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Port details
py-resdk Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics
20.0.0 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 20.0.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-20 04:24:12
Last Update: 2024-02-29 07:18:32
Commit Hash: 5d4139f
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.
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:
  • ${PYTHON_PKGNAMEPREFIX}resdk>0:biology/py-resdk@${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 py39-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 py39-resdk listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-resdk
Package flavors (<flavor>: <package>)
  • py39: py39-resdk
distinfo:
TIMESTAMP = 1698476837 SHA256 (resdk-20.0.0.tar.gz) = 56728eac8971c7f4c7eca2573a4783bb75373a083b2c1e0a8066e5267a7328df SIZE (resdk-20.0.0.tar.gz) = 256197

Packages (timestamps in pop-ups are UTC):
py39-resdk
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest20.0.020.0.0-20.0.020.0.0---
FreeBSD:13:quarterly20.0.020.0.0--20.0.0-20.0.0-
FreeBSD:14:latest20.0.020.0.0-20.0.020.0.0---
FreeBSD:14:quarterly20.0.020.0.0--20.0.0-20.0.0-
FreeBSD:15:latest20.0.020.0.0n/a20.0.0n/a-20.0.020.0.0
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. py39-setuptools>0 : devel/py-setuptools@py39
  2. py39-setuptools-scm>=6.4.0 : devel/py-setuptools-scm@py39
  3. py39-wheel>0 : devel/py-wheel@py39
  4. python3.9 : lang/python39
  5. py39-build>=0 : devel/py-build@py39
  6. py39-installer>=0 : devel/py-installer@py39
Test dependencies:
  1. py39-pytest>=7,1 : devel/py-pytest@py39
  2. python3.9 : lang/python39
Runtime dependencies:
  1. py39-aiohttp>0 : www/py-aiohttp@py39
  2. py39-boto3>0 : www/py-boto3@py39
  3. py39-botocore-stubs>0 : www/py-botocore-stubs@py39
  4. py39-chardet<=5.2.0,1 : textproc/py-chardet@py39
  5. py39-openpyxl>0 : textproc/py-openpyxl@py39
  6. py39-pandas>=1.0.0 : math/py-pandas@py39
  7. py39-pytz>=2018.4 : devel/py-pytz@py39
  8. py39-requests>=2.6.0 : www/py-requests@py39
  9. py39-slumber>=0.7.1 : www/py-slumber@py39
  10. py39-tqdm>0 : misc/py-tqdm@py39
  11. py39-tzlocal>=1.5.1 : devel/py-tzlocal@py39
  12. py39-wrapt>0 : devel/py-wrapt@py39
  13. py39-xlrd>0 : textproc/py-xlrd@py39
  14. py39-mypy-boto3-s3>0 : devel/py-mypy-boto3-s3@py39
  15. python3.9 : lang/python39
This port is required by:
for Run
  1. 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:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/r/resdk/
  2. https://pypi.org/packages/source/r/resdk/
Collapse this list.

Number of commits found: 27

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
20.0.0
29 Feb 2024 07:18:32
commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454commit hash: 5d4139f8bdb67bd6e8328422f9762661bd0d6454 files touched by this commit
Charlie Li (vishwin) search for other commits by this committer
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
commit hash: bb97b107cebb25f350dab46cb07cef97609759becommit hash: bb97b107cebb25f350dab46cb07cef97609759becommit hash: bb97b107cebb25f350dab46cb07cef97609759becommit hash: bb97b107cebb25f350dab46cb07cef97609759be files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
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
commit hash: 191490a4ef56ad5a42cbf0c4101d336bd46bc908commit hash: 191490a4ef56ad5a42cbf0c4101d336bd46bc908commit hash: 191490a4ef56ad5a42cbf0c4101d336bd46bc908commit hash: 191490a4ef56ad5a42cbf0c4101d336bd46bc908 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: update 19.0.1 → 20.0.0

Reported by:	portscout
19.0.1
28 Aug 2023 06:31:28
commit hash: f97472faf9161e540bcec8268b52ecdfcf827b21commit hash: f97472faf9161e540bcec8268b52ecdfcf827b21commit hash: f97472faf9161e540bcec8268b52ecdfcf827b21commit hash: f97472faf9161e540bcec8268b52ecdfcf827b21 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: update 19.0.0 → 19.0.1

Reported by:	portscout
19.0.0
25 Aug 2023 03:24:38
commit hash: 61ea32a58c1a5f63580f1e9d801c2fce164ef945commit hash: 61ea32a58c1a5f63580f1e9d801c2fce164ef945commit hash: 61ea32a58c1a5f63580f1e9d801c2fce164ef945commit hash: 61ea32a58c1a5f63580f1e9d801c2fce164ef945 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: update 18.0.0 → 19.0.0

Reported by:	portscout
18.0.0
18 Jul 2023 00:53:09
commit hash: 9a80a6ee5e8ebf5c279b3d7a9e7e8b7dbabbaf0acommit hash: 9a80a6ee5e8ebf5c279b3d7a9e7e8b7dbabbaf0acommit hash: 9a80a6ee5e8ebf5c279b3d7a9e7e8b7dbabbaf0acommit hash: 9a80a6ee5e8ebf5c279b3d7a9e7e8b7dbabbaf0a files touched by this commit
Charlie Li (vishwin) search for other commits by this committer
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
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>
18.0.0
26 Jun 2023 22:51:39
commit hash: a3855d8a75c967c69607b44e45408315137a15cdcommit hash: a3855d8a75c967c69607b44e45408315137a15cdcommit hash: a3855d8a75c967c69607b44e45408315137a15cdcommit hash: a3855d8a75c967c69607b44e45408315137a15cd files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 17.0.0 → 18.0.0

Reported by:	portscout
17.0.0
27 Apr 2023 08:36:47
commit hash: 66fef84e5490d359c6708b17ea7b448da8a675b2commit hash: 66fef84e5490d359c6708b17ea7b448da8a675b2commit hash: 66fef84e5490d359c6708b17ea7b448da8a675b2commit hash: 66fef84e5490d359c6708b17ea7b448da8a675b2 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 16.0.0 → 17.0.0

Reported by:	portscout
16.0.0_2
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
16.0.0_1
04 Apr 2023 18:29:11
commit hash: 1730e97e049085a8fe5536788d214cbfc4eb3123commit hash: 1730e97e049085a8fe5536788d214cbfc4eb3123commit hash: 1730e97e049085a8fe5536788d214cbfc4eb3123commit hash: 1730e97e049085a8fe5536788d214cbfc4eb3123 files touched by this commit
Antoine Brodin (antoine) search for other commits by this committer
USE_PYTHON=pep517: bump PORTREVISION
16.0.0
05 Feb 2023 19:05:02
commit hash: f5890bd3cbc66a805bfc04a1a45688b5a3e68c50commit hash: f5890bd3cbc66a805bfc04a1a45688b5a3e68c50commit hash: f5890bd3cbc66a805bfc04a1a45688b5a3e68c50commit hash: f5890bd3cbc66a805bfc04a1a45688b5a3e68c50 files touched by this commit
Charlie Li (vishwin) search for other commits by this committer
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 View all of this commit message)
16.0.0_1
05 Feb 2023 18:16:47
commit hash: de6965254c3a007efcf697c3d455b54d2aeb2383commit hash: de6965254c3a007efcf697c3d455b54d2aeb2383commit hash: de6965254c3a007efcf697c3d455b54d2aeb2383commit hash: de6965254c3a007efcf697c3d455b54d2aeb2383 files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
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
commit hash: 29ec6d22d557b9dac349cde0220db6b9e1180008commit hash: 29ec6d22d557b9dac349cde0220db6b9e1180008commit hash: 29ec6d22d557b9dac349cde0220db6b9e1180008commit hash: 29ec6d22d557b9dac349cde0220db6b9e1180008 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 15.0.0 → 16.0.0

Reported by:	portscout
15.0.0
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
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)
15.0.0
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)
15.0.0
07 Jun 2022 00:38:49
commit hash: 97850626d50919c4c7aad2ba0b5be90ca6df1596commit hash: 97850626d50919c4c7aad2ba0b5be90ca6df1596commit hash: 97850626d50919c4c7aad2ba0b5be90ca6df1596commit hash: 97850626d50919c4c7aad2ba0b5be90ca6df1596 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 14.1.0 -> 15.0.0

Reported by:	portscout
14.1.0
27 Apr 2022 17:38:25
commit hash: fedffc237c1385edf91277373ce802cef77aac7fcommit hash: fedffc237c1385edf91277373ce802cef77aac7fcommit hash: fedffc237c1385edf91277373ce802cef77aac7fcommit hash: fedffc237c1385edf91277373ce802cef77aac7f files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 14.0.0 -> 14.1.0

Reported by:	portscout
14.0.0
19 Jan 2022 18:10:01
commit hash: 738dbb9b6736a3f5b681bc9714cf2f3c16a6b8e8commit hash: 738dbb9b6736a3f5b681bc9714cf2f3c16a6b8e8commit hash: 738dbb9b6736a3f5b681bc9714cf2f3c16a6b8e8commit hash: 738dbb9b6736a3f5b681bc9714cf2f3c16a6b8e8 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 13.8.0 -> 14.0.0

Reported by:	portscout
13.8.0
30 Dec 2021 05:15:52
commit hash: d4592076c8ff4bab0c51b4a0345a91eb9cc6dce3commit hash: d4592076c8ff4bab0c51b4a0345a91eb9cc6dce3commit hash: d4592076c8ff4bab0c51b4a0345a91eb9cc6dce3commit hash: d4592076c8ff4bab0c51b4a0345a91eb9cc6dce3 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 13.7.0 -> 13.8.0

Reported by:	portscout
13.7.0
18 Nov 2021 06:33:39
commit hash: bcfb23816bd707e2ec4443d711212c2388208d12commit hash: bcfb23816bd707e2ec4443d711212c2388208d12commit hash: bcfb23816bd707e2ec4443d711212c2388208d12commit hash: bcfb23816bd707e2ec4443d711212c2388208d12 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 13.6.0 -> 13.7.0

Reported by:	portscout
13.6.0
22 Oct 2021 08:57:04
commit hash: a90a3d3623d653bbee690d3f262e4f656c97e7c5commit hash: a90a3d3623d653bbee690d3f262e4f656c97e7c5commit hash: a90a3d3623d653bbee690d3f262e4f656c97e7c5commit hash: a90a3d3623d653bbee690d3f262e4f656c97e7c5 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
Author: takefu
biology/py-resdk: Update 13.4.0 -> 13.6.0

PR:		259351
13.4.0
17 Aug 2021 17:29:42
commit hash: 21c779f88ef7540b13fa2164360ea04d6579e5abcommit hash: 21c779f88ef7540b13fa2164360ea04d6579e5abcommit hash: 21c779f88ef7540b13fa2164360ea04d6579e5abcommit hash: 21c779f88ef7540b13fa2164360ea04d6579e5ab files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
Author: wen heping
biology/py-resdk: Update 13.3.0 -> 13.4.0
13.3.0
24 May 2021 07:26:50
commit hash: 191694478f466f184531a0c4342f44dfef2666e1commit hash: 191694478f466f184531a0c4342f44dfef2666e1commit hash: 191694478f466f184531a0c4342f44dfef2666e1commit hash: 191694478f466f184531a0c4342f44dfef2666e1 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 13.2.0 -> 13.3.0

Reported by:	portscout
13.2.0
05 May 2021 19:56:26
commit hash: 4e9b2197ad8ecf3597606b04d945f50ab6fb9c5acommit hash: 4e9b2197ad8ecf3597606b04d945f50ab6fb9c5acommit hash: 4e9b2197ad8ecf3597606b04d945f50ab6fb9c5acommit hash: 4e9b2197ad8ecf3597606b04d945f50ab6fb9c5a files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-resdk: Update 13.1.0 -> 13.2.0

Reported by:	portscout
13.1.0
20 Apr 2021 04:22:01
commit hash: b9f16eadc90f774bff9030ef7b8511ba1a392464commit hash: b9f16eadc90f774bff9030ef7b8511ba1a392464commit hash: b9f16eadc90f774bff9030ef7b8511ba1a392464commit hash: b9f16eadc90f774bff9030ef7b8511ba1a392464 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and
Resolwe Bioinformatics

Number of commits found: 27