[sage-devel] Re: 9.2 Beta0 build issue under Ubuntu 19.10

2020-05-29 Thread John H Palmieri
The glpk test failures are being discussed at https://trac.sagemath.org/ticket/29493. On Friday, May 29, 2020 at 1:19:51 PM UTC-7, Andy Howell wrote: > > I originally sent this to sage-release when 9.1 was released. I see the > same test failures under 9.2.beta0. I didn't see a way to make

Re: [sage-devel] New Python version requirement for Sage?

2020-05-27 Thread John H Palmieri
The particular ticket in question deals with matplotlib, which has Python as a dependency, so I think we can safely build with "Sage's Python 3", which should be at least 3.6. If we can accommodate older version of Python for the rest of the Sage build — and I think we can, given the current

Re: [sage-devel] Error installing package openblas-0.3.6.p0 on mac

2020-05-18 Thread John H Palmieri
There is a link given to the log file in the first few lines of the original post. On Monday, May 18, 2020 at 8:57:35 PM UTC-7, Justin C. Walker wrote: > > Please include the full log for openblas. > > Thanks! > > > On May 18, 2020, at 17:05 , Valentin Buciumas > wrote: > > > > Hello, > >

Re: [sage-devel] remove log_html() and other log_*()

2020-05-08 Thread John H Palmieri
On Friday, May 8, 2020 at 2:17:25 PM UTC-7, Michael Orlitzky wrote: > > There are some duplicates in there (I've wasted enough time on it), but > it matches things that a regex never will. That function is implemented > by the following code, which belongs in a third-party library and not >

Re: [sage-devel] remove log_html() and other log_*()

2020-05-08 Thread John H Palmieri
On Friday, May 8, 2020 at 9:51:34 AM UTC-7, Michael Orlitzky wrote: > > On 5/8/20 12:11 PM, John H Palmieri wrote: > > > > They accomplish different things: one searches the global name space and > > the other searches the source code. > > > > Examp

Re: [sage-devel] remove log_html() and other log_*()

2020-05-08 Thread John H Palmieri
On Friday, May 8, 2020 at 3:08:21 AM UTC-7, Dima Pasechnik wrote: > > On Fri, May 8, 2020 at 10:37 AM Markus Wageringel > > wrote: > > > > Am Freitag, 8. Mai 2020 09:03:08 UTC+2 schrieb Sebastian Oehms: > >> > >> But if we talk about users who are not interested in code and strings, >

Re: [sage-devel] remove log_html() and other log_*()

2020-05-07 Thread John H Palmieri
On Thursday, May 7, 2020 at 9:58:55 AM UTC-7, John H Palmieri wrote: > > > > On Thursday, May 7, 2020 at 4:40:52 AM UTC-7, Michael Orlitzky wrote: >> >> On 5/6/20 11:28 PM, John H Palmieri wrote: >> > >> > And to clarify, this is what you expec

Re: [sage-devel] remove log_html() and other log_*()

2020-05-07 Thread John H Palmieri
On Thursday, May 7, 2020 at 4:40:52 AM UTC-7, Michael Orlitzky wrote: > > On 5/6/20 11:28 PM, John H Palmieri wrote: > > > > And to clarify, this is what you expect users to use instead of > > search_src? ;) > > > And to clarify, neither you no

Re: [sage-devel] remove log_html() and other log_*()

2020-05-06 Thread John H Palmieri
On Sunday, May 3, 2020 at 4:48:49 PM UTC-7, Michael Orlitzky wrote: > > On 5/2/20 1:55 PM, John H Palmieri wrote: > > > > OMG, why does "sage -grep" use the "find" command? > > > > Others have pointed out that "-r" isn't standar

Re: [sage-support] How to use notebook in sage 9.0?

2020-05-06 Thread John H Palmieri
Silly question, but are you sure you are starting up Sage 9.0 when you do all of this ("sage --notebook" or "sage --sh")? If you give an explicit path to the Sage 9.0 version, does that help? Do you have any Sage-related environment variables which could be interfering with things? On

Re: [sage-devel] remove log_html() and other log_*()

2020-05-02 Thread John H Palmieri
On Saturday, May 2, 2020 at 11:37:57 AM UTC-7, Sébastien Labbé wrote: > > > > On Saturday, May 2, 2020 at 7:55:25 PM UTC+2, John H Palmieri wrote: >> >> >> >> On Saturday, May 2, 2020 at 9:59:18 AM UTC-7, Sébastien Labbé wrote: >>> >>> &

Re: [sage-devel] remove log_html() and other log_*()

2020-05-02 Thread John H Palmieri
On Saturday, May 2, 2020 at 9:59:18 AM UTC-7, Sébastien Labbé wrote: > > > I feel the same way about functions like search_src() that badly >> reimplement grep (even if they still work). >> > > I am fine with getting rid of the log_* functions, but I definitively want > search_src(),

[sage-devel] Re: Proposal: Deprecate all of sage.finance, sage.media, sage.stats in 9.1

2020-05-01 Thread John H Palmieri
Did you mean 9.2? It's too late to add deprecations to 9.1, in my opinion. On Friday, May 1, 2020 at 2:19:32 PM UTC-7, Matthias Koeppe wrote: > > These modules have a very limited amount of code, seem to have seen no > major development for about 10 years, and are (with minor exceptions) >

Re: [sage-devel] remove log_html() and other log_*()

2020-05-01 Thread John H Palmieri
There is a tradeoff. If I want to search the Sage source code, running "search_src(...)" in Sage is easy, and it's in our documentation, so people might find it. Running '!grep -R -n ... "$SAGE_ROOT"/src/sage' is not quite as easy; if you want the line numbers, you need -n, and it also requires

Re: [sage-devel] remove log_html() and other log_*()

2020-04-30 Thread John H Palmieri
On Thursday, April 30, 2020 at 11:15:31 AM UTC-7, Dima Pasechnik wrote: > > > > On Thu, 30 Apr 2020, 19:10 John H Palmieri, > wrote: > >> >> >> On Thursday, April 30, 2020 at 9:20:00 AM UTC-7, Michael Orlitzky wrote: >>> >>> On 4/30/20 11

Re: [sage-devel] remove log_html() and other log_*()

2020-04-30 Thread John H Palmieri
On Thursday, April 30, 2020 at 9:20:00 AM UTC-7, Michael Orlitzky wrote: > > On 4/30/20 11:16 AM, Dima Pasechnik wrote: > > > > I think we should just remove this completely, as ipython nowadays has > > %history magic which certainly can do the same as log_text() > > > > +1 > > I feel the

[sage-support] Re: Extended Operations on Symbols

2020-04-26 Thread John H Palmieri
sage: var('q') q sage: (q+q^(-1))^(1/2) sqrt(q + 1/q) (By the way, I'm not sure I would call using a fraction field "naive".) On Sunday, April 26, 2020 at 9:01:35 AM UTC-7, Jin Guu wrote: > > I am writing a calculator for various 'q' quantities, and often find that > I need to manipulate

Re: [sage-devel] Re: A possible defect in hypergraph generator of Graph module

2020-04-21 Thread John H Palmieri
On Tuesday, April 21, 2020 at 7:59:18 PM UTC-7, John H Palmieri wrote: > > > > On Tuesday, April 21, 2020 at 5:26:00 PM UTC-7, Dima Pasechnik wrote: >> >> On Wed, Apr 22, 2020 at 2:56 AM k2wagle wrote: >> > >> > Tried this just now, ge

Re: [sage-devel] Re: A possible defect in hypergraph generator of Graph module

2020-04-21 Thread John H Palmieri
On Tuesday, April 21, 2020 at 5:26:00 PM UTC-7, Dima Pasechnik wrote: > > On Wed, Apr 22, 2020 at 2:56 AM k2wagle > > wrote: > > > > Tried this just now, getting the same error. Open a ticket please. > > This error is already in Sage 9.0 - and this is an example from the > manual! > > It's

[sage-support] Re: How to modify the index of a matrix

2020-04-20 Thread John H Palmieri
On Monday, April 20, 2020 at 1:01:24 PM UTC-7, Emmanuel Zuñiga wrote: > > Hello, i would like to know how to modify the index of a matrix in > sagemath. As an example, we all know that every object begins in 0, m[0] > and that kind of things. > Now, i need to modify this. to add one to the

[sage-devel] Proposal for Sage 9.2: require "./configure" before "make"

2020-04-18 Thread John H Palmieri
Several of us are in favor of requiring that, in order to build Sage, people should have to run "./configure" before running "make". I would further propose that "make" should not itself then run "configure". Some advantages: - This is the same procedure used with many other software packages.

Re: [sage-support] simple desolve_tides_mpfr crash, even for SageMath Cell Server

2020-04-16 Thread John H Palmieri
Maybe SageCell doesn't have the optional package "tides" installed. This is the same error I see on my own computer without "tides". On Thursday, April 16, 2020 at 9:26:21 AM UTC-7, slelievre wrote: > > Here is the error after executing the original poster's code in SageCell. > >

Re: [sage-devel] Re: archlinux: some system package not recognized

2020-04-14 Thread John H Palmieri
I would suggest two things: $ brew install pkg-config and then before building Sage, while in SAGE_ROOT: $ source .homebrew-build-env Then try ./configure to see what it says at the end about system packages. On Tuesday, April 14, 2020 at 6:21:40 AM UTC-7, David Coudert wrote: > > I

[sage-release] Re: Sage 9.1.beta9 released

2020-04-13 Thread John H Palmieri
On Wednesday, April 1, 2020 at 3:02:49 PM UTC-7, Matthias Köppe wrote: > > Another variation to try is to use " . .homebrew-build-env " > before the build, which sets some environment variables so that homebrew's > "keg-only packages" are found. > Among other things, this affects libpng via

Re: [sage-support] Sage Crash report

2020-04-09 Thread John H Palmieri
Did you look at the file "README.md"? It suggests building in parallel to speed things up. Have you tried that? On Thursday, April 9, 2020 at 12:35:58 PM UTC-7, hbetx9 wrote: > > I htink I know what I did, somehow I change the prefix to a directory that > didn't exist. I'm recompiling to see

Re: [sage-support] Building on Catalina

2020-04-08 Thread John H Palmieri
When I have had problems with libpng, it has helped to do "brew install pkg-config". If you happened to start building Sage and then upgraded Homebrew and/or Xcode in the middle of that, or if you've installed any new Homebrew packages, you should probably start over with "make distclean"

[sage-devel] Re: Where to propose addition of change log and updates of documentation ...

2020-04-08 Thread John H Palmieri
On Wednesday, April 8, 2020 at 3:30:44 PM UTC-7, Matthias Koeppe wrote: > > On Wednesday, April 8, 2020 at 7:53:07 AM UTC-7, rana-aerea rossa wrote: >> >> I need someone to tell me where to propose three kinds of changes of >> Sagemath. >> (1) I guess Sagemath misses change log for some time.

[sage-release] Re: Sage 9.1.beta9 released

2020-04-01 Thread John H Palmieri
On Wednesday, April 1, 2020 at 11:05:31 AM UTC-7, John H Palmieri wrote: > > > > On Tuesday, March 31, 2020 at 7:15:10 PM UTC-7, John H Palmieri wrote: >> >> >> >> On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote: >>> >>>

[sage-release] Re: Sage 9.1.beta9 released

2020-04-01 Thread John H Palmieri
On Tuesday, March 31, 2020 at 7:15:10 PM UTC-7, John H Palmieri wrote: > > > > On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote: >> >> On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote: >>> >>> Here's the

[sage-release] Re: Sage 9.1.beta9 released

2020-03-31 Thread John H Palmieri
On Tuesday, March 31, 2020 at 6:21:42 PM UTC-7, Matthias Köppe wrote: > > On Tuesday, March 31, 2020 at 8:02:48 PM UTC-4, John H Palmieri wrote: >> >> Here's the strange part: if I add the package libpng, then Sage doesn't >> build. With these packages, it builds and p

[sage-devel] Re: ecl build failure when building sage

2020-03-31 Thread John H Palmieri
When the build fails, there should be a message like: The following package(s) may have failed to build... * package: ecl last build time: ... log file:... build directory: /build/directory/is/here/ Check the build directory listed at the end for the file config.log. It

[sage-release] Re: Sage 9.1.beta9 released

2020-03-30 Thread John H Palmieri
r SageMath should install SPKG gmp... ## > ## ## > configure:10415: will use system package and not install SPKG gmp > > > > This seems to come from AX_ABSOLUTE_HEADER > > > > On Monday, March 30, 2020 at 12:18:41 PM

Re: [sage-release] Re: Sage 9.1.beta9 released

2020-03-30 Thread John H Palmieri
ote: > > I vaguely recall seeing similar errors on Homebrew, they were due to > stale Homebrew. Could you try updating it? > > On Tue, Mar 31, 2020 at 12:23 AM John H Palmieri > wrote: > > > > I should also mention that I have built every beta from scratch

[sage-release] Re: Sage 9.1.beta9 released

2020-03-29 Thread John H Palmieri
On OS X with a homebrew installation of Python 3.7.7 I get some failures, mostly to do with pari, including messages like this: PARI/GP ERROR: *** bug in PARI/GP (Segmentation Fault), please report. and this: fatal error: 'gmp.h' file not found #include "gmp.h" ^~~

[sage-support] Re: deprecation warning about "`\QQ`" and "\*"

2020-03-29 Thread John H Palmieri
On Sunday, March 29, 2020 at 12:24:38 AM UTC-7, rana-aere wrote: > > Thank you for clear instructions. > I used the codes to compare how doctoring of the method _macaulay2_init_ > is displayed. > > sage-8.9 (command line and jupyter) > > ``` > Init docstring: x.__init__(...) initializes x; see

[sage-support] Re: deprecation warning about "`\QQ`" and "\*"

2020-03-28 Thread John H Palmieri
On Saturday, March 28, 2020 at 7:07:53 AM UTC-7, rana-aere wrote: > > > > I am compiling binary-pkg and encountered a deprecation warning. > The warning appeared when I invoked sage from command line. > (Technically, it was after messages of patching.) > > The warning reads > > ``` >

[sage-devel] Re: Installing TOPCOM

2020-03-25 Thread John H Palmieri
Please use "sage -i topcom" (lowercase). "topcom" is the newer version of "TOPCOM", which is the old, outdated, package. That may not help, but it's worth a try. On Wednesday, March 25, 2020 at 9:50:01 AM UTC-7, Tyler L. Kelly wrote: > > Dear all, > > I was sent here in trying to install

Re: [sage-devel] Inherit Method but keep Documentation?

2020-03-18 Thread John H Palmieri
What about my_method = Mother.my_method my_method.__doc__ = "new docstring" Does that do what you want? On Wednesday, March 18, 2020 at 9:22:31 PM UTC-7, David Roe wrote: > > > > On Wed, Mar 18, 2020 at 10:58 PM Michael Jung > wrote: > >> Damn it. Then I another question: Would it cause a

Re: [sage-devel] sagenb dependencies

2020-03-12 Thread John H Palmieri
twisted, too, I think. On Wednesday, March 11, 2020 at 4:25:21 PM UTC-7, François Bissey wrote: > > The flask packages definitely should be made optional. > > > On 12/03/2020, at 12:02 PM, Antonio Rojas > wrote: > > > > sagenb was made optional, but its dependencies (such as flask-* >

[sage-devel] glpk and the message "Long-step dual simplex will be used"

2020-03-10 Thread John H Palmieri
Ticket #24824 upgraded glpk to version 4.65, patching it so it doesn't print a warning message "Long-step dual simplex will be used". What should we do about system-wide installations of glpk? I recently installed it using homebrew, and the result was that Sage failed lots of tests, all

[sage-release] Re: Sage 9.1.beta2 released

2020-01-30 Thread John H Palmieri
On Thursday, January 30, 2020 at 12:23:34 AM UTC-8, Markus Wageringel wrote: > > > > Also, the directory `build/pkgs/sage_conf/src/` contains untracked > autogenerated files. This makes `configure` fail if one tries to checkout a > previous beta. > > I see this too. I don't understand why it

[sage-devel] Re: Unable to build sage after git trac config

2020-01-30 Thread John H Palmieri
On Wednesday, January 29, 2020 at 3:04:12 PM UTC-8, Vipul Gupta wrote: > > Hello, > I am using Ubuntu 18.04.3 LTS with sage version 9.1 beta 2 > After using below command > git clone git://github.com/sagemath/sage.git > cd sage > git checkout develop > make > Okay up to here. Before doing the

[sage-devel] Re: Should Sage fiddle with .sage file permissions?

2020-01-27 Thread John H Palmieri
On Monday, January 27, 2020 at 9:59:04 AM UTC-8, Matthias Koeppe wrote: > > On Monday, January 27, 2020 at 9:34:41 AM UTC-5, Marc Mezzarobba wrote: >> >> >> I just noticed that Sage unconditionally changes the permissions of the >> DOT_SAGE directory to rwx--- even after the user manually

Re: [sage-support] sage with python3, mpmath

2020-01-14 Thread John H Palmieri
/libintmath.py", > line 161 ? Just interesting :) > > вторник, 14 января 2020 г., 21:20:05 UTC+3 пользователь John H Palmieri > написал: >> >> Sorry, I meant Sage *9.1.beta0*. >> >> On Tuesday, January 14, 2020 at 10:18:41 AM UTC-8, John H Palmieri wro

Re: [sage-support] sage with python3, mpmath

2020-01-14 Thread John H Palmieri
Sorry, I meant Sage *9.1.beta0*. On Tuesday, January 14, 2020 at 10:18:41 AM UTC-8, John H Palmieri wrote: > > Just to confirm: everything works with Sage 9.0.beta1, built with Python > 2. Fails with Sage built with Python 3. > > > On Tuesday, January 14, 2020 at 5:55:51 A

Re: [sage-support] sage with python3, mpmath

2020-01-14 Thread John H Palmieri
Just to confirm: everything works with Sage 9.0.beta1, built with Python 2. Fails with Sage built with Python 3. On Tuesday, January 14, 2020 at 5:55:51 AM UTC-8, Александр Ватузов wrote: > > https://trac.sagemath.org/ticket/29009#ticket > > вторник, 14 января 2020 г., 16:36:27 UTC+3

[sage-devel] Re: Building 9.0 on macOS: test suite failure with cython-0.29.12.p0 and nose-1.3.7

2020-01-11 Thread John H Palmieri
It is safe to build without setting SAGE_CHECK. Also, some packages are known to fail their test suites — see https://groups.google.com/d/msg/sage-devel/abysgIIVGZI/fF7efL9RAwAJ, for example. On Saturday, January 11, 2020 at 2:40:04 AM UTC-8, Szabolcs Horvát wrote: > > Hello everyone, > > I

[sage-devel] Bug with Smith normal form for matrices over GF(4) on OS X

2020-01-08 Thread John H Palmieri
Dave Witte Morris pointed out the following bug (now trac 28970): M = random_matrix(GF(4), 70, 70) def test_matrix(iterations=50):for k in range(iterations): S,U,V = M.smith_form() print(k) if not S == U * M * V: raise ValueError On OS X, this will

[sage-devel] Re: drop python2 compatibility in 9.1 ?

2020-01-05 Thread John H Palmieri
Can someone with trac admin access and know-how add a 9.2 milestone, so people can develop for 9.2 if they want to focus on dropping Python 2 support? Meanwhile, 9.1 should include a deprecation warning when people use './configure --with-python=2'. On Sunday, January 5, 2020 at 1:06:21 PM

[sage-support] Re: Problems Compiling 9.0

2020-01-03 Thread John H Palmieri
On Friday, January 3, 2020 at 11:54:04 AM UTC-8, finotti wrote: > > I'm trying to build version 9.0 from source under Linux (Debian > Unstable/Sid). The machine has Intel Core i7-8700 CPU and 48GB of RAM. > > Below is the end of the compilation: > > [snip] > > [twisted-16.3.0.p0] Finished

[sage-devel] Re: sage-system-python use in runtime

2019-12-31 Thread John H Palmieri
On Monday, December 30, 2019 at 9:57:25 PM UTC-8, Isuru Fernando wrote: > > I'm trying to build sage 9.0.rc1 for conda. For conda what I do is I run, > 1. Run configure > 2. cp src/bin/* to /bin > 3. cp src/ext/* to /share/sage/ext > 4. run `python setup.py install` in src > > This has worked

Re: [sage-release] Re: Sage 9.0.beta8 released

2019-12-02 Thread John H Palmieri
On Monday, December 2, 2019 at 9:15:49 AM UTC-8, John H Palmieri wrote: > > > > On Monday, December 2, 2019 at 3:12:12 AM UTC-8, E. Madison Bray wrote: >> >> On Mon, Dec 2, 2019 at 6:50 AM John H Palmieri >> wrote: >> > >> > Broken with a Pytho

Re: [sage-release] Re: Sage 9.0.beta8 released

2019-12-02 Thread John H Palmieri
On Monday, December 2, 2019 at 3:12:12 AM UTC-8, E. Madison Bray wrote: > > On Mon, Dec 2, 2019 at 6:50 AM John H Palmieri > wrote: > > > > Broken with a Python 2 build. Do we care? > > > > In particular, SageNB is not built with Python 2, but the docteste

[sage-release] Re: Sage 9.0.beta8 released

2019-12-01 Thread John H Palmieri
Broken with a Python 2 build. Do we care? In particular, SageNB is not built with Python 2, but the doctester thinks it should be: ./sage -t -p --all --long --logfile=logs/ptestlong.log Running doctests with ID 2019-12-01-19-23-00-d57c8cb5. Git branch: develop Using

[sage-release] Re: Sage 9.0.beta7 released

2019-11-27 Thread John H Palmieri
It's okay with Python 3, but I'm getting a failure on OS X when built with Python 2: sage -t --long --warn-long 68.2 src/sage/libs/pynac/pynac.pyx ** File "src/sage/libs/pynac/pynac.pyx", line 295, in

Re: [sage-devel] Re: Significant slowdown of basic arithmetic

2019-11-23 Thread John H Palmieri
On Saturday, November 23, 2019 at 12:38:35 PM UTC-8, vdelecroix wrote: > > Le 23/11/2019 à 11:34, John H Palmieri a écrit : > > By the way, Integer(1r) is also faster with Python 2 than with Python 3. > > By how much? Does it explain the 25% slowdown of the original post?

Re: [sage-devel] Re: Significant slowdown of basic arithmetic

2019-11-23 Thread John H Palmieri
It's not actually Sage 8.9 vs. 9.0, it is? Rather it's Python 2 vs. Python 3. On my computer, I see the same timings with Python 3 builds of 8.9 and 9.0.beta6, but things look faster with Python 2 builds of 8.9 and 9.0.beta6. By the way, Integer(1r) is also faster with Python 2 than with Python

Re: [sage-release] Re: Sage 9.0.beta6 released

2019-11-21 Thread John H Palmieri
I have what looks like a very similar setup: `pkg-config --libs libpng` returns the same thing, I have symlinks for those two files, but matplotlib finds libpng just fine. Did you do 'make distclean' after reinstalling libpng and pkg-config? What does "brew list" say? On Thursday, November

Re: [sage-release] Re: Sage 9.0.beta6 released

2019-11-19 Thread John H Palmieri
The problems with incremental building and Python 2 vs. Python 3 are being tracked at https://trac.sagemath.org/ticket/28742 On Tuesday, November 19, 2019 at 6:57:36 AM UTC-8, Dima Pasechnik wrote: > > On Tue, Nov 19, 2019 at 1:59 PM E. Madison Bray > wrote: > > > > On Tue, Nov 19, 2019 at

[sage-devel] Re: Chain Complexes and homology

2019-11-13 Thread John H Palmieri
Sage is not using very sophisticated methods for computing homology. If anyone wants to implement something better, they are certainly welcome to. I may try to look at the paper, but it may take me a while to get to it. -- John On Wednesday, November 13, 2019 at 4:48:18 PM UTC-8, Salvatore

[sage-devel] Testing Sage's packages

2019-11-13 Thread John H Palmieri
I just set SAGE_CHECK=yes and tried to build Sage on several platforms: OS X and a virtual machine running Ubuntu. Summary: Failed on both: - gap: looks like some sort of string-vs-bytes problem (https://trac.sagemath.org/ticket/28728) - cvxopt: fails with a Python 3 build, hangs (at least on

[sage-devel] Re: Package installation/uninstallation confusion

2019-11-11 Thread John H Palmieri
I created https://trac.sagemath.org/ticket/28721 to add documentation for these to the developer's guide. Needs review. John On Thursday, November 7, 2019 at 8:27:32 AM UTC-8, John H Palmieri wrote: > > These shell functions are defined and documented in > SAGE_ROOT/build/bin/

[sage-devel] Re: Package installation/uninstallation confusion

2019-11-07 Thread John H Palmieri
These shell functions are defined and documented in SAGE_ROOT/build/bin/sage-dist-helpers. In my opinion they should also be documented in the developer's guide, but they don't seem to be. On Thursday, November 7, 2019 at 6:35:05 AM UTC-8, Simon King wrote: > > Hi Dima, > > On 2019-11-06,

Re: [sage-devel] Re: Package installation/uninstallation confusion

2019-11-06 Thread John H Palmieri
Simon, you should look at the json file for p_group_cohomology to see if it contains all of the installed files, or if indeed some are not listed. If everything is there, there is no need to split it into two packages, unless I'm missing something. On Wednesday, November 6, 2019 at 9:33:04

Re: [sage-support] Re: sage building with python3

2019-11-04 Thread John H Palmieri
If you want to build Sage for use with Python 3, you should do $ make distclean $ ./configure --with-python=3 $ make Where does this fail for you? On Monday, November 4, 2019 at 8:21:04 AM UTC-8, Александр Ватузов wrote: > > No, I am building sage only for using it with python3. So I need to

[sage-devel] Re: OSX Catalina works

2019-11-03 Thread John H Palmieri
lled xcode from the > appsrtore I am using the latest versions av I am using: > > ProductName:Mac OS X > ProductVersion:10.15.1 > BuildVersion:19B88 > Xcode 11.2 > Build version 11B52 > > Andrew > > > > > On Saturday, 2 November 2019 05:45:

Re: [sage-support] Re: sage building with python3

2019-11-03 Thread John H Palmieri
Since trac #28426 (merged pretty recently), when building with Python 3, we do not build Python 2. Before that, we always built both. On Sunday, November 3, 2019 at 12:57:02 PM UTC-8, Dima Pasechnik wrote: > > I am surprised we still even build python2 by default. Isn't it an > optional

Re: [sage-devel] Re: Optional and experimental packages

2019-11-01 Thread John H Palmieri
/28687: change scons from optional to experimental. I thought briefly of trying to upgrade it instead, but I don't really care about the package, so someone else who is actually interested will have to do that. John On Friday, November 1, 2019 at 1:27:34 PM UTC-7, John H Palmieri wrote

Re: [sage-devel] Re: Optional and experimental packages

2019-11-01 Thread John H Palmieri
Note that "sage --sws2rst ..." relies on sagenb, and therefore will only work with Sage built with Python 2. In any case, https://trac.sagemath.org/ticket/28685 upgrades to beautifulsoup4, which is compatible with Python 3. On Friday, November 1, 2019 at 3:43:32 AM UTC-7, kcrisman wrote: > >

[sage-devel] Re: OSX Catalina works

2019-11-01 Thread John H Palmieri
I just upgraded a different machine to Catalina. This one didn't have Xcode or homebrew installed beforehand, so I installed Xcode, its command-line tools, and homebrew's gcc. Then I built Sage and it worked. I have now installed a bunch of other homebrew packages relevant to Sage, and the

Re: [sage-devel] Re: OSX Catalina works

2019-11-01 Thread John H Palmieri
If you have the time, could you try uninstalling Xcode and then reinstalling it? You might also try uninstalling and reinstalling homebrew's gcc and any other homebrew components that are relevant to Sage. There may be some remnants of previously installed software that is somehow interfering.

Re: [sage-devel] MacOS 10.15.1: gfortran does not compile in sage-8.9

2019-10-30 Thread John H Palmieri
I tried building several version of gfortran by hand on 10.15, but I couldn't succeed, whereas I could with 10.14. I didn't try just upgrading Sage's gfortran/gcc package to 9.x. On Wednesday, October 30, 2019 at 3:21:58 PM UTC-7, François Bissey wrote: > > I suspect gcc/gfortran shipped with

[sage-devel] Re: MacOS 10.15.1: gfortran does not compile in sage-8.9

2019-10-30 Thread John H Palmieri
I also had problems with Sage's gfortran package with OS X Catalina. I instead installed homebrew (https://brew.sh), and used homebrew to install their gcc package. This should install gfortran, which Sage will find as part of its configure process, thereby bypassing Sage's gfortran package.

Re: [sage-devel] Re: OSX Catalina works

2019-10-29 Thread John H Palmieri
On Tuesday, October 29, 2019 at 4:45:53 AM UTC-7, Andrew wrote: > > Thanks Dima > > On Tuesday, 29 October 2019 17:51:02 UTC+11, Dima Pasechnik wrote: >> >> Did you run >> >> xcode-select --install >> >> after Xcode upgrade? >> > > Yes, the command line tools are correctly installed but, as

[sage-devel] Re: Optional and experimental packages

2019-10-28 Thread John H Palmieri
Oops, I spoke too soon. Two more files had failures: - sage -t --long src/sage/databases/stein_watkins.py # 20 doctests failed - sage -t --long src/sage/interfaces/frobby.py # 12 doctests failed On Monday, October 28, 2019 at 3:02:23 PM UTC-7, John H Palmieri wrote: > > With a Python 3

[sage-devel] Optional and experimental packages

2019-10-28 Thread John H Palmieri
With a Python 3 build of Sage on OS X 10.14.6, I decided to install as many optional and experimental packages as I could. The results: *Optional:* - the following packages failed to build, and the reason wasn't completely obvious: awali buckygen cbc gambit gdb mpi4py - the following

Re: [sage-devel] Switch to Python 3 by default

2019-10-26 Thread John H Palmieri
+1 On Saturday, October 26, 2019 at 5:27:51 PM UTC-7, vdelecroix wrote: > > > https://trac.sagemath.org/ticket/28660 > > > Le 26/10/2019 à 17:20, François Bissey a écrit : > > +1 > > > >> On 27/10/2019, at 12:58 PM, Vincent Delecroix <20100.d...@gmail.com > > wrote: > >> > >> +1 > >> >

[sage-support] Re: failure to re-install ipython

2019-10-25 Thread John H Palmieri
On Friday, October 25, 2019 at 2:59:36 AM UTC-7, Dima Pasechnik wrote: > > in the Sage 9.0.beta2 I get > > [ipython-5.8.0] Successfully installed ipython-5.8.0 > [ipython-5.8.0] Cleaning up... > [ipython-5.8.0] Removed build tracker '/tmp/pip-req-tracker-h6h22jg5' > [ipython-5.8.0] >

Re: [sage-devel] Python 3 and flushing output from external libraries

2019-10-24 Thread John H Palmieri
On Thursday, October 24, 2019 at 10:57:09 AM UTC-7, Dima Pasechnik wrote: > > On Thu, Oct 24, 2019 at 6:48 PM Nils Bruin > > wrote: > > > > On Thursday, October 24, 2019 at 10:29:48 AM UTC-7, Nils Bruin wrote: > >> > >> > >> I guess via ctypes it would be possible too. > > > > > >

Re: [sage-devel] Python 3 and flushing output from external libraries

2019-10-24 Thread John H Palmieri
On Wednesday, October 23, 2019 at 9:49:56 PM UTC-7, Nils Bruin wrote: > > On Wednesday, October 23, 2019 at 2:47:54 PM UTC-7, John H Palmieri wrote: >> >> >> >> On Wednesday, October 23, 2019 at 1:41:35 PM UTC-7, Nils Bruin wrote: >>> >>> On Wedne

Re: [sage-devel] Python 3 and flushing output from external libraries

2019-10-23 Thread John H Palmieri
On Wednesday, October 23, 2019 at 1:41:35 PM UTC-7, Nils Bruin wrote: > > On Wednesday, October 23, 2019 at 1:26:46 PM UTC-7, John Cremona wrote: >> >> >> That all looks very complicated. Before I fixed the eclib source code >> the previous method did work, namely to flush stdout and stderr

Re: [sage-devel] Python 3 and flushing output from external libraries

2019-10-23 Thread John H Palmieri
side-library > > is it what would work for us? > > On Wed, 23 Oct 2019, 20:06 John H Palmieri, > wrote: > >> >> >> On Monday, September 9, 2019 at 2:06:21 PM UTC-7, Jeroen Demeyer wrote: >>> >>> On Mon, Sep 9, 2019 at 7:51 PM John H Palmieri >&g

Re: [sage-devel] Python 3 and flushing output from external libraries

2019-10-23 Thread John H Palmieri
On Monday, September 9, 2019 at 2:06:21 PM UTC-7, Jeroen Demeyer wrote: > > On Mon, Sep 9, 2019 at 7:51 PM John H Palmieri > wrote: > > I am writing to ask for help fixing a Python 3 problem. On some > platforms, there are Python 3 doctest failures in > > >

Re: [sage-devel] Question about deprecation warnings: when do they appear in doctests vs. real life?

2019-10-19 Thread John H Palmieri
ey have the deprecated behavior in > a function they've written. > David > > On Sat, Oct 19, 2019 at 2:56 PM John H Palmieri > wrote: > >> Here is a doctest from sage/rings/integer.pyx: >> >> sage: Integer('012') >> doctest:...: DeprecationWa

[sage-devel] Question about deprecation warnings: when do they appear in doctests vs. real life?

2019-10-19 Thread John H Palmieri
Here is a doctest from sage/rings/integer.pyx: sage: Integer('012') doctest:...: DeprecationWarning: use 0o as octal prefix instead of 0 If you do not want this number to be interpreted as octal, remove the leading zeros. See http://trac.sagemath.org/17413 for

Re: [sage-devel] Re: sagemath 8.9 is not complied on macOS Catalina with python3

2019-10-18 Thread John H Palmieri
On Friday, October 18, 2019 at 10:25:07 AM UTC-7, Dima Pasechnik wrote: > > Hi John, > > On Fri, Oct 18, 2019 at 5:08 PM John H Palmieri > wrote: > > > > I have compiled it without any problems. You should not be using gcc > from homebrew, but rather the ver

[sage-devel] Re: sagemath 8.9 is not complied on macOS Catalina with python3

2019-10-18 Thread John H Palmieri
I have compiled it without any problems. You should not be using gcc from homebrew, but rather the version of gcc installed by Xcode or its command-line tools. That might help. (You should install the homebrew gcc package to get gfortran, but at least for me, installing homebrew's gcc

[sage-devel] Need help with Python 3, doctesting framework, and patchbot

2019-10-17 Thread John H Palmieri
With a Python 3 build of Sage, there are three files which exhibit failures only (or primarily?) when running the Sage patchbot. This is being tracked at https://trac.sagemath.org/ticket/28622. Can anyone help figure out the problem and how to fix it? To see the problem, cd to SAGE_ROOT, run

Re: [sage-devel] OSX Catalina works

2019-10-13 Thread John H Palmieri
A few days ago, after the Catalina release, I used Homebrew to build gcc, and it worked. Well, it built from source, which took a while, but it built a version of gfortran which worked well enough to build Sage. (As far as I know, it's completely functional, but the only reason I install

Re: [sage-support] SageMath installation in macOS Catalina

2019-10-09 Thread John H Palmieri
On Wednesday, October 9, 2019 at 4:51:48 AM UTC-7, David Joyner wrote: > > > > On Wed, Oct 9, 2019 at 7:42 AM Dima Pasechnik > wrote: > >> >> >> On Wed, Oct 9, 2019 at 6:34 AM David Joyner > > wrote: >> >>> >>> >>> On Wed, Oct 9, 2019 at 7:14 AM Dima Pasechnik >> > wrote: >>> Hi,

Re: [sage-devel] scipy fails to build Sage 8.9 - MacOS 10.14.6

2019-10-08 Thread John H Palmieri
On OS X, Sage by default should use the system's "gcc" (which is actually clang), so it's okay to not have a symlink connecting gcc-9 to gcc in /usr/local/bin. What you really need is /usr/local/bin/gfortan, and homebrew should provide that. John On Tuesday, October 8, 2019 at 3:56:24 PM

[sage-devel] Package installation/uninstallation confusion

2019-09-27 Thread John H Palmieri
I have been testing new versions of Simon King's p-group cohomology package. The current version doesn't work with Python 3, and he has been working (#28414) to fix this. My workflow: 1. check out his git branch 2. run ./sage -f -c p_group_cohomology 3. report any issues 4.

Re: [sage-devel] Re: Build failure at matplotlib-2.2.4 and sagenb-1.1.2 on OS X

2019-09-25 Thread John H Palmieri
Could you also trying using Homebrew to install gfortran? On Wednesday, September 25, 2019 at 12:09:55 PM UTC-7, Ben Salisbury wrote: > > Ok, I tried the Homebrew route, and still the build failed. First, the > computer successfully executed the following: > > brew install

[sage-devel] Re: Build failure at matplotlib-2.2.4 and sagenb-1.1.2 on OS X

2019-09-24 Thread John H Palmieri
On Tuesday, September 24, 2019 at 10:12:17 AM UTC-7, Ben Salisbury wrote: > > Hi, > > I'm attempting to build Sage from the develop branch on a new office > computer running OS X 10.14.6. I've installed Xcode and Command Line Tools > (or at least I thought I had), and I'm getting a build

[sage-devel] Re: Poll: three.js as the default 3d viewer in Sage

2019-09-23 Thread John H Palmieri
+1 for threejs I tried to compare the two: in a single Jupyter notebook, I plotted the same function with both viewers. threejs produced the plot faster, and it was snappier when rotating, zooming, etc. (This is with both Firefox and Safari on OS X.) Same from the command-line: the threejs

Re: [sage-release] Sage 8.9.rc0 released

2019-09-12 Thread John H Palmieri
On Thursday, September 12, 2019 at 12:30:34 PM UTC-7, Dima Pasechnik wrote: > > On Thu, Sep 12, 2019 at 5:55 PM John Cremona > wrote: > > > > On ubuntu, upgrade from previous beta, python3 configured: make > ptestlong succeeds except for > > > > sage -t --long --warn-long 81.2

Re: [sage-release] Sage 8.9.beta9 released

2019-09-12 Thread John H Palmieri
On Friday, September 6, 2019 at 3:13:07 AM UTC-7, E. Madison Bray wrote: > > On Fri, Sep 6, 2019 at 11:36 AM E. Madison Bray > wrote: > > > > Consistently getting a test failure on Cygwin related to some oddity in > GAP: > > > > sage -t --long --warn-long 109.3 src/sage/tests/cmdline.py >

[sage-release] Re: Sage 8.9.rc0 released

2019-09-11 Thread John H Palmieri
On Wednesday, September 11, 2019 at 4:36:46 PM UTC-7, Volker Braun wrote: > > As always, you can get the latest beta version from the "develop" git > branch. Alternatively, the self-contained source tarball is at > http://www.sagemath.org/download-latest.html > OS X + Python 3: All tests

Re: [sage-devel] Python 3 and flushing output from external libraries

2019-09-09 Thread John H Palmieri
On Monday, September 9, 2019 at 2:06:21 PM UTC-7, Jeroen Demeyer wrote: > > On Mon, Sep 9, 2019 at 7:51 PM John H Palmieri > wrote: > > I am writing to ask for help fixing a Python 3 problem. On some > platforms, there are Python 3 doctest failures in > > >

[sage-devel] Python 3 and flushing output from external libraries

2019-09-09 Thread John H Palmieri
I am writing to ask for help fixing a Python 3 problem. On some platforms, there are Python 3 doctest failures in - libs/eclib/interface.py (#28454) - rings/polynomial/polynomial_rational_flint.pyx (#28334) and both occur for the same reason: warning messages printed by C or C++ libraries are

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