| Port details |
- py-pyteomics Python modules for proteomics data analysis
- 4.7.5 science
 =2      4.7.3Version of this port present on the latest quarterly branch. - Maintainer: sunpoet@FreeBSD.org
- Port Added: 2015-11-02 09:24:59
- Last Update: 2024-10-25 15:56:47
- Commit Hash: df8e2d1
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: APACHE20
- WWW:
- https://pyteomics.readthedocs.io/en/latest/
- https://github.com/levitsky/pyteomics
- Description:
- 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
The goal of the Pyteomics project is to provide a versatile, reliable and
well-documented set of open tools for the wide proteomics community. One of the
project's key features is Python itself, an open source language increasingly
popular in scientific programming. The main applications of the library are
reproducible statistical data analysis and rapid software prototyping.
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}pyteomics>0:science/py-pyteomics@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/science/py-pyteomics/ && make install clean
- To add the package, run one of these commands:
- pkg install science/py-pyteomics
- pkg install py311-pyteomics
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 py311-pyteomics listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-pyteomics
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1729856288
SHA256 (pyteomics-4.7.5.tar.gz) = 382aeaa8b921bdd2a7e5b4aa9fe46c6184bb43701205a845b4b861ee3e88f46a
SIZE (pyteomics-4.7.5.tar.gz) = 236493
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:
-
- py311-setuptools>=0 : devel/py-setuptools@py311
- py311-wheel>=0 : devel/py-wheel@py311
- python3.11 : lang/python311
- py311-build>=0 : devel/py-build@py311
- py311-installer>=0 : devel/py-installer@py311
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-pandas>=0.17,1 : math/py-pandas@py311
- py311-matplotlib>=0 : math/py-matplotlib@py311
- py311-numpy>=0,1 : math/py-numpy@py311
- py311-lxml>=0 : devel/py-lxml@py311
- py311-sqlalchemy14>=0 : databases/py-sqlalchemy14@py311
- py311-lxml>=0 : devel/py-lxml@py311
- py311-numpy>=0,1 : math/py-numpy@py311
- python3.11 : lang/python311
- There are no ports dependent upon this port
Configuration Options:- ===> The following configuration options are available for py311-pyteomics-4.7.5:
DF=on: DataFrame support
GRAPHICS=on: Graphics support
TDA=on: Target-decoy approach support
UNIMOD=on: Unimod database support
XML=on: XML support
===> Use 'make config' to modify these settings
- Options name:
- science_py-pyteomics
- USES:
- python
- 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 |
|---|
4.7.5
25 Oct 2024 15:56:47
 |
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.7.5
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.7.4
14 Oct 2024 05:25:45
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.7.4
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.7.3
04 Aug 2024 17:14:10
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.7.3
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.7.2
19 May 2024 17:15:51
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.7.2
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.7.1_1
09 Mar 2024 14:06:14
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Convert to USE_PYTHON=pep517
- Bump PORTREVISION for package change |
4.7.1
06 Mar 2024 22:31:12
|
Max Brazhnikov (makc) |
science/py-pyteomics: update to 4.7.1
PR: 277087
Approved by: maintainer timeout |
4.7
21 Feb 2024 15:07:59
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.7
- Update WWW and clean up pkg-descr
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.6
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> |
4.6
27 May 2023 04:09:57
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.6
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.5.6_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
4.5.6
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
4.5.6
30 Dec 2022 09:05:06
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.5.6
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
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) |
4.5.5
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  ) |
4.5.5
31 Aug 2022 11:41:13
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.5.5
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.5.4
30 Jul 2022 05:58:16
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.5.4
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.5.3
25 Mar 2022 13:37:13
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.5.3
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.5.2
28 Feb 2022 12:46:24
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.5.2
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.5
21 Sep 2021 22:23:38
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.5
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.4.2_1
11 May 2021 21:47:18
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Change RUN_DEPENDS from py-sqlalchemy13 to py-sqlalchemy14
- Bump PORTREVISION for dependency change |
4.4.2
10 May 2021 20:13:20
|
Thierry Thomas (thierry) |
math/py-matplotlib: chase minimum Python version in dependent ports
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.
PR: 255347
Reported by: sunpoet |
4.4.2
02 May 2021 19:45:37
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Remove PYNUMPY |
4.4.2
18 Apr 2021 05:44:06
|
Po-Chuan Hsieh (sunpoet) |
science/py-pyteomics: Update to 4.4.2
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.4.1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
4.4.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
4.4.1
26 Jan 2021 17:37:47
 |
sunpoet |
Update to 4.4.1
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.4.0
21 Nov 2020 09:20:52
|
sunpoet |
Update to 4.4.0
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.3.3
02 Oct 2020 07:31:12
|
sunpoet |
Update to 4.3.3
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.3.2
19 Sep 2020 14:15:43
|
antoine |
Unbreak bulk -a |
4.3.2
05 Sep 2020 21:32:55
|
sunpoet |
Update version requirement of RUN_DEPENDS |
4.3.2
21 May 2020 20:44:52
|
sunpoet |
Add DF, GRAPHICS, TDA, UNIMOD and XML options |
4.3.2
21 May 2020 04:58:55
|
sunpoet |
Update to 4.3.2
- Update WWW
Changes: https://github.com/levitsky/pyteomics/releases
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.2
01 Mar 2020 06:49:00
|
sunpoet |
Update to 4.2
Changes: https://bitbucket.org/levitsky/pyteomics/src/default/CHANGELOG
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.1.2_1
26 Jul 2019 20:46:57
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330 |
4.1.2
09 Jun 2019 16:52:36
|
sunpoet |
Update to 4.1.2
Changes: https://bitbucket.org/levitsky/pyteomics/src/default/CHANGELOG
https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.1.1
25 May 2019 22:03:26
|
sunpoet |
Update to 4.1.1
Changes: https://pyteomics.readthedocs.io/en/latest/changelog.html |
4.1
18 Apr 2019 18:00:53
|
sunpoet |
Update to 4.1
- Update pkg-descr
- Update WWW
- Take maintainership
Changes: https://pyteomics.readthedocs.io/en/latest/changelog.html |
3.5.1_1
12 Dec 2018 01:35:36
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590 |
3.5.1
29 Nov 2018 21:58:22
|
makc |
science/py-pyteomics:
- Update to 3.5.1 and enable for all Python versions |
3.4.2_1
20 Jun 2018 17:05:44
|
mat |
Use PY_FLAVOR for dependencies.
FLAVOR is the current port's flavor, it should not be used outside of
this scope.
Sponsored by: Absolight |
3.4.2_1
25 Apr 2018 16:42:38
|
amdmi3 |
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
they now redirect to anyway. All new urls checked to return 200,
I've fixed a couple of them in the process.
Approved by: portmgr blanket, mat |
3.4.2_1
10 Mar 2018 17:46:06
|
gerald |
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079). |
3.4.2
30 Nov 2017 15:50:34
 |
mat |
Convert Python ports to FLAVORS.
Ports using USE_PYTHON=distutils are now flavored. They will
automatically get flavors (py27, py34, py35, py36) depending on what
versions they support.
There is also a USE_PYTHON=flavors for ports that do not use distutils
but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if
using distutils but flavors are not wanted.
A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
added to cope with Python ports that did not have the Python
PKGNAMEPREFIX but are flavored.
USES=python now also exports a PY_FLAVOR variable that contains the (Only the first 15 lines of the commit message are shown above ) |
3.4.2
02 Jul 2017 16:10:25
|
sunpoet |
Update to 3.4.2
- Sort USE_PYTHON
Changes: https://bitbucket.org/levitsky/pyteomics/src/default/CHANGELOG |
3.4.1
22 Feb 2017 01:45:24
|
vanilla |
Update to 3.4.1. |
3.4
01 Dec 2016 23:52:39
|
jhale |
Update to 3.4
Add LICENSE_FILE
PR: 214198
Submitted by: Jochen Neumeister <joneum@bsdproject.de> |
2.4.0_1
07 Nov 2016 12:24:07
|
amdmi3 |
- Add LICENSE
- Add NO_ARCH |
2.4.0_1
20 Oct 2016 15:58:13
|
rakuco |
Reassign makc's ports back to the pool.
See "Maintainer Reset" in
https://www.freebsd.org/portmgr/policies_contributors.html. makc's last commit
was in March 31st (r412218), and his ports have been timing out since at least
July (r418155).
I also emailed him 2 weeks ago and have received no response so far. |
2.4.0_1
01 Apr 2016 14:25:18
|
mat |
Remove ${PORTSDIR}/ from dependencies, categories r, s, t, and u.
With hat: portmgr
Sponsored by: Absolight |
2.4.0_1
02 Nov 2015 09:24:50
|
makc |
Rename my ports to comply with Python ports policy
Requested by: koobs |
As an Amazon Associate I earn from qualifying purchases.