igraph, python-igraph: Update to 0.8.3
Closed this issue · 86 comments
(from #30611)
Released Oct 8, 2020. https://igraph.org/
the previous update was in #27597, where we also disabled blas/lapack inteface; perhaps it can make a comeback here.
This ticket also adds package texttable version 1.6.3, a dependency of python_igraph.
source tarballs: see checksums.ini
Upstream: Reported upstream. No feedback yet.
CC: @kiwifb @dcoudert @dimpase @slel @isuruf
Component: packages: optional
Author: David Coudert, Dima Pasechnik
Branch: 938d704
Reviewer: Dima Pasechnik, Matthias Koeppe
Issue created by migration from https://trac.sagemath.org/ticket/30899
Description changed:
---
+++
@@ -1 +1,3 @@
(from #30611)
+
+Released Oct 8, 2020. https://igraph.org/source at https://github.com/igraph/igraph/releases/download/0.8.3/igraph-0.8.3.tar.gz
Description changed:
---
+++
@@ -1,3 +1,5 @@
(from #30611)
Released Oct 8, 2020. https://igraph.org/
+
+the previous update was in #27597, where we also disabled blas/lapack inteface; perhaps it can make a comeback here.This version of igraph is also in homebrew https://formulae.brew.sh/formula/igraph. I don't think we are currently checking whether graph is a system package or not.
We also need python_igraph (https://igraph.org/python/), right ?
Description changed:
---
+++
@@ -3,3 +3,9 @@
Released Oct 8, 2020. https://igraph.org/
the previous update was in #27597, where we also disabled blas/lapack inteface; perhaps it can make a comeback here.
+
+---
+source:
+- https://github.com/igraph/igraph/releases/download/0.8.3/igraph-0.8.3.tar.gz
+- https://files.pythonhosted.org/packages/b8/42/a5a462b7d42f2e9b148250e2299fb7abdd7c699cef5d45487bbbd1695bd8/python-igraph-0.8.3.tar.gz
+I tried to update to 0.8.3 on macOS 10.15.7. Compilation went well, but I have the following issues:
sapristi:sage dcoudert$ ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.3.beta1, Release Date: 2020-11-07 │
│ Using Python 3.9.0. Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable. ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: import igraph
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-1-73ffca960e68> in <module>
----> 1 import igraph
~/sage/local/lib/python3.9/site-packages/igraph/__init__.py in <module>
33 # W0401: wildcard import
34 from igraph._igraph import *
---> 35 from igraph.clustering import *
36 from igraph.cut import *
37 from igraph.configuration import Configuration
~/sage/local/lib/python3.9/site-packages/igraph/clustering.py in <module>
36 from igraph.drawing.colors import ClusterColoringPalette
37 from igraph.statistics import Histogram
---> 38 from igraph.summary import _get_wrapper_for_width
39 from igraph.utils import str_to_orientation
40
~/sage/local/lib/python3.9/site-packages/igraph/summary.py in <module>
9 from itertools import islice
10 from math import ceil
---> 11 from texttable import Texttable
12 from textwrap import TextWrapper
13
ModuleNotFoundError: No module named 'texttable'
and
sage: from sage.features import PythonModule
sage: F = PythonModule("igraph", spkg="python_igraph", url="http://igraph.org")
sage: F.is_present()
FeatureTestResult('igraph', False)
I don't know what to do
New commits:
d2f206d | trac #30899: update to 0.8.3 |
Branch: public/30899_igraph
python-igraph has new dependencies that need to be added. pycairo and texttable
https://pypi.org/project/texttable/
https://pypi.org/project/pycairo/
We may be able to do without pycairo (which in turns will require cairo either as a spkg or system package, may be it is already required, that need to be checked).
Indeed python-igraph used to vendor texttable but this was changed:
Careful, it's texttable, not textable (both exist on PyPI).
as far as cairo and pycairo are concerned, we can add them, why not?
cairo is potentially opening a nest of dependencies, so if skipping it was possible, I think that would be preferable.
Branch pushed to git repo; I updated commit sha1. New commits:
373c82b | trac #30899: add texttable |
Author: David Coudert
Description changed:
---
+++
@@ -8,4 +8,5 @@
source:
- https://github.com/igraph/igraph/releases/download/0.8.3/igraph-0.8.3.tar.gz
- https://files.pythonhosted.org/packages/b8/42/a5a462b7d42f2e9b148250e2299fb7abdd7c699cef5d45487bbbd1695bd8/python-igraph-0.8.3.tar.gz
+- https://files.pythonhosted.org/packages/f5/be/716342325d6d6e05608e3a10e15f192f3723e454a25ce14bc9b9d1332772/texttable-1.6.3.tar.gz
I added texttable and it seems ok now on my side. Not sure I did it the right way...
checksums.ini needs upstream_url (see #30895)
spkg-check.in looks incomplete.
The error handling in spkg-install.in can be removed - the function sdh_pip_install already takes care of it
Branch pushed to git repo; I updated commit sha1. New commits:
2f8d505 | addded upstream_url's |
Branch pushed to git repo; I updated commit sha1. New commits:
63d3718 | remove unneeded error handling |
Branch pushed to git repo; I updated commit sha1. New commits:
9626cf9 | use pkg-config to check for libxml |
What else should be done if we want to use a local installation of igraph (e.g., homebrew) ?
Branch pushed to git repo; I updated commit sha1. New commits:
ccad4b3 | added missing quotes |
Add system package information in distros/ (see https://repology.org/project/igraph/versions) and add spkg-configure.m4
python_igraph by default vendors libigraph, to avoid it one needs to follow
https://github.com/igraph/python-igraph#linking-to-an-existing-igraph-installation
But I don't know how this can be done with our sdh_pip_install, which does not accept arguments other than ..
You can use the same method that we use in numpy: Use setup.py bdist_wheel and then sdh_store_and_pip_install_wheel.
Unless someone wants to give it a try now, I propose to postpone the use of system package to another ticket.
Replying to @dcoudert:
Unless someone wants to give it a try now, I propose to postpone the use of system package to another ticket.
The tricky part is to take care of comment:20 - I'll write the spkg-configure for igraph once this is done, but 1st things 1st.
Branch pushed to git repo; I updated commit sha1. New commits:
af23430 | build wheel and install |
igraph does not build on macOS 10.5 with Xcode 12.
[igraph-0.8.3] /bin/bash ../libtool --tag=CC --mode=compile clang -DHAVE_CONFIG_H -I. -I.. -O3 -DIGRAPH_VERIFY_FINALLY_STACK=0 -I../include -I../include -I../src/CHOLMOD/Include -I../src/CHOLMOD/Include -I../src/AMD/Include -I../src/AMD/Include -I../src/COLAMD/Include -I../src/COLAMD/Include -I../src/SuiteSparse_config -I../src/SuiteSparse_config -DNPARTITION -DNTIMER -DNCAMD -Wall -I../src/prpack -DPRPACK_IGRAPH_SUPPORT -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -O3 -c -o AMD/Source/libigraph_la-amd_1.lo `test -f 'AMD/Source/amd_1.c' || echo './'`AMD/Source/amd_1.c
[igraph-0.8.3] In file included from CHOLMOD/Supernodal/cholmod_super_numeric.c:80:
[igraph-0.8.3] CHOLMOD/Supernodal/t_cholmod_super_numeric.c:510:17: error: implicit declaration of function 'dsyrk_' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
[igraph-0.8.3] BLAS_dsyrk ("L", "N",
[igraph-0.8.3] ^
[igraph-0.8.3] ../src/CHOLMOD/Include/cholmod_blas.h:331:2: note: expanded from macro 'BLAS_dsyrk'
[igraph-0.8.3] BLAS_DSYRK (uplo, trans, &N, &K, alpha, A, &LDA, beta, C, &LDC) ; \
[igraph-0.8.3] ^
[igraph-0.8.3] ../src/CHOLMOD/Include/cholmod_blas.h:132:20: note: expanded from macro 'BLAS_DSYRK'
[igraph-0.8.3] #define BLAS_DSYRK igraphdsyrk_
[igraph-0.8.3] ^
[igraph-0.8.3] ./igraph_lapack_internal.h:86:29: note: expanded from macro 'igraphdsyrk_'
[igraph-0.8.3] #define igraphdsyrk_ dsyrk_
[igraph-0.8.3] ^
no surprise, it's very old code they vendor for no good reason, too. I'll open an issue with upstream.
The following fixes the problem
--- a/build/pkgs/igraph/spkg-install.in
+++ b/build/pkgs/igraph/spkg-install.in
@@ -4,6 +4,7 @@ You need libxml2 to run igraph. On Ubuntu and Debian Linux, installing the build
exit 1
fi
+export CFLAGS="$CFLAGS -Wno-strict-prototypes -Wno-implicit-function-declaration"
cd src
sdh_configure --with-external-blas --with-external-lapack --with-external-glpk
sdh_makeBranch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
3ff4fd8 | build wheel and install |
Branch pushed to git repo; I updated commit sha1. New commits:
7e97772 | spkg-configure and distros hints for igraph |
Changed author from David Coudert to David Coudert, Dima Pasechnik
Reviewer: Dima Pasechnik
+upstream_url=https://github.com/foutaise/texttable/archive/vVERSION.tar.gz
better to use pypi.io URLs
Replying to @mkoeppe:
+upstream_url=https://github.com/foutaise/texttable/archive/vVERSION.tar.gzbetter to use pypi.io URLs
I don't know where to get a nice url there. there are links to pypi.org there with ugly hashes.
It should be of the following form (try it)
https://pypi.io/packages/source/t/texttable/texttable-VERSION.tar.gz
Branch pushed to git repo; I updated commit sha1. New commits:
5970390 | get texttable tarball from pypi |
Branch pushed to git repo; I updated commit sha1. New commits:
bb1b510 | igraph in conda, too |
The distros files are missing the extension ".txt"
Branch pushed to git repo; I updated commit sha1. New commits:
978d9a4 | trac #30899: add missing .txt extensions |
I renamed the files.
I have a doubt for gentoo.txt: on page https://repology.org/project/igraph/versions it's written dev-libs/igraph but our file contains only igraph. Should I change to dev-libs/igraph ?
Replying to @dcoudert:
I renamed the files.
I have a doubt for
gentoo.txt: on page https://repology.org/project/igraph/versions it's writtendev-libs/igraphbut our file contains onlyigraph. Should I change todev-libs/igraph?
igraph would be fine. dev-libs/igraph would be useful to lift ambiguities if there were several igraph packages across different categories. That being said you should check what was done for other packages. If we have a convention of using the "long" package name you should follow it.
Branch pushed to git repo; I updated commit sha1. New commits:
938d704 | trac #30899: correct gentoo.txt and add freebsd.txt |
the convention is dev-libs/igraph. I also added a file for freebsd ports.
OK, needs final review?
python-igraph is on pypi https://pypi.org/project/python-igraph/ so we should use it as upstream instead of
upstream_url=https://github.com/igraph/python-igraph/releases/download/VERSION/python-igraph-VERSION.tar.gz
github generated tarballs sometimes have issues.
I am not sure about using sage-python23 , aren't we phasing that out to use plain python3 or python?
Replying to @kiwifb:
I am not sure about using
sage-python23, aren't we phasing that out to use plainpython3orpython?
I copied this from numpy's spkg-install. I suppose here should be a ticket that does away with sage-python23 at some point.
Replying to @kiwifb:
python-igraph is on pypi https://pypi.org/project/python-igraph/ so we should use it as upstream instead of
upstream_url=https://github.com/igraph/python-igraph/releases/download/VERSION/python-igraph-VERSION.tar.gzgithub generated tarballs sometimes have issues.
this tarball is not github-generated, it's a manually uploaded one. cf
https://github.com/igraph/igraph/releases/tag/0.8.3
Replying to @dimpase:
Replying to @kiwifb:
python-igraph is on pypi https://pypi.org/project/python-igraph/ so we should use it as upstream instead of
upstream_url=https://github.com/igraph/python-igraph/releases/download/VERSION/python-igraph-VERSION.tar.gzgithub generated tarballs sometimes have issues.
this tarball is not github-generated, it's a manually uploaded one. cf
https://github.com/igraph/igraph/releases/tag/0.8.3
that's definitely a good thing. I won't insist on pypi.
I tried with a homebrew install of igraph and then sage -I python_igraph and it's working well. I don't know for other systems.
Branch pushed to git repo; I updated commit sha1. New commits:
348569b | trac #30899: use python3 istead of sage-python23 |
build/pkgs/python_igraph/spkg-install.in also has sage-python23
Branch pushed to git repo; I updated commit sha1. New commits:
cf66e4c | trac #30899: missing change |
I don't like these sage-python23 -> python3 changes.
I don't see why this python3 is guaranteed to be the correct python.
In fact, no package at the moment uses python3 to run setup.py, while about a dozen
packages use sage-python23.
I really think until #30731 is done, we should continue using sage-python23.
Sorry I didn't check earlier.
I don't know how to remove the 2 lasts commits (I'm still at git beginner level...). Otherwise I can push a revert commit.
Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:
OK, I was able to remove the last 2 commits (and so revert to sage-python23). I had to do a forced push.
Replying to @dimpase:
I don't like these sage-python23 -> python3 changes.
We will switch over in #30371 - and I agree that it is better for uniformity if we don't do this package by package.
I don't see why this python3 is guaranteed to be the correct python.
It is actually guaranteed by our installation.
- When there is a suitable system python3.x, then Sage creates a venv over it and installs a
python3symlink in$SAGE_LOCAL/bin(which is in$PATHand not shadowed by what is in front of it), sopython3works. - When there is no suitable system python3.x, then Sage builds one and installs a binary in
$SAGE_LOCAL/bin, sopython3also works.
(Side note: After #22731/#30013, the above is still true, but with$SAGE_VENV/bininstead of$SAGE_LOCAL/bin.)
Description changed:
---
+++
@@ -5,8 +5,5 @@
the previous update was in #27597, where we also disabled blas/lapack inteface; perhaps it can make a comeback here.
---
-source:
-- https://github.com/igraph/igraph/releases/download/0.8.3/igraph-0.8.3.tar.gz
-- https://files.pythonhosted.org/packages/b8/42/a5a462b7d42f2e9b148250e2299fb7abdd7c699cef5d45487bbbd1695bd8/python-igraph-0.8.3.tar.gz
-- https://files.pythonhosted.org/packages/f5/be/716342325d6d6e05608e3a10e15f192f3723e454a25ce14bc9b9d1332772/texttable-1.6.3.tar.gz
+source tarballs: see `checksums.ini`
Description changed:
---
+++
@@ -4,6 +4,8 @@
the previous update was in #27597, where we also disabled blas/lapack inteface; perhaps it can make a comeback here.
+This ticket also adds package `texttable` version 1.6.3, a dependency of `python_igraph`.
+
---
source tarballs: see `checksums.ini`
lgtm
Changed reviewer from Dima Pasechnik to Dima Pasechnik, Matthias Koeppe
Looks good. Given that this is an optional package, we can defer the actual portability tests to the automatic run of the GH Actions when it is merged into a beta release.
Upstream: Reported upstream. No feedback yet.
I've opened igraph/igraph#1547 in regard of XCode 12 issue (solved with CFLAGS here).
Changed branch from public/30899_igraph to 938d704
Volker, the upstream tarball for python_igraph seems to be missing on the mirrors. Note that make download has been repaired - so it should be easy to check if anything is missing