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Port details
py-python-libsbml LibSBML Python API
5.20.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 5.20.1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-08-17 21:33:06
Last Update: 2023-12-03 12:02:23
Commit Hash: 4135d03
Also Listed In: python
License: LGPL21
WWW:
https://sbml.org/Main_Page
Description:
Python binding for libsbml - Systems Biology Markup Language (SBML) read/write library.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

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:
  • ${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR}
To install the port:
cd /usr/ports/biology/py-python-libsbml/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-python-libsbml
  • pkg install py39-python-libsbml
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-python-libsbml listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-python-libsbml
Package flavors (<flavor>: <package>)
  • py39: py39-python-libsbml
distinfo:
TIMESTAMP = 1687747738 SHA256 (python-libsbml-5.20.1.tar.gz) = 5a10f0a494ba03ffda5190430f80a15516357d2d17698b928a01cbd2e231bf45 SIZE (python-libsbml-5.20.1.tar.gz) = 48808000

Packages (timestamps in pop-ups are UTC):
py39-python-libsbml
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest5.20.15.20.1-5.20.15.20.1---
FreeBSD:13:quarterly5.20.15.20.15.20.15.20.15.20.15.20.15.20.15.20.1
FreeBSD:14:latest5.20.15.20.15.19.05.20.15.20.15.19.0-5.19.0
FreeBSD:14:quarterly5.20.15.20.1-5.20.15.20.15.20.15.20.15.20.1
FreeBSD:15:latest5.20.15.20.1n/a5.20.1n/a5.20.15.20.15.20.1
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake-core
  2. swig : devel/swig
  3. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  2. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/py-PySCeS

Configuration Options:
No options to configure
Options name:
biology_py-python-libsbml
USES:
python
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://github.com/sbmlteam/python-libsbml/releases/download/v5.20.1/
Collapse this list.

Number of commits found: 11

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
5.20.1
03 Dec 2023 12:02:23
commit hash: 4135d03c4dfc53060604c924d2849763ec47f01fcommit hash: 4135d03c4dfc53060604c924d2849763ec47f01fcommit hash: 4135d03c4dfc53060604c924d2849763ec47f01fcommit hash: 4135d03c4dfc53060604c924d2849763ec47f01f files touched by this commit
Ruslan Makhmatkhanov (rm) search for other commits by this committer
biology/py-python-libsbml: relax python version requirement

According to [1] python-libsbml supports Python 3.11 since version 5.19.2

[1] https://github.com/sbmlteam/python-libsbml/releases/tag/v5.19.2

PR:		275494
Approved by:	portmgr (blanket)
5.20.1
26 Jul 2023 07:04:04
commit hash: 246333eca493bcd5568689f249dc16d2046d3900commit hash: 246333eca493bcd5568689f249dc16d2046d3900commit hash: 246333eca493bcd5568689f249dc16d2046d3900commit hash: 246333eca493bcd5568689f249dc16d2046d3900 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-python-libsbml: Use CMAKE_BUILD_PARALLEL_LEVEL env var for
parallelization
5.20.1
26 Jul 2023 06:20:26
commit hash: 8221f161dcf785939e3766a00ab19caba308386dcommit hash: 8221f161dcf785939e3766a00ab19caba308386dcommit hash: 8221f161dcf785939e3766a00ab19caba308386dcommit hash: 8221f161dcf785939e3766a00ab19caba308386d files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-python-libsbml: Parallelize build
5.20.1
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
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>
5.20.1
26 Jun 2023 15:53:03
commit hash: 45027c0066d01a3ddaefcf99a72d9f84970fff21commit hash: 45027c0066d01a3ddaefcf99a72d9f84970fff21commit hash: 45027c0066d01a3ddaefcf99a72d9f84970fff21commit hash: 45027c0066d01a3ddaefcf99a72d9f84970fff21 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-python-libsbml: Update 5.19.0 → 5.20.1

Reported by:	portscout
5.19.0
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
5.19.0
09 Sep 2022 20:32:24
commit hash: e942e560c468063b850b05ae3df340b36f24c7b5commit hash: e942e560c468063b850b05ae3df340b36f24c7b5commit hash: e942e560c468063b850b05ae3df340b36f24c7b5commit hash: e942e560c468063b850b05ae3df340b36f24c7b5 files touched by this commit
Daniel Engberg (diizzy) search for other commits by this committer
*/*: Update path set in BUILD_DEPENDS for CMake

Commit b23ea4e2d2f51b53d8915fe9fd7b4efbdd575e38 changed its location to
devel/cmake-core

Approved by:	portmgr (blanket)
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
5.19.0
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
5.19.0
03 Nov 2021 18:26:41
commit hash: c7f13313cda239c91fba6fa7bb775817379f0fcdcommit hash: c7f13313cda239c91fba6fa7bb775817379f0fcdcommit hash: c7f13313cda239c91fba6fa7bb775817379f0fcdcommit hash: c7f13313cda239c91fba6fa7bb775817379f0fcd files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
biology/py-python-libsbml: limit supported python versions, fix build

- Cap supported python verions with 3.9. Fails with 3.10:

  Traceback (most recent call last):
    File
"/wrkdirs/usr/ports/biology/py-python-libsbml/work-py310/python-libsbml-5.19.0/libsbml_source/src/bindings/python/doc-converter/rewrite_pydoc.py",
line 121, in <module>
      from formatter import NullWriter, AbstractFormatter
  ModuleNotFoundError: No module named 'formatter'

- Fix library stripping to unbreak port with python != 3.8

Approved by:	portmgr blanket
5.19.0
17 Aug 2021 21:30:07
commit hash: 10875d93bb728801a61c3d78a1e140718fd0cfdfcommit hash: 10875d93bb728801a61c3d78a1e140718fd0cfdfcommit hash: 10875d93bb728801a61c3d78a1e140718fd0cfdfcommit hash: 10875d93bb728801a61c3d78a1e140718fd0cfdf files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-python-libsbml: New port: LibSBML Python API

Number of commits found: 11