Re: [sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
an isolated upgrade to 0.18 probably won't fly. And indeed, jedi is used in ipython, not only in jupyter. Perhaps one can update only ipython, and leave jupyter for later? I don't know. On Tue, Feb 9, 2021 at 8:23 PM 'jonatha...@googlemail.com' via sage-devel wrote: > > Downgrading to jedi 0.15, I instead get the error (after long wait time) > > /usr/lib/python3.7/inspect.py:718: DeprecationWarning: > sage.interacts.debugger is deprecated because it is meant for the deprecated > Sage Notebook > See https://trac.sagemath.org/27531 for details. > if hasattr(object, '__module__'): > > All rather strange to me. To be clear. I'm not using jupyter, I'm just on the > shell. > > jonatha...@googlemail.com schrieb am Dienstag, 9. Februar 2021 um 21:10:49 > UTC+1: >> >> The jedi upgrade (to 0.18.0) does not fix the error, but does change the log: >> >> >> >> jonatha...@googlemail.com schrieb am Dienstag, 9. Februar 2021 um 21:05:20 >> UTC+1: >>> >>> Actually the error is reproducible: >>> >>> def foo(): return 2 >>> foo() >>> foo() >>> >>> What makes it crash is hitting TAB after opening the parenthesis and then >>> completing it and hitting enter. >>> >>> Matthias Koeppe schrieb am Dienstag, 9. Februar 2021 um 17:56:31 UTC+1: A Jupyter upgrade is in https://trac.sagemath.org/ticket/31280 - which needs some help On Tuesday, February 9, 2021 at 6:52:51 AM UTC-8 Dima Pasechnik wrote: > > it looks like https://github.com/davidhalter/jedi/issues/1615 > and our version of jedi is older than the fix there. > Upgrade jedi (if this is possible without a full ipython/jupyter > upgrade, don't know) ? > > On Tue, Feb 9, 2021 at 1:56 PM 'jonatha...@googlemail.com' via > sage-devel wrote: > > > > > > Dear all, > > > > sage crashes once in a while hard with some strange error. > > > > Does anyone know what is going on? This is somewhat new. Not > > reproducible. > > > > Happened to me maybe 3 or 4 times now at various occasions. > > > > Jonathan > > > > -- > > You received this message because you are subscribed to the Google > > Groups "sage-devel" group. > > To unsubscribe from this group and stop receiving emails from it, send > > an email to sage-devel+...@googlegroups.com. > > To view this discussion on the web visit > > https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com. > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/d4e347a9-ead5-401e-906b-7159ebd2679fn%40googlegroups.com. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq2URJb5A-qzVZ8YD5vJpV9RDU%2B6O7RyrbBt2N-drQ9L4w%40mail.gmail.com.
Re: [sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
Downgrading to jedi 0.15, I instead get the error (after long wait time) /usr/lib/python3.7/inspect.py:718: DeprecationWarning: sage.interacts.debugger is deprecated because it is meant for the deprecated Sage Notebook See https://trac.sagemath.org/27531 for details. if hasattr(object, '__module__'): All rather strange to me. To be clear. I'm not using jupyter, I'm just on the shell. jonatha...@googlemail.com schrieb am Dienstag, 9. Februar 2021 um 21:10:49 UTC+1: > The jedi upgrade (to 0.18.0) does not fix the error, but does change the > log: > > > > jonatha...@googlemail.com schrieb am Dienstag, 9. Februar 2021 um > 21:05:20 UTC+1: > >> Actually the error is reproducible: >> >> def foo(): return 2 >> foo() >> foo() >> >> What makes it crash is hitting TAB after opening the parenthesis and then >> completing it and hitting enter. >> >> Matthias Koeppe schrieb am Dienstag, 9. Februar 2021 um 17:56:31 UTC+1: >> >>> A Jupyter upgrade is in https://trac.sagemath.org/ticket/31280 - which >>> needs some help >>> >>> On Tuesday, February 9, 2021 at 6:52:51 AM UTC-8 Dima Pasechnik wrote: >>> it looks like https://github.com/davidhalter/jedi/issues/1615 and our version of jedi is older than the fix there. Upgrade jedi (if this is possible without a full ipython/jupyter upgrade, don't know) ? On Tue, Feb 9, 2021 at 1:56 PM 'jonatha...@googlemail.com' via sage-devel wrote: > > > Dear all, > > sage crashes once in a while hard with some strange error. > > Does anyone know what is going on? This is somewhat new. Not reproducible. > > Happened to me maybe 3 or 4 times now at various occasions. > > Jonathan > > -- > You received this message because you are subscribed to the Google Groups "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+...@googlegroups.com. > To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com. >>> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/d4e347a9-ead5-401e-906b-7159ebd2679fn%40googlegroups.com.
Re: [sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
The jedi upgrade (to 0.18.0) does not fix the error, but does change the
log:
jonatha...@googlemail.com schrieb am Dienstag, 9. Februar 2021 um 21:05:20
UTC+1:
> Actually the error is reproducible:
>
> def foo(): return 2
> foo()
> foo()
>
> What makes it crash is hitting TAB after opening the parenthesis and then
> completing it and hitting enter.
>
> Matthias Koeppe schrieb am Dienstag, 9. Februar 2021 um 17:56:31 UTC+1:
>
>> A Jupyter upgrade is in https://trac.sagemath.org/ticket/31280 - which
>> needs some help
>>
>> On Tuesday, February 9, 2021 at 6:52:51 AM UTC-8 Dima Pasechnik wrote:
>>
>>> it looks like https://github.com/davidhalter/jedi/issues/1615
>>> and our version of jedi is older than the fix there.
>>> Upgrade jedi (if this is possible without a full ipython/jupyter
>>> upgrade, don't know) ?
>>>
>>> On Tue, Feb 9, 2021 at 1:56 PM 'jonatha...@googlemail.com' via
>>> sage-devel wrote:
>>> >
>>> >
>>> > Dear all,
>>> >
>>> > sage crashes once in a while hard with some strange error.
>>> >
>>> > Does anyone know what is going on? This is somewhat new. Not
>>> reproducible.
>>> >
>>> > Happened to me maybe 3 or 4 times now at various occasions.
>>> >
>>> > Jonathan
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> Groups "sage-devel" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> an email to sage-devel+...@googlegroups.com.
>>> > To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com.
>>>
>>>
>>>
>>
--
You received this message because you are subscribed to the Google Groups
"sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to sage-devel+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/sage-devel/703602b5-2699-4a57-a71d-bfb7de676db0n%40googlegroups.com.
***
IPython post-mortem report
{'commit_hash': 'd0b255042',
'commit_source': 'installation',
'default_encoding': 'UTF-8',
'ipython_path':
'/srv/public/kliem/sage/local/lib/python3.7/site-packages/IPython',
'ipython_version': '7.13.0',
'os_name': 'posix',
'platform': 'Linux-4.19.0-10-amd64-x86_64-with-debian-10.8',
'sys_executable': '/srv/public/kliem/sage/local/bin/python3',
'sys_platform': 'linux',
'sys_version': '3.7.3 (default, Jul 25 2020, 13:03:44) \n[GCC 8.3.0]'}
***
***
Crash traceback:
---
---
TypeErrorPython 3.7.3: /srv/public/kliem/sage/local/bin/python3
Tue Feb 9 21:09:23 2021
A problem occurred executing Python code. Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
/srv/public/kliem/sage/src/bin/sage-ipython in
1 #!/usr/bin/env sage-python
2 # -*- coding: utf-8 -*-
3 """
4 Sage IPython startup script.
5 """
6
7 # Display startup banner. Do this before anything else to give the user
8 # early feedback that Sage is starting.
9 from sage.misc.banner import banner
10 banner()
11
12 from sage.repl.interpreter import SageTerminalApp
13
14 app = SageTerminalApp.instance()
15 app.initialize()
---> 16 app.start()
global app.start = >
/srv/public/kliem/sage/local/lib/python3.7/site-packages/IPython/terminal/ipapp.py
in start(self=)
341 if self.log_level <= logging.INFO: print()
342
343 def _pylab_changed(self, name, old, new):
344 """Replace --pylab='inline' with --pylab='auto'"""
345 if new == 'inline':
346 warnings.warn("'inline' not available as pylab backend, "
347 "using 'auto' instead.")
348 self.pylab = 'auto'
349
350 def start(self):
351 if self.subapp is not None:
352 return self.subapp.start()
353 # perform any prexec steps:
354 if self.interact:
355 self.log.debug("Starting IPython's mainloop...")
--> 356 self.shell.mainloop()
self.shell.mainloop = >
357 else:
358 self.log.debug("IPython not interactive...")
359 if not self.shell.last_execution_succeeded:
360 sys.exit(1)
361
362 def load_default_config(ipython_dir=None):
363 """Load the default config file from the default ipython_dir.
364
365 This is useful for
Re: [sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
Actually the error is reproducible: def foo(): return 2 foo() foo() What makes it crash is hitting TAB after opening the parenthesis and then completing it and hitting enter. Matthias Koeppe schrieb am Dienstag, 9. Februar 2021 um 17:56:31 UTC+1: > A Jupyter upgrade is in https://trac.sagemath.org/ticket/31280 - which > needs some help > > On Tuesday, February 9, 2021 at 6:52:51 AM UTC-8 Dima Pasechnik wrote: > >> it looks like https://github.com/davidhalter/jedi/issues/1615 >> and our version of jedi is older than the fix there. >> Upgrade jedi (if this is possible without a full ipython/jupyter >> upgrade, don't know) ? >> >> On Tue, Feb 9, 2021 at 1:56 PM 'jonatha...@googlemail.com' via >> sage-devel wrote: >> > >> > >> > Dear all, >> > >> > sage crashes once in a while hard with some strange error. >> > >> > Does anyone know what is going on? This is somewhat new. Not >> reproducible. >> > >> > Happened to me maybe 3 or 4 times now at various occasions. >> > >> > Jonathan >> > >> > -- >> > You received this message because you are subscribed to the Google >> Groups "sage-devel" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to sage-devel+...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com >> . >> > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/e2745da7-79f0-461b-bd99-29ae299002b8n%40googlegroups.com.
Re: [sage-devel] Trouble building cython
On Tuesday, February 9, 2021 at 9:09:32 AM UTC-8 zsc...@gmail.com wrote: > I see that the link I posted to the installation from source documentation > doesn't mention autoconf/automake, but I would have thought some other > package would have already installed them. Probably since homebrew is all > bottles now they don't automatically get installed anymore if you are not > building locally. > > But Dima is right, it's probably best practice to brew install the > packages listed in the file build/pkgs/_bootstrap/distros/homebrew.txt. > >> >> The installation manual does not mention the bootstrapping prerequisites because users installing source releases will not need them. Bootstrapping is only needed when developers use branches from git that make changes to packages or build scripts. However the developer's manual should be updated to discuss bootstrapping. There is a ticket for improvements to this manual - https://trac.sagemath.org/ticket/29784 - which needs help. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/43f209e5-8536-4685-8c9d-78e5eeb0aa84n%40googlegroups.com.
Re: [sage-devel] Trouble building cython
I see that the link I posted to the installation from source documentation doesn't mention autoconf/automake, but I would have thought some other package would have already installed them. Probably since homebrew is all bottles now they don't automatically get installed anymore if you are not building locally. But Dima is right, it's probably best practice to brew install the packages listed in the file build/pkgs/_bootstrap/distros/homebrew.txt. On Tuesday, February 9, 2021 at 10:43:00 AM UTC-5 dim...@gmail.com wrote: > On Tue, Feb 9, 2021 at 3:32 PM Trevor Karn wrote: > > > > I uninstalled and reinstalled homebrew and that got rid of the brew > doctor warnings. I then brewed the suggested packages from the Sage link > Zachary provided and the packages listed at the end of the output of > configure. > > > > Then from SAGE_ROOT I ran > > > > make distclean > > source .homebrew-build-env > > ./bootstrap -d > > ./configure > > make -j4 build > > > > In the end this seems to be working. Thank you so much Dima and Zachary > for your help. > > > > The reason for running ./bootstrap with the -d flag was because that is > what an error message told me to do. Without -d flag: > > > > trevorkarn@Trevors-MacBook-Air sage % source .homebrew-build-env > > > > trevorkarn@Trevors-MacBook-Air sage % ./bootstrap > > > > rm -rf config configure build/make/Makefile-auto.in > > > > rm -f src/doc/en/installation/*.txt > > > > rm -rf src/doc/en/reference/spkg/*.rst > > > > rm -f src/doc/en/reference/repl/*.txt > > > > rm -f environment.yml > > > > rm -f src/environment.yml > > > > rm -f environment-optional.yml > > > > rm -f src/environment-optional.yml > > > > src/doc/bootstrap:92: installing src/doc/en/installation/arch.txt and > src/doc/en/installation/arch-optional.txt > > > > src/doc/bootstrap:92: installing src/doc/en/installation/debian.txt and > src/doc/en/installation/debian-optional.txt > > > > src/doc/bootstrap:92: installing src/doc/en/installation/fedora.txt and > src/doc/en/installation/fedora-optional.txt > > > > src/doc/bootstrap:92: installing src/doc/en/installation/cygwin.txt and > src/doc/en/installation/cygwin-optional.txt > > > > src/doc/bootstrap:92: installing src/doc/en/installation/homebrew.txt > and src/doc/en/installation/homebrew-optional.txt > > > > src/doc/bootstrap:66: installing environment.yml, > environment-optional.yml, src/environment.yml and > src/environment-optional.yml > > > > src/doc/bootstrap:103: installing src/doc/en/reference/spkg/*.rst > > > > src/doc/bootstrap:182: installing src/doc/en/reference/repl/options.txt > > > > bootstrap:73: installing 'config/config.rpath' > > > > ./bootstrap: line 118: aclocal: command not found > > > > Bootstrap failed. Either install autotools or run bootstrap with > > > > the -d option to download the auto-generated files instead. > > build/pkgs/_bootstrap/distros/homebrew.txt > > contains a list of dev packages recommended for Homebrew. > (and with these installed, ./bootstrap should complete without errors) > > I wonder whether any of these are printed at the end of the ./configure > run. > > > > > > > > Best Regards, > > > > Trevor Karn > > > > > > On Tue, Feb 9, 2021 at 4:06 AM Dima Pasechnik wrote: > >> > >> On Tue, Feb 9, 2021 at 4:07 AM Zachary Scherr wrote: > >> > > >> > I need to sign off for the night, but the numpy error is definitely > related to gfortran. If you have gcc installed via homebrew then it should > come with the latest version of gfortran. You can see from your config.log > file that gfortran is not found: > >> > > >> > configure:7281: checking for gfortran > >> > configure:7311: result: no > >> > > >> > and other standard homebrew packages are not found, like openblas: > >> > > >> > configure:12171: checking BLAS library > >> > configure:12190: result: openblas > >> > configure:12239: checking whether any of gfortran is installed as or > will be installed as SPKG > >> > configure:12243: result: yes; install openblas as well > >> > configure:13540: no suitable system package found for SPKG openblas > >> > > >> > are you aware if you have gcc and openblas installed via homebrew? I > also see that you didn't run "source .homebrew-build-env" before running > ./configure since I don't see certain items on your path. If you go to the > sage installation guide at > https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation > > you can see a list of homebrew packages you might want to have before > installing sage. I think if you get everything in working order with > homebrew then you shouldn't have any issues installing sage. Here is my > best suggestion as to what to try: > >> > > >> > - fix all "brew doctor" warnings. This might not be necessary, but I > get worried when I see so many warnings. You can probably just delete all > the suggested files and you should be fine. > >> > > >> > - install all the recommended homebrew packages. If any are already >
Re: [sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
A Jupyter upgrade is in https://trac.sagemath.org/ticket/31280 - which needs some help On Tuesday, February 9, 2021 at 6:52:51 AM UTC-8 Dima Pasechnik wrote: > it looks like https://github.com/davidhalter/jedi/issues/1615 > and our version of jedi is older than the fix there. > Upgrade jedi (if this is possible without a full ipython/jupyter > upgrade, don't know) ? > > On Tue, Feb 9, 2021 at 1:56 PM 'jonatha...@googlemail.com' via > sage-devel wrote: > > > > > > Dear all, > > > > sage crashes once in a while hard with some strange error. > > > > Does anyone know what is going on? This is somewhat new. Not > reproducible. > > > > Happened to me maybe 3 or 4 times now at various occasions. > > > > Jonathan > > > > -- > > You received this message because you are subscribed to the Google > Groups "sage-devel" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to sage-devel+...@googlegroups.com. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com > . > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/f7fa64f7-bafb-4f0e-9391-662ca6c020d7n%40googlegroups.com.
Re: [sage-devel] Trouble building cython
On Tue, Feb 9, 2021 at 3:32 PM Trevor Karn wrote: > > I uninstalled and reinstalled homebrew and that got rid of the brew doctor > warnings. I then brewed the suggested packages from the Sage link Zachary > provided and the packages listed at the end of the output of configure. > > Then from SAGE_ROOT I ran > > make distclean > source .homebrew-build-env > ./bootstrap -d > ./configure > make -j4 build > > In the end this seems to be working. Thank you so much Dima and Zachary for > your help. > > The reason for running ./bootstrap with the -d flag was because that is what > an error message told me to do. Without -d flag: > > trevorkarn@Trevors-MacBook-Air sage % source .homebrew-build-env > > trevorkarn@Trevors-MacBook-Air sage % ./bootstrap > > rm -rf config configure build/make/Makefile-auto.in > > rm -f src/doc/en/installation/*.txt > > rm -rf src/doc/en/reference/spkg/*.rst > > rm -f src/doc/en/reference/repl/*.txt > > rm -f environment.yml > > rm -f src/environment.yml > > rm -f environment-optional.yml > > rm -f src/environment-optional.yml > > src/doc/bootstrap:92: installing src/doc/en/installation/arch.txt and > src/doc/en/installation/arch-optional.txt > > src/doc/bootstrap:92: installing src/doc/en/installation/debian.txt and > src/doc/en/installation/debian-optional.txt > > src/doc/bootstrap:92: installing src/doc/en/installation/fedora.txt and > src/doc/en/installation/fedora-optional.txt > > src/doc/bootstrap:92: installing src/doc/en/installation/cygwin.txt and > src/doc/en/installation/cygwin-optional.txt > > src/doc/bootstrap:92: installing src/doc/en/installation/homebrew.txt and > src/doc/en/installation/homebrew-optional.txt > > src/doc/bootstrap:66: installing environment.yml, environment-optional.yml, > src/environment.yml and src/environment-optional.yml > > src/doc/bootstrap:103: installing src/doc/en/reference/spkg/*.rst > > src/doc/bootstrap:182: installing src/doc/en/reference/repl/options.txt > > bootstrap:73: installing 'config/config.rpath' > > ./bootstrap: line 118: aclocal: command not found > > Bootstrap failed. Either install autotools or run bootstrap with > > the -d option to download the auto-generated files instead. build/pkgs/_bootstrap/distros/homebrew.txt contains a list of dev packages recommended for Homebrew. (and with these installed, ./bootstrap should complete without errors) I wonder whether any of these are printed at the end of the ./configure run. > > > Best Regards, > > Trevor Karn > > > On Tue, Feb 9, 2021 at 4:06 AM Dima Pasechnik wrote: >> >> On Tue, Feb 9, 2021 at 4:07 AM Zachary Scherr wrote: >> > >> > I need to sign off for the night, but the numpy error is definitely >> > related to gfortran. If you have gcc installed via homebrew then it >> > should come with the latest version of gfortran. You can see from your >> > config.log file that gfortran is not found: >> > >> > configure:7281: checking for gfortran >> > configure:7311: result: no >> > >> > and other standard homebrew packages are not found, like openblas: >> > >> > configure:12171: checking BLAS library >> > configure:12190: result: openblas >> > configure:12239: checking whether any of gfortran is installed as or will >> > be installed as SPKG >> > configure:12243: result: yes; install openblas as well >> > configure:13540: no suitable system package found for SPKG openblas >> > >> > are you aware if you have gcc and openblas installed via homebrew? I also >> > see that you didn't run "source .homebrew-build-env" before running >> > ./configure since I don't see certain items on your path. If you go to >> > the sage installation guide at >> > https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation >> > you can see a list of homebrew packages you might want to have before >> > installing sage. I think if you get everything in working order with >> > homebrew then you shouldn't have any issues installing sage. Here is my >> > best suggestion as to what to try: >> > >> > - fix all "brew doctor" warnings. This might not be necessary, but I get >> > worried when I see so many warnings. You can probably just delete all the >> > suggested files and you should be fine. >> > >> > - install all the recommended homebrew packages. If any are already >> > installed then maybe try "brew reinstall" to make sure it is installed >> > properly. If you think you have homebrew gcc installed then you should be >> > able to do "which gfortran" and "gfortran --version". That should >> > hopefully show you that you have gfortran 10.2.0_3. >> > >> > - in your sage folder under the develop branch you should run the commands >> > I mentioned, and don't skip out on "source .homebrew-build-env": >> > >> > >> make distclean >> > >> ./bootstrap >> > >> source .homebrew-build-env >> > >> ./configure >> > >> > Before running "make -j4 build" you can look at config.log and make sure >> > that it picked up all of the relevant homebrew
Re: [sage-devel] Trouble building cython
I uninstalled and reinstalled homebrew and that got rid of the brew doctor warnings. I then brewed the suggested packages from the Sage link Zachary provided and the packages listed at the end of the output of configure. Then from SAGE_ROOT I ran make distclean source .homebrew-build-env ./bootstrap -d ./configure make -j4 build In the end this seems to be working. Thank you so much Dima and Zachary for your help. The reason for running ./bootstrap with the -d flag was because that is what an error message told me to do. Without -d flag: trevorkarn@Trevors-MacBook-Air sage % source .homebrew-build-env trevorkarn@Trevors-MacBook-Air sage % ./bootstrap rm -rf config configure build/make/Makefile-auto.in rm -f src/doc/en/installation/*.txt rm -rf src/doc/en/reference/spkg/*.rst rm -f src/doc/en/reference/repl/*.txt rm -f environment.yml rm -f src/environment.yml rm -f environment-optional.yml rm -f src/environment-optional.yml src/doc/bootstrap:92: installing src/doc/en/installation/arch.txt and src/doc/en/installation/arch-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/debian.txt and src/doc/en/installation/debian-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/fedora.txt and src/doc/en/installation/fedora-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/cygwin.txt and src/doc/en/installation/cygwin-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/homebrew.txt and src/doc/en/installation/homebrew-optional.txt src/doc/bootstrap:66: installing environment.yml, environment-optional.yml, src/environment.yml and src/environment-optional.yml src/doc/bootstrap:103: installing src/doc/en/reference/spkg/*.rst src/doc/bootstrap:182: installing src/doc/en/reference/repl/options.txt bootstrap:73: installing 'config/config.rpath' ./bootstrap: line 118: aclocal: command not found Bootstrap failed. Either install autotools or run bootstrap with the -d option to download the auto-generated files instead. Best Regards, Trevor Karn On Tue, Feb 9, 2021 at 4:06 AM Dima Pasechnik wrote: > On Tue, Feb 9, 2021 at 4:07 AM Zachary Scherr wrote: > > > > I need to sign off for the night, but the numpy error is definitely > related to gfortran. If you have gcc installed via homebrew then it should > come with the latest version of gfortran. You can see from your config.log > file that gfortran is not found: > > > > configure:7281: checking for gfortran > > configure:7311: result: no > > > > and other standard homebrew packages are not found, like openblas: > > > > configure:12171: checking BLAS library > > configure:12190: result: openblas > > configure:12239: checking whether any of gfortran is installed as or > will be installed as SPKG > > configure:12243: result: yes; install openblas as well > > configure:13540: no suitable system package found for SPKG openblas > > > > are you aware if you have gcc and openblas installed via homebrew? I > also see that you didn't run "source .homebrew-build-env" before running > ./configure since I don't see certain items on your path. If you go to the > sage installation guide at > https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation > you can see a list of homebrew packages you might want to have before > installing sage. I think if you get everything in working order with > homebrew then you shouldn't have any issues installing sage. Here is my > best suggestion as to what to try: > > > > - fix all "brew doctor" warnings. This might not be necessary, but I > get worried when I see so many warnings. You can probably just delete all > the suggested files and you should be fine. > > > > - install all the recommended homebrew packages. If any are already > installed then maybe try "brew reinstall" to make sure it is installed > properly. If you think you have homebrew gcc installed then you should be > able to do "which gfortran" and "gfortran --version". That should > hopefully show you that you have gfortran 10.2.0_3. > > > > - in your sage folder under the develop branch you should run the > commands I mentioned, and don't skip out on "source .homebrew-build-env": > > > > >> make distclean > > >> ./bootstrap > > >> source .homebrew-build-env > > >> ./configure > > > > Before running "make -j4 build" you can look at config.log and make sure > that it picked up all of the relevant homebrew packages. > > > > > source .homebrew-build-env > > should be run before ./bootstrap > > > as well, ./confugure at the end of its run outputs an advice on > packages that can still be installed. > > > > > > > > > On Monday, February 8, 2021 at 10:52:43 PM UTC-5 Trevor Karn wrote: > >> > >> Here is the new one. Thanks so much for all of your help on this, > Zachary. > >> > >> > >> Best Regards, > >> > >> Trevor Karn > >> > >> > >> On Mon, Feb 8, 2021 at 9:40 PM Zachary Scherr wrote: > >>> > >>> At some point you should deal with those warnings, but
Re: [sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
it looks like https://github.com/davidhalter/jedi/issues/1615 and our version of jedi is older than the fix there. Upgrade jedi (if this is possible without a full ipython/jupyter upgrade, don't know) ? On Tue, Feb 9, 2021 at 1:56 PM 'jonatha...@googlemail.com' via sage-devel wrote: > > > Dear all, > > sage crashes once in a while hard with some strange error. > > Does anyone know what is going on? This is somewhat new. Not reproducible. > > Happened to me maybe 3 or 4 times now at various occasions. > > Jonathan > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq0VD2oTk35cfK7U3VPOy%3DsngxqJiwAD1LTDq612ov%3D4sQ%40mail.gmail.com.
Re: [sage-devel] Re: Help needed with adding user packages as optional/experimental packages
Le 09/02/2021 à 02:22, Matthias Koeppe a écrit : On Monday, February 8, 2021 at 10:42:59 AM UTC-8 Matthias Koeppe wrote: I think it should be the responsibility of the downstream package to define a versioning policy - define when they plan to drop support for a particular Sage version. Then we can use an appropriate version constraint in the "install-requires.txt" file for this package in build/pkgs. Another thing that a downstream package can do is declare an "install_requires" on the Sage library, specifying a supported range of versions. Then we should be able to use the dependency resolution by pip to be sure to install a compatible version. > Note https://trac.sagemath.org/ticket/30912 updates the metadata of the Sage library, defining the distribution name "sagemath-standard". (Another distribution that could be used for versioning is "sage_conf".) Also note the pip dependency resolver has just changed with the update to pip 20.3.3 in #30589 (see https://pip.pypa.io/en/latest/user_guide/#changes-to-the-pip-dependency-resolver-in-20-2-2020). I think that the most important thing we care about is the answer to What is the most recent version of package X that runs on Sage version Y? On the downstream side, one could just add a requirement sagemath>=Y meaning that sagemath < Y is not supported. However, I don't know enough of pip to understand how to make "pip install X" retrieve the information. Would that work out of the box with sage 9.3.beta7? Best Vincent -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/0d4438e8-7332-4680-50d0-380715320394%40gmail.com.
[sage-devel] AttributeError: module 'sage.sandpiles.all' has no attribute 'absolute_import'
Dear all,
sage crashes once in a while hard with some strange error.
Does anyone know what is going on? This is somewhat new. Not reproducible.
Happened to me maybe 3 or 4 times now at various occasions.
Jonathan
--
You received this message because you are subscribed to the Google Groups
"sage-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to sage-devel+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/sage-devel/53367a09-45ff-4ebf-bcca-88766b0b77e9n%40googlegroups.com.
***
IPython post-mortem report
{'commit_hash': 'd0b255042',
'commit_source': 'installation',
'default_encoding': 'utf-8',
'ipython_path':
'/home/jonathan/Applications/sage/local/lib/python3.8/site-packages/IPython',
'ipython_version': '7.13.0',
'os_name': 'posix',
'platform': 'Linux-5.4.0-65-generic-x86_64-with-glibc2.29',
'sys_executable': '/home/jonathan/Applications/sage/local/bin/python3',
'sys_platform': 'linux',
'sys_version': '3.8.5 (default, Jul 28 2020, 12:59:40) \n[GCC 9.3.0]'}
***
***
Crash traceback:
---
---
KeyError Python 3.8.5: /home/jonathan/Applications/sage/local/bin/python3
Tue Feb 9 14:50:23 2021
A problem occurred executing Python code. Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
~/Applications/sage/local/lib/python3.8/site-packages/jedi/cache.py in
wrapper(self=, *args=(), **kwargs={})
108 try:
--> 109 return dct[key]
dct = {}
key = ((), frozenset())
110 except KeyError:
KeyError: ((), frozenset())
During handling of the above exception, another exception occurred:
---
KeyError Python 3.8.5: /home/jonathan/Applications/sage/local/bin/python3
Tue Feb 9 14:50:23 2021
A problem occurred executing Python code. Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
~/Applications/sage/local/lib/python3.8/site-packages/jedi/cache.py in
wrapper(self=,
*args=('get_signature_params',), **kwargs={})
108 try:
--> 109 return dct[key]
dct = {(('get_api_type',), frozenset()): 'function', (('is_instance',),
frozenset()): True, (('getattr_paths', '__class__'), frozenset()):
[, )>], (('py__class__',), frozenset()):
,
(('py__doc__',), frozenset()): '', (('get_repr',), frozenset()):
'
1 #!/usr/bin/env sage-python
2 # -*- coding: utf-8 -*-
3 """
4 Sage IPython startup script.
5 """
6
7 # Display startup banner. Do this before anything else to give the user
8 # early feedback that Sage is starting.
9 from sage.misc.banner import banner
10 banner()
11
12 from sage.repl.interpreter import SageTerminalApp
13
14 app = SageTerminalApp.instance()
15 app.initialize()
---> 16 app.start()
global app.start = >
~/Applications/sage/local/lib/python3.8/site-packages/IPython/terminal/ipapp.py
in start(self=)
341 if self.log_level <= logging.INFO: print()
342
343 def _pylab_changed(self, name, old, new):
344 """Replace --pylab='inline' with --pylab='auto'"""
345 if new == 'inline':
346 warnings.warn("'inline' not available as pylab backend, "
347 "using 'auto' instead.")
348 self.pylab = 'auto'
349
350 def start(self):
351 if self.subapp is not None:
352 return self.subapp.start()
353 # perform any prexec steps:
354 if self.interact:
355 self.log.debug("Starting IPython's mainloop...")
--> 356 self.shell.mainloop()
self.shell.mainloop = >
357 else:
358 self.log.debug("IPython not interactive...")
359 if not self.shell.last_execution_succeeded:
360 sys.exit(1)
361
362 def load_default_config(ipython_dir=None):
363 """Load the default config file from the default ipython_dir.
364
365 This is useful for embedded shells.
366 """
367 if ipython_dir is None:
368 ipython_dir = get_ipython_dir()
369
370 profile_dir = os.path.join(ipython_dir, 'profile_default')
371 app = TerminalIPythonApp()
[sage-devel] Re: [GSoC Mentors Announce] Now Accepting GSoC 2021 Mentoring Organization Applications until Feb 19
This year is difficult for all of us and we lack motivation for this edition of GSoC. On the other end, it is more important than ever to push/motivate/help students. Other Sagemath contributors than the usual could be involved in mentoring activity. I think many contributors are not really aware of this program and what it means. Furthermore, this year the GSoC period has been shortened (by half) and so it is no longer necessary to be around till end of August. This could be an extra motivation to attract new mentors. Concerning the admin part, I don't know how heavy it is, what it means exactly, etc. Of course, if we are too few ready to help/mentor for GSoC this year we can pass. Le lundi 8 février 2021 à 15:17:43 UTC+1, mmarco a écrit : > I have participated as mentor other years... but this year I just don't > think I have the needed energy. > > I think Harald's proposal to pass this year and reconsider the next one > makes sense (sadly). > El domingo, 7 de febrero de 2021 a las 17:54:07 UTC+1, > harald@gmail.com escribió: > >> Hi, a word from my side: I would really like to stop being admin as well >> and hope someone else can take over. I'm the one writing the application >> each year and I could this time around, but in general I want to focus on >> other things after all those years. >> >> Despite that, looks like there are only two mentors. Feels like this is >> below the threshold where it makes sense to pursue this? Maybe we should >> pass this year and re-evaluate for the next one? >> >> -- Harald >> >> >> >> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/575fa23b-caa5-4216-ba51-951769175219n%40googlegroups.com.
Re: [sage-devel] possible bug: kernel of ring homomorphism
Thank you for reporting this problem. I have opened https://trac.sagemath.org/ticket/31367 for it and will provide a fix there shortly. Akos M schrieb am Montag, 8. Februar 2021 um 11:42:59 UTC+1: > It seems that unfortunately the problem persists for multivariate rings as > well: > > A. = QQ[] > B. = QQ[] > H = B.quotient(B.ideal([B.2])) > f = A.hom([H.0, H.1], H) > f > f.kernel() > > Ring morphism: > From: Multivariate Polynomial Ring in t, u over Rational Field > To: Quotient of Multivariate Polynomial Ring in x, y, z over Rational > Field by the ideal (z) > Defn: t |--> xbar >u |--> ybar > Ideal (-t, -u, 0) of Multivariate Polynomial Ring in t, u over Rational > Field > > I have the impression that the fact that the ring homomorphism is to a > quotient ring introduces the error, but that's just a wild guess. > On Monday, February 8, 2021 at 11:09:52 AM UTC+1 dim...@gmail.com wrote: > >> A wild guess would be that it's due to univariate and multivariate >> rings handled by different backends in Sage, one sees this kinds of >> corner cases errors. >> >> On Mon, Feb 8, 2021 at 10:06 AM John Cremona >> wrote: >> > >> > It looks like a bug to me. f.kernel() expands to >> > f._inverse_image_ideal(f.codomain().zero_ideal()) and >> > f.codomain().zero_ideal() looks OK so the problem must be in the >> > inverse image. The author is apparently Simon King (2011). Simon, >> > can you help? >> > >> > John >> > >> > On Mon, 8 Feb 2021 at 09:20, Akos M wrote: >> > > >> > > Hi, >> > > >> > > I'm not sure whether this is a bug or not, but the kernel of a ring >> homomorphism to a quotient ring gives unexpected results: >> > > >> > > A. = QQ[] >> > > B. = QQ[] >> > > H = B.quotient(B.ideal([B.1])) >> > > f = A.hom([H.0], H) >> > > f >> > > f.kernel() >> > > >> > > outputs: >> > > >> > > Ring morphism: From: Univariate Polynomial Ring in t over Rational >> Field >> > > To: Quotient of Multivariate Polynomial Ring in x, y over Rational >> Field by the ideal (y) Defn: t |--> xbar >> > > Principal ideal (t) of Univariate Polynomial Ring in t over Rational >> Field >> > > >> > > whereas the kernel of f:A[t]->B[x,y]->B[x,y]/(y), for f(t)=x should >> be (0). >> > > >> > > Is this a bug? >> > > >> > > Thanks, >> > > Akos >> > > >> > > -- >> > > You received this message because you are subscribed to the Google >> Groups "sage-devel" group. >> > > To unsubscribe from this group and stop receiving emails from it, >> send an email to sage-devel+...@googlegroups.com. >> > > To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-devel/3eeea5f7-4ea2-4586-bbb6-04d00c0d4fa9n%40googlegroups.com. >> >> >> > >> > -- >> > You received this message because you are subscribed to the Google >> Groups "sage-devel" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to sage-devel+...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-devel/CAD0p0K45OKUuLWegC6sXWHoTWs9ppPf7htmZ1wVyBo_O08%3DNTw%40mail.gmail.com. >> >> >> > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/806d3b24-3f01-49b5-89e1-50e218b427d0n%40googlegroups.com.
Re: [sage-devel] Trouble building cython
On Tue, Feb 9, 2021 at 4:07 AM Zachary Scherr wrote: > > I need to sign off for the night, but the numpy error is definitely related > to gfortran. If you have gcc installed via homebrew then it should come with > the latest version of gfortran. You can see from your config.log file that > gfortran is not found: > > configure:7281: checking for gfortran > configure:7311: result: no > > and other standard homebrew packages are not found, like openblas: > > configure:12171: checking BLAS library > configure:12190: result: openblas > configure:12239: checking whether any of gfortran is installed as or will be > installed as SPKG > configure:12243: result: yes; install openblas as well > configure:13540: no suitable system package found for SPKG openblas > > are you aware if you have gcc and openblas installed via homebrew? I also see > that you didn't run "source .homebrew-build-env" before running ./configure > since I don't see certain items on your path. If you go to the sage > installation guide at > https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation > you can see a list of homebrew packages you might want to have before > installing sage. I think if you get everything in working order with > homebrew then you shouldn't have any issues installing sage. Here is my best > suggestion as to what to try: > > - fix all "brew doctor" warnings. This might not be necessary, but I get > worried when I see so many warnings. You can probably just delete all the > suggested files and you should be fine. > > - install all the recommended homebrew packages. If any are already > installed then maybe try "brew reinstall" to make sure it is installed > properly. If you think you have homebrew gcc installed then you should be > able to do "which gfortran" and "gfortran --version". That should hopefully > show you that you have gfortran 10.2.0_3. > > - in your sage folder under the develop branch you should run the commands I > mentioned, and don't skip out on "source .homebrew-build-env": > > >> make distclean > >> ./bootstrap > >> source .homebrew-build-env > >> ./configure > > Before running "make -j4 build" you can look at config.log and make sure that > it picked up all of the relevant homebrew packages. > > source .homebrew-build-env should be run before ./bootstrap as well, ./confugure at the end of its run outputs an advice on packages that can still be installed. > > > > On Monday, February 8, 2021 at 10:52:43 PM UTC-5 Trevor Karn wrote: >> >> Here is the new one. Thanks so much for all of your help on this, Zachary. >> >> >> Best Regards, >> >> Trevor Karn >> >> >> On Mon, Feb 8, 2021 at 9:40 PM Zachary Scherr wrote: >>> >>> At some point you should deal with those warnings, but I don't think that >>> is what is causing your problems (although they are probably symptomatic of >>> other possible issues). >>> >>> The config.log file you posted earlier is picking up a lot of packages that >>> were built by sage and not from homebrew. Do you have the config.log file >>> that you got after running make distclean? >>> >>> On Monday, February 8, 2021 at 10:10:01 PM UTC-5 Trevor Karn wrote: brew doctor is giving lots of errors about unbrewed files: trevorkarn@Trevors-MacBook-Air sage % brew doctor Please note that these warnings are just used to help the Homebrew maintainers with debugging if you file an issue. If everything you use Homebrew for is working fine: please don't worry or file an issue; just ignore this. Thanks! Warning: Unbrewed dylibs were found in /usr/local/lib. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted. Unexpected dylibs: /usr/local/lib/libtcl8.6.dylib /usr/local/lib/libtk8.6.dylib Warning: Unbrewed header files were found in /usr/local/include. If you didn't put them there on purpose they could cause problems when building Homebrew formulae, and may need to be deleted. Unexpected header files: /usr/local/include/fakemysql.h /usr/local/include/fakepq.h /usr/local/include/fakesql.h /usr/local/include/itcl.h /usr/local/include/itcl2TclOO.h /usr/local/include/itclDecls.h /usr/local/include/itclInt.h /usr/local/include/itclIntDecls.h /usr/local/include/itclMigrate2TclCore.h /usr/local/include/itclTclIntStubsFcn.h /usr/local/include/mysqlStubs.h /usr/local/include/odbcStubs.h /usr/local/include/pqStubs.h /usr/local/include/tcl.h /usr/local/include/tclDecls.h /usr/local/include/tclOO.h /usr/local/include/tclOODecls.h /usr/local/include/tclPlatDecls.h
