2012
+==================
.. toctree::
:maxdepth: 1
.. figure:: /pics/coffeeart/IMG_6647.JPG
+.. raw:: html
+
+ <script type="text/javascript">
+ $(document).ready(function(){
+ $('.figure img').each(function() {
+ $(this).wrap('<a class="figurelink" href="' + $(this).attr('src') + '" rel="coffee"></a>');
+ });
+ $('a.figurelink').fancybox();
+ });
+ </script>
# General information about the project.
project = u'Debian Neuroscience Package Repository'
-copyright = u'2009-2011, NeuroDebian Team'
+copyright = u'2009-2012, NeuroDebian Team <team@neuro.debian.net>'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# 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
# "<project> v<release> documentation".
html_title = project
--- /dev/null
+.. _support:
+
+Contacts
+========
+
+`Email us directly <team@neuro.debian.net>`_ with any "private"
+communication. Otherwise please use our public mailing lists, which
+exist not only to provide user-support but also to establish
+communication channels within the NeuroDebian community
+
+.. _chap_mailinglists:
+
+* neurodebian-users_: Discussions and support of NeuroDebian users
+
+* neurodebian-upstream_: General discussions and knowledge sharing
+ among developers of neuroscience software. We also use it
+ to update you with summaries of recent relevant developments in
+ Debian project
+
+* neurodebian-devel_: Technical mailing list for discussions on
+ NeuroDebian development
+
+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 <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
+<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
+`Experimental Psychology Debian packaging project
+<http://alioth.debian.org/projects/pkg-exppsy>`_) 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
+================
+
+We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
+Italian espresso <coffeeart>`.
+
+.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
+
+Thanks to the following institutions and individuals for hosting a mirror:
+
+* `Department of Psychological and Brain Sciences at Dartmouth College`_
+ *[us-nh]* (primary mirror)
+* `Department of Experimental Psychology at the University of Magdeburg`_
+ *[de-md]*
+* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
+* `Paul Ivanov`_ *[us-ca]*
+* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
+ *[us-tn]*
+* `Australia's research and education network (AARNET)
+ <http://www.aarnet.edu.au>`_ *[au]*
+* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
+* Iaroslav Iurchenko *[ua]*
+* `Nikolaus Valentin Haenel`_ *[de-v]*
+* `INCF G-Node at Ludwig-Maximilians-Universität München <http://www.g-node.org>`_ *[de-m]*
+
+If your are interested in mirroring the repository, please see the :ref:`faq`.
+
+.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
+.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
+.. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
+.. _Paul Ivanov: http://www.pirsquared.org
+.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
+.. _Nikolaus Valentin Haenel: http://haenel.co
+
+.. _chap_popularity:
+
+Popularity
+==========
+
+.. raw:: html
+
+ <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
+
+Popularity Contest
+------------------
+
+We encourage you to participate in the `popularity
+contest <http://popcon.debian.org>`_ (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
+<http://popcon.debian.org/>`__ or `Ubuntu
+<http://popcon.ubuntu.com/>`__) you can see/get statistics for
+submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
+know that you are already contributing back to the community.
+
+
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 <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
- anyone using Debian-derived distributions this package repository was created
- initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
- <http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
- NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
- all these projects -- and we are constantly working on enriching this
- environment with as many additional relevant software as possible.
-
-
-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
- using the Debian operating system, and therefore the ultimate goal is to get
- all relevant software **into Debian**.
+.. raw:: html
+
+ <div class="expandinstructions">Click on an item to expand it</div>
+
+.. container:: foldup
+
+ 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 <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
+ anyone using Debian-derived distributions this package repository was created
+ initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
+ <http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
+ NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
+ all these projects -- and we are constantly working on enriching this
+ environment with as many additional relevant software as possible.
+
+
+ Why is NeuroDebian not a Pure Blend?
+ This is in the works, but...
+
+ 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 using
+ the Debian operating system, and therefore the ultimate goal is to get all
+ relevant software **into Debian**.
+
+ However, various reasons exist that prevent a particular software from
+ entering Debian. Some are temporary, i.e. a package is already useable, but
+ some technical bits do not meet Debian's standards (yet) or a licensing issue
+ needs to be resolved first. For some software the licensing is so restrictive
+ that it cannot be distributed by Debian, and hence cannot even go into its
+ *non-free* branch. Unfortunately, sometimes these issues cannot be solved to
+ a degree that is acceptable for Debian. For some other packages Debian itself
+ is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
+ sometimes over 1GB <pkg_fsl-first-data>`).
+
+ NeuroDebian aims to be a platform that provides a staging area for
+ neuroscience software packages on their way into Debian. All packages are
+ properly registered in the relevant `Debian Pure Blends`_, e.g.
+ `Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
+ Debian these efforts already provide a suitable framework for this purpose,
+ and hence there is no need to establish yet another one.
+
+ .. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
+ .. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
+ .. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
+
+
+ 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
+ projects <projects>`, each listing a number of tasks that need to be done.
+
+ If you found something you are interested in, please email the
+ neurodebian-devel_ mailing list and let us know about it. Thanks!
+
- However, various reasons exist that prevent a particular software from
- entering Debian. Some are temporary, i.e. a package is already useable, but
- some technical bits do not meet Debian's standards (yet) or a licensing issue
- needs to be resolved first. For some software the licensing is so restrictive
- that it cannot be distributed by Debian, and hence cannot even go into its
- *non-free* branch. Unfortunately, sometimes these issues cannot be solved to
- a degree that is acceptable for Debian. For some other packages Debian itself
- is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
- sometimes over 1GB <pkg_fsl-first-data>`).
-
- NeuroDebian aims to be a platform that provides a staging area for
- neuroscience software packages on their way into Debian. All packages are
- properly registered in the relevant `Debian Pure Blends`_, e.g.
- `Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
- Debian these efforts already provide a suitable framework for this purpose,
- and hence there is no need to establish yet another one.
-
-.. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
-.. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
-.. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
+ 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
+ packaging itself is available in some version control system -- typically in
+ the Git repositories of the `pkg-exppsy group on Debian's Alioth server`_, or
+ another VCS, or on http://mentors.debian.net.
+
+ The only difference is that a particular package becomes available through the
+ NeuroDebian repository before it has passed all checks for compliance with
+ Debian's standards. But even after a package becomes part of Debian the
+ NeuroDebian repository continues to provide binary packages of new versions
+ for a certain set of Debian and Ubuntu releases (aka backports).
+
+ .. _ITPs: http://www.debian.org/devel/wnpp
+ .. _pkg-exppsy group on Debian's Alioth server: http://alioth.debian.org/projects/pkg-exppsy/
+
+
+ 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
+ packages in Debian, instead of having to directly contribute to countless
+ child-distributions. After the appearance of new packages in Debian, Ubuntu
+ typically synchronizes them quickly and they become available in the *Ubuntu
+ universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
+ release. We are not constantly rebuilding of all available NeuroDebian
+ packages for new Ubuntu releases. Therefore, you might find some packages
+ temporarily being available for older Ubuntu releases only -- until the point
+ when a new package version is made and gets built for all currently supported
+ releases.
+
+
+ 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 <team@neuro.debian.net>`_.
+
+
+ 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:
+
+ * You can approach packaging it yourself. Start by filing an ITP_ (Intent to
+ package) bugreport) and `ask us <team@neuro.debian.net>`_ to mentor your
+ upload to Debian_, if you are not a Debian developer.
+
+ * `Contact us <team@neuro.debian.net>`_ -- 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
+ <http://www.debian.org/doc/debian-policy/ch-archive.html>`_. The *non-free*
+ section contains packages that have certain restrictions regarding **your
+ freedom** to employ them for a particular purpose. In contrast, for packages
+ in the *main* section your are completely free to do whatever and in whatever
+ context you like. Regardless of the actual license or archive section, all
+ packages in NeuroDebian are provided free of charge and under the licensing
+ terms of the original developers.
+
+ .. _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::
+
+ 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::
+ WARNING: The following packages cannot be authenticated!
+ ...
+ Install these packages without verification [y/N]?
-I want to help. How do I get involved?
---------------------------------------
+ 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:
- 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
- projects <projects>`, each listing a number of tasks that need to be done.
-
- If you found something you are interested in, please email the
- neurodebian-devel_ mailing list and let us know about it. Thanks!
+ 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::
-When does a package migrate from NeuroDebian into Debian proper?
-----------------------------------------------------------------
+ apt-key add #file#
- 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
- packaging itself is available in some version control system -- typically in
- the Git repositories of the `pkg-exppsy group on Debian's Alioth server`_, or
- another VCS, or on http://mentors.debian.net.
+ 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).
- The only difference is that a particular package becomes available through the
- NeuroDebian repository before it has passed all checks for compliance with
- Debian's standards. But even after a package becomes part of Debian the
- NeuroDebian repository continues to provide binary packages of new versions
- for a certain set of Debian and Ubuntu releases (aka backports).
-.. _ITPs: http://www.debian.org/devel/wnpp
-.. _pkg-exppsy group on Debian's Alioth server: http://alioth.debian.org/projects/pkg-exppsy/
+ How can I cite NeuroDebian?
+ Please cite the following paper:
-
-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
- packages in Debian, instead of having to directly contribute to countless
- child-distributions. After the appearance of new packages in Debian, Ubuntu
- typically synchronizes them quickly and they become available in the *Ubuntu
- universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
- release. We are not constantly rebuilding of all available NeuroDebian
- packages for new Ubuntu releases. Therefore, you might find some packages
- temporarily being available for older Ubuntu releases only -- until the point
- when a new package version is made and gets built for all currently supported
- releases.
-
-
-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 <team@neuro.debian.net>`_.
-
-
-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:
-
-* You can approach packaging it yourself. Start by filing an ITP_ (Intent to
- package) bugreport) and `ask us <team@neuro.debian.net>`_ to mentor your
- upload to Debian_, if you are not a Debian developer.
-
-* `Contact us <team@neuro.debian.net>`_ -- 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
- <http://www.debian.org/doc/debian-policy/ch-archive.html>`_. The *non-free*
- section contains packages that have certain restrictions regarding **your
- freedom** to employ them for a particular purpose. In contrast, for packages
- in the *main* section your are completely free to do whatever and in whatever
- context you like. Regardless of the actual license or archive section, all
- packages in NeuroDebian are provided free of charge and under the licensing
- terms of the original developers.
-
-.. _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::
-
- 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::
-
- 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:
-
-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::
-
- 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).
-
-
-How can I cite NeuroDebian?
----------------------------
-
-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
- <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
- *Frontiers in Neuroinformatics*, 6:22.
+ Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
+ next step: An integrated, community-driven computing platform for neuroscience
+ <http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
+ *Frontiers in Neuroinformatics*, 6:22.
.. include:: link_names.txt
.. _WELCOme:
-***************************************************
- Welcome to the Ultimate Platform for Neuroscience
-***************************************************
+*********************************************
+ The Ultimate Neuroscience Software Platform
+*********************************************
-.. 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 <pkg_tocs>`. 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 <repository_howto>` 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
-<chap_derivatives>` projects. Please see the :ref:`faq` for more information
-about the goals of this project, and :ref:`read what people say about it
-<testimonials>`. Take a look at the :ref:`list of our current and planned
-projects <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
.. raw:: html
- <p>
- <a href="pkgs.html"><img border="0" src="_static/package.png" title="Software package list" /></a>
- <a href="pkglists/pkgs-by_release-datasets_(data).html"><img border="0" src="_static/datasets.png" title="Dataset package list" /></a>
- <a href="vm.html"><img border="0" src="_static/machine.png" title="Get NeuroDebian for your non-Debian computer" /></a>
- <a href="debian/pool"><img border="0" src="_static/pool.png" title="Go to the package pool (deep and cold, only for experts)" /></a>
- <a href="projects.html"><img border="0" src="_static/workarea.png" title="Current and planned projects: Get involved!" /></a>
- <a href="derivatives.html"><img border="0" src="_static/derivatives.png" title="NeuroDebian Derivatives" /></a>
- <a href="blog/index.html"><img border="0" src="_static/rssfeeds.png" title="NeuroDebian Insider Blog" /></a>
- </p>
+ <div class="linkmore"><a href="/publications.html">more publications</a></div>
+ <div class="clearer"></div>
+ <!-- for dynamic quote update via javascript -->
+ <hr />
+ <div id="randomquote" title="Feedback from the community">
+
+.. quotes::
+ :random: 1
+
+.. raw:: html
+
+ </div><!-- randomquote -->
+ <div class="linkmore"><a href="/testimonials.html">more testimonials</a></div>
.. _Ubuntu: http://www.ubuntu.com
+.. _repository_howto:
+.. _chap_installation:
+
+Get NeuroDebian
+===============
+
+.. include:: reposetup.rst
+
.. _news:
News
limit: 10,
rate: 300000});
</script>
-
-For more news and information see our :ref:`blog <blog>`. Older news items are
-available on identi.ca_. Follow us on identi.ca_ (preferred) or twitter_ to
-subscribe to the NeuroDebian news.
+ <div class="nojavascriptinstructions">
+ The news widget requires javascript
+ </div>
.. _identi.ca: http://identi.ca/neurodebian
.. _twitter: http://twitter.com/NeuroDebian
-.. _repository_howto:
-
-
-
-How to use this repository
-==========================
-
-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.
-
-.. include:: sources_lists
-
-Once this is done, you have to update the package index and you are ready to
-install packages. Use your favorite package manager, e.g. synaptic, adept. In
-the terminal you can use :command:`apt-get`::
-
- sudo apt-get update
- sudo apt-get install mricron
-
-.. note::
-
- Not every package is available for all distributions/releases. For information
- about which package version is available for which release and architecture,
- please have a look at the corresponding package pages.
.. raw:: html
- <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
+ <hr />
+ <div id="sitemap">
-Popularity Contest
-------------------
+* **About**
+* :ref:`Team <chap_team>`
+* :ref:`chap_popularity`
+* :ref:`FAQ <faq>`
+* :ref:`Blog <blog>`
+* :ref:`chap_publications`
+* :ref:`testimonials`
+* :ref:`coffeeart`
-We encourage you to participate in the `popularity
-contest <http://popcon.debian.org>`_ (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::
+.. start a new list
- sudo dpkg-reconfigure popularity-contest
+* **Services**
+* :ref:`Software <pkg_tocs>`
+* :ref:`Data <toc_pkgs_for_suite_data>`
+* :ref:`Appliance <chap_vm>`
-.. note::
+.. start a new list
- 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::
+* **Community**
+* :ref:`Mailing lists <chap_mailinglists>`
+* `OpenHatch <https://openhatch.org/+projects/NeuroDebian>`_
+* `Identi.ca <http://identi.ca/neurodebian>`_
+* `Twitter <http://twitter.com/NeuroDebian>`_
+* `Google+ <https://plus.google.com/104292290917252528951>`_
+* `YouTube <http://www.youtube.com/neurodebian>`_
+* `GitHub <https://github.com/neurodebian>`_
- 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
-<http://popcon.debian.org/>`__ or `Ubuntu
-<http://popcon.ubuntu.com/>`__) you can see/get statistics for
-submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
-know that you are already contributing back to the community.
-
-.. _chap_installation:
+.. start a new list
-Ways to use NeuroDebian
-=======================
+* **Related**
+* `Debian <http://www.debian.org>`_
+* `Debian Med <http://www.debian.org/devel/debian-med>`_
+* `INCF <http://software.incf.org/software/neurodebian>`_
+* `NITRC <http://www.nitrc.org/projects/neurodebian>`_
-Virtual machine
----------------
-
-If you are not running Debian_ on a particular machine a :ref:`chap_vm` is
-provided as a convenient testing and evaluation environment. After a few
-simple steps to setup the virtual machine, you will be able to use NeuroDebian_
-as an integral part of your existing working environment without any sacrifice.
-The virtual machine is also a suitable environment to temporarily deploy
-neuroscience software on machines running other operating systems, e.g. for the
-purpose of teaching a neuroimaging data analysis course in a multipurpose
-computer lab.
-
-
-Debian installation
--------------------
-
-Having been exposed to the wonders of NeuroDebian_ you are no longer
-satisfied with your previous choice of operating system? We would
-recommend installing Debian_ to replace or complement (dual-boot) your
-existing OS. Please visit `"Getting Debian"
-<http://www.debian.org/distrib/>`_ to obtain the images for your
-hardware architecture and then simply add |repos|.
-
-
-.. _chap_team:
-
-
-The team
-========
-
-`Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
-<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
-`Experimental Psychology Debian packaging project
-<http://alioth.debian.org/projects/pkg-exppsy>`_) 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:
-
-Contacts
-========
+.. raw:: html
-`Email us directly <team@neuro.debian.net>`_ with any "private"
-communication. Otherwise please use our public mailing lists, which
-exist not only to provide user-support but also to establish
-communication channels within the NeuroDebian community
-
-* neurodebian-users_: Discussions and support of NeuroDebian users
-
-* neurodebian-upstream_: General discussions and knowledge sharing
- among developers of neuroscience software. We also use it
- to update you with summaries of recent relevant developments in
- Debian project
-
-* neurodebian-devel_: Technical mailing list for discussions on
- NeuroDebian development
-
-You are welcome also to join #neurodebian IRC room on OFTC network if
-you have quick questions or want to join a live discussion.
-
-Acknowledgements
-================
-
-We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
-Italian espresso <coffeeart>`.
-
-.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
-
-Thanks to the following institutions and individuals for hosting a mirror:
-
-* `Department of Psychological and Brain Sciences at Dartmouth College`_
- *[us-nh]* (primary mirror)
-* `Department of Experimental Psychology at the University of Magdeburg`_
- *[de-md]*
-* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
-* `Paul Ivanov`_ *[us-ca]*
-* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
- *[us-tn]*
-* `Australia's research and education network (AARNET)
- <http://www.aarnet.edu.au>`_ *[au]*
-* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
-* Iaroslav Iurchenko *[ua]*
-* `Nikolaus Valentin Haenel`_ *[de-v]*
-* `INCF G-Node at Ludwig-Maximilians-Universität München <http://www.g-node.org>`_ *[de-m]*
-
-If your are interested in mirroring the repository, please see the :ref:`faq`.
-
-.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
-.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
-.. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
-.. _Paul Ivanov: http://www.pirsquared.org
-.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
-.. _Nikolaus Valentin Haenel: http://haenel.co
-
-
-Publications
-============
-
-Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
-<http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
-given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
-Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
-[`video <http://youtu.be/8t6znEOEDVo>`_]
-
-Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
-OR Just using Debian is not enough
-<http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
-Talk given at the workshop "Debian for Scientific Facilities Days" at the
-European Synchrotron Radiation Facility (ESRF), Grenoble, France.
-
-Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
-next step: An integrated, community-driven computing platform for neuroscience
-<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
-6:22.
-
-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*,
-University of Edinburgh, Edinburgh, UK.
-
-Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
-contemporary research in neuroimaging: PyMVPA and NeuroDebian
-<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
-*Talk given at the University of Pennsylvania School of Medicine*,
-Philadelphia, PA, USA.
-
-Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
-NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
-*Talk given at the Max-Planck-Institute for Human Cognitive and Brain
-Sciences*, Leipzig, Germany.
-
-Hanke, M. (2011). `More than batteries included: NeuroDebian
-<_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
-*Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
-Paris, France.
-
-Halchenko, Y. O. (2011). `Ï€'s in Debian or Scientific Debian: NumPy, SciPy and beyond
-<_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
-*Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
-Paris, France.
-
-Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
-<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
-*Frontiers in Neuroinformatics, 5:8*.
-
-Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
-platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
-*Poster presented at the annual meeting of the Organisation for Human Brain
-Mapping*, Quebec City, Canada.
-
-Hanke, M. (2011). `Integrating Condor into the Debian operating system
-<_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
-*Talk given at* `CondorWeek 2011
-<http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
-Madison, Wisconsin, USA.
-
-Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
-SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
-Neuroscience*, San Diego, USA.
-
-Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
-(2010). `Having trouble getting your Nature paper? Maybe you are not using the
-right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
-annual meeting of the Society for Neuroscience*, San Diego, USA.
-
-Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
-neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
-*Talk given at* DebConf10_, New York City, USA. [video:
-`low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
-`high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
-
-Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
-efficiency in cognitive neuroscience research with NeuroDebian
-<_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
-meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
-
-Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
-statistical learning, and open-source software to make research more
-efficient, more open, and more fun
-<_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
-`Dartmouth College`_, New Hampshire, USA.
-
-.. _DebConf10: http://debconf10.debconf.org/
-.. _Dartmouth College: http://www.dartmouth.edu/
+ </div><div class="clearer"></div>
+ <hr />
.. toctree::
pkgs
spread
vm
+ publications
coffeeart
photoalbum
projects
testimonials
testimonials-topics
+ vm_welcome
+ derivatives
+
+.. are these supposed to be visible?
+.. toctree::
+ :hidden:
+
+ machines
+ todo
+
+.. toctree::
+ :hidden:
+ :glob:
+
+ pkgs/*
+ pkglists/*
.. probably should be purged altogether
.. toctree::
:hidden:
- booth_sfn2010
- datasets
livecd
quotes-nihr01
quotes-nitrc
- sources_lists
- vm_welcome
+ dump
.. include:: link_names.txt
.. include:: substitutions.txt
+
+.. raw:: html
+
+ <script type="text/javascript">
+ $(document).ready(function($) {
+ //setInterval(function(){
+ $.get('testimonials.html', function(data) {
+ var quotes = $("blockquote", data);
+ var idx = Math.floor(quotes.length * Math.random());
+ $('#randomquote').html(quotes[idx]);
+ }); // update callback
+ //}, 60000); // set interval
+ }); // doc ready
+ //$("h1").html("NeuroDebian <span style=\"font-size:14px\">— the ultimate neuroscience software platform</span>")
+
+ function foldbuttontoggle(foldname) {
+ var foldid = '#' + foldname;
+ var buttonid = foldid + 'button';
+ $(buttonid).on('click', function() {
+ $('#' + foldname).slideToggle();
+ if ($(buttonid).html() == "↓↓↓") {
+ $(buttonid).html("↑↑↑");
+ }
+ else {
+ $(buttonid).html("↓↓↓");
+ }
+ });
+ $(foldid).slideUp();
+ $(buttonid).html("↓↓↓");
+ };
+
+ </script>
--- /dev/null
+Install a package
+=================
+
+Step 1
+------
+
+*[skip this steps if your machine is already configured to use this repository]*
+
+.. include:: reposetup.rst
+
+Step 2
+------
+
+To install the ``###pkgname###`` package on your system or virtual machine,
+open a terminal and execute the following command::
+
+ sudo apt-get install ###pkgname###
+
+.. raw:: html
+
+ <script type="text/javascript">
+ var split = location.search.replace('?', '').split('=')
+ if ( split[0] == 'p' ) {
+ $(document.body).html($(document.body).html().replace('###pkgname###', split[1]));
+ }
+ </script>
Promotion
---------
+.. raw:: html
+
+ <div class="expandinstructions">Click on an item to expand it</div>
+
* `Publications <http://neuro.debian.net/index.html#publications>`_ and
promotional materials
- - `Debian / NeuroDebian tri-fold
+ - `(Neuro)Debian tri-fold
<http://neuro.debian.net/_files/brochure_debian-neurodebian.pdf>`_
* Conferences presence of the team presenting Debian_,
NeuroDebian_, and related work:
-
**May 2-6, 2011** `Paradyn/Condor Week <http://www.cs.wisc.edu/condor/ParadynCondorWeek2011>`_, Madison, Wisconsin, USA
Hanke, M. `Talk: Integrating Condor into the Debian operating system <http://www.cs.wisc.edu/condor/ParadynCondorWeek2011/presentations/hanke-condor-debian.pdf>`__
**June 26-30, 2011** `HBM 2011 <http://www.humanbrainmapping.org/HBM2011>`_, Québec City, Canada
**July 21-23, 2011** `PsychoPy Workshop and Codesprint <https://scanlab.psych.yale.edu/public/psychopy>`_, New Haven, CT, USA
**August 25-30, 2011** `EuroSciPy 2011/ Python in NeuroScience <http://www.euroscipy.org/conference/euroscipy2011>`_, Paris, France
-
2011/08/27, 16:30 -- 17:00, Scientific track
- Halchenko, Yaroslav O. `Talk: π's in Debian or Scientific Debian: NumPy,
- SciPy and beyond <http://www.euroscipy.org/talk/4379>`__
+ Halchenko, Yaroslav O. `Talk: π's in Debian or Scientific Debian: NumPy,
+ SciPy and beyond <http://www.euroscipy.org/talk/4379>`__
2011/08/29, 14:00 -- 14:30, Neuroimaging data processing
Halchenko, Yaroslav O. `Talk: The virtues and sins of PyMVPA <http://pythonneuro.sciencesconf.org/899>`__
2011/08/30, 10:30 -- 10:45, Workflows and pipelines for data processing
Hanke, M. `Talk: More than batteries included: NeuroDebian <http://pythonneuro.sciencesconf.org/883>`__
2011/08/30, 12:00 -- 12:15, Data management and databasing
- Hanke, M. `Talk: NiBabel: Conductor for a cacophony of neuro-imaging file formats <http://pythonneuro.sciencesconf.org/901>`__
+ Hanke, M. `Talk: NiBabel: Conductor for a cacophony of neuro-imaging file formats <http://pythonneuro.sciencesconf.org/901>`__
**September 8, 2011** `INCF Cross-Task Force Hackathon <http://atlasing.incf.org/wiki/Sept8>`_, Boston, MA, USA
**November 12-16, 2011** `SfN 2011 <http://www.sfn.org/am2011/>`_, Washington, District Columbia, USA
Booth #3207
- `Invite us <mailto:team@neuro.debian.net>`_
+* `Invite us <mailto:team@neuro.debian.net>`_ to talk about NeuroDebian.
* `Inviting contributions and new members to join the NeuroDebian project
<https://openhatch.org/+projects/NeuroDebian>`_
--- /dev/null
+
+.. _chap_publications:
+
+************
+Publications
+************
+
+This is a list of publication from the NeuroDebian team on various
+NeuroDebian-related topics:
+
+Hanke, M. (2012). `Share your tools! But fear the wombat! Seriously.
+<http://neuro.debian.net/_files/Hanke_FearTheWombat_Brainhack2012.pdf>`_ *Talk
+given at* `Brainhack <http://brainhack.org/2012/04/06/brainhack-2012-unconference>`_ 2012 at the
+Max-Planck-Institute for Human Cognitive and Brain Sciences*, Leipzig, Germany.
+[`video <http://youtu.be/8t6znEOEDVo>`_]
+
+Hanke, M. (2012). `Computational and cognitive neuroscience boosted by Debian
+OR Just using Debian is not enough
+<http://neuro.debian.net/_files/Hanke_UsingDebianIsNotEnough_ESRF2012.pdf>`_.
+Talk given at the workshop "Debian for Scientific Facilities Days" at the
+European Synchrotron Radiation Facility (ESRF), Grenoble, France.
+
+Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
+next step: An integrated, community-driven computing platform for neuroscience
+<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_. *Frontiers in Neuroinformatics*,
+6:22.
+
+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*,
+University of Edinburgh, Edinburgh, UK.
+
+Halchenko, Y. O. & Hanke, M. (2012). `Environments for efficient
+contemporary research in neuroimaging: PyMVPA and NeuroDebian
+<_files/HalchenkoHanke_ContemporaryNeuroimaging_PENN2012.pdf>`_.
+*Talk given at the University of Pennsylvania School of Medicine*,
+Philadelphia, PA, USA.
+
+Hanke, M. (2012). `Rock solid, brand new, everyday, for free, not a joke:
+NeuroDebian <_files/Hanke_NeuroDebian_MPI2012.pdf>`_.
+*Talk given at the Max-Planck-Institute for Human Cognitive and Brain
+Sciences*, Leipzig, Germany.
+
+Hanke, M. (2011). `More than batteries included: NeuroDebian
+<_files/Hanke_NeuroDebian_EuroSciPy2011.pdf>`_.
+*Talk given at the Python in Neuroscience satellite of EuroScipy 2011*,
+Paris, France.
+
+Halchenko, Y. O. (2011). `Ï€'s in Debian or Scientific Debian: NumPy, SciPy and beyond
+<_files/Halchenko_EuroScipy11_3_14s_in_Debian.pdf>`_.
+*Talk given at* `EuroScipy 2011 <http://www.euroscipy.org/talk/4379>`_,
+Paris, France.
+
+Hanke, M. & Halchenko, Y. O. (2011). `Neuroscience runs on GNU/Linux
+<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00008/full>`_.
+*Frontiers in Neuroinformatics, 5:8*.
+
+Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). `NeuroDebian -- versatile
+platform for brain-imaging research <_files/NeuroDebian_HBM2011.png>`_
+*Poster presented at the annual meeting of the Organisation for Human Brain
+Mapping*, Quebec City, Canada.
+
+Hanke, M. (2011). `Integrating Condor into the Debian operating system
+<_files/Hanke_CondorDebianIntegration_CondorWeek2011.pdf>`_.
+*Talk given at* `CondorWeek 2011
+<http://www.cs.wisc.edu/condor/CondorWeek2011/wednesday_condor.html>`_,
+Madison, Wisconsin, USA.
+
+Hanke, M. & Halchenko, Y. O. (2010). :ref:`Report from the Debian booth at
+SfN2010 <chap_debian_booth_sfn2010>`. *Annual meeting of the Society for
+Neuroscience*, San Diego, USA.
+
+Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D.
+(2010). `Having trouble getting your Nature paper? Maybe you are not using the
+right tools? <_files/NeuroDebian_SfN2010.png>`_ *Poster presented at the
+annual meeting of the Society for Neuroscience*, San Diego, USA.
+
+Hanke, M., Halchenko, Y. O. (2010). `Debian: The ultimate platform for
+neuroimaging research <_files/HankeHalchenko_NeuroDebianDebConf10.pdf>`_.
+*Talk given at* DebConf10_, New York City, USA. [video:
+`low resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/low/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_,
+`high resolution <http://meetings-archive.debian.net/pub/debian-meetings/2010/debconf10/high/1310_1310_Debian_The_ultimate_platform_for_neuroimaging_research.ogv>`_]
+
+Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). `Improving
+efficiency in cognitive neuroscience research with NeuroDebian
+<_files/NeuroDebian_CNS2010.pdf>`_. *Poster presented at the annual
+meeting of the Cognitive Neuroscience Society*, Montréal, Canada.
+
+Halchenko, Y. O., Hanke, M. (2009). `An ecosystem of neuroimaging,
+statistical learning, and open-source software to make research more
+efficient, more open, and more fun
+<_files/HalchenkoHanke_FossEcosystemDC09.pdf>`_. *Talk given at*
+`Dartmouth College`_, New Hampshire, USA.
+
+.. _DebConf10: http://debconf10.debconf.org/
+.. _Dartmouth College: http://www.dartmouth.edu/
+.. _chap_popularity:
+
+
--- /dev/null
+Imagine very fine instructions for reporting a bug against ``###pkgname###``
+
+.. raw:: html
+
+ <script type="text/javascript">
+ var split = location.search.replace('?', '').split('=')
+ if ( split[0] == 'p' ) {
+ $(document.body).html($(document.body).html().replace('###pkgname###', split[1]));
+ }
+ </script>
--- /dev/null
+First select what kind of operating system you are using, and then choose a
+download server close to you:
+
+.. include:: sources_lists
+
+.. raw:: html
+
+ <div class="nojavascriptinstructions">
+ This form requires javascript. If disabled, incomplete instructions are
+ displayed below</div>
+ <div id="repoconfig">
+ <div class="nojavascriptinstructions">
+ Instructions for Debian-derived systems
+ </div>
+ <p>Select desired components:<br />
+ <table><tr>
+ <td><input type="radio" name="components" value="libre"></td>
+ <td><strong>only</strong> software with guaranteed freedoms<br />
+ <span style=font-size:75%>all packages are
+ <a href="http://www.debian.org/social_contract#guidelines">DSFG</a>-compliant,
+ with permission to use, modify, re-distribute under any condition</span></td></tr>
+ <tr><td><input type="radio" name="components" value="full"></td>
+ <td>all software<br />
+ <span style=font-size:75%>
+ individual packages may have restrictive licenses and you are required to
+ check license-compliance manually
+ </span></td></tr>
+ </table>
+ <div class="reposetup">
+
+You can enable NeuroDebian on your system by simply copying and pasting the
+following two commands into a terminal window. This will add the NeuroDebian
+repository to your native package management system, and you will be able to
+install neuroscience software the same way as any other package.
+
+.. raw:: html
+
+ <pre id="code">
+ After selecting a release the setup code will be shown here.
+ </pre>
+
+Now you can update the package index and you are ready to install packages.
+Simply execute the following command in a terminal::
+
+ sudo apt-get update
+
+You are ready to go -- enjoy NeuroDebian!
+
+.. note::
+
+ Not every package is available for all distributions/releases. For information
+ about which package version is available for which release and architecture,
+ please have a look at the corresponding package pages.
+
+.. raw:: html
+
+ </div> <!-- end reposetup -->
+ </div> <!-- end repoconfig -->
+
+ <div id="vmsetup">
+ <div class="nojavascriptinstructions">
+ Instructions for non-Debian systems
+ </div>
+
+For all non-Debian operating systems we recommend to deploy NeuroDebian as a
+`virtual appliance`_ (virtual machine) -- this will only take a few minutes.
+On all modern hardware (built within
+the last 3-4 years) a virtual appliance is a convenient solution to run
+NeuroDebian simultaneously with the primary operating system -- without
+noticeable performance loss. To start using NeuroDebian:
+
+1. Download this image file:
+
+.. raw:: html
+
+ <div id="vmimagedownload">
+ <a href="http://neuro.debian.net/debian/vm/">NeuroDebian images</a>
+ </div>
+
+2. Import this image into VirtualBox_. If you do not have VirtualBox_
+ installed yet, visit the `VirtualBox download page
+ <http://www.virtualbox.org/wiki/Downloads>`_ and get an installer for your
+ system (installers for Windows, Linux, Mac and Solaris are available).
+
+3. Finish the configuration by following :ref:`the instructions on setting up
+ the virtual appliance <chap_vm>`. `[Virtual machine
+ setup video tutorial] <http://www.youtube.com/watch?v=eqfjKV5XaTE>`_
+
+
+
+
+You are ready to go -- enjoy NeuroDebian!
+
+.. note::
+
+ If you still running an older VirtualBox 3.x, download one of the image files
+ listed below. These older releases are distributed as a `zip` file. Please
+ extract all files from the `.zip` file, using appropriate software
+ for your operating system.
+
+ * `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
+
+ * `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
+
+.. raw:: html
+
+ </div> <!-- end vmsetup -->
+
+.. _virtual appliance: http://en.wikipedia.org/wiki/Virtual_appliance
+.. _VirtualBox: http://www.virtualbox.org
+
+.. raw:: html
+
+ <script type="text/javascript">
+ function createvmdownload(rel, mir) {
+ var img_version = '6.0.5';
+ var img_suffix;
+ var base_url;
+ var img_url;
+ var md5sum_url;
+ if (rel == 'win32') {
+ img_suffix = 'i386';
+ } else {
+ img_suffix = 'amd64';
+ };
+ if(mir in mirrors) {
+ base_url = mirrors[mir] + '/vm/';
+ img_url = base_url + 'NeuroDebian_' + img_version + '_' + img_suffix + '.ova';
+ md5sum_url = base_url + 'MD5SUMS';
+ } else {
+ return 'Internal error';
+ };
+ return '<blockquote><a href="' + img_url
+ + '">Virtual applicance image</a> [<a title="Verify image integrity by dowloading this file and running `md5sum -c MD5SUMS`" href="'
+ + md5sum_url
+ + '">MD5SUM</a>, <a title="Verify authenticity of the MD5SUM file by downloading this file and running `gpg –verify MD5SUMS.gpg`" href="'
+ + md5sum_url + '.gpg">MD5SUM.gpg</a>]</blockquote>' ;
+
+ };
+
+ function createrepourl(rel, mir, comp) {
+ if(mir in mirrors) {
+ var retrepo = "wget -O- http://neuro.debian.net/lists/" + rel + "."
+ + mir + "." + comp + " | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list\n"
+ + "sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9\n";
+ return retrepo;
+ }
+
+ };
+
+ function update_by_form() {
+ var rel = $("#release").val();
+ var mir = $("#mirror").val();
+ var comp = $('input[name="components"]:checked').val();
+ if (rel != '' && mir != '') {
+ if (rel in {'win32':'', 'win64':'', 'mac':''}) {
+ $('#vmimagedownload').html(createvmdownload(rel, mir));
+ $('#vmsetup').slideDown();
+ $('#repoconfig').slideUp();
+ } else {
+ $('#vmsetup').slideUp();
+ $('#repoconfig').slideDown();
+ if (comp == undefined) {
+ $('.reposetup').slideUp();
+ } else {
+ $('#code').text(createrepourl(rel, mir, comp));
+ $('.reposetup').slideDown();
+ }
+ };
+ }
+ else
+ {
+ $('#repoconfig').slideUp();
+ $('#vmsetup').slideUp();
+ };
+ };
+
+ $(document).ready(function($) {
+ update_by_form();
+ $('#repoconfig').hide()
+ $('.reposetup').hide();
+ $('#vmsetup').hide()
+ $('#release').change(update_by_form);
+ $('#mirror').change(update_by_form);
+ $('input[name=components]:radio').change(update_by_form);
+ });
+
+ </script>
Testimonials
============
+Here is some feedback we got from the neuroscience community on various
+occasions. On this page it is grouped by its origin (i.e. `research
+institutions`_, `research software projects`_, `individual laboratories and
+researchers`_). Alternatively, you can read testimonials related to specific
+topics:
+
+* :ref:`testimonials_open_science`
+* :ref:`testimonials_standardization`
+* :ref:`testimonials_vm`
+
.. None so far replied
..
.. Organizations
.. :group: Organizations
-By Topic
---------
-
-* :ref:`testimonials_open_science`
-* :ref:`testimonials_standardization`
-* :ref:`testimonials_vm`
-
-
Research Institutions
---------------------
NeuroDebian Virtual Machine
===========================
+`Installation`_ | `Working with the virtual machine`_ | `Troubleshooting`_ |
+`What has changed`_
+
.. quotes::
:random: 1
:tags: vm
-For those who are not yet running a Debian-based operation system we offer a
-`virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
-from a Debian-based research environment on other operating systems.
-This virtual machine initially comes as a compact Debian installation that can,
-once installed, be equipped with a large variety of neuroscience software with
-just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
+For all systems running a non-Debian-based operation system, such as MS Windows
+or Mac OS X, we offer a `virtual machine`_ that can be equipped with a large
+variety of neuroscience software with just a few mouse clicks (e.g. AFNI_,
+FSL_, PyMVPA_).
.. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
-
-Downloads
----------
-
-Stable (6.x series)
-~~~~~~~~~~~~~~~~~~~
-
-Based on current stable `Debian 6.0 (squeeze)`_ release. This VM
-provides a stable, well tested environment with the most of the recent
-releases available from NeuroDebian.
-
-* `NeuroDebian 6.0.6 image (32bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_i386.ova>`_ [~559MB]
-
- *This image should work on virtually all systems that are supported by*
- VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
- is not compatible with a host machine.*
-
-* `NeuroDebian 6.0.6 image (64bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_amd64.ova>`_ [~576MB]
-
- *This image only works on 64bit host machines with active hardware
- virtualization support. The should include all recent Apple hardware and most
- 64bit Windows systems.*
-
-Development (to be 7.x series)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Based on upcoming `Debian 7.0 (wheezy)`_ release. Although already
-quite stable, there might be outstanding issues. This VM also
-switches from GNOME_ (v.2) desktop environment to XFCE4_. We
-recommend this VM over a stable one for anyone needing recent releases
-of tools not available for the stable VM (e.g. recent pandas) --
-**getting a complete "Scientific Python" stack with 100s of other
-Python modules was never easier**. Moreover your feedback might also
-be valuable to polish upcoming Debian wheezy release and NeuroDebian
-VM 7.0.
-
-* `NeuroDebian 6.999.b4.20121231 image (32bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.999.b4.20121231_i386.ova>`_ [~656MB]
-
-* `NeuroDebian 6.999.b4.20121231 image (64bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.999.b4.20121231_amd64.ova>`_ [~660MB]
-
-
-Historical
-~~~~~~~~~~
-
-Virtual appliances above carry guest additions for 4.x series of the
-VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
-virtual appliances:
-
-* `NeuroDebian 6.0.2 image (32bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
-
-* `NeuroDebian 6.0.2 image (64bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
-
-.. note::
-
- This older virtual appliances are distributed as a `zip` file. Please
- extract all files from the `.zip` file, using appropriate software
- for your operating system.
-
-.. note::
-
- You can verify that you have downloaded archives correctly using
- `md5sums -c MD5SUMS
- <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
- the authenticity of the `MD5SUMS
- <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
- --verify MD5SUMS.gpg
- <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
- NeuroDebian archive key.
-
-* `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
- Solaris)
-
- *This webpage offers installers of the VirtualBox application, as well as the
- documentation.*
-
-Changes
--------
-
-6.999.b4.20121231 -- 31 Dec 2012
-
- * Based on beta 4 release of debian-installer_ for wheezy
- * Comes with XFCE4_ instead of GNOME_
-
-6.0.6 -- 01 Oct 2012
-
- * Updated core system to Debian squeeze 6.0.6
-
-6.0.5 -- 10 Nov 2011
-
- * Updated core system to Debian squeeze 6.0.3
- * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
-
- - ``~/host`` is now symlinked to correct path ``/media/sf_host``
- - ``brain`` user is added to ``vboxsf`` group so mounted host
- directories should become readily available
-
- * Root partition size and swap space got doubled in size (40GB
- and 2GB correspondingly). Space is allocated dynamically so
- the actual size of the virtual drive should not grow unless
- you use it
-
-6.0.4 -- 13 Jun 2011
-
- * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
-
-6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
-
- * Updated to Debian squeeze 6.0.1
- * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
- * Appliance is available as a single file (.ova) ready for the import
-
-6.0.2 -- 08 Feb 2011
-
-6.0.1 -- 01 Dec 2010
-
-Documentation
--------------
-
The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
GNOME_ desktop environment. All installed software comes from standard Debian
-packages, or prospective Debian packages from NeuroDebian. This means that all
-contained software is readily available for any system running a Debian
-operating system (or a recent Ubuntu release). The virtual machine can be seen
-as a showcase of what Debian for neuroscience research feels like. Moreover,
-once downloaded this virtual machine can be kept up to date, just as any other
+packages, or prospective Debian packages from NeuroDebian. The virtual machine
+can be seen as a showcase of what Debian for neuroscience research feels like.
+Once downloaded this virtual machine can be kept up to date, just as any other
Debian installation. Using convenient graphical package management tools users
will benefit from security bug fixes provided by the Debian project for the
whole operating system, as well as from software updates for
neuroscience-related packages.
+Even on Debian-based systems this virtual machine is an excellent way to
+maintain an analysis environment that remains identical throughout the lifetime
+of a study and that can be archived alongside acquired data and publications.
+This is a much more practical way than freezing the entire software stack of a
+whole workstation, where it quickly becomes troublesome to combine the desire
+for latest research methodology for new studies and the need for stability for
+ongoing projects.
+
+.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
+.. _GNOME: http://www.gnome.org/
Installation
~~~~~~~~~~~~
-The following video shows how to get the NeuroDebian virtual machine running
-on your machine. The installation is shown for Mac OS X. It should, however, be
-very similar on a Windows box. If you cannot watch the video, please take a
-look at the written instructions below.
+The following instructions demonstrate how to install the NeuroDebian virtual
+machine -- here shown exemplary for Mac OS X, but the procedure is virtually
+identical on a Windows box. There is also a video tutorial at coffee break
+length. `[Virtual machine setup video tutorial]
+<http://www.youtube.com/watch?v=eqfjKV5XaTE>`_.
-.. raw:: html
-
- <iframe title="YouTube video player"
- class="youtube-player"
- type="text/html"
- width="640"
- height="375"
- src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
- frameborder="0"></iframe>
-
-First download and install a recent version of VirtualBox_. VirtualBox is a
-virtualization software that is freely available for Windows, MacOS X, Solaris,
-and Linux. VirtualBox comes with a comprehensive manual that should answer
-potential questions regarding installation and maintenance.
+If you don't have t already, first download and install a recent version of
+VirtualBox_. VirtualBox is a virtualization software that is freely available
+for Windows, MacOS X, Solaris, and Linux. VirtualBox comes with a comprehensive
+manual that should answer potential questions regarding installation and
+maintenance.
.. _VirtualBox: http://www.virtualbox.org
-Next, download the most recent version of the NeuroDebian virtual machine from
-the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file
-menu.
+Obtain the most recent version of the NeuroDebian virtual machine by visiting
+http://neuro.debian.net and selecting your operating system and a download
+server on the frontpage.
+
+Start VirtualBox and select "Import Appliance" from the file menu.
.. image:: pics/vm_import_app.jpg
.. image:: pics/vm_settings.jpg
-The virtual machine logs yourself in automatically. The name of the virtual
-machine user is `brain` and the password is `neurodebian`. The *root* password
-is also `neurodebian`. In most cases, however, you should not be forced to type
-the password, since `sudo` is configured to work without it.
+The virtual machine logs yourself in automatically. This is the default account:
+
+:user: brain
+:password: neurodebian
+
+:root password: neurodebian
+
+In most cases you should not be forced to type the password, because ``sudo``
+is configured to work without it.
.. note::
Working with the virtual machine
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The next video is a demonstration of some basic desktop integration features.
-It shows how to use the virtual machine in full-screen and seamless mode, shared
-folder access, software installation, as well as suspending and resuming the
-virtual machine.
-
-.. raw:: html
-
- <iframe title="YouTube video player"
- class="youtube-player"
- type="text/html"
- width="640"
- height="375"
- src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
- frameborder="0"></iframe>
+The NeuroDebian virtual machine has very low maintenance demands. We have
+prepared a short video demo that shows most typical procedures that you will
+probably perform while working with NeuroDebian inside a virtual machine:
+use the virtual machine in full-screen and seamless mode, shared folder access,
+software installation, as well as suspending and resuming the
+virtual machine. `[Virtual machine handling video tutorial]
+<http://www.youtube.com/watch?v=OV7fYSEoOeQ>`_
.. _chap_vm_troubleshooting:
Troubleshooting
~~~~~~~~~~~~~~~
-Updating the VM or installing new packages doesn't work.
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ Updating the VM or installing new packages doesn't work
+ The VM uses as service that tries to figure out the best/closest package
+ repository for you. In some network environments this service might not work
+ well, or not at all. To check if this is a problem, you can modify the
+ respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need
+ to use ``sudo`` for that) and replace the package repository URL with a
+ mirror close to you. A comprehensive list of mirrors is available at:
+ http://www.debian.org/mirror/list
+
+ Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
+ URL. For example, in Canada you might want to change::
+
+ deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+
+ to::
+
+ deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+
+ Only modify lines that refer to ``geomirror`` (all of them), but do **not**
+ modify entries for ``security.debian.org``.
+
+ Our proxy setup at work prevents APT from downloading packages
+ APT needs to be told how to access the proxy. Talk to your local sysadmin
+ and ask for the proxy's address (maybe a username and password too), as well
+ as the ports for HTTP and FTP proxies. With this information add the
+ following lines in the file, /etc/apt/apt.conf.d/80proxy. This will ensure
+ that after an upgrade changes won't be lost::
+
+ Acquire::http::proxy "http://<username>:<password>@<proxy>:<port>/";
+ Acquire::ftp::proxy "ftp://<username>:<password>@<proxy>:<port>/";
+ Acquire::https::proxy "https://<username>:<password>@<proxy>:<port>/";
+
+ I cannot hear sounds played in the virtual machine
+ By default the sound is muted. To enable playback launch the mixer applet by
+ clicking on the mixer icon in the task bar. Unmute the master volume
+ control. Now click on the "Volume control" to load the channel mixer dialog.
+ Unmute the "Master" and "PCM" channels and raise the volume as desired. You
+ should now be able to hear sounds played within the virtual machines through
+ your host computer's speakers.
+
+ My VM lost mounted host directories after upgrading from VirtualBox from 3.x to 4.x
+ NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
+ 3.x series of VirtualBox and some initial versions of VirtualBox in
+ 4.x series have failed to mount host directories properly.
+ VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
+ series. If you nevertheless want to upgrade guest additions within
+ NeuroDebian VM, please rebuild the version available from the
+ backports::
+
+ sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
+ sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
+ virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+
+ and reboot VM.
+
+
+What has changed
+----------------
+
+.. container:: foldup
- The VM uses as service that tries to figure out the best/closest package
- repository for you. In some network environments this service might not work
- well, or not at all. To check if this is a problem, you can modify the
- respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
- use ``sudo`` for that) and replace the package repository URL with a mirror
- close to you. A comprehensive list of mirrors is available at:
- http://www.debian.org/mirror/list
+ .. container:: expandinstructions
- Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
- URL. For example, in Canada you might want to change::
+ Click on an item to expand it
- deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+ 6.999.b4.20121231 -- 31 Dec 2012
- to::
+ * Based on beta 4 release of debian-installer_ for wheezy
+ * Comes with XFCE4_ instead of GNOME_
- deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+ 6.0.6 -- 01 Oct 2012
+ * Updated core system to Debian squeeze 6.0.6
- Only modify lines that refer to ``geomirror`` (all of them), but do **not**
- modify entries for ``security.debian.org``.
+ 6.0.5 -- 10 Nov 2011
+ * Updated core system to Debian squeeze 6.0.3
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
-I cannot hear sounds played in the virtual machine.
+ - ``~/host`` is now symlinked to correct path ``/media/sf_host``
+ - ``brain`` user is added to ``vboxsf`` group so mounted host
+ directories should become readily available
- By default the sound is muted. To enable playback launch the mixer applet by
- clicking on the mixer icon in the task bar. Unmute the master volume control.
- Now click on the "Volume control" to load the channel mixer dialog. Unmute
- the "Master" and "PCM" channels and raise the volume as desired. You should
- now be able to hear sounds played within the virtual machines through your
- host computer's speakers.
+ * Root partition size and swap space got doubled in size (40GB
+ and 2GB correspondingly). Space is allocated dynamically so
+ the actual size of the virtual drive should not grow unless
+ you use it
-I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
-mounted host directories.
+ 6.0.4 -- 13 Jun 2011
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
- NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
- 3.x series of VirtualBox and some initial versions of VirtualBox in
- 4.x series have failed to mount host directories properly.
- VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
- series. If you nevertheless want to upgrade guest additions within
- NeuroDebian VM, please rebuild the version available from the
- backports::
+ 6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
+ * Updated to Squeeze 6.0.1
+ * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
+ * Appliance is available as a single file (.ova) ready for the import
- sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
- sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
- virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+ 6.0.2 -- 08 Feb 2011
+ * Minor update
- and reboot VM.
+ 6.0.1 -- 01 Dec 2010
+ * Minor update
.. include:: link_names.txt
projects / neurodebian.git / commitdiff
