Commit graph

272210 commits

Author SHA1 Message Date
adam
c76e2d7c6f py-alembic: update to 0.9.6
0.9.6

feature

[feature] [commands] The alembic history command will now make use of the revision environment env.py unconditionally if the revision_environment configuration flag is set to True. Previously, the environment would only be invoked if the history specification were against a database-stored revision token.

bug

[bug] [commands] Fixed a few Python3.6 deprecation warnings by replacing StopIteration with return, as well as using getfullargspec() instead of getargspec() under Python 3.

[bug] [commands] An addition to 441 fixed in 0.9.5, we forgot to also filter for the + sign in migration names which also breaks due to the relative migrations feature.

[bug] [autogenerate] Fixed bug expanding upon the fix for 85 which adds the correct module import to the “inner” type for an ARRAY type, the fix now accommodates for the generic sqlalchemy.types.ARRAY type added in SQLAlchemy 1.1, rendering the inner type correctly regardless of whether or not the Postgresql dialect is present.

[bug] [mysql] Fixed bug where server default comparison of CURRENT_TIMESTAMP would fail on MariaDB 10.2 due to a change in how the function is represented by the database during reflection.

[bug] [autogenerate] Fixed bug where comparison of Numeric types would produce a difference if the Python-side Numeric inadvertently specified a non-None “scale” with a “precision” of None, even though this Numeric type will pass over the “scale” argument when rendering. Pull request courtesy Ivan Mmelnychuk.

[bug] [batch] The name of the temporary table in batch mode is now generated off of the original table name itself, to avoid conflicts for the unusual case of multiple batch operations running against the same database schema at the same time.

[bug] [autogenerate] A ForeignKeyConstraint can now render correctly if the link_to_name flag is set, as it will not attempt to resolve the name from a “key” in this case. Additionally, the constraint will render as-is even if the remote column name isn’t present on the referenced remote table.

[bug] [runtime] [py3k] Reworked “sourceless” system to be fully capable of handling any combination of: Python2/3x, pep3149 or not, PYTHONOPTIMIZE or not, for locating and loading both env.py files as well as versioning files. This includes: locating files inside of __pycache__ as well as listing out version files that might be only in versions/__pycache__, deduplicating version files that may be in versions/__pycache__ and versions/ at the same time, correctly looking for .pyc or .pyo files based on if pep488 is present or not. The latest Python3x deprecation warnings involving importlib are also corrected.
2017-10-18 16:29:01 +00:00
adam
51d22134aa py-rpy: update to 2.9.0
Release 2.9.0:

New features

- New module :mod:`rpy2.situation` to extract and report informations
  about the environment, such as where is the R HOME, what is the
  version of R, what is the version of R rpy2 was built with, etc...
  The module is also designed to be run directly and provide diagnostics:
  `python -m rpy2.situation`.

- :meth:`Environment.values`, :meth:`Environment.pop`,
  :meth:`Environment.popitems`, :meth:`Environment.clear`
  to match :meth:`dict.values`,
  :meth:`dict.pop`, :meth:`dict.popitems`, :meth:`dict.clear`.

- :class:`VectorOperationsDelegator` now has a method `__matmul__` to implement
  Python's matrix multiplication operator (PEP-0645).

- A rule to convert R POSIXct vectors to pandas Timestamp vectors was added.

- method :meth:`_repr_html_` for R vectors to display HTML in jupyter.


Changes

- Starting several times the singleton :class:`EventProcessor` longer results
  in a :class:`RuntimeError`.

- The target version for the R package `dplyr` mapped is now 0.7.1, and
  :func:`rpy2.robjects.lib.dplyr.src_dt` and
  :func:`rpy2.robjects.lib.dplyr.src_desc` are no longer present.

- :meth:`Environment.keys` is now a iterator to match :meth:`dict.keys`,
  also an interator in Python 3.

- Target version of `ggplot2` library is 2.2.1.

- Option `stringsasfactors` in the constructor for the class `DataFrame`. If `False`, the
  strings are no longer converted to factors. When converting from pandas data frames
  the default is to no longer convert columns of strings to factors.

- The R "magic" for jupyter is now more consistently using the conversion system, and the
  use of custom converters through the magic argument `-c` will work as expected.

- Docker-related files moved to directory docker/ (where variants image for rpy2 are available)


Bugs fixed

- :func:`numpy.float128` is not available on all platforms. The unit test
  for it is now skipped on systems where it is not present

- R pairlist objects can now be sliced.

- Passing parameters names that are empty string to R function was
  causing a segfault.

- Trying to build an atomic R vector from a Python object that has a length,
  but it not a sequence nor an iterator was causing a segfault
2017-10-18 16:17:12 +00:00
adam
87deec87c5 R: pkgsrc changes
PkgSrc changes:
* On Darwin, use Aqua interface instead of X11
* Cairo support also requires Pango
* Allow Cairo with other backends, not only X11 (e.g. to make it work on Darwin)
2017-10-18 16:14:30 +00:00
wen
1b7b4dcdbd Updated www/p5-Dancer2 to 0.205002 2017-10-18 14:00:56 +00:00
wen
26824b1ee1 Update to 0.205002
Upstream changes:
0.205002  2017-10-17 16:08:25-05:00 America/Chicago

    [ BUG FIXES ]
    * GH #1362: Make cookies http_only by default (David Precious)
    * GH #1366: Use proper shebang on dancer script and make EU::MM do the job
    * GH #1373: Unset Dancer environment vars before testing (Alberto Sim繭es)
    * GH #1380: Consider class of error displayed when using show_errors
      (Nick Tonkin).
    * GH #1383: Remove Deflater from default app skeleton (Pierre Vigier)
    * GH #1385: Fix links inside the documentation (Alberto Sim繭es)
    * GH #1390: Honour no_server_tokens config in error responses (Russell
      @veryrusty Jenkins)

    [ DOCUMENTATION ]
    * GH #1285: Add "Default Template Variables" section to manual (simbabque)
    * GH #1312: Fix docs for Dancer2::Core::Route->match, which takes a request
      object (simbabque).
    * GH #1368: Don't allow XSS in tutorial (simbabque)
    * GH #1383: Remove full URL on links to third party modules (Alberto Simoes)
    * GH #1395: Customize TT behavior via subclassing (simbabque).
2017-10-18 13:58:16 +00:00
gavan
80c9ac7b8f Update cyrus-imapd24 to 2.4.20 2017-10-18 12:06:55 +00:00
gavan
9ff0abf568 Update cyrus-imapd24 to 2.4.20
Changes in 2.4.19:

  * Complete backport of the new (2.5 and later) IMAP IDLE implementation
    (thanks Thomas Jarosh). This fixes a bunch of bugs and race conditions
    that were inherent to the older implementation
  * New option "imapidletimeout" overrides "timeout" specifically for
    connections in IDLE state
  * OpenSSL 1.1.0 is now supported
  * Fixed: imap ENABLED doesn't print * ENABLED when nothing new enabled
  * Fixed: mailbox lock management over rename (thanks Thomas Jarosh)
  * Fixed: added overflow protection to urlfetch range checks
  * Fixed: lmtpd can now deliver when mupdate server isn't available
    (thanks Michael Menge)
  * Fixed task 227: service processes no longer divide by zero when
    invoked with -T 0 argument (thanks Ian Batten and Jens Erat)
  * Fixed task 229: ctl_cyrusdb now uses database paths from imapd.conf
    (thanks Simon Matter)
  * Fixed bug #3862: mailbox database changes now rolled back on mupdate
    failure during rename (thanks Michael Menge)
  * Fixed: XFER to 2.5 and later no longer downgrades index to oldest version
  * Fixed: nonsensical "TEXT.MIME" section now handled as "HEADER"
  * Fixed: added missing 'auditlog: ' prefix to backend connections
    (thanks Wolfgang Breyha)
  * Fixed: IMAP SEARCH crash on some platforms
  * Fixed: memory leaks in IMAP SEARCH and IMAP APPEND
  * Fixed Issue #1967: EXISTS count reported earlier if fetching past size
    of previous message set

Changes in 2.4.20:

  * Fixed: lmtpd crash
  * Fixed: auth_pts will now error if its configured socket path is too
    long for its buffer
2017-10-18 12:06:31 +00:00
joerg
f9d30b1cc4 Explicitly depend on the extraction tools here as SKIP_DEPENDS doesn't
make the dependency visible. It also helps bulk builds on platforms
without native bzcat.
2017-10-18 11:15:39 +00:00
fhajny
d06fa9d434 doc: Updated devel/ivykis to 0.42.2 2017-10-18 11:05:31 +00:00
fhajny
3aa89e6f65 Update devel/ivykis to 0.42.2.
- Fix crash in __iv_event_run_pending_events().
- Hold a reference on the main loop for each registered iv_event.
2017-10-18 11:05:22 +00:00
fhajny
76250bfbf2 doc: Updated sysutils/rsyslog to 8.30.0 2017-10-18 11:01:19 +00:00
fhajny
40e926602b Update sysutils/rsyslog* to 8.30.0.
- CHANGE OF BEHAVIOUR: all variables are now case-insensitive by
  default
- core: handle (JSON) variables in case-insensitive way
- imjournal: made switching to persistent journal in runtime possible
- mmanon: complete refactor and enhancements
  - add pseudonymization mode
  - add address randomization mode
  - add support for IPv6 (this also supports various replacement
    modes)
  - in IPv4 address recognition
  - in IPv4 simple mode to-be-anonymized bits can get wrong
- imfile: add "fileoffset" metadata
- RainerScript: add ltrim and rtrim functions
- core: report module name when suspending action
- core: add ability to limit number of error messages going to stderr
- tcpsrv subsystem: improvate clarity of some error messages
- imptcp: include module name in error msg
- imtcp: include module name in error msg
- tls improvement: better error message if certificate file cannot be
  read
- omfwd: slightly improved error messages during config parsing
- ommysql improvements
- ommysql bugfix: do not duplicate entries on failed transaction
- imtcp bugfix: parameter priorityString was ignored
- template/bugfix: invalid template option conflict detection
- core/actions: fix handling of data-induced errors
- core/action bugfix: no "action suspended" message during retry
  processing
- core/ratelimit bugfix: race can lead to segfault
- core bugfix: rsyslog aborts if errmsg is generated in early startup
- core bugfix: informational messages was logged with error severity
- core bugfix: --enable-debugless build was broken
- queue bugfix: file write error message was incorrect
- omrelp bugfix:  segfault when rebindinterval parameter is used
- omkafka bugfix: invalid load of failedmsg file on startup if
  disabled
- kafka bugfix: problem on invalid kafka configuration values
- imudp bugfix: UDP oversize message not properly handled
- core bugfix: memory corruption during configuration parsing
- core bugfix: race on worker thread termination during shutdown
- omelasticsearch: avoid ES5 warnings while sending json in bulkmode
- omelasticsearch bugfix: incompatibility with newer ElasticSearch
  version
- imptcp bugfix: invalid mutex addressing on some platforms
- imptcp bugfix: do not accept missing port in legacy listener
  definition
2017-10-18 11:01:05 +00:00
fhajny
39dcaee4b7 doc: Updated devel/librdkafka to 0.11.1 2017-10-18 10:00:14 +00:00
fhajny
85e7fbda6e Update devel/librdkafka to 0.11.1.
Noteworthy critical bug fixes
- Fix OpenSSL instability on Windows (fix thread id callback) - the
  bug resulted in SSL connections being torn down for no apparent
  reason.
- Fetch response fix: read all MessageSets, not just the first one.

Enhancements
- Add api.version.request.timeout.ms
- Point users to documentation when attempting to use Java security
  properties

Fixes:
- Adjust log level for partial message reads when debug is enabled
- Allow app metadata() requests regardless of outstanding metadata
  requests
- Proper size calculation from flags2str to include nul
- Thread-safe rd_strerror()
- Proper re-sends of ProduceRequests in-transit on connection down
- Producer: invalid offsets reported back when
  produce.offset.report=false
- Consumer: Message Null Key/Value were messed up
- Fix metadata querying for topics with LEADER_UNAVAIL set
- Treat request __TIMED_OUT as a retryable error
- Let timed out ProduceRequests result in MSG_TIMED_OUT error code for
  messages
- Fix crash on leader rejoin when outstanding assignor metadata
- sasl_cyrus: Fix dangling stack ptr to sasl_callback_t
2017-10-18 10:00:04 +00:00
maya
947acf41e1 g95: fix build on linux
force passing asprintf test which is incorrectly not found due to FORTIFY
pass LIBRARY_PATH so crtn.o and crti.o are found on Ubuntu & friends

Note many reporters need to install g++-multilib as a package to overcome
the errors they reported in the bugs (missing <sys/cdefs.h>)

PR pkg/51198, PR pkg/51690, PR pkg/52116
2017-10-18 09:38:23 +00:00
adam
5b08c21ff0 Updated security/py-keyring, www/py-notebook 2017-10-18 08:30:30 +00:00
adam
b194a75c31 py-notebook: update to 5.2.0
5.2.0
Allow setting token via jupyter_token env.
Fix some errors caused by raising 403 in get_current_user.
Register contents_manager.files_handler_class directly.
Ensure that keyboard shortcuts are disabled when editing them.
Make all files in the dashboard editable by default and provide a whitelist of viewable file extensions.
The root directory of the notebook server should never be hidden.
Fix notebook require config to match tools/build-main.
Give page constructor default arguments.
Fix codemirror.less to match codemirror's expected padding layout.
Addx-xsrftoken to access-control-allow-headers.
Buffer messages when websocket connection is interrupted.
Load locale dynamically only when not en-us.
Changed key strength to 2048 bits.
Resyncjsversion with python version.
Allow copy operation on modified, read-only notebook.
Update error handling on apihandlers.
Test python 3.6 on travis, drop 3.3.
Avoid base64-literals in image tests.
Upgrade xterm.js to 2.9.2.
Changed all python variables named file to file_name to not override built_in file.
Add more doc tests.
Typos fix.
Rename and update license.
Travis builds doc.
Pull request i18n.
Factor out output_prompt_function, as is done with input prompt.
Use rfc5987 encoding for filenames.
Added path to the resources metadata, the same as in from_filename(...) in nbconvert.exporters.py.
Make "extrakeys" consistent for notebook and editor.
Bidi support.
2017-10-18 08:29:27 +00:00
adam
072c38ba60 py-keyring: update to 10.4.0
10.4.0
In Kwallet, pass mainloop to SessionBus.
Unpin pywin32-ctypes, but blacklist known incompatible versions.
2017-10-18 07:22:53 +00:00
minskim
1e0a90e531 doc: Added security/ruby-openvas-omp version 0.0.4 2017-10-17 19:39:36 +00:00
minskim
99373de2e5 security/Makefile: Add ruby-openvas-omp 2017-10-17 19:39:19 +00:00
minskim
64a183d46f securitiy/ruby-openvas-omp: Import version 0.0.4
This library is used for communication with OpenVAS manager over
OMP. You can start, stop, pause and resume scan. Watch progress and
status of scan, download report, etc.
2017-10-17 19:38:12 +00:00
adam
d623e610dc Updated devel/py-entrypoints, www/py-nbformat, www/py-nbconvert, fonts/py-fonttools 2017-10-17 18:47:33 +00:00
adam
a34999aa6b py-fonttools: update to 3.17.0
3.17.0:
- [svgPathPen] Added an ``SVGPathPen`` that translates segment pen commands
  into SVG path descriptions. Copied from Tal Leming's ``ufo2svg.svgPathPen``
  https://github.com/typesupply/ufo2svg/blob/d69f992/Lib/ufo2svg/svgPathPen.py
- [reverseContourPen] Added ``ReverseContourPen``, a filter pen that draws
  contours with the winding direction reversed, while keeping the starting
  point.
- [filterPen] Added ``ContourFilterPen`` to manipulate contours as a whole
  rather than segment by segment.
- [arrayTools] Added ``Vector`` class to apply math operations on an array
  of numbers, and ``pairwise`` function to loop over pairs of items in an
  iterable.
- [varLib] Added support for building and interpolation of ``cvar`` table
2017-10-17 18:45:27 +00:00
adam
478bbd6af1 Removed devel/py-ipython1 successor devel/py-ipython 2017-10-17 18:44:14 +00:00
adam
b45b0f8321 Make ipython versioned dependency 2017-10-17 18:37:22 +00:00
minskim
31ef2e2e78 doc: Added security/ruby-nessus_rest version 0.1.6 2017-10-17 18:34:22 +00:00
minskim
6794e1cfcb security/Makefile: Add ruby-nessus_rest 2017-10-17 18:33:52 +00:00
minskim
c0a79151b0 security/ruby-nessus_rest: Import version 0.1.6
Ruby library for Nessus (version 6+) JSON/REST interface. This library
is used for communication with Nessus over REST interface. You can
start, stop, pause and resume scan. Watch progress and status of scan,
download report, etc.
2017-10-17 18:33:09 +00:00
adam
d5ac3f022a py-nbconvert: update to 5.3.1
5.3.1
MANIFEST.in updated to include LICENSE and scripts/ when creating sdist.
2017-10-17 18:31:40 +00:00
adam
27448a0ab4 py-nbformat: update to 4.4.0
4.4.0:
- Explicitly state that metadata fields can be ignored.
- Introduce official jupyter namespace inside metadata (``metadata.jupyter``).
- Introduce ``source_hidden`` and ``outputs_hidden`` as official front-end
  metadata fields to indicate hiding source and outputs areas. **NB**: These
  fields should not be used to hide elements in exported formats.
- Fix ending the redundant storage of signatures in the signature database.
- :func:`nbformat.validate` can be set to not raise a ValidationError if
  additional properties are included.
- Fix for errors with connecting and backing up the signature database.
- Dict-like objects added to NotebookNode attributes are now transformed to be
  NotebookNode objects; transformation also works for `.update()`.
2017-10-17 18:30:02 +00:00
adam
1b055e7373 Make ipython versioned dependency 2017-10-17 18:28:53 +00:00
adam
e4392ae6e5 Removed ipython from BUILD_DEPENDS: it is needed for testing, but will cause circular dependencies 2017-10-17 18:19:07 +00:00
minskim
a1cbaf88c9 doc: Added security/ruby-nexpose version 7.1.1 2017-10-17 18:18:13 +00:00
minskim
aed3bc53b8 security/Makefile: Add ruby-nexpose 2017-10-17 18:17:51 +00:00
minskim
c27c36eb7e security/ruby-nexpose: Import version 7.1.1
nexpose is the official gem package for the Ruby Nexpose API client
library.
2017-10-17 18:15:18 +00:00
adam
5939e6929f py-entrypoints: update to 0.2.3
0.2.3:
Bug fixes
2017-10-17 18:06:44 +00:00
fhajny
cfba3fe087 Enable erlang-eimp 2017-10-17 15:10:19 +00:00
fhajny
798c53d3a3 doc: Added graphics/erlang-eimp version 1.0.1 2017-10-17 15:09:33 +00:00
fhajny
c98020802b Add eimp 1.0.1 as graphics/erlang-eimp.
eimp is an Erlang/Elixir application for manipulating graphic
images using external C libraries. It supports WebP, JPEG, PNG
and GIF.
2017-10-17 15:09:21 +00:00
fhajny
a0fe7690c4 doc: Updated chat/ejabberd to 17.09 2017-10-17 14:55:45 +00:00
fhajny
f9166c6910 Update chat/ejabberd to 17.09.
Admin
- Harden ejabberdctl
- Fix ejabberdctl quoting when using iex
- Call earlier deps configure scripts during compilation
- Fix iexdebug and iexlive commands
- Quote $PEER in ping command to avoid hostnames containing "-" being
  interpreted as arithmetic
- Docker: Sync containers from rroemhild and add instructions in
  README
- Use eimp instead of ImageMagick calls for thumbnails creation
- Add forgotten caching options to the validator
- Fix 'make install' to work with new output from rebar list-deps
- Rewrite muc_register_nick and muc_unregister_nick to be DB
  independent
- WebAdmin: Fix deletion of multiple offline messages

Encryption
- Add support for XEP-0368 in outgoing s2s: SRV records for XMPP over
  TLS
- Deprecate s2s_use_starttls: required_trusted
- Don't attempt to access(2) a certificate file
- Let 'domain_certfile' take higher precedence instead of s2s_certfile
  or c2s_certfile

Databases
- mysql.sql: Use multi-column index on username/ID
- Use forked repo of Riak Erlang client to support OTP20

Modules
- mod_avatar: New module with support for legacy and modern clients
- mod_block_strangers: Introduce option 'allow_transports'
- mod_block_strangers: Block messages from strangers before
  mod_mam/mod_offline processing
- mod_http_upload: Don't ignore 'custom_headers'
- mod_muc: Improve presence-error and unavailable of multi-session
  occupants
- mod_multicast: Fix start and reading of configured limits
- mod_mam: Simplify check for anon MUC JID filtering
- mod_mam: Refuse filtering anon MUC queries by JID
- mod_privacy: Explicitly match against
- mod_register: Introduce 'redirect_url' option
- mod_stream_mgmt: Delete 'c2s_init' hook
- mod_vcard_xupdate: Also replace vcard-x-update in direct presences

PubSub
- Fix get_items/get_item calls
- Add correct order when requesting all items
- Implement '6.5.7 Requesting the Most Recent Items'
- Fix RSM support on SQL
- Add RSM support on mnesia
- Fix node_options: default options only apply on first plugin
- Broadcast updated node configuration
- Enforce controls on publish and delete items

Miscelanea
- Preserve correct order of deserialized XML elements
- Suppress push notifications for online clients
- Extract strings and prepare translation files works again
2017-10-17 14:55:36 +00:00
fhajny
112e9b4bad doc: Updated net/erlang-xmpp to 1.1.15 2017-10-17 14:53:30 +00:00
fhajny
b5e0734d1a Update net/erlang-xmpp to 1.1.15
- Updating fast_xml to version 1.1.24.
- Updating p1_utils to version 1.0.10.
- Updating stringprep to version 1.0.10.
- Compatibility with R19.3+
- XEP-0084 (User Avatar) support
2017-10-17 14:53:22 +00:00
fhajny
ba7fe0edcb doc: Updated net/erlang-esip to 1.0.16 2017-10-17 14:52:54 +00:00
fhajny
aee8a3a8a4 Update net/erlang-esip to 1.0.16.
- Updating stun to version 1.0.15.
- Updating fast_tls to version 1.0.16.
- Updating p1_utils to version 1.0.10.
- Compatibility with R20
2017-10-17 14:52:43 +00:00
fhajny
910c09e2e9 doc: Updated net/erlang-stun to 1.0.15 2017-10-17 14:51:53 +00:00
fhajny
d96415ac93 Update net/erlang-stun to 1.0.15
- Updating fast_tls to version 1.0.16.
- Updating p1_utils to version 1.0.10.
2017-10-17 14:51:42 +00:00
fhajny
db47e2614d doc: Updated databases/erlang-p1_pgsql to 1.1.4 2017-10-17 14:51:26 +00:00
fhajny
6122910ab9 Update databases/erlang-p1_pgsql to 1.1.4
- Update coverall script
2017-10-17 14:51:17 +00:00
fhajny
e6d43b81d2 doc: Updated databases/erlang-p1_mysql to 1.0.4 2017-10-17 14:51:01 +00:00