Support more system-site packages #36256
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On Debian for |
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Thanks, this works. |
Our system package lists are generated with a special case that looks for SAGE_PYTHON_PACKAGE_CHECK when spkg-configure.m4 is present. The rpy2 package already had an spkg-configure.m4 relating to --disable-r, but its spkg-configure.m4 did not use SAGE_PYTHON_PACKAGE_CHECK. As a result, it was erroneously included in the package list. We now use SAGE_PYTHON_PACKAGE_CHECK for the usual "check" phase of SAGE_SPKG_CONFIGURE, which both allows the user to use rpy2 from the system and fixes the package list.
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Rebased away. |
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Documentation preview for this PR (built with commit 905419a; changes) is ready! 🎉 |
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On Conda the Conda provided rpy2 package seems to be rejected, see ci. Is this according to design? Also there are a lot of errors that certain system packages couldn't be used. |
Nothing is being detected because More generally though, we just enabled hundreds of system packages without much consideration for whether or not the popular versions of those packages actually work for sage. Conda (or any distro) won't be expected to work until someone tries to install all of these packages as system packages and then runs through the test suite and fixes all of the bugs they hit. It's still an experimental feature that, more than anything, lets us start fixing said bugs without having to jump through hoops. |
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I experimented with using this facility under Python 3.11.4 installed by pyenv. Here are more The latter can be fixed by ln -s ~/.pyenv/versions/3.11.5/share/jupyter/nbconvert/ ~/work/software/sage/local/var/lib/sage/venv-python3.11/share/jupyter/
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I can't really say. I'm not a notebook user anyway, but I also haven't even started to sort out the notebook issues with system site packages enabled. If I had to bet though, I'd go with: version mismatches. Our ipython and notebook are outdated, but many of their dependencies are missing bounds in
I'm happy to have them but can we do it in a new ticket that isn't positively reviewed already? Note also that jupyter_packaging is being removed in #36267 |
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Follow-up ticket please... |
Please see #36276 |
This is a continuation of sagemath#36256 - Fixes sagemath#36301 - Fixes https://groups.google.com/g/sage- release/c/1wOBmhvNJqc/m/Jk14VAbjBAAJ (hence marked critical) ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies - sagemath#36296: to use an up to date Sphinx - sagemath#36267: updated ipympl, etc Also, a Jupyter/Python issue was uncovered there, which might need work. URL: sagemath#36276 Reported by: Dima Pasechnik Reviewer(s): Matthias Köppe, Michael Orlitzky
This is a continuation of sagemath#36256 - Fixes sagemath#36301 - Fixes https://groups.google.com/g/sage- release/c/1wOBmhvNJqc/m/Jk14VAbjBAAJ (hence marked critical) ### 📝 Checklist <!-- Put an `x` in all the boxes that apply. --> <!-- If your change requires a documentation PR, please link it appropriately --> <!-- If you're unsure about any of these, don't hesitate to ask. We're here to help! --> <!-- Feel free to remove irrelevant items. --> - [x] The title is concise, informative, and self-explanatory. - [x] The description explains in detail what this PR is about. - [x] I have linked a relevant issue or discussion. - [ ] I have created tests covering the changes. - [ ] I have updated the documentation accordingly. ### ⌛ Dependencies - sagemath#36296: to use an up to date Sphinx - sagemath#36267: updated ipympl, etc Also, a Jupyter/Python issue was uncovered there, which might need work. URL: sagemath#36276 Reported by: Dima Pasechnik Reviewer(s): Matthias Köppe, Michael Orlitzky
Add boilerplate for a few more python packages to be detected with
--enable-system-site-packages.Marked as critical because it repairs rpy2 system package on ubuntu/debian