| Port details |
- py-resdk Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics
- 21.2.1 biology
 =2      21.2.0Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2021-04-20 04:24:12
- Last Update: 2024-11-11 03:54:22
- Commit Hash: 335c5d9
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: APACHE20
- WWW:
- https://github.com/genialis/resolwe-bio-py
- Description:
- Resolwe SDK for Python supports interaction with Resolwe server and its
extension Resolwe Bioinformatics. You can use it to upload and inspect
biomedical data sets, contribute annotations, run analysis, and write pipelines.
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}resdk>0:biology/py-resdk@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-resdk/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-resdk
- pkg install py311-resdk
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-resdk listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-resdk
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1731244665
SHA256 (resdk-21.2.1.tar.gz) = 5b231e655674f0362e72846bbf66e36afe82f595acbca32dbc77656517c21f2e
SIZE (resdk-21.2.1.tar.gz) = 258693
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-setuptools-scm>=6.4.0 : devel/py-setuptools-scm@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:
-
- py311-pytest>=7,1 : devel/py-pytest@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-aiohttp>=3.9.3 : www/py-aiohttp@py311
- py311-boto3>0 : www/py-boto3@py311
- py311-botocore-stubs>0 : www/py-botocore-stubs@py311
- py311-chardet<=5.2.0,1 : textproc/py-chardet@py311
- py311-openpyxl>0 : textproc/py-openpyxl@py311
- py311-packaging>0 : devel/py-packaging@py311
- py311-pandas>0 : math/py-pandas@py311
- py311-pytz>0 : devel/py-pytz@py311
- py311-requests>0 : www/py-requests@py311
- py311-slumber>=0.7.1 : www/py-slumber@py311
- py311-tqdm>0 : misc/py-tqdm@py311
- py311-tzlocal>0 : devel/py-tzlocal@py311
- py311-wrapt>0 : devel/py-wrapt@py311
- py311-xlrd>0 : textproc/py-xlrd@py311
- py311-mypy-boto3-s3>0 : devel/py-mypy-boto3-s3@py311
- python3.11 : lang/python311
- This port is required by:
- for Run
-
- biology/py-orange3-bioinformatics
Configuration Options:- No options to configure
- Options name:
- biology_py-resdk
- 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 |
|---|
21.2.1
11 Nov 2024 03:54:22
 |
Yuri Victorovich (yuri)
Author: Älven |
biology/py-resdk: update 21.2.0 → 21.2.1
PR: 282669 |
21.2.0
12 Jul 2024 08:58:00
|
Yuri Victorovich (yuri) |
biology/py-resdk: update 21.1.0 → 21.2.0
Reported by: portscout |
21.1.0
06 Apr 2024 01:04:45
|
Yuri Victorovich (yuri) |
biology/py-resdk: update 20.0.0 → 21.1.0
Reported by: portscout |
20.0.0
29 Feb 2024 07:18:32
|
Charlie Li (vishwin) |
devel/py-setuptools-scm: update to 8.0.4
Directory and PORTNAME changed to match normalised name in release
tarball; consumers updated to match.
Although setuptools itself is specified as a run dependency in the
Python package metadata, it is currently left out here to prevent
environment pollution until at least PR 270510 is committed.
Additionally, this version of setuptools-scm requires setuptools>=61,
which means this version is only meant for USE_PYTHON=pep517 ports
as all USE_PYTHON=distutils ports will switch to devel/py-setuptools58
also after PR 270510. science/py-emmet-core is switched to
devel/py-setuptools_scm7 accordingly, as it specifies setuptools-scm<8.
devel/py-{flit-scm,hatch-vcs} have ${PY_SETUPTOOLS} added to
RUN_DEPENDS to compensate.
Further details: https://wiki.freebsd.org/Python/setuptools
Reported by: yuri
Co-authored by: matthew
Exp-run by: antoine (earlier iteration)
Approved by: yuri (science/py-emmet-core, previous iteration)
PR: 272134
Differential Revision: https://reviews.freebsd.org/D39288 |
20.0.0
08 Dec 2023 20:55:13
|
Thierry Thomas (thierry) |
biology/py-resdk: relax chardet limitation
It accepts chardet-5.2.0.
PR: 275630
Approved by: yuri@ (maintainer) |
20.0.0
30 Oct 2023 02:31:22
|
Yuri Victorovich (yuri) |
biology/py-resdk: update 19.0.1 → 20.0.0
Reported by: portscout |
19.0.1
28 Aug 2023 06:31:28
|
Yuri Victorovich (yuri) |
biology/py-resdk: update 19.0.0 → 19.0.1
Reported by: portscout |
19.0.0
25 Aug 2023 03:24:38
|
Yuri Victorovich (yuri) |
biology/py-resdk: update 18.0.0 → 19.0.0
Reported by: portscout |
18.0.0
18 Jul 2023 00:53:09
|
Charlie Li (vishwin) |
devel/py-setuptools: convert individual consumers to ${PY_SETUPTOOLS}
Currently a no-op, but in the future outputs the correct setuptools
port depending on whether USES_PYTHON=distutils is specified.
With hat: python
PR: 270510, 270358 |
18.0.0
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> |
18.0.0
26 Jun 2023 22:51:39
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 17.0.0 → 18.0.0
Reported by: portscout |
17.0.0
27 Apr 2023 08:36:47
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 16.0.0 → 17.0.0
Reported by: portscout |
16.0.0_2
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
16.0.0_1
04 Apr 2023 18:29:11
|
Antoine Brodin (antoine) |
USE_PYTHON=pep517: bump PORTREVISION |
16.0.0
05 Feb 2023 19:05:02
|
Charlie Li (vishwin) |
Revert "Mk/Uses/python.mk: Fix USE_PYTHON=pep517: always compile and install
bytecode"
Despite installer's default behaviour to compile and install bytecode,
we are not doing so going forward at stage/package time. [0] During
initial development and qualification of PEP-517 framework support,
compiling and installing bytecode at stage/package time was considered,
but was found problematic, fragile and ultimately unreliable, both
currently and historically (with USE_PYTHON=distutils), due to our
fixed plist requirement. While the living binary distribution format
(wheel) specification [1] says to compile bytecode, that is in the
pure Python package management context (pip, etc); nuance always
exists when interacting with "system" package management.
Additionally, "bytecode is an implementation detail of the CPython
interpreter. No guarantees are made that bytecode will not be added, (Only the first 15 lines of the commit message are shown above  ) |
16.0.0_1
05 Feb 2023 18:16:47
|
Po-Chuan Hsieh (sunpoet) |
Mk/Uses/python.mk: Fix USE_PYTHON=pep517: always compile and install bytecode
- While I'm here, use long options for easier reading [1][2]
- Bump PORTREVISION of dependent ports (USE_PYTHON=pep517) for package change
It fixes build_fs_violation of dependent ports in poudriere (with -t flag).
It is also the default behavior of installer [2].
from py-sphinx log:
=>> Checking for staging violations... done
=>> Error: Filesystem touched during stage (files must install to ${STAGEDIR}):
extra: usr/local/lib/python3.9/site-packages/importlib_metadata/__pycache__
=>> Cleaning up wrkdir
from installer documentation:
--compile-bytecode
Possible choices: 0, 1, 2
generate bytecode for the specified optimization level(s) (default=0, 1)
--no-compile-bytecode
don’t generate bytecode for installed modules
Default: False
With hat: python
Reference: https://pypa-build.readthedocs.io/en/stable/ [1]
https://installer.pypa.io/en/stable/cli/installer/ [2] |
16.0.0
28 Jan 2023 06:56:38
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 15.0.0 → 16.0.0
Reported by: portscout |
15.0.0
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) |
15.0.0
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 ) |
15.0.0
07 Jun 2022 00:38:49
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 14.1.0 -> 15.0.0
Reported by: portscout |
14.1.0
27 Apr 2022 17:38:25
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 14.0.0 -> 14.1.0
Reported by: portscout |
14.0.0
19 Jan 2022 18:10:01
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 13.8.0 -> 14.0.0
Reported by: portscout |
13.8.0
30 Dec 2021 05:15:52
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 13.7.0 -> 13.8.0
Reported by: portscout |
13.7.0
18 Nov 2021 06:33:39
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 13.6.0 -> 13.7.0
Reported by: portscout |
13.6.0
22 Oct 2021 08:57:04
|
Yuri Victorovich (yuri)
Author: takefu |
biology/py-resdk: Update 13.4.0 -> 13.6.0
PR: 259351 |
13.4.0
17 Aug 2021 17:29:42
|
Yuri Victorovich (yuri)
Author: wen heping |
biology/py-resdk: Update 13.3.0 -> 13.4.0 |
13.3.0
24 May 2021 07:26:50
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 13.2.0 -> 13.3.0
Reported by: portscout |
13.2.0
05 May 2021 19:56:26
|
Yuri Victorovich (yuri) |
biology/py-resdk: Update 13.1.0 -> 13.2.0
Reported by: portscout |
13.1.0
20 Apr 2021 04:22:01
|
Yuri Victorovich (yuri) |
New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and
Resolwe Bioinformatics |
As an Amazon Associate I earn from qualifying purchases.