igraph, python-igraph: Update to 0.8.3

[mkoeppe]

(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.

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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

[dimpase]

comment:2

source at https://github.com/igraph/igraph/releases/download/0.8.3/igraph-0.8.3.tar.gz

[dcoudert]

comment:4

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 ?

[dcoudert]

comment:5

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

[dcoudert]

Commit: d2f206d

[dcoudert]

Branch: public/30899_igraph

[kiwifb]

comment:6

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).

[slel]

comment:7

Indeed python-igraph used to vendor texttable but this was changed:

igraph/python-igraph@60194fb

Careful, it's texttable, not textable (both exist on PyPI).

https://pypi.org/project/texttable/

[dimpase]

comment:8

as far as cairo and pycairo are concerned, we can add them, why not?

[kiwifb]

comment:9

cairo is potentially opening a nest of dependencies, so if skipping it was possible, I think that would be preferable.

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

373c82b

trac #30899: add texttable

[sagetrac-git]

Changed commit from d2f206d to 373c82b

[dcoudert]

Author: David Coudert

[dcoudert]

comment:11

I added texttable and it seems ok now on my side. Not sure I did it the right way...

[mkoeppe]

comment:12

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

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

2f8d505

addded upstream_url's

[sagetrac-git]

Changed commit from 373c82b to 2f8d505

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

63d3718

remove unneeded error handling

[sagetrac-git]

Changed commit from 2f8d505 to 63d3718

[sagetrac-git]

Changed commit from 63d3718 to 9626cf9

[slel]

comment:47

Replying to @kiwifb:

I am not sure about using sage-python23 , aren't we
phasing that out to use plain python3 or python?

Yes, see #30731.

[sagetrac-git]

Changed commit from 938d704 to 348569b

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

348569b

trac #30899: use python3 istead of sage-python23

[dimpase]

comment:49

build/pkgs/python_igraph/spkg-install.in also has sage-python23

[sagetrac-git]

Changed commit from 348569b to cf66e4c

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

cf66e4c

trac #30899: missing change

[dimpase]

comment:51

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.

[dcoudert]

comment:52

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.

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

[sagetrac-git]

Changed commit from cf66e4c to 938d704

[dcoudert]

comment:54

OK, I was able to remove the last 2 commits (and so revert to sage-python23). I had to do a forced push.

[mkoeppe]

comment:55

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 python3 symlink in $SAGE_LOCAL/bin (which is in $PATH and not shadowed by what is in front of it), so python3 works.
• When there is no suitable system python3.x, then Sage builds one and installs a binary in $SAGE_LOCAL/bin, so python3 also works.
  (Side note: After Replace "$SAGE_LOCAL/bin" by more specific variables to make Sage easier to package, use in venvs #22731/src/bin/sage-env: Make sure $SAGE_VENV/bin is at the beginning of the PATH #30013, the above is still true, but with $SAGE_VENV/bin instead of $SAGE_LOCAL/bin.)

[dimpase]

comment:58

lgtm

[mkoeppe]

Changed reviewer from Dima Pasechnik to Dima Pasechnik, Matthias Koeppe

[mkoeppe]

comment:59

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.

[dimpase]

Upstream: Reported upstream. No feedback yet.

[dimpase]

comment:60

I've opened igraph/igraph#1547 in regard of XCode 12 issue (solved with CFLAGS here).

[vbraun]

Changed branch from public/30899_igraph to 938d704

[mkoeppe]

comment:62

Follow up in #27921, running the libxml2 check via a script package

[mkoeppe]

Changed commit from 938d704 to none

[mkoeppe]

comment:63

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