Add SHA512 digests for distfiles for audio category

Problems found with existing distfiles:
/pub/pkgsrc/distfiles/amp-0.7.6.tgz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-music-32000-1.0.8.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-music-48000-1.0.8.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-en-us-callie-32000-1.0.22.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-en-us-callie-48000-1.0.22.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-fr-ca-june-32000-1.0.18.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-fr-ca-june-48000-1.0.18.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-ru-RU-elena-16000-1.0.12.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-ru-RU-elena-32000-1.0.12.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-ru-RU-elena-48000-1.0.12.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-ru-RU-elena-8000-1.0.12.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-fr-ca-june-32000-1.0.18.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-fr-ca-june-48000-1.0.18.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-ru-RU-elena-32000-1.0.13.tar.gz
/pub/pkgsrc/distfiles/freeswitch/freeswitch-sounds-ru-RU-elena-48000-1.0.13.tar.gz
/pub/pkgsrc/distfiles/kid3-3.3.0.tar.gz
/pub/pkgsrc/distfiles/libdca-0.0.5.tar.bz2
/pub/pkgsrc/distfiles/mp3to.gz
/pub/pkgsrc/distfiles/squeezeboxserver-7.5.1-noCPAN.tgz
No changes made to these file.

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for archivers category

Problems found with existing distfile for eagle:
distfiles/bicom101.zip
distfiles/szip-2.1nb3/szip-2.1.tar.gz
distfiles/xmill-0.9.1.tar.gz
No changes made to these distinfo files.

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for cross category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for benchmarks category

Problems found with existing distfile for superpi:
distfiles/super_pi-20030927/super_pi.tar.gz
No changes were made to the superpi/distinfo file.

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.
distfiles/eagle-lin32-7.4.0.run

(agc)

Add SHA512 digests for distfiles for cad category

Problems found with existing distfile for eagle:
distfiles/eagle-lin32-7.4.0.run
No changes made to eagle/distinfo file.

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for filesystems category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for finance category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for geography category

One mismatched digest found in geography/libmemphis02:
# package libmemphis02
recorded SHA1 (memphis-0.2.3.tar.gz) = dbc2f61e49b996dc9ca91df0de9a08eb7adbfa9b
calculated SHA1 (memphis-0.2.3.tar.gz) = 85993bce12c3616fcf6e7682a70b9605883edec2
No changes were made to the libmemphis02 distinfo file

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for ham category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for mbone category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for news category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for parallel category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for wm category

Problems found with existing distfiles:
distfiles/fvwm-1.24r.tar.gz

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for time category

Problems found with mismatching existing digests for:
distfiles/asclock-classic-1.0.tar.gz
distfiles/asclock-gtk-2.1.10beta.tar.gz
distfiles/asclock-xlib-2.0.11.tar.gz
distfiles/emiclock-2.0.2.tar.gz

Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden).  All existing
SHA1 digests retained for now as an audit trail.

(agc)

Add SHA512 digests for distfiles for shells category

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Pass --disable-smpegtest to configure. Test is known to sometimes hang.
I've seen it happen on Darwin.

(tnn)

Fixed patch detection in distinfo files

Up to now, all files whose names started with "patch-" were considered
patch files. This was wrong, since e.g. devel/patch also has distfiles
with the same naming pattern.

(rillig)

Fixed order of lines in distinfo

(rillig)

Updated graphics/sane-backends to 1.0.25nb1

(leot)

INT_MIN and DBL_MIN are respectively included in <limits.h> and <float.h>.
Fixes build on Linux.
PKGREVISION++

Noted and patch provided by Matthias Ferdinand via pkgsrc-users@.

(leot)

Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

(agc)

Updated fonts/umefont-ttf to 0.560

(ryoon)

Update to 0.560

* Workaround for WRKSRC.

Status:
Unadjusted glyphs (characters; 1st pass): Uninode 8869-8b95
Unadjusted glyphs (Bushu; 1st pass): Koromo, Gonben

(ryoon)

Updated net/owncloudclient to 2.0.2

(ryoon)

Update to 2.0.2

Changelog:
Release 2.0.2 October 22nd 2015

    csync_file_stat_s: Save a bit of memory
    Shibboleth: Add our base user agent to WebKit
    SelectiveSync: Increase folder list timeout to 60
    Propagation: Try another sync on 423 Locked (#3387)
    Propagation: Make 423 Locked a soft error (#3387)
    Propagation: Reset upload blacklist if a chunk succeeds
    Application: Fix crash on early shutdown (#3898)
    Linux: Don't show settings dialog always when launched twice (#3273, #3771, #3485)
    win32 vio: Add the OPEN_REPARSE_POINTS flag to the CreateFileW call. (#3813)
    AccountSettings: only expand root elements on single click.
    AccountSettings: Do not allow to expand the folder list when disconnected.
    Use application SHORT name for the name of the MacOSX pkg file (ownBrander).
    FolderMan: Fix for removing a syncing folder (#3843)
    ConnectionMethodDialog: Don't be insecure on close (#3863)
    Updater: Ensure folders are not removed (#3747)
    Folder settings: Ensure path is cleaned (#3811)
    Propagator: Simplify sub job finished counting (#3844)
    Share dialog: Hide settings dialog before showing (#3783)
    UI: Only expand 1 level in folder list (#3585)
    UI: Allow folder expanding from button click (#3585)
    UI: Expand folder treeview on single click (#3585)
    GUI: Change tray menu order (#3657)
    GUI: Replace term "sign in" with "Log in" and friends.
    SetupPage: Fix crash caused by uninitialized Account object.
    Use a themable WebDAV path all over.
    Units: Back to the "usual" mix units (JEDEC standard).
    csync io: Full UNC path support on Win (#3748)
    Tray: Don't use the tray workaround with the KDE theme (#3706, #3765)
    ShareDialog: Fix folder display (#3659)
    AccountSettings: Restore from legacy only once (#3565)
    SSL Certificate Error Dialog: show account name (#3729)
    Tray notification: Don't show a message about modified folder (#3613)
    PropagateLocalRemove: remove entries from the DB even if there was an error.
    Settings UI improvements (eg. #3713, #3721, #3619 and others)
    Folder: Do not create the sync folder if it does not exist (#3692)
    Shell integration: don't show share menu item for top level folders
    Tray: Hide while modifying menus (#3656, #3672)
    AddFolder: Improve remote path selection error handling (#3573)
    csync_update: Use excluded_traversal() to improve performance (#3638)
    csync_excluded: Add fast _traversal() function (#3638)
    csync_exclude: Speed up significantly (#3638)
    AccountSettings: Adjust quota info design (#3644, #3651)
    Adjust buttons on remove folder/account questions (#3654)

Release 2.0.1 September 1st 2015

    AccountWizard: fix when the theme specifies an override URL (#3699)

Release 2.0.0 August 25th 2015

    Add support for multiple accounts (#3084)
    Do not sync down new big folders from server without users consent (#3148)
    Integrate Selective Sync into the default UI
    OS X: Support native finder integration for 10.10 Yosemite (#2340)
    Fix situation where client would not reconnect after timeout (#2321)
    Use SI units for the file sizes
    Improve progress reporting during sync (better estimations, show all files, show all bandwidth)
    Windows: Support paths >255 characters (#57) by using Windows API instead of POSIX API
    Windows, OS X: Allow to not sync hidden files (#2086)
    OS X: Show file name in UI if file has invalid UTF-8 in file name
    Sharing: Make use of Capability API (#3439)
    Sharing: Do not allow sharing the root folder (#3495)
    Sharing: Show thumbnail
    Client Updater: Check for updates periodically, not only once per run (#3044)
    Windows: Remove misleading option to remove sync data (#3461)
    Windows: Do not provoke AD account locking if password changes (#2186)
    Windows: Fix installer when installing unprivileged (#2616, #2568)
    Quota: Only refresh from server when UI is shown
    SSL Button: Show more information
    owncloudcmd: Fix --httpproxy (#3465)
    System proxy: Ask user for credentials if needed
    Several fixes and performance improvements in the sync engine
    Network: Try to use SSL session tickets/identifiers. Check the SSL button to see if they are used.
    Bandwidth Throttling: Provide automatic limit setting for downloads (#3084)
    Systray: Workaround for issue with Qt 5.5.0 (#3656)

(ryoon)

Updated www/php-owncloud to 8.2.0

(ryoon)

Update to 8.2.0

Changelog:
Version 8.2.0 October 20th 2015
Major new ownCloud release, more info in announcement blog. Summary:

    Updated design
    New sidebar
    Rewritten Gallery app
    Updated text editor
    Notifications
    Policy for retaining deleted files and file versions
    Encrypt/decrypt commands
    Many additions to occ command tool for admins
    Improved mime type handling
    Security Hardening
    ownCloud API work: Modular Authentication support, Capabilities Manager and Query Builder and more
    Many small improvements

(ryoon)

Updated devel/nspr to 4.10.10

(ryoon)

Update to 4.10.10

Changelog:
Not available.
Required by upcoming Firefox 42.

(ryoon)

Updated shells/zsh to 5.1.1

(ryoon)

Update to 5.1.1

Changelog:
Changes from 5.1 to 5.1.1
-------------------------

5.1.1 is primarily a bug fix release; however, a few minor features were
added.

The ZLE variables YANK_ACTIVE, YANK_START and YANK_END have been added
and are useful for managing highlighting.

The zsh-specific pattern match range tests have been supplemented with
[:INCOMPLETE:] and [:INVALID:] to help detect the state of partially
read multibyte character strings.

(ryoon)

Updated audio/pulseaudio to 7.1

(ryoon)

Update to 7.1

Changelog:
Since we had a couple of annoying bugs in 7.0, we thought it'd be a
good idea to do a 7.1 to address those.

Changes at a glance:

  * Fix a crasher when using srbchannel
  * Fix a build system typo that caused symlinks to turn up in /
  * Make Xonar cards work better
  * Other minor  bug fixes and improvements

(ryoon)

No need to build flock(1) when we are only interested in libuuid.
Fixes build on Darwin.

(tnn)

extraneous parenthesis crept in in Darwin conditional

(tnn)

Updated devel/py-mercurial to 3.6

(wiz)

Update py-mercurial to 3.6:

Mercurial 3.6 (2015-11-1)

Regularly scheduled feature release.

1.1. commands

    bookmark: do not crash when active bookmark is forward and --date is used
    bookmarks: don't deactivate on no-op update (issue4901)
    clone: fix updaterev to update to latest branch changeset (issue4528)
    clonebundles: support for seeding clones from pre-generated bundles
    commit: abort when a committemplate is not changed (BC)
    help: distinguish sections when multiple match (issue4802)
    help: pass around ui to doc loader (API)
    help: pass around ui to rewriter hooks (API)
    merge: perform all premerges before any merges (BC)
    merge: abort on file/directory case folding collisions (issue4892)
    phases: return zero for no-op operations (issue4751) (BC)
    resolve: perform all premerges before performing any file merges (BC)

1.2. core

    cmdutil: make in-memory changes visible to external editor (issue4378)
    cmdutil: stop tryimportone from using dirstateguard (BC)
    context: don't hex encode all unknown 20 char revision specs (issue4890)
    dirstate: batch calls to statfiles (issue4878)
    parsers: fix infinite loop or out-of-bound read in fm1readmarkers (issue4888)
    revlog: add an aggressivemergedelta option
    revlog: change generaldelta delta parent heuristic
    revset: do not fall through to revspec for literal: branch (issue4838)
    revsets: makes follow() supports file patterns (issue4757) (BC)
    templater: add new docheader/footer components for XML (issue4135)
    templater: create string unescape helper (issue4798)
    templater: do not pre-evaluate generator keyword at runsymbol (issue4868)
    templater: introduce {latesttag()} function to match a pattern (issue4184)
    templater: switch ctx of list expression to rev of revset() (BC)
    ui: change default path fallback mechanism (issue4796)
    util: use tuple accessor to get accurate st_mtime value (issue4836)
    wireproto: properly parse false boolean args (BC)

1.3. extensions

    histedit: use one editor when multiple folds happen in a row (issue3524) (BC)
    largefiles: better handling of merge of largefiles that are not available
    mq: generate patch names from first line of description
    rebase: avoid losing branch commits with --keepbranch (issue4835)
    rebase: fix warning about ignoring tool option on rebase continue (issue4698)
    rebase: fix wrong 'no changes to commit' when using --collapse
    rebase: on abort delete rebase state file no matter what
    rebase: properly abort when destination is public (issue4896)
    rebase: properly handle chains of markers with missing nodes
    shelve: bundle using bundle2 if repository is general delta (issue4862)
    shelve: delete shelve statefile on any exception during abort
    shelve: restore shelved dirstate explicitly after aborting transaction
    shelve: restore unshelved dirstate explicitly after aborting transaction

1.4. hgweb

    hgweb: consume generator inside context manager (issue4756)
    hgweb: ensure both foreground and background colors are specified (issue4872)
    hgweb: overwrite cwd to resolve file patterns relative to repo (issue4568)

1.5. unsorted

    builddeb: actually run make when building the deb (issue4778)
    buildrpm: mkdir -p two needed directories (issue4779)
    bundle2: don't try to recover from a GeneratorExit (issue4785)
    bundle: extend the format of --type to support version and compression
    debian: install bash completion as hg and not mercurial (issue4900)
    debian: install hgk as part of mercurial-common (issue4829)
    dispatch: error out on invalid -R path even if optionalrepo (issue4805) (BC)
    dispatch: stop warning about EPIPE in --debug mode
    graphmod: compute slow revset query once prior to reachableroots (issue4782)
    highlight: add highlightfiles config option which takes a fileset (issue3005)
    highlight: add option to prevent content-only based fallback
    highlight: exit early on textual and unknown files (issue3005)
    incoming: request a bundle2 when possible (BC)
    localrepo: recreate phasecache if changelog was modified (issue4855)
    lock: loop a finite number of times in trylock (issue4787)
    mercurial: add debugextensions command (issue4676)
    minirst: don't treat top level item as children of last item (issue4803)
    notify: fix fromauthor setting for 'incoming' hook type (issue4194)
    posix: shellquote do not require quoting for "+" (issue4818)
    reachableroots: verify integer range of heads argument (issue4775)
    revpair: restrict odd-range handling to top-level x:y expression (issue4774)
    revrange: drop old-style parser in favor of revset (API)
    test-merge-tools: include /usr/sbin in path for sysctl (issue4813)
    traceback: allow providing a local support contact point
    treemanifest: rework lazy-copying code (issue4840)
    windows: read all global config files, not just the first (issue4491) (BC)
    worker: restore old countcpus code (issue4869)

(wiz)

-midori-0.5.11 (hi jmcneill)

(dholland)

midori

(dholland)

Needs libXScrnSaver; PR 50387 from YAMASHIRO Jun.

(dholland)

dieharder was updated to 3.31.1

(agc)

+ sudo-1.8.15.

(taca)

appease pkglint

(tnn)

Use ${COMPILER_INCLUDE_DIRS} instead of hardcoded /usr/include

(tnn)

note xquartz in TODO

(tnn)

Updated x11/modular-xorg-{server,xephyr} to 1.17.4

(tnn)

Update to modular-xorg-{server,xephyr}-1.17.4

1.17.4:
Fixes an uninitialized fd_set

1.17.3:
Various bugfixes across the board.  The most visible changes include
fixing GLX extension setup under Xwayland and other non-Xorg servers
(enabling core contexts in more scenarios), and various stability fixes
to glamor and the Present extension.

(tnn)

+confuse-2.8

(bsiegert)

fix build with clang

(tnn)

Fix sysconfdir

(markd)

Fix sysconfdir.

(markd)

don't include libcddb bl3.mk twice

(tnn)

Fix dependencies.

(markd)

Import syslog-ng Python bindings as sysutils/py-syslog-ng.

(fhajny)

Updated multimedia/mpv to 0.12.0

(leot)

Update multimedia/mpv to mpv-0.12.0.

pkgsrc changes:
o mpv does not build on NetBSD<7 because it needs sem_timedwait(3),
  add the various not supported versions to NOT_FOR_PLATFORM.
o Bump waf requried version to reflect upstream.

Changes:
Release 0.12.0
==============
NOTE: This release changes the default format for youtube-dl and removes some
workarounds related to MPEG DASH support. However, the required changes to
FFmpeg code are not in any FFmpeg release yet (as of 2015-10-29), so for now,
playing DASH streams requires using FFmpeg git master. You can work around
this by using the --ytdl-format=best option.

Features
--------
New
~~~
- vo_opengl: support new VAAPI EGL interop (requires Mesa 11)
- vo_opengl: vaapi: add Wayland support
- bring back the x11 video output
- vo_opengl: support all kinds of GBRP formats

Removed
~~~~~~~
- video: remove VDA support (VideoToolbox is preferred)

Behavior
--------
- vo_opengl: enable X11 EGL backend by default (disabled for NVIDIA due to
  driver bugs)
- ytdl: don't override user-set format in no-video mode
- sub: adjust behavior on mismatching video/subtitle aspect ratio

Options and Commands
--------------------
Added
~~~~~
- audio: add option for falling back to ao_null
- options: add support for client certificate authentication
- input: add key name for U+3000 IDEOGRAPHIC SPACE
- player: add audio drop/duplicate mode to video-sync

Changed
~~~~~~~
- vo_opengl: remove sharpen scalers, add sharpen sub-option
- vo_opengl: make sw suboption work without explicit backend selection
- command: make time properties unavailable if timestamp is unknown
- command: do not return 0 for bitrate if unknown (make property unavailable
  instead)
- vo_opengl: make the default debanding settings less excessive
- ytdl: disable --all-subs if "sub-lang" is in raw-options

Removed
~~~~~~~
- video: remove user-controllable PTS sorting (--pts-association-mode)

Fixes and Minor Enhancements
----------------------------
- player: fix another --force-window bug
- player: add wav to list of external audio file extensions
- ao_alsa: fix failure to find any sample format
- player: make stop command actually stop in all cases
- audio: various fixes related to audio device hotplugging
- vo_xv: fix crash with --wid
- ytdl: Remove DASH hacks, use DASH by default
- player: be slightly less prone to framedrop in display sync mode
- sd_lavc: extend subtitle resolution if images go outside video frame
- player: offset chapter display by start time
- command: make bitrate properties work correctly for external tracks
- w32_common: disable IME
- player: fix display-sync A/V calculation on high playback speeds
- player: fix display sync A/V difference estimation on drops
- player: raise display sync desync tolerance

(leot)

Updated print/cups-filters to 1.1.0

(leot)

Update print/cups-filters to cups-filters-1.1.0.

Changes:
CHANGES IN V1.1.0
- Version numbering scheme changed: Releases with feature
  addition/change have the minor number increased now, pure
  bug fix releases get the revision number increased, to make
  use of the minor number which stayed zero all the time.
- cups-browsed: Added "DefaultOptions" directive to
  cups-browsed.conf to allow defining default option settings
  for local queues to be generated for newly appearing remote
  printers.
- cups-browsed: Removed assert() calls which remained from
  copy and paste in the very beginning of the development of
  cups-browsed.  assert() is only for use during debugging and
  should not be used in production code.
- cups-browsed: Let option settings of a generated print queue
  be saved before taking the queue down so that when the remote
  printer appears again all user changes get restored, making
  user changes permanent on generated queues.
- foomatic-rip: Fixed string length for shell path constant, to
  work also with systems having longer paths (Bug #1325)
- cups-browsed: Added a mode in which IP-based device URIs
  for the generation of local print queues are used, for
  cases with problems in local host name resolution.
- foomatic-rip: Use -dFirstPage=... and -dLastPage=... only
  if really needed (Bug #1324).
- cups-browsed, implicitclass: Make the load-balancing
  configurable so that one can select whether the jobs get
  queued up locally like in a CUPS class or whether they get
  immediately distributed to the remote servers letting them
  queue up there.

(leot)

GNU_CONFIGURE=yes must be set before bsd.prefs.mk is included.
Also LOCALBASE -> PREFIX

(tnn)

Add devel/ivykis

(fhajny)

Added devel/ivykis version 0.39

(fhajny)

Import ivykis 0.39 as devel/ivykis.

ivykis is a thin wrapper over various OS'es implementation of I/O
readiness notification facilities (such as poll(2), kqueue(2))
and is mainly intended for writing portable high-performance
network servers.

(fhajny)

Remove wx option, depended on removed wxGTK26.

(wiz)

+ cairo-1.14.4, cairo-gobject-1.14.4, colordiff-1.0.16,
  cups-filters-1.1.0, dbus-1.10.2, gsl-2.0, gst-plugins1-base-1.6.1,
  gst-plugins1-good-1.6.1, gst-plugins1-ugly-1.6.1, gstreamer1-1.6.1,
  libopenmpt-0.2.5705beta15, musicpd-0.19.11, ocaml-findlib-1.5.6,
  py-cryptography-1.1, py-markdown-2.6.3, py-vdirsyncer-0.7.0,
  x264-devel-20151031.

(wiz)

Updated math/py-networkx to 1.10

(wiz)

Update py-networkx to 1.10, based on PR 50383 by Derouiche.

API changes

    [#1501] connected_components, weakly_connected_components, and strongly_connected_components return now a generator of sets of nodes. Previously the generator was of lists of nodes. This PR also refactored the connected_components and weakly_connected_components implementations making them faster, especially for large graphs.
    [#1547] The func_iter functions in Di/Multi/Graphs classes are slated for removal in NetworkX 2.0 release. func will behave like func_iter and return an iterator instead of list. These functions are deprecated in NetworkX 1.10 release.

New functionalities

    [#823] A enumerate_all_cliques function is added in the clique package (networkx.algorithms.clique) for enumerating all cliques (including nonmaximal ones) of undirected graphs.
    [#1105] A coloring package (networkx.algorithms.coloring) is created for graph coloring algorithms. Initially, a greedy_color function is provided for coloring graphs using various greedy heuristics.
    [#1193] A new generator edge_dfs, added to networkx.algorithms.traversal, implements a depth-first traversal of the edges in a graph. This complements functionality provided by a depth-first traversal of the nodes in a graph. For multigraphs, it allows the user to know precisely which edges were followed in a traversal. All NetworkX graph types are supported. A traversal can also reverse edge orientations or ignore them.
    [#1194] A find_cycle function is added to the networkx.algorithms.cycles package to find a cycle in a graph. Edge orientations can be optionally reversed or ignored.
    [#1210] Add a random generator for the duplication-divergence model.
    [#1241] A new networkx.algorithms.dominance package is added for dominance/dominator algorithms on directed graphs. It contains a immediate_dominators function for computing immediate dominators/dominator trees and a dominance_frontiers function for computing dominance frontiers.
    [#1269] The GML reader/parser and writer/generator are rewritten to remove the dependence on pyparsing and enable handling of arbitrary graph data.
    [#1280] The network simplex method in the networkx.algorithms.flow package is rewritten to improve its performance and support multi- and disconnected networks. For some cases, the new implementation is two or three orders of magnitude faster than the old implementation.
    [#1286] Added the Margulis窶敵abber窶敵alil graph to networkx.generators.
    [#1306] Added the chordal p-cycle graph, a mildly explicit algebraic construction of a family of 3-regular expander graphs. Also, moves both the existing expander graph generator function (for the Margulis-Gabber-Galil expander) and the new chordal cycle graph function to a new module, networkx.generators.expanders.
    [#1314] Allow overwriting of base class dict with dict-like: OrderedGraph, ThinGraph, LogGraph, etc.
    [#1321] Added to_pandas_dataframe and from_pandas_dataframe.
    [#1322] Added the Hopcroft窶適arp algorithm for finding a maximum cardinality matching in bipartite graphs.
    [#1336] Expanded data keyword in G.edges and added default keyword.
    [#1338] Added support for finding optimum branchings and arborescences.
    [#1340] Added a from_pandas_dataframe function that accepts Pandas DataFrames and returns a new graph object. At a minimum, the DataFrame must have two columns, which define the nodes that make up an edge. However, the function can also process an arbitrary number of additional columns as edge attributes, such as 窶�weight窶�.
    [#1354] Expanded layout functions to add flexibility for drawing subsets of nodes with distinct layouts and for centering each layout around given coordinates.
    [#1356] Added ordered variants of default graph class.
    [#1360] Added harmonic centrality to network.algorithms.centrality.
    [#1390] The generators.bipartite have been moved to algorithms.bipartite.generators. The functions are not imported in the main namespace, so to use it, the bipartite package has to be imported.
    [#1391] Added Kanevsky窶冱 algorithm for finding all minimum-size separating node sets in an undirected graph. It is implemented as a generator of node cut sets.
    [#1399] Added power function for simple graphs
    [#1405] Added fast approximation for node connectivity based on White and Newman窶冱 approximation algorithm for finding node independent paths between two nodes.
    [#1413] Added transitive closure and antichains function for directed acyclic graphs in algorithms.dag. The antichains function was contributed by Peter Jipsen and Franco Saliola and originally developed for the SAGE project.
    [#1425] Added generator function for the complete multipartite graph.
    [#1427] Added nonisomorphic trees generator.
    [#1436] Added a generator function for circulant graphs to the networkx.generators.classic module.
    [#1437] Added function for computing quotient graphs; also created a new module, networkx.algorithms.minors.
    [#1438] Added longest_path and longest_path_length for DAG.
    [#1439] Added node and edge contraction functions to networkx.algorithms.minors.
    [#1445] Added a new modularity matrix module to networkx.linalg, and associated spectrum functions to the networkx.linalg.spectrum module.
    [#1447] Added function to generate all simple paths starting with the shortest ones based on Yen窶冱 algorithm for finding k shortest paths at algorithms.simple_paths.
    [#1455] Added the directed modularity matrix to the networkx.linalg.modularity_matrix module.
    [#1474] Adds triadic_census function; also creates a new module, networkx.algorithms.triads.
    [#1476] Adds functions for testing if a graph has weighted or negatively weighted edges. Also adds a function for testing if a graph is empty. These are is_weighted, is_negatively_weighted, and is_empty.
    [#1481] Added Johnson窶冱 algorithm; one more algorithm for shortest paths. It solves all pairs shortest path problem. This is johnson at algorithms.shortest_paths
    [#1414] Added Moody and White algorithm for identifying k_components in a graph, which is based on Kanevsky窶冱 algorithm for finding all minimum-size node cut-sets (implemented in all_node_cuts #1391).
    [#1415] Added fast approximation for k_components to the networkx.approximation package. This is based on White and Newman approximation algorithm for finding node independent paths between two nodes (see #1405).

Removed functionalities

    [#1236] The legacy ford_fulkerson maximum flow function is removed. Use edmonds_karp instead.

Miscellaneous changes

    [#1192] Support for Python 2.6 is dropped.

(wiz)

Updated math/py-sympy to 0.7.6.1

(wiz)

Update to 0.7.6.1, based on PR 50382 by derouiche.

0.7.6.1

This is a small bugfix release over SymPy 0.7.6, primarily to fix issues with printing in the Jupyter notebook.
Changes

    Fix pretty printing in the Jupyter notebook and Jupyter qtconsole for Jupyter 4.0.

    The deprecated linearization method in the mechanics module no longer fails to execute.

0.7.6

Major changes

    New module calculus.finite_diff for generating finite difference formulae approximating derivatives of arbitrary order on arbitrarily spaced grids.

    New module physics.optics for symbolic computations related to optics.

    geometry module now supports 3D geometry.

    Support for series expansions at a point other then 0 or oo. See PR #2427.

    Rules for the intersection of integer ImageSets were added. See PR #7587. We can now do things like {2⋅m | m ∊ ℤ} ∩ {3⋅n | n ∊ ℤ} = {6⋅t | t ∊ ℤ} and {2⋅m | m ∊ ℤ} ∩ {2⋅n + 1 | n ∊ ℤ} = ∅

    dsolve module now supports system of ODEs including linear system of ODEs of 1st order for 2 and 3 equations and of 2nd order for 2 equations. It also supports homogeneous linear system of n equations.

    New support for continued fractions, including iterators for partial quotients and convergents, and reducing a continued fraction to a Rational or a quadratic irrational.

    Support for Egyptian fraction expansions, using several different algorithms.

    Addition of generalized linearization methods to physics.mechanics.

    Use an LRU cache by default instead of an unbounded one. See PR #7464. Control cache size by the environment variable SYMPY_CACHE_SIZE (default is 500). SYMPY_CACHE_SIZE=None restores the unbounded cache.

    Added fastcache as an optional dependency. Requires v0.4 or newer. Control via SYMPY_CACHE_SIZE. May result in significant speedup. See PR #7737.

    New experimental module physics.unitsystems for computation with dimensions, units and quantities gathered into systems. This opens the way to dimensional analysis and better quantity calculus. The old module physics.units will stay available until the new one reaches a mature state. See PR #2628.

    New Complement class to represent relative complements of two sets. See Pr #7462.

    New trigonometric functions (asec, acsc), many enhancements for other trigonometric functions (PR #7500).

    New Contains class to represent the relation "is an element of" (see PR #7989).

    The code generation tools (code printers, codegen, autowrap, and ufuncify) have been updated to support a wider variety of constructs, and do so in a more robust way. Major changes include added support for matrices as inputs/outputs, and more robust handling of conditional (Piecewise) statements.

    ufuncify now uses a backend that generates actual numpy.ufuncs by default through the use of the numpy C api. This allows broadcasting on all arguments. The previous cython and f2py backends are still accessible through the use of the backend kwarg.

    CodeGen now generates code for Octave and Matlab from SymPy expressions. This is supported by a new CodePrinter with interface octave_code. For example octave_code(Matrix([[x**2, sin(pi*x*y), ceiling(x)]])) gives the string [x.^2 sin(pi*x.*y) ceil(x)].

    New general 3D vector package at sympy.vector. This package provides a 3D vector object with the Del, gradient, divergence, curl, and operators. It supports arbitrary rotations of Cartesian coordinate systems and arbitrary locations of points.

Backwards compatibility breaks and deprecations

    All usage of inequalities (>, >=, <, <=) on SymPy objects will now return SymPy's S.true or S.false singletons instead of Python's True or False singletons. Code that checks for, e.g., (a < b) is True should be changed to (a < b) == True or (a < b) == S.true. Use of is is not recommended here.

    The subset() method in sympy.core.sets is marked as being deprecated and will be removed in a future release (issue). Instead, the is_subset() method should be used.

    Previously, if you compute the series expansion at a point other than 0, the result was shifted to 0. Now SymPy returns the usual series expansion, see PR #2427.

    In physics.mechanics, KanesMethod.linearize has a new interface. Old code should be changed to use this instead. See docstring for information.

    physics.gaussopt has been moved to physics.optics.gaussopt. You can still import it from the previous location but it may result in a deprecation warning.

    This is the last release with the bundled mpmath library. In the next release you will have to install this library from the official site.

    Previously lambdify would convert Matrix to numpy.matrix by default. This behavior is being deprecated, and will be completely phased out with the release of 0.7.7. To use the new behavior now set the modules kwarg to [{'ImmutableMatrix': numpy.array}, 'numpy']. If lambdify will be used frequently it is recommended to wrap it with a partial as so: lambdify = functools.partial(lambdify, modules=[{'ImmutableMatrix': numpy.array}, 'numpy']). For more information see #7853 and the lambdify doc string.

    Set.complement doesn't exists as an attribute anymore. Now we have a method Set.complement(<universal_set>) which complements the given universal set.

    Removed is_finite assumption (see #7891). Use instead a combination of "is_bounded and is_nonzero" assumptions.

    is_bounded and is_unbounded assumptions were renamed to is_finite and is_infinite (see #7947).

    Removed is_infinitesimal assumption (see #7995).

    Removed is_real property for Sets, use set.is_subset(Reals) instead (see #7996).

    For generic symbol x (SymPy's symbols are not bounded by default), inequalities with oo are no longer evaluated as they were before, e.g. x < oo no longer evaluates to True). See #7861.

    CodeGen has been refactored to make it easier to add other languages. The main high-level tool is still utilities.codegen.codegen. But if you previously used the Routine class directly, note its __init__ behaviour has changed; the new utilities.codegen.make_routine is recommended instead and by default retains the previous C/Fortran behaviour. If needed, you can still instantiate Routine directly; it only does minimal sanity checking on its inputs. See #8082.

    FiniteSet([1, 2, 3, 4]) syntax not supported anymore, use FiniteSet(1, 2, 3, 4) instead See #7622.

Minor changes

    Updated the parsing module to allow sympification of lambda statements to their SymPy equivalent.
    Lambdify can now use numexpr by specifying modules='numexpr'
    Use with evaluate(False) context manager to control automatic evaluation. E.g. with evaluate(False): x + x is actually x + x, not 2*x
    IndexedBase and Indexed are changed to be commutative by default
    sympy.core.sets moved to sympy.sets
    Changes in sympy.sets:
        Infinite Range is now allowed. See PR #7741
        is_subset(): The is_subset() method deprecates the subset() method. self.is_subset(other) checks if self is a subset of other. This is different from self.subset(other), which checked if other is a subset of self.
        is_superset(): A new method is_superset() method is now available. self.is_superset(other) checks if self is a superset of other.
        is_proper_subset and is_proper_superset: Two new methods allow checking if one set is the proper subset and proper superset of another respectively. For eg. self.is_proper_subset(other) and self.is_proper_superset(other) checks if self is the proper subset of other and if self is the proper superset of other respectively.
        is_disjoint(): A new method for checking if two sets are disjoint.
        powerset(): A new method powerset() has been added to find the power set of a set.
        The cardinality of a ProductSet can be found using the len() function.
    Changes in sympy.plot.plot_implicit:
        The plot_implicit function now also allows explicitly specifying the symbols to plot on the X and Y axes. If not specified, the symbols will be assigned in the order they are sorted.
        The plot_implicit function also allows axes labels for the plot to be specified.
    rules for simplification of ImageSet were added PR#7625. As a result {x | x ∊ ℤ} now simplifies to ℤ and {sin(n) | n ∊ {tan(m) | m ∊ ℤ}} automatically simplifies to {sin(tan(m)) | m ∊ ℤ}
    coth(0) now returns Complex Infinity. See #7634
    dioptre is added to physics.units #7782
    replace now respects commutativity #7752
    The CCodePrinter gracefully handles Symbols which have string representations that match C reserved words. #8199
    limit function now returns an unevaluated Limit instance if it can't compute given limit, see #8213

0.7.5

Major changes

    The version of mpmath included in SymPy has been updated to 0.18.

    New routines for efficiently compute the dispersion of a polynomial or a pair thereof.

    Fancy indexing of matrices is now provided, e.g. A[:, [1, 2, 5]] selects all rows and only 3 columns.

    Enumeration of multiset partitions is now based on an implementation of Algorithm 7.1.2.5M from Knuth's The Art of Computer Programming. The new version is much faster, and includes fast methods for enumerating only those partitions with a restricted range of sizes, and counting multiset partitions. (See the new file sympy.utilities.enumerative.py.)

    distance methods were added to Line and Ray to compute the shortest distance to them from a point.

    The normal_lines method was added to Ellipse to compute the lines from a point that strike the Ellipse at a normal angle.

    inv_quick and det_quick were added as functions in solvers.py to facilitate fast solution of small symbolic matrices; their use in solve has reduced greatly the time needed to solve such systems.

    solve_univariate_inequality has been added to sympy.solvers.inequalities.py.

    as_set attribute for Relationals and Booleans has been added.

    Several classes and functions strictly associated with vector calculus were moved from sympy.physics.mechanics to a new package sympy.physics.vector. (PRs #2732 #2862 #2894)

    New implementation of the Airy functions Ai and Bi and their derivatives Ai' and Bi' (called airyai, airybi, airyaiprime and airybiprime, respectively). Most of the usual features of SymPy special function are present. Notable exceptions are Gruntz limit computation helpers and meijerg special functions integration code.

    Euler-Lagrange equations (function euler_equations) in a new package sympy.calculus (PR #2431).

Minor changes

    Some improvements to the gamma function.

    generate_bell now generates correct permutations for any number of elements.

    It is no longer necessary to provide nargs to objects subclassed from Function unless an eval class method is not defined. (If eval is defined, the number of arguments will be inferred from its signature.)

    geometric Point creation will be faster since simplification is done only on Floats

    Some improvements to the intersection method of the Ellipse.

    solutions from solve of equations involving multiple log terms are more robust

    idiff can now return higher order derivatives

    Added to_matrix() method to sympy.physics.vector.Vector and sympy.physics.dyadic.Dyadic. (PR #2686).

    Printing improvements for sympy.physics.vector objects and mechanics printing. (PRs #2687, #2728, #2772, #2862, #2894)

    Functions with LaTeX symbols now print correct LaTeX. (PR #2772)

    init_printing has several new options, including a flag print_builtin to prevent SymPy printing of basic Python types (PR #2683), and flags to let you supply custom printers (PR #2894).

    improvements in evaluation of imageset for Intervals (PR #2723).

    Set properties to determine boundary and interior (PR #2744).

    input to a function created by lambdify no longer needs to be flattened.

Backwards compatibility breaks and deprecations

    the submatrix method of matrices was removed; access the functionality by providing slices or list of rows/columns to matrix directly, e.g. A[:, [1, 2]].

    Matrix([]) and Matrix([[]]) now both return a 0x0 matrix

    terms_gcd no longer removes a -1.0 from expressions

    extract_multiplicatively will not remove a negative Number from a positive one, so (4*x*y).extract_multiplicatively(-2*x) will return None.

    the shape of the result from M.cross(B) now has the same shape as matrix M.

    The factorial of negative numbers is now zoo instead of 0. This is consistent with the definition factorial(n) = gamma(n + 1).

    1/0 returns zoo, not oo (PR #2813).

    zoo.is_number is True (PR #2823).

    oo < I raises TypeError, just as for finite numbers (PR #2734).

    1**oo == nan instead of 1, better documentation for Pow class (PR #2606).

(wiz)