Commit graph

291335 commits

Author SHA1 Message Date
adam
9de881e5c7 py-peewee: updated to 3.8.1
3.8.1

New features
Sqlite SearchField now supports the match() operator, allowing full-text search to be performed on a single column (as opposed to the whole table).

Changes
Remove minimum passphrase restrictions in SQLCipher integration.

Bugfixes
Support inheritance of ManyToManyField instances.
Ensure operator overloads are invoked when generating filter expressions.
Fix incorrect scoring in Sqlite BM25, BM25f and Lucene ranking algorithms.
Support string field-names in data dictionary when performing an ON CONFLICT ... UPDATE query, which allows field-specific conversions to be applied.
2019-01-08 08:37:59 +00:00
tron
bb7cef4a09 Note update of the "mutt" package to version 1.11.2 2019-01-08 08:01:28 +00:00
tron
b602b3b637 mutt: Update to version 1.11.2
This is a  bug fix release.
2019-01-08 08:01:04 +00:00
wiz
048e459509 doc/TODO: add some
+ calibre-3.37.0, mutt-1.11.2.
2019-01-08 06:03:06 +00:00
markd
8da6abdac1 {py-,}protobuf: don't share the patches directory
some patches only apply to py-protobuf.
2019-01-08 05:56:19 +00:00
schmonz
b714f3376c doc: Updated devel/libtai to 0.60nb6 2019-01-08 03:57:16 +00:00
schmonz
f526638b1c Add the latest leap second. Generate leapsecs.dat during build. Install
static library with sensible permissions. Bump PKGREVISION.
2019-01-08 03:57:11 +00:00
kre
e32c76ac3a + bash-5 readline-8 2019-01-08 01:20:02 +00:00
schmonz
a36608f5d4 doc: Updated net/vpnc-script to 20180226 2019-01-07 22:32:22 +00:00
schmonz
3c1c411358 Update to 20180226. From the changelog:
- Support routes with different devs and gateways
- Revive route cleanup for /sbin/route code
- Support split-exclude rules from Pulse gateway
- Check if resolved is enabled in nsswitch.conf prior to using it
- Add support for systemd-resolved
2019-01-07 22:32:17 +00:00
schmonz
cdb32d71bb doc: Updated net/openconnect to 8.01 2019-01-07 22:23:57 +00:00
schmonz
0d2fe9a06d Update to 8.01. From the changelog:
- Fix memset_s() arguments.
- Fix OpenBSD build.
- Clear form submissions (which may include passwords) before freeing (CVE-2018-20319).
- Allow form responses to be provided on command line.
- Add support for SSL keys stored in TPM2.
- Fix ESP rekey when replay protection is disabled.
- Drop support for GnuTLS older than 3.2.10.
- Fix --passwd-on-stdin for Windows to not forcibly open console.
- Fix portability of shell scripts in test suite.
- Add Google Authenticator TOTP support for Juniper.
- Add RFC7469 key PIN support for cert hashes.
- Add protocol method to securely log out the Juniper session.
- Relax requirements for Juniper hostname packet response to support old gateways.
- Add API functions to query the supported protocols.
- Verify ESP sequence numbers and warn even if replay protection is disabled.
- Add support for PAN GlobalProtect VPN protocol (--protocol=gp).
- Reorganize listing of command-line options, and include information on supported protocols.
- SIGTERM cleans up the session similarly to SIGINT.
2019-01-07 22:23:52 +00:00
schmonz
af53e0023a Get a copy of dnsroots.global from djbdns and use the copy as
CONF_FILES. Fixes build on NetBSD that somehow wasn't broken on OS X.
2019-01-07 19:45:48 +00:00
jaapb
6f1e5443eb doc: Updated lang/ocaml to 4.07.1nb1 2019-01-07 18:52:36 +00:00
jaapb
0426d7fcb1 Updated lang/ocaml to compile on aarch64 and revbump.
A few patches to the configure script to recognise the combination of
NetBSD and aarch64, and a few changes to the Makefile to make sure we've
got the right combination of options for the PLIST. It now compiles on my
Pinebook.
2019-01-07 18:52:23 +00:00
kleink
69fbf3d0f3 Added www/py-flask-cors version 3.0.7. 2019-01-07 18:04:28 +00:00
kleink
ec0a01ff44 www: + py-flask-cors. 2019-01-07 18:03:27 +00:00
kleink
500bd41900 www/py-flask-cors: Import Flask-Cors 3.0.7.
A Flask extension for handling Cross Origin Resource Sharing (CORS),
making cross-origin AJAX possible.

This package has a simple philosophy, when you want to enable CORS, you
wish to enable it for all use cases on a domain. This means no mucking
around with different allowed headers, methods, etc. By default,
submission of cookies across domains is disabled due to the security
implications, please see the documentation for how to enable
credential'ed requests, and please make sure you add some sort of
CSRF protection before doing so!
2019-01-07 18:02:45 +00:00
leot
ab00dc4e8b doc: Updated misc/nyancat to 1.5.2 2019-01-07 17:41:43 +00:00
leot
e67316def6 nyancat: Update to 1.5.2
Changes:
1.5.2
-----
 - Misc bugfixes
 - Fix typos
2019-01-07 17:41:33 +00:00
adam
edc044f36f Updated textproc/py-sphinxcontrib-bibtex, www/py-paste 2019-01-07 17:15:01 +00:00
adam
a48703250d py-paste: update to 3.0.9
3.0.6
* Revert the changes in the 3.0.5, which introduced unexpected errors in
  paste/httpserver.py when using SSL.
2019-01-07 17:14:41 +00:00
adam
1cb83e91fb py-sphinxcontrib-bibtex: updated to 0.4.2
0.4.2:
* Drop Python 3.3 support, add Python 3.7 support.
* Work around issue with sphinx-testing on Fedora
2019-01-07 17:00:33 +00:00
wiz
fc99dc8ee7 doc: Updated emulators/mame to 0.205 2019-01-07 15:51:33 +00:00
wiz
57ac217d02 mame: update to 0.205.
With Christmas just over, it’s time for the final MAME release for
2018, and what a year it’s been!

MAME 0.205 is no different. Newly supported arcade systems include
Unico’s Magic Purple, and Visco’s never-before-seen prototype Pastel
Island. The latter ties in nicely with improved video emulation
for the SSV platform (yes, this fixes other long-standing glitches,
too). Newly playable machines include Konami’s Tobe! Polystars,
Evil Night and Total Vice. Yes, Konami M2 emulation is finally
here! Be aware that there’s still a lot of room for performance
optimisation on this system.

Putting arcade systems aside for a moment, this release includes
support for Dance Dance Revolution Strawberry Shortcake, and the
Nintendo Game & Watch titles Oil Panic and Squish. Interestingly,
there are no other emulators or simulators for Squish, and it hasn’t
been included in any of Nintendo’s Game & Watch collections. It
seems to draw inspiration from the Famicom game Devil World.

There are hundreds more Commodore 64 cassettes in the software list
now, and quite a few more BBC ROMs as well. Software lists have
been added for the Nascom computers, along with updates to the boot
ROM choices and better keyboard emulation. We’ve also created a
skeleton driver and documented the known software for the Chinese
Monon Color console. In a last-minute addition we added support
for new version 2 .WOZ floppy images on the Apple II family.
2019-01-07 15:51:23 +00:00
wiz
3f38a9b1b3 doc: Updated x11/xcursorgen to 1.0.7 2019-01-07 15:49:30 +00:00
wiz
04dc9125f5 xcursorgen: update to 1.0.7.
Alan Coopersmith (10):
      configure: Drop AM_MAINTAINER_MODE
      autogen.sh: Honor NOCONFIGURE=1
      Fix type mismatch warnings for loop index variables
      Include more information in error messages
      Use asprintf if available, instead of malloc+strcpy+strcat
      Convert to X.Org standard code style
      Update README for gitlab migration
      Add README.md to EXTRA_DIST in Makefile.am
      Update configure.ac bug URL for gitlab migration
      xcursorgen 1.0.7

Emil Velikov (1):
      autogen.sh: use quoted string variables

Mihail Konev (1):
      autogen: add default patch prefix

Peter Hutterer (1):
      autogen.sh: use exec instead of waiting for configure to finish

Tobias Stoeckmann (1):
      Fix null pointer dereference on very large images.
2019-01-07 15:49:21 +00:00
bacon
385a79042f ncbi-blast+: Upgrade to 2.8.1
Support for new BLAST database format
Increased makeblastdb output file size limit to 4GB
Other minor bug fixes and enhancements

OK wiz@
2019-01-07 15:00:10 +00:00
schmonz
dcb9592476 doc: Updated net/djbdns-run to 20190107 2019-01-07 14:02:01 +00:00
schmonz
31940d97a1 With the 'inet6' option, depend on djbdnscurve6 instead of djbdns.
Extract most of MESSAGE to README.pkgsrc.

Remove vestigial Red Hat chkconfig stanza from main control script (we
have pkgtools/rc.d-boot now).

Use CONF_FILES where applicable.

rc.d script defaults:
- Tag log entries like qmail-run's; for instance, "nbtinydns" and
  "nbdnscache" become "nbdjbdns/tiny" and "nbdjbdns/cache".
- Have tinydns listen on the network.
- Auto-rebuild CDBs as needed on service start.

Bump version.
2019-01-07 14:01:55 +00:00
he
03d0b2236b Add a comment to the patch, and add the netbsd-stdint.h
header for NetBSD/powerpc, so that the macppc version builds.
Thanks to maya@ for the hint.
No revision bump, as this is only a build fix for NetBSD/powerpc.
2019-01-07 13:46:14 +00:00
adam
8b300389bd Added www/py-django-timezone-field, www/py-django-celery-beat 2019-01-07 13:00:34 +00:00
adam
a3834eae95 py-django-celery-beat: updated to 1.4.0
1.4.0:
- Fix migrations dependencies.
- Added the DJANGO_CELERY_BEAT_TZ_AWARE setting.

1.3.0:
- Fix transaction handling while syncing the schedule.
- Fix schedule type validation logic.
- Scheduler no longer forgets the tasks after first schedule change.
- Fix race condition for schedule_changed() resulting in erroneously closed connections.
- Add support for task priorities when using RabbitMQ or Redis as broker.
- Disabled tasks are now correctly deleted from the schedule.
- Added name as search filter.

1.2.0:
- Allow timezone-aware Cron schedules.
- Retry later in case of InterfaceError in sync.
- Show Periodic Task Description in panel admin.
- Fix CrontabSchedule example.
- Support Periodic Tasks with a start date and one-off tasks.
- Fixes a problem with beat not reconnecting to MySQL (server restart, network problem, etc.) when checking if schedule has changed.
- Add toggle admin action which allows to activate disabled tasks or deactivate enabled tasks.
- Add fields validation for CrontabSchedule.
- Drop support for Django<1.11.
- Fix task heap invalidation bug which prevented scheduled tasks from running when syncing tasks from the database.
- Raise a ValidationError when more than one type (solar, crontab or interval) of schedule is provided.
2019-01-07 12:59:35 +00:00
adam
e8725ece18 py-django-timezone-field: added version 3.0
A Django app providing database and form fields for pytz timezone objects.
2019-01-07 12:56:22 +00:00
adam
65a2a4d6b9 Updated time/py-pytz, graphics/py-Pillow 2019-01-07 10:16:37 +00:00
adam
1843357622 py-Pillow: updated to 5.4.1
5.4.1:
- File closing: Only close __fp if not fp
- Fix build for Termux
- PNG: Detect MIME types
- PNG: Handle IDAT chunks after image end
2019-01-07 10:16:20 +00:00
adam
072e0284fd py-pytz: updated to 2018.9
2018.9:
Unknown changes.
2019-01-07 10:05:42 +00:00
adam
b205742e9f Updated multimedia/mkvtoolnix, net/py-smb 2019-01-07 09:13:29 +00:00
adam
e9220ddb08 py-smb: updated to 1.1.26
Version 1.1.26:
Prevents OperationError from being raised when listPath() operation does not return any matching file results.
SMBConnection is now a context manager
2019-01-07 09:13:13 +00:00
adam
bb15e407dd mkvtoolnix: updated to 30.1.0
Version 30.1.0 "Forever And More":

Bug fixes
* build system: fixed building on non-UTF-8 locales.
* MKVToolNix GUI: multiplexer: implemented a workaround for drag & drop not
  working on macOS with Qt 5.12 due to a bug in Qt 5.12.
* MKVToolNix GUI: chapter editor: when opening a Matroska/WebM file that
  doesn't contain chapters and later saving chapters back to them, the editor
  was truncating the file down to a couple of KB in size.
2019-01-07 09:12:40 +00:00
adam
0c327703b7 Updated devel/py-hypothesis, security/libsodium, devel/py-test, devel/py-test-cov 2019-01-07 08:44:18 +00:00
adam
c223d7e7ef py-test-cov: updated to 2.6.1
2.6.1:
* Added support for Pytest 4.1.
* Various test and docs fixes.
* Fixed the "Module already imported".
2019-01-07 08:43:55 +00:00
adam
e57f574e78 py-test: updated to 4.1.0
pytest 4.1.0:
Removals
* pytest.mark.parametrize: in previous versions, errors raised by id functions were suppressed and changed into warnings. Now the exceptions are propagated, along with a pytest message informing the node, parameter value and index where the exception occurred.
* Remove legacy internal warnings system: config.warn, Node.warn. The pytest_logwarning now issues a warning when implemented.
See our docs on information on how to update your code.
* Removed support for yield tests - they are fundamentally broken because they don’t support fixtures properly since collection and test execution were separated.
See our docs on information on how to update your code.
* Removed support for applying marks directly to values in @pytest.mark.parametrize. Use pytest.param instead.
See our docs on information on how to update your code.
* Removed Metafunc.addcall. This was the predecessor mechanism to @pytest.mark.parametrize.
See our docs on information on how to update your code.
* Removed support for passing strings to pytest.main. Now, always pass a list of strings instead.
See our docs on information on how to update your code.
* [pytest] section in setup.cfg files is not longer supported, use [tool:pytest] instead. setup.cfg files are meant for use with distutils, and a section named pytest has notoriously been a source of conflicts and bugs.
Note that for pytest.ini and tox.ini files the section remains [pytest].
* Removed the deprecated compat properties for node.Class/Function/Module - use pytest.Class/Function/Module now.
See our docs on information on how to update your code.
* Removed the implementation of the pytest_namespace hook.
See our docs on information on how to update your code.
* Removed request.cached_setup. This was the predecessor mechanism to modern fixtures.
See our docs on information on how to update your code.
* Removed the deprecated PyCollector.makeitem method. This method was made public by mistake a long time ago.
* Removed support to define fixtures using the pytest_funcarg__ prefix. Use the @pytest.fixture decorator instead.
See our docs on information on how to update your code.
* Calling fixtures directly is now always an error instead of a warning.
See our docs on information on how to update your code.
* Remove Node.get_marker(name) the return value was not usable for more than a existence check.
Use Node.get_closest_marker(name) as a replacement.
* The deprecated record_xml_property fixture has been removed, use the more generic record_property instead.
See our docs for more information.
* An error is now raised if the pytest_plugins variable is defined in a non-top-level conftest.py file (i.e., not residing in the rootdir).
See our docs for more information.
* Remove testfunction.markername attributes - use Node.iter_markers(name=None) to iterate them.

Deprecations
* Deprecated the pytest.config global.
See https://docs.pytest.org/en/latest/deprecations.html#pytest-config-global for rationale.
* Passing the message parameter of pytest.raises now issues a DeprecationWarning.
It is a common mistake to think this parameter will match the exception message, while in fact it only serves to provide a custom message in case the pytest.raises check fails. To avoid this mistake and because it is believed to be little used, pytest is deprecating it without providing an alternative for the moment.
If you have concerns about this, please comment on issue 3974.
* Deprecated raises(..., 'code(as_a_string)') and warns(..., 'code(as_a_string)').
See https://docs.pytest.org/en/latest/deprecations.html#raises-warns-exec for rationale and examples.

Features
* A warning is now issued when assertions are made for None.
This is a common source of confusion among new users, which write:
assert mocked_object.assert_called_with(3, 4, 5, key="value")
When they should write:
mocked_object.assert_called_with(3, 4, 5, key="value")
Because the assert_called_with method of mock objects already executes an assertion.
This warning will not be issued when None is explicitly checked. An assertion like:
assert variable is None
will not issue the warning.
* Richer equality comparison introspection on AssertionError for objects created using attrs or dataclasses (Python 3.7+, backported to 3.6).
* CACHEDIR.TAG files are now created inside cache directories.
Those files are part of the Cache Directory Tagging Standard, and can be used by backup or synchronization programs to identify pytest’s cache directory as such.
* pytest.outcomes.Exit is derived from SystemExit instead of KeyboardInterrupt. This allows us to better handle pdb exiting.
* Updated the --collect-only option to display test descriptions when ran using --verbose.
* Restructured ExceptionInfo object construction and ensure incomplete instances have a repr/str.
* pdb: added support for keyword arguments with pdb.set_trace.
It handles header similar to Python 3.7 does it, and forwards any other keyword arguments to the Pdb constructor.
This allows for __import__("pdb").set_trace(skip=["foo.*"]).
* Added ini parameter junit_duration_report to optionally report test call durations, excluding setup and teardown times.
The JUnit XML specification and the default pytest behavior is to include setup and teardown times in the test duration report. You can include just the call durations instead (excluding setup and teardown) by adding this to your pytest.ini file:
[pytest]
junit_duration_report = call
* -ra now will show errors and failures last, instead of as the first items in the summary.
This makes it easier to obtain a list of errors and failures to run tests selectively.
* pytest.importorskip now supports a reason parameter, which will be shown when the requested module cannot be imported.

Bug Fixes
* -p now accepts its argument without a space between the value, for example -pmyplugin.
* approx again works with more generic containers, more precisely instances of Iterable and Sized instead of more restrictive Sequence.
* Ensure that node ids are printable.
* Fixed raises(..., 'code(string)') frame filename.
* Display actual test ids in --collect-only.

Improved Documentation
* Markers example documentation page updated to support latest pytest version.
* Update cache documentation example to correctly show cache hit and miss.
* Improved detailed summary report documentation.

Trivial/Internal Changes
* Changed the deprecation type of --result-log to PytestDeprecationWarning.
2019-01-07 08:38:01 +00:00
adam
82a78d166a libsodium: updated to 1.0.17
Version 1.0.17
- Bug fix: sodium_pad() didn't properly support block sizes >= 256 bytes.
- JS/WebAssembly: some old iOS versions can't instantiate the WebAssembly
module; fall back to Javascript on these.
- JS/WebAssembly: compatibility with newer Emscripten versions.
- Bug fix: crypto_pwhash_scryptsalsa208sha256_str_verify() and
crypto_pwhash_scryptsalsa208sha256_str_needs_rehash() didn't return
EINVAL on input strings with a short length, unlike their high-level
counterpart.
- Added a workaround for Visual Studio 2010 bug causing CPU features
not to be detected.
- Portability improvements.
- Test vectors from Project Wycheproof have been added.
- New low-level APIs for arithmetic mod the order of the prime order group:
crypto_core_ed25519_scalar_random(), crypto_core_ed25519_scalar_reduce(),
crypto_core_ed25519_scalar_invert(), crypto_core_ed25519_scalar_negate(),
crypto_core_ed25519_scalar_complement(), crypto_core_ed25519_scalar_add()
and crypto_core_ed25519_scalar_sub().
- New low-level APIs for scalar multiplication without clamping:
crypto_scalarmult_ed25519_base_noclamp() and
crypto_scalarmult_ed25519_noclamp(). These new APIs are especially useful
for blinding.
- sodium_sub() has been implemented.
- Support for WatchOS has been added.
- getrandom(2) is now used on FreeBSD 12+.
- The nonnull attribute has been added to all relevant prototypes.
- More reliable AVX512 detection.
- Javascript/Webassembly builds now use dynamic memory growth.
2019-01-07 08:36:03 +00:00
adam
744451446a py-hypothesis: updated to 3.86.5
3.86.5:
This is a docs-only patch, which fixes some typos and removes a few hyperlinks for deprecated features.

3.86.4:
This release changes the order in which the shrinker tries to delete data. For large and slow tests this may significantly improve the performance of shrinking.

3.86.3:
This release fixes a bug where certain places Hypothesis internal errors could be raised during shrinking when a user exception occurred that suppressed an exception Hypothesis uses internally in its generation.

The two known ways to trigger this problem were:

Errors raised in stateful tests’ teardown function.
Errors raised in finally blocks that wrapped a call to data.draw.
These cases will now be handled correctly.

3.86.2:
This patch is a docs-only change to fix a broken hyperlink.

3.86.1:
This patch fixes issue 1732, where integers() would always return long values on Python 2.

3.86.0:
This release ensures that infinite numbers are never generated by floats() with allow_infinity=False, which could previously happen in some cases where one bound was also provided.

The trivially inconsistent min_value=inf, allow_infinity=False now raises an InvalidArgumentError, as does the inverse with max_value. You can still use just(inf) to generate inf without violating other constraints.
2019-01-07 08:31:28 +00:00
schmonz
b7ada6e391 Use RCD_SCRIPTS_DIR in MESSAGE and README.pkgsrc, and SUBST_VARS the latter. 2019-01-07 04:29:46 +00:00
bacon
ba39e252d3 doc: Added biology/canu version 1.8 2019-01-07 02:35:02 +00:00
bacon
aefc835978 Add canu 2019-01-07 02:34:21 +00:00
bacon
94e269c682 biology/canu: import canu-1.8
Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

Canu is a hierarchical assembly pipeline which runs in four steps:

    Detect overlaps in high-noise sequences using MHAP

    Generate corrected sequence consensus

    Trim corrected sequences

    Assemble trimmed corrected sequences
2019-01-07 02:33:17 +00:00
wiz
37d4115594 doc/TODO: add some
+ ImageMagick-7.0.8.23, fish-3.0.0, gobject-introspection-1.58.3,
  libxml2-2.9.9, libxslt-1.1.33, mc-4.8.22, meld-3.20.0,
  py-libxml2-2.9.9, py-libxslt-1.1.33, syncthing-1.0.0,
  zsh-autosuggestions-0.5.0.
2019-01-07 00:19:09 +00:00