| Port details |
- py-ete3 Framework for the analysis and visualization of trees
- 3.1.3 biology
 =2      3.1.3Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2020-05-16 00:13:16
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: GPLv3
- WWW:
- http://etetoolkit.org/
- Description:
- ETE is a Python programming toolkit that assists in the automated manipulation,
analysis and visualization of phylogenetic trees. It provides a wide range of
tree handling options, node annotation features and specialized features to deal
with phylogenetic trees (i.e automatic orthology and paralogy detection,
phylostratigraphy, tree reconciliation, etc). ETE implements also an interactive
tree visualization system based on a a highly customizable tree drawing engine
(PDF and SVG tree images). Although ETE is developed as a tool for phylogenetic
analysis, it is also used to handle other types of hierarchical trees
(i.e. clustering results).
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}ete3>0:biology/py-ete3@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-ete3/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-ete3
- pkg install py39-ete3
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-ete3 listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-ete3
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1687816760
SHA256 (ete3-3.1.3.tar.gz) = 06a3b7fa8ed90187b076a8dbbe5b1b62acee94201d3c6e822f55f449601ef6f2
SIZE (ete3-3.1.3.tar.gz) = 4768608
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-lxml>0 : devel/py-lxml@py39
- py39-six>0 : devel/py-six@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- py39-qt5-pyqt>=5.15.9 : devel/py-qt5-pyqt@py39
- Test dependencies:
-
- py39-pytest>=7,1 : devel/py-pytest@py39
- python3.9 : lang/python39
- py39-qt5-pyqt>=5.15.9 : devel/py-qt5-pyqt@py39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-lxml>0 : devel/py-lxml@py39
- py39-six>0 : devel/py-six@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- py39-qt5-pyqt>=5.15.9 : devel/py-qt5-pyqt@py39
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_py-ete3
- USES:
- python pyqt:5 shebangfix
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
3.1.3
27 Jun 2023 19:34:34
 |
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
3.1.3
26 Jun 2023 22:51:39
|
Yuri Victorovich (yuri) |
biology/py-ete3: Update 3.1.2 → 3.1.3
Reported by: portscout |
3.1.2_8
25 Apr 2023 15:17:15
|
Christian Weisgerber (naddy) |
audio/opus: bump consumers after update to 1.4 |
3.1.2_7
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
3.1.2_6
09 Mar 2023 11:15:07
|
Loïc Bartoletti (lbartoletti) |
PyQt: Update to latest versions
- PyQt5: update to 5.15.9
- PyQt6: upate to 6.4.2
- PyQt6-sip: update to 13.4.1
- PyQt5-sip: update to 12.11.1
- PyQt-builder: update to 1.14.1
- sip: upate to 6.7.7
PR: 269751
Exp-run by: antoine |
3.1.2_5
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
3.1.2_5
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
3.1.2_5
06 Aug 2022 22:23:11
|
Yuri Victorovich (yuri) |
biology/py-ete3: Add tests |
3.1.2_5
07 Mar 2022 17:39:13
|
Loïc Bartoletti (lbartoletti) |
devel/py-qt5, devel/py-sip: Update versions
- Update sip to 6.5.1
- Update PyQt5 to 5.15.6
- Update PyQtChart, PyQtNetworkAuth and PyQtWebengine to 5.15.5
- Update PyQtSip to 12.9.1
- Update PyQtBuilder to 1.12.2
- Add ${_MAKE_JOBS} for pyqt.mk (reported by Tatsuki Makino)
PR: 261685
Exp-run by: antoine |
3.1.2_4
27 Jan 2022 06:12:26
|
Loïc Bartoletti (lbartoletti) |
PyQt: Update sip to 6.5.0, reintroduce sip4 and simplify PyQt framework.
SIP:
As mentioned in the update from sip to sip5, this is a transitional version
to remove what is deprecated in sip4.
Sip6 completely removes the deprecated parts.
Unfortunately, some ports — mostly cura things — can not use sip6, so we
reintroduce sip4.
PyQt:
At the same time, we took the opportunity to simplify PyQT and propose only one
package as for devel/pyside2. */py-qt5-* have been merged — excepted chart,
networkauth and webengine — into devel/py-qt5-pyqt.
This allows us to be in adequacy with the packages that the author of these (Only the first 15 lines of the commit message are shown above ) |
3.1.2_4
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
3.1.2_4
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
3.1.2_4
16 Mar 2021 09:29:54
 |
lbartoletti |
PyQt5: Update PyQt5 to 5.15.4 and py-qtbuilder to 1.9.1
PR: 254218
Exp-run by: antoine |
3.1.2_3
08 Mar 2021 06:49:18
|
lbartoletti |
PyQt5: Update PyQt5 to 5.15.3, QScintilla2 to 2.12.0, py-qtbuilder to 1.9.0
* PyQt5: update to 5.15.3
This is a minor feature and bug-fix release. There are corresponding releases of
the other PyQt5-related packages.
- Added the missing QImage.setAlphaChannel().
- Support for the QtNetworkAuth library has been moved to a separate
PyQtNetworkAuth package.
- Wheels no longer bundle the corresponding Qt libraries and instead
automatically install them from an external wheel.
* QScintilla2: update to 2.12.0
This adds support for Qt6 and removes support for Qt4.
- Change the new distname (again)i due to a conflict
- Use the new sip-build system
* devel/py-qtbuilder: update to 1.9.0
* devel/py-sip: fix flavor for sip-distinfo
PR: 253865
Exp-run by: antoine |
3.1.2_2
15 Dec 2020 17:56:00
|
lbartoletti |
Update PyQt5 to 5.15.2, sip to 5.5.0, py-qtbuilder to 1.6.0 and py-qt5-sip to
12.8.1
PR: 251764
Exp-run by: antoine |
3.1.2_1
08 Dec 2020 20:03:07
|
lbartoletti |
Update Qt/PySide2 to 5.15.2 / PyQt to 5.15.1 / SIP to 5.4.0
This commit combines several updates.
- Update Qt to 5.12.2
- Update PyQt to 5.15.1
- Since PySide 5.15.1 is broken with Qt 5.15.2, so PySide and Shiboken are also
updated to 5.15.2.
- Update sip to 5.4.0
SIP is a collection of tools to create Python bindings for C and C++ libraries
and used by PyQt and wxPython. There are some changes with sip5 [1]:
- python 3.5+ is required
- sip drops support of old deprecated methods as sipdistutils & cie.
- this version breaks also PyQt5 extension ABI. SIP files will be installed in
${PYTHON_SITELIBDIR}/PyQt${_PYQT_VERSION}/bindings
- some ports will use the new pyqtbuilder package with the pyproject.toml setup.
Instead if the project have a setup.py, you should use sip-build to build it.
- if a port needs sip, it should also needs pysip. BTW, py-qt5-core requires
pysip, so that should be enough for PyQt packages.
(Only the first 15 lines of the commit message are shown above ) |
3.1.2_1
05 Oct 2020 15:50:04
|
lbartoletti |
Update PyQt to 5.15.0, py-sip to 4.19.24 and qscintilla2 to 2.11.5
- Update PyQt to 5.15.0, py-sip to 4.19.24 and qscintilla2 to 2.11.5
- Use pypi for PYQT [1]
- Add devel/py-qt5-sip (Don't use it for now. It will be used in future updates
of PyQt with py-sip >= 5)
- Add missing py-qt5 ports: comms/py-qt5-sensors, devel/py-qt5-location,
devel/py-qt5-remoteobjects, net/py-qt5-networkauth
- Strip libs
- Refactor *_PATH and *_PORT parts
[1] RiverBankComputing doesn't offer links to download latest version of some
ports
PR: 247369
Reviewed by: tcberner
Differential Revision: https://reviews.freebsd.org/D25749
Exp-run by: antoine |
3.1.2
02 Sep 2020 03:54:05
|
yuri |
biology/py-ete3: Update 3.1.1 -> 3.1.2
Reported by: portscout |
3.1.1
16 May 2020 00:13:09
|
yuri |
New port: biology/py-ete3: Framework for the analysis and visualization of trees |
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