Pyteomics is a collection of lightweight and handy tools for Python
that help to handle various sorts of proteomics data. Pyteomics
provides a growing set of modules to facilitate the most common
tasks in proteomics data analysis, such as:
* calculation of basic physico-chemical properties of polypeptides:
. mass and isotopic distribution
. charge and pI
. chromatographic retention time
* access to common proteomics data:
. MS or LC-MS data
. FASTA databases
. search engines output
* easy manipulation of sequences of modified peptides and proteins
WWW: https://pypi.python.org/pypi/pyteomics
- Tighten COMMENT text
- Drop shlib ABI versions from LIB_DEPENDS
- Rename DOCS option to DOXYGEN to reflect its evil nature, and disable
it by default (of course)
- Clean up Makefile while here, reformat port description
Changes:
* Totally revamped implementation of FXThreadPool. The new FXThreadPool
is organized about a lock-free queue, with semaphores managing
synchronization between producer- and worker-threads. Thus, threads
never block unless two edge conditions are reached: either the
task-queue is empty, in which case worker threads will block (nothing
to do), or task queue is filled up, and producer thread will block
(no room in queue). An important new capability is for an additional
thread to enter into the task-processing loop temporarily. Finally,
the thread starting FXThreadPool, as well as the worker threads
belonging to the FXThreadPool now have a thread-local variable
referencing the FXThreadPool. This allows the threads involved to
locate the address of the FXThreadPool, for instance to create an
FXTaskGroup.
* New FXTaskGroup class manages groups of task to be executed in parallel
on a FXThreadPool. Tasks started through the FXTaskGroup interface are
guaranteed to be completed within the lifetime of the FXTaskGroup
instance.
* New FXParallelInvoke and FXParallelFor template functions to implement
parallel function call, and parallel for loop. This uses the new
FXTaskGroup, and indirectly, FXThreadPool.
* Pass optional stacksize when constructing FXWorker. Added stacksize
option to FXThreadPool with which new workers will be started.
* FXBarrier wait primitive now sports API's to change break-through
threshold, and forced-release option.
* FXSemaphore now has API's for timed wait, and try-wait for non-blocking
semaphore decrement.
* Added additional atomic variable types in FXAtomic.h.
* Added check for maximum dash-pattern length in FXDC and FXDCWindow.
* Fixed some issues with FXStat of files.
* Off-by-one error fixed in FXRex counted repeat of complex subpatterns.
* Clear internal text pointers in FXRex prior to a match.
* Added a few missing print-patterns to Adie.stx syntax file.
* Added FXSemaphore-protected queue class FXSemaQueue; this is itself a
wrapper around FXPtrQueue.
* Added lock-free queue class FXLFQueue.
* Numeric conversion issues fixed in fxstrtod.cpp; in particular, some
corner cases now give more accurate results.
* The function fxscanf.cpp does no longer eat the "e" when scanning for a
number, unless actually followed by digits.
* Switch to statvfs() from statfs() in FXStat.
* Indexing operator added to FXAutoPtr.
* Added new class FXScopedThread. FXScopedThread automatically performs a
join() upon destruction.
Changes:
* Correct esponja bug for windows : in windows you cannot
remove a file when it is still open !
* Patch by C Deleuze for a few fixes in info mode.
Incompatible Changes
====================
* layout redo/undo has been removed.
Normal Changes
==============
* Add halfpage up/down bindings to copy mode.
* Session choosing fixed to work with unattached sessions.
* New window options window-status-last-{attr,bg,fg} to denote the last
window which was active.
* Scrolling in copy-mode now scrolls the region without moving the mouse
cursor.
* run-shell learnt '-t' to specify the pane to use when displaying output.
* Support for middle-click pasting.
* choose-tree learns '-u' to start uncollapsed.
* select-window learnt '-T; to toggle to the last window if it's already
current.
* New session option 'assume-paste-time' for pasting text versus
key-binding actions.
* choose-* commands now work outside of an attached client.
* Aliases are now shown for list-commands command.
* Status learns about formats.
* Free-form options can be set with set-option if prepended with an '@'
sign.
* capture-pane learnt '-p' to send to stdout, and '-e' for capturing
escape sequences, and '-a' to capture the alternate screen, and '-P' to
dump pending output.
* Many new formats added (client_session, client_last_session, etc.)
* Control mode, which is a way for a client to send tmux commands.
Currently more useful to users of iterm2.
* resize-pane learnt '-x' and '-y' for absolute pane sizing.
* Config file loading now reports errors from all files which are loaded
via the 'source-file' command.
* 'copy-pipe' mode command to copy selection and pipe the selection to a
command.
* Changes panes can now emit focus notifications for certain applications
which use those.
* run-shell and if-shell now accept format placeholders.
* resize-pane learnt '-Z' for zooming a pane temporarily.
* new-session learnt '-A' to make it behave like attach-session.
* set-option learnt '-o' to prevent setting an option which is already
set.
* capture-pane and show-options learns '-q' to silence errors.
* New command 'wait-for' which blocks a client until woken up again.
* Resizing panes will now reflow the text inside them.
* Lots and lots of bug fixes, fixing memory-leaks, etc.
* Various manpage improvements.
PR: 177435 (with minor modifications)
Submitted by: Yasuhiro KIMURA <yasu@utahime.org>
that if found in a @(un)exec pkgng will force to push them in post_deinstallation script.
This allows not to hardcode anymore those in the pkgng binary.
uses Tor's control protocol to help developers program against the Tor process,
enabling them to build things similar to Vidalia and arm.
WWW: https://stem.torproject.org/
- Apply upstream patches to plug a memory leak, etc.
- Move CLuceneConfig.cmake to DATADIR as other ports do.
- Fix several problems found by Clang and make it build cleanly.
Submitted by: Kishore Ramareddy (kishore at niksun dot com)
(initial version) [1]
