[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-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

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-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-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-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-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-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-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

[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-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-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

[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

[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-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 > >> >

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-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-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

[sage-devel] Re: Wrong python in Sage shell?

2019-08-29 Thread John H Palmieri
On Thursday, August 29, 2019 at 7:15:51 AM UTC-7, Frédéric Chapoton wrote: > > Hello > > Somebody (else) should make sure that every single remaining piece of > python2 is removed from a python3 sage. In particular, we should not build > python2 at all. > See

[sage-devel] Re: Grepping Trac

2019-08-02 Thread John H Palmieri
On Friday, August 2, 2019 at 1:36:36 PM UTC-7, Nils Bruin wrote: > > On Friday, August 2, 2019 at 11:39:47 AM UTC-7, Timo Kaufmann wrote: >> >> Hi! >> >> As part of my packaging workflow, I find myself pasting error messages >> into the trac search pretty frequently to discover if something is

[sage-devel] signature missing in introspection some of the time

2019-07-20 Thread John H Palmieri
See https://ask.sagemath.org/question/47214/help-doesnt-show-function-call/. Some of the time when you evaluate blah? the signature is not present. Is this a bug or is it intended? I like this behavior: sage: A = SteenrodAlgebra() sage: A.antipode? Signature: B.antipode(self, *args)

Re: [sage-devel] sage foundation ???

2019-06-25 Thread John H Palmieri
I am writing to follow up on this. The University of Washington has now stopped accepting donations to the Sage Foundation fund. People looking for ways to donate in support of Sage will need to find other avenues for that, and I encourage people to create those avenues if they know how. Of

[sage-devel] Re: Installation gets stuck when it tries to download zeromq-4.2.5.tar.gz

2019-06-18 Thread John H Palmieri
On Tuesday, June 18, 2019 at 10:12:06 AM UTC-7, Parth Dubal wrote: > > I tried to download manually and put it into upstream directory but it is > already present and the installation didn't even reach to that step. I > don't understand, if it was already downloaded earlier then why the >

[sage-devel] Re: Installation gets stuck when it tries to download zeromq-4.2.5.tar.gz

2019-06-18 Thread John H Palmieri
On Tuesday, June 18, 2019 at 8:47:31 AM UTC-7, Parth Dubal wrote: > > Hi, > > I tried three times to install sage as described in github on my virtual > machine (Ubuntu 19) but the installation gets stuck for hours at the point > of downloading zeromq-4.2.5.tar.gz. I am running ubuntu on

Re: [sage-devel] Apple deprecates Python

2019-06-08 Thread John H Palmieri
On Saturday, June 8, 2019 at 8:56:09 AM UTC-7, Dima Pasechnik wrote: > > > > On Sat, 8 Jun 2019 16:50 John H Palmieri, > wrote: > >> >> >> On Saturday, June 8, 2019 at 1:25:11 AM UTC-7, vdelecroix wrote: >>> >>> Le 07/06/2019 à 16:44,

Re: [sage-devel] Apple deprecates Python

2019-06-08 Thread John H Palmieri
On Saturday, June 8, 2019 at 1:25:11 AM UTC-7, vdelecroix wrote: > > Le 07/06/2019 à 16:44, Jeroen Demeyer a écrit : > > On 2019-06-07 16:38, E. Madison Bray wrote: > >> While I agree it's part of an annoying trend, this is one change I > >> welcome: The Python interpreter shipped in OSX has

Re: [sage-devel] Apple deprecates Python

2019-06-07 Thread John H Palmieri
On Friday, June 7, 2019 at 7:44:03 AM UTC-7, Jeroen Demeyer wrote: > > On 2019-06-07 16:38, E. Madison Bray wrote: > > While I agree it's part of an annoying trend, this is one change I > > welcome: The Python interpreter shipped in OSX has always *always* > > been broken and unusable > >

Re: [sage-devel] Re: Errors from MacOS build with Python3

2019-05-30 Thread John H Palmieri
docutils-0.14 > > I'll run make ptest-python3 as you suggest. > > Thanks again > > Brian > > > > On Thu, May 30, 2019 at 3:19 PM John H Palmieri > wrote: > >> >> >> On Thursday, May 30, 2019 at 2:15:12 PM UTC-7, Brian Ball wrote: >>> >&g

[sage-devel] Re: Errors from MacOS build with Python3

2019-05-30 Thread John H Palmieri
On Thursday, May 30, 2019 at 2:15:12 PM UTC-7, Brian Ball wrote: > > I built sage 8.7 with python 3.6. > What do you mean by "built"? Did you run "make"? If so, did it complete without error? (I would find that surprising, since "make" should build the documentation.) What does the file

[sage-devel] Are Sage library files supposed to pass when using "sage -tp --file-iterations=N FILES"?

2019-05-30 Thread John H Palmieri
If I run ./sage -tp --file-iterations=2 src/sage/algebras/ then I get many doctest failures. Is this expected? Is something broken when using the "--file-iterations" flag? -- sage -t src/sage/algebras/free_algebra.py # 1

Re: [sage-devel] error building pynormaliz with 8.8.beta6

2019-05-29 Thread John H Palmieri
On Wednesday, May 29, 2019 at 5:52:26 PM UTC-7, Michael Orlitzky wrote: > > On 5/28/19 5:09 PM, Sébastien Labbé wrote: > > > > $ cd > /home/slabbe/GitBox/sage/local/var/tmp/sage/build/pynormaliz-2.5/src > > $ strace sh congiure > > ... > > 4000 lines in total including: > > ... > >

Re: [sage-devel] Would anybody like...progress bars?

2019-05-23 Thread John H Palmieri
There is also the "warn-long" flag: sage -t --warn-long 3.2 FILE should tell you all tests in FILE that take more than 3.2 seconds. On Thursday, May 23, 2019 at 4:05:04 PM UTC-7, Travis Scrimshaw wrote: > > sage -t --verbose (or -tp of course) > > Best, > Travis > > > On Friday, May 24,

[sage-devel] Re: Printing a matrix of large size

2019-05-18 Thread John H Palmieri
Did you try "print(mat.str())"? On Saturday, May 18, 2019 at 6:37:02 PM UTC-7, Kwankyu Lee wrote: > > Hi, > > If mat is a matrix of large size, it is displayed in a short form: > > sage: mat > 22 x 32 dense matrix over Finite Field of size 2 (use the '.str()' method > to see the entries) > > >

[sage-devel] Re: CHomP

2019-05-03 Thread John H Palmieri
On Friday, May 3, 2019 at 10:22:25 AM UTC-7, Salvatore Stella wrote: > > Hi All, > has anyone tried installing CHomP recently? For me it fails applying > patches. > It is an old-style package and apparently it is very stale; does it > provide > any tangible speedup in

Re: [sage-devel] patchbot questions

2019-04-24 Thread John H Palmieri
On Tuesday, April 23, 2019 at 12:18:13 AM UTC-7, Daniel Krenn wrote: > > On 23.04.19 01:37, John H Palmieri wrote: > > I was running a patchbot successfully until some time last week. For > > reasons I don't understand, I did "git pull" on the patchbot, and now it

[sage-devel] patchbot questions

2019-04-22 Thread John H Palmieri
I was running a patchbot successfully until some time last week. For reasons I don't understand, I did "git pull" on the patchbot, and now it won't run with Python 2, complaining File "sage_patchbot/plugins.py", line 309 yield from names ^ SyntaxError: invalid syntax Do I

[sage-devel] Re: python3 status report (mi-april of last python2 year)

2019-04-19 Thread John H Palmieri
What does sage: C Set partitions of {'a', 'c', 'b'} reveal? Is it helpful, or can it be omitted? Maybe it's good enough to do sage: C = SetPartitions(["a", "b", "c"]) sage: C.cardinality() 5 sage: sorted(C) [{{'a'}, {'b'}, {'c'}}, {{'a'}, {'b', 'c'}}, {{'a', 'b'}, {'c'}}, {{'a', 'b', 'c'}},

[sage-devel] Re: Matrix exponentials of diagonal matrices.

2019-04-16 Thread John H Palmieri
On Tuesday, April 16, 2019 at 8:30:13 PM UTC-7, Nils Bruin wrote: > > On Tuesday, April 16, 2019 at 8:06:06 PM UTC-7, Brian Fitzpatrick wrote: >> >> >> Is this a bug? >> >> Looks like it. The problem seems to be that "sparse matrices over SR" > aren't special cased the way dense matrices are

[sage-devel] Re: frozensets in doctests / for display in Python3

2019-04-16 Thread John H Palmieri
Is the printed order important? If not, you can change the doctest to something else that is actually testing something relevant, maybe like sage: 'B' in frozenset() True or sage: (define the frozenset S somehow) sage: S == frozenset(['A', 'B', 'C']) True Or if

Re: [sage-devel] Polyhedron.vertices() function call behaviour

2019-04-11 Thread John H Palmieri
Can you provide details of how you created the polyhedron? As David said, Q.vertices() should make a copy before returning the result, and I would like to recreate this so I can fix it. On Thursday, April 11, 2019 at 9:21:42 PM UTC-7, Narayanan Narayanan wrote: > > Thank you David. Using

[sage-devel] Re: building documentation with python3.6 and topcom installed

2019-04-04 Thread John H Palmieri
What happens when you run this version of Sage and do sage: PointConfiguration.set_engine('internal') # to make doctests independent of TOPCOM sage: p = PointConfiguration([[-1,-1],[1,1],[1,0],[0,1],[0,0]]) and then if that succeeds, plot p? What if you omit the first line and just

[sage-devel] "@experimental" decorator, doctests, and py2 vs. py3

2019-04-04 Thread John H Palmieri
I am confused about how Sage's doctests work with a deprecation warning, for example as coming from the @experimental decorator. Here is a snippet from the top of rings/padics/padic_lattice_element.py: sage: R = ZpLC(2) doctest:...: FutureWarning: This class/method/function is marked as

[sage-devel] Re: load() function doesn't pop up a PNG viewer

2019-04-03 Thread John H Palmieri
On Wednesday, April 3, 2019 at 4:20:43 PM UTC-7, Yagamy Light wrote: > > > > On Thursday, 4 April 2019 01:58:09 UTC+3, John H Palmieri wrote: >> >> >> >> On Wednesday, April 3, 2019 at 3:13:43 PM UTC-7, Yagamy Light wrote: >>> >>> >

[sage-devel] Re: load() function doesn't pop up a PNG viewer

2019-04-03 Thread John H Palmieri
On Wednesday, April 3, 2019 at 3:13:43 PM UTC-7, Yagamy Light wrote: > > > > On Wednesday, 3 April 2019 22:42:15 UTC+3, Samuel Lelievre wrote: >> >> >> >> Le mercredi 3 avril 2019 17:43:51 UTC+2, Yagamy Light a écrit : >>> >>> # Steps to reproduce (in terms of terminal comands: >>> >>> $ cat

[sage-devel] Re: How docstrings generate html

2019-03-24 Thread John H Palmieri
On Sunday, March 24, 2019 at 12:21:43 PM UTC-7, Chaman Agrawal wrote: > > I was trying to contribute through a ticket related to documentation but I > am not sure how docstrings are generating HTML and have doubts. > 1) It is ignoring all the function of with names like __function_name__ >

Re: [sage-devel] Re: how does the res/mod in "geng" work?

2019-03-21 Thread John H Palmieri
It's part of nauty. > On Thu, Mar 21, 2019 at 9:58 PM John H Palmieri > wrote: > >> >> >> On Thursday, March 21, 2019 at 9:38:03 PM UTC-7, Ai Bo wrote: >>> >>> Saw this in the document: >>> res/mod : only generate subset res out of subsets 0..mod-1

[sage-devel] Re: how does the res/mod in "geng" work?

2019-03-21 Thread John H Palmieri
On Thursday, March 21, 2019 at 9:38:03 PM UTC-7, Ai Bo wrote: > > Saw this in the document: > res/mod : only generate subset res out of subsets 0..mod-1 > It would help if you gave some context for this. I'm guessing that most Sage users won't know what "geng" is. I certainly didn't. I found

Re: [sage-devel] Re: internet tests failing

2019-03-15 Thread John H Palmieri
On Friday, March 15, 2019 at 3:31:33 AM UTC-7, Dima Pasechnik wrote: > > On Thu, Mar 14, 2019 at 7:51 PM John H Palmieri > wrote: > > > > I'm seeing the same failure on a Mac running the most recent OS X. I > have openssl 1.1.1a installed on this machine, and

[sage-devel] Re: pretty print latex doctest error

2019-03-14 Thread John H Palmieri
On Thursday, March 14, 2019 at 1:46:38 PM UTC-7, kcrisman wrote: > > I just ran the following command, and amazingly got only one timeout and > one error. The rest is fine. > > ./sage -tp 3 -T 600 --optional=sage,python2,latex src/sage > >

[sage-devel] Re: internet tests failing

2019-03-14 Thread John H Palmieri
I'm seeing the same failure on a Mac running the most recent OS X. I have openssl 1.1.1a installed on this machine, and I see the error in Sage. Then I did './sage -i openssl' and './sage -f python2', and I still see the error. The Python 2 log file does not list ssl among the modules which

[sage-devel] Recommendation for Mac OS X users on Sage's cutting edge

2019-03-11 Thread John H Palmieri
For those of you who use OS X and also like to do incremental upgrades to Sage's most recent beta release, I would suggest running 'make distclean' and then 'make'. Why? Previous versions of Sage have broken file manifests for its packages – not broken on linux, only OS X – so package

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