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Use pipenv to create venv for development #30371

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mkoeppe opened this issue Aug 15, 2020 · 672 comments
Closed

Use pipenv to create venv for development #30371

mkoeppe opened this issue Aug 15, 2020 · 672 comments

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@mkoeppe
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mkoeppe commented Aug 15, 2020

We modify src/setup.py to support editable installs via pipenv (pipenv install -e ., which invokes pip install --editable). Since distribution continues using build/pkgs/sagelib/src/setup.py, the changes to src/setup.py made in this ticket do not affect the existing build process of the Sage library.

With this ticket, the following code works:

./bootstrap
./configure --enable-editable
make build-local
cd src
mkdir .venv
pipenv install --dev --ignore-pipfile
pipenv run pip install -e . --upgrade --exists-action=i --no-build-isolation
pipenv run sage-runtests --all

Instead of the first three commands, one can of course also use tox -e local-sudo-standard build-local.
It generates a virtual env in src/.venv that contains all necessary Python packages, and an editable install of sage.
Moreover, the installation of some packages might fail (depending on your system configuration). In this case one can manually build it using sage and then install the sage-built wheel in the pipenv. For example,

make fpylll
cd src && pipenv run pip install <sage>/local/var/lib/sage/venv-python3.8/var/lib/sage/wheels/fpylll-0.5.6-cp38-cp38-linux_x86_64.whl

The output of the added GH workflow is available here: https://github.com/sagemath/sagetrac-mirror/actions?query=workflow%3A%22Build+%26+Test+using+pipenv%22+branch%3Apublic%2Fbuild%2Finplace
Most tests are working, but a few are failing. Only a few tests are failing:

sage -t --random-seed=0 sage/misc/sagedoc.py  # 4 doctests failed
sage -t --random-seed=0 sage/docs/conf.py  # 1 doctest failed
sage -t --random-seed=0 sage/matrix/matrix_integer_dense.pyx  # 1 doctest failed
sage -t --random-seed=0 sage/cpython/dict_del_by_value.pyx  # 2 doctests failed
sage -t --random-seed=0 sage/tests/cmdline.py  # 8 doctests failed

TODO (as followup tickets):

Previous tickets on in-place builds, editable installs:

Depends on #30779
Depends on #30672
Depends on #30673
Depends on #30709
Depends on #30706
Depends on #30901
Depends on #31080
Depends on #29850
Depends on #29314
Depends on #30937
Depends on #30935
Depends on #30731
Depends on #30859
Depends on #30923
Depends on #30910
Depends on #30944
Depends on #30770
Depends on #31216
Depends on #31029
Depends on #30912
Depends on #31357
Depends on #31362
Depends on #31365
Depends on #31377

CC: @tobiasdiez @kiwifb @jhpalmieri @isuruf

Component: build

Keywords: sd111

Author: Tobias Diez

Branch/Commit: public/build/inplace @ c736e0c

Issue created by migration from https://trac.sagemath.org/ticket/30371

@mkoeppe mkoeppe added this to the sage-9.3 milestone Aug 15, 2020
@tobiasdiez
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comment:1

I've worked a bit on it. The current commit is a semi-working prototype, in the sense that all cython files are successfully compiled to C files if invoked via python src/setup.py build_ext --inplace. The second compilation of the c files does not yet work.

I had problems that none of the source cython files were correctly found on my system (wsl) and that a few dependencies in the current build files were not met ('linbox', 'Singular', 'm4ri', 'zlib', 'cblas'). For this reason, I started from scratch and only included what was needed so far. Any pointers to how to install these dependencies (I think they are needed for the second compilation).


New commits:

bc6e272Semi-working prototype for inplace compilation

@tobiasdiez
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Commit: bc6e272

@tobiasdiez
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Branch: public/build/inplace

@mkoeppe
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mkoeppe commented Aug 18, 2020

comment:2

I don't really have time to look into this before the 9.2 release. But if you are looking for where include directories are determined, take a look at sage_setup.command.sage_build_cython

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sagetrac-git mannequin commented Aug 19, 2020

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

58452ceMake in-place compilation work

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sagetrac-git mannequin commented Aug 19, 2020

Changed commit from bc6e272 to 58452ce

@tobiasdiez
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comment:4

The command ./sage src/setup.py build_ext --inplace runs now fine for me. I had to change quite a few things to make it work, and found it easier to completely start over using cythonize instead of using the existing build_cython code. The resulting code is a minimal working version. Please let me know which features of the existing build_cython file you would like to keep (to be honest, I don't really understand what some of the code there is doing, and why its needed).

The code definitely needs cleanup, but otherwise is ready for a first round of review.

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sagetrac-git mannequin commented Aug 19, 2020

Changed commit from 58452ce to 1a99228

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sagetrac-git mannequin commented Aug 19, 2020

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

1a99228Update gitignore

@mkoeppe
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mkoeppe commented Aug 19, 2020

comment:7
--- a/.gitignore
+++ b/.gitignore
@@ -99,7 +99,18 @@ gitlab-build-docker.log
 /src/build
 /src/Makefile
 /src/bin/sage-env-config
-/build/bin/sage-build-env-config
+/build

this is not good. Our /build/ contains important files of the sage distribution

@mkoeppe
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mkoeppe commented Aug 19, 2020

comment:8

And the changes removing old python2 code really need to go on a separate ticket

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sagetrac-git mannequin commented Aug 19, 2020

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

22b27a0Remove global gitignore of build folder

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sagetrac-git mannequin commented Aug 19, 2020

Changed commit from 1a99228 to 22b27a0

@tobiasdiez
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comment:10

Ok, I was under the assumption that the build folder is for build artifacts. If this would be the case, then I suppose it would be better to whitelist those files in the build folder that needs to be checked-in. I've now replaced the global build ignore, by a more fine-grained statement which only ignores the "temporary" files.

Concerning the changes about old Python2 code, I've created #30397.

@mkoeppe
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mkoeppe commented Aug 20, 2020

comment:11

Replying to @tobiasdiez:

I was under the assumption that the build folder is for build artifacts.

No, not at all.

@mkoeppe
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mkoeppe commented Aug 20, 2020

comment:12

The changes I see in setup.py don't seem to fit so well into the plan I have regarding modularization of sagelib. See #29705 and #28925 (which needs help).

@tobiasdiez
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comment:13

I wasn't aware of your changes in #28925. I guess what I'm proposing is a different strategy for the source discovery. The approach in #28925 is to change the source files themselves and enrich them by some form of metadata that decides in which distribution / package they land. Here I was proposing to specify the distribution of the files in the setup.py file. I guess both strategies have pros and cons. The main reason for me was that it seems the responsibility of the setup.py file to construct the distribution; why should the source file need to care about where they are used/included? I.e classical example of separation of concerns. I think, it's also the more flexible approach since it's easy to include a source file into multiple distributions etc. Moreover, you also gain a bit of performance at build time since you don't need to parse the files for some magic comments. What do you think?

@mkoeppe
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mkoeppe commented Aug 20, 2020

comment:14

Replying to @tobiasdiez:

[...] Here I was proposing to specify the distribution of the files in the setup.py file. I guess both strategies have pros and cons. The main reason for me was that it seems the responsibility of the setup.py file to construct the distribution; why should the source file need to care about where they are used/included? I.e classical example of separation of concerns. [...]

One more thing to be aware of is that (1) setup.py by itself actually is not able to control what goes into the source distribution. In #29865 (where I prepare some experimental subset distributions), I additionally use MANIFEST.in to control that.

Separation of concerns is, of course, desirable. But so is locality: (2) My plan for splitting up the distribution is driven to a large extent by the dependencies on different sets of C/C++ libraries. And these are already encoded in Cython distutils directives.

Also I have explored a little bit the packaging options beyond using setuptools (in part motivated because of the shortcoming (1)). See #29854 (flit), #29810 (poetry). Unfortunately currently there does not seem to be a proper mainstream solution for the source layout that we want to keep (a monolithic source tree in src/sage). For example, flit (and even pip out-of-directory installs) do not handle symbolic links well. In the long term, I was hoping to transform sage_setup to implement the PEP 517 API directly (see #29845). That's another reason why I would be reluctant to hard-code distribution information in setup.py.

In any case, I am hoping to have a broader discussion about all of this on sage-devel at the beginning of the 9.3 cycle.

@tobiasdiez
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comment:15

Separation of concerns is, of course, desirable. But so is locality: (2) My plan for splitting up the distribution is driven to a large extent by the dependencies on different sets of C/C++ libraries. And these are already encoded in Cython distutils directives.

One could also take this as an argument to remove the distutil dependency directives and put them into the setup.py, giving you locality and separation of concerns.

Anyway, my goal with this PR is not to redesign or modularize the build. I just wanted to have a working inplace build. For this moving the distribution declaration to setup.py was the easiest option, and I quite liked this also from a conceptual point of view. But if the current way is preferred, I change it back of course.
Anything else that needs to be changed?

@mkoeppe
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mkoeppe commented Aug 20, 2020

comment:16

Replying to @tobiasdiez:

One could also take this as an argument to remove the distutil dependency directives and put them into the setup.py, giving you locality and separation of concerns.

Ha, no, we just moved them there. Getting rid of the messy file modules_list.py was an achievement in the present cycle. See #29706

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mkoeppe commented Aug 20, 2020

comment:17

Replying to @tobiasdiez:

Anything else that needs to be changed?

I haven't really had a chance to look at it in more detail yet, sorry. Soon...

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sagetrac-git mannequin commented Aug 23, 2020

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

55d00d7Merge branch 'develop' of git://trac.sagemath.org/sage into public/build/inplace

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sagetrac-git mannequin commented Aug 23, 2020

Changed commit from 22b27a0 to 55d00d7

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Dependencies: #30397

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sagetrac-git mannequin commented Aug 23, 2020

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

8404a5dRemove old python 2 code from cython files
e9c06e3Readd constants in build script
811b78cRemove unused import
32daec5Merge branch 'public/build/removeOldCode' of git://trac.sagemath.org/sage into public/build/inplace
40f3503Fix merge problem

@jhpalmieri
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comment:484

I don't have any opinion about the code, so I am not the right person to review this, but I did get a lot of doctest failures when following the directions in the ticket:

sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/env.py  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/superseded.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/cython.py  # 21 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/inline_fortran.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/cachefunc.pyx  # 54 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/session.pyx  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/randstate.pyx  # 25 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/inherit_comparison.pyx  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/sagedoc.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/nested_class.pyx  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/lazy_attribute.pyx  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/sageinspect.py  # 35 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/sage_eval.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/misc/persist.pyx  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/elliptic_curves/ell_rational_field.py  # 21 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/elliptic_curves/lseries_ell.py  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/generic/algebraic_scheme.py  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/generic/homset.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/fano_variety.py  # 137 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/divisor_class.pyx  # 50 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/points.py  # 108 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/library.py  # 74 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/toric_subscheme.py  # 104 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/variety.py  # 229 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/divisor.py  # 234 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/weierstrass.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/weierstrass_covering.py  # 9 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/chow_group.py  # 159 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/homset.py  # 72 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/morphism.py  # 194 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/sheaf/klyachko.py  # 101 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/schemes/toric/sheaf/constructor.py  # 29 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/crypto/classical.py  # 16 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/parallel/decorate.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/graphics.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/contour_plot.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/line.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/arrow.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/tachyon.py  # 24 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/index_face_set.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/platonic.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/base.pyx  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/implicit_surface.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/implicit_plot3d.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/parametric_plot3d.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/plot/plot3d/parametric_surface.pyx  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/manifolds/differentiable/vectorfield.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/manifolds/differentiable/tangent_vector.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/constellation.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/tutorial.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/quickref.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/permutation.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/designs/ext_rep.py  # Killed due to abort
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/posets/posets.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/root_system/weyl_group.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/combinat/matrices/latin.py  # 45 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/lfunctions/zero_sums.pyx  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/lfunctions/lcalc.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/lfunctions/sympow.py  # 10 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/ext/memory_allocator.pxd  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/ext/memory_allocator.pyx  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/doctest/control.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/doctest/forker.py  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/features/__init__.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/benchmark.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/cmdline.py  # 8 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/gap_packages.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/books/judson-abstract-algebra/groups-sage.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/books/judson-abstract-algebra/cyclic-sage.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/books/judson-abstract-algebra/homomorph-sage.py  # 11 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/books/judson-abstract-algebra/sylow-sage.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/tests/books/computational-mathematics-with-sagemath/combinat_doctest.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/algebras/orlik_terao.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/algebras/orlik_solomon.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/repl/interpreter.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/repl/interface_magic.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/repl/ipython_extension.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/repl/load.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/galois_group.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/class_function.py  # 137 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/generic.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/symgp_conjugacy_class.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/permgroup_morphism.py  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/permgroup.py  # 44 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/cubegroup.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/constructor.py  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/permgroup_element.pyx  # 10 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/perm_gps/partn_ref/data_structures.pyx  # 9 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/abelian_gps/dual_abelian_group_element.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/abelian_gps/abelian_group_morphism.py  # 15 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/groups/abelian_gps/abelian_group.py  # 64 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/docs/instancedoc.pyx  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/arith/misc.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/arith/long.pxd  # 14 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/libs/gap/element.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/libs/gap/libgap.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/cpython/dict_del_by_value.pyx  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/cpython/wrapperdescr.pxd  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/cpython/string.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/cpython/cython_metaclass.pyx  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/cpython/getattr.pyx  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modular/abvar/abvar.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modular/arithgroup/congroup_gamma0.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modular/arithgroup/congroup_gammaH.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modular/arithgroup/arithgroup_perm.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modular/modform/constructor.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modular/hecke/submodule.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/functions/other.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/functions/exp_integral.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/functions/generalized.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/functions/piecewise.py  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/binary_code.pyx  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/databases.py  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/linear_code.py  # 22 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/golay_code.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/kasami_codes.pyx  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/two_weight_db.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/code_constructions.py  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/linear_code_no_metric.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/coding/goppa_code.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/integer_ring.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/integer.pyx  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/infinity.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/integer_fake.pxd  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/tate_algebra_ideal.pyx  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/rational_field.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/number_field/galois_group.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/number_field/number_field.py  # 26 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/number_field/number_field_element.pyx  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/number_field/totallyreal_rel.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/polynomial_ring.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/polynomial_element.pyx  # 8 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/ore_polynomial_element.pyx  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/multi_polynomial.pyx  # 8 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/multi_polynomial_ring_base.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/multi_polynomial_ideal.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/polynomial/groebner_fan.py  # 118 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/finite_rings/galois_group.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/finite_rings/element_pari_ffelt.pyx  # 11 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/finite_rings/element_givaro.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/finite_rings/integer_mod_ring.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/finite_rings/integer_mod.pyx  # 4 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/rings/finite_rings/finite_field_givaro.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/graphs/connectivity.pyx  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/graphs/generic_graph.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/graphs/graph_decompositions/fast_digraph.pyx  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/symbolic/expression.pyx  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/symbolic/constants.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/symbolic/pynac.pxi  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/symbolic/integration/integral.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/symbolic/integration/external.py  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/cone_catalog.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/fan_morphism.py  # 92 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/fan.py  # 85 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/toric_plotter.py  # 12 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/lattice_polytope.py  # 196 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/cone.py  # 17 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/fan_isomorphism.py  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/polyhedron/ppl_lattice_polytope.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/polyhedron/base_ZZ.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/polyhedron/backend_normaliz.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/polyhedron/palp_database.py  # 23 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/polyhedron/base.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/geometry/triangulation/element.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/calculus/calculus.py  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modules/free_module_element.pyx  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modules/filtered_vector_space.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modules/with_basis/invariant.py  # 74 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/modules/with_basis/representation.py  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/structure/parent_old.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/structure/element.pyx  # 37 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/structure/factory.pyx  # 8 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/structure/element.pxd  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/structure/parent.pyx  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/categories/primer.py  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/categories/finite_dimensional_modules_with_basis.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/categories/pushout.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/categories/modules_with_basis.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/matrix/matrix1.pyx  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/tachyon.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/expect.py  # 49 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/mwrank.py  # 9 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/ecm.py  # 12 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/qsieve.py  # 7 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/interface.py  # 31 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/gap3.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/gap.py  # 143 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/tests.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage/interfaces/giac.py  # 140 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage_setup/find.py  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 sage_docbuild/__init__.py  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/ja/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/ja/tutorial/tour_advanced.rst  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/ja/tutorial/interfaces.rst  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/ru/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/ru/tutorial/tour_advanced.rst  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/ru/tutorial/interfaces.rst  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/pt/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/pt/tutorial/tour_advanced.rst  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/pt/tutorial/interfaces.rst  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/de/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/de/tutorial/tour_advanced.rst  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/de/tutorial/interfaces.rst  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/fr/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/fr/tutorial/tour_advanced.rst  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/fr/tutorial/interfaces.rst  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/es/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/developer/coding_in_other.rst  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/tutorial/tour_groups.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/tutorial/tour_advanced.rst  # 2 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/tutorial/interfaces.rst  # 5 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/constructions/rep_theory.rst  # 18 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/constructions/polynomials.rst  # 13 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/constructions/rings.rst  # 6 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/constructions/linear_algebra.rst  # 3 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/constructions/groups.rst  # 18 doctests failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/thematic_tutorials/coding_theory.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/thematic_tutorials/explicit_methods_in_number_theory/elliptic_curves.rst  # 1 doctest failed
sage -t --warn-long 64.4 --random-seed=60140155690716510157027757823734981182 doc/en/thematic_tutorials/lie/weyl_groups.rst  # 1 doctest failed

Some come from

pkgconfig.pkgconfig.PackageNotFoundError: fflas-ffpack not found

and I also see some instances of errors like

File "doc/es/tutorial/tour_groups.rst", line 29, in doc.es.tutorial.tour_groups
Failed example:
    G.random_element()           # random output (resultado aleatorio)
Exception raised:
    Traceback (most recent call last):
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/sage/interfaces/gap.py", line 1155, in _start
        raise OSError("GAP workspace too old")
    OSError: GAP workspace too old

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/sage/interfaces/expect.py", line 492, in _start
        self._expect = SageSpawn(cmd,
      File "sage/interfaces/sagespawn.pyx", line 65, in sage.interfaces.sagespawn.SageSpawn.__init__
        with ContainChildren(silent=True):
      File "sage/interfaces/sagespawn.pyx", line 66, in sage.interfaces.sagespawn.SageSpawn.__init__
        spawn.__init__(self, *args, **kwds)
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/.venv/lib/python3.9/site-packages/pexpect/pty_spawn.py", line 205, in __init__
        self._spawn(command, args, preexec_fn, dimensions)
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/.venv/lib/python3.9/site-packages/pexpect/pty_spawn.py", line 276, in _spawn
        raise ExceptionPexpect('The command was not found or was not ' +
    pexpect.exceptions.ExceptionPexpect: The command was not found or was not executable: gap.

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/sage/interfaces/gap.py", line 654, in _eval_line
        self._start()
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/sage/interfaces/gap.py", line 1166, in _start
        Expect._start(self, "Failed to start GAP.")
      File "/Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/sage/interfaces/expect.py", line 503, in _start
        raise RuntimeError("unable to start %s because the command %r failed: %s\n%s" %
    RuntimeError: unable to start gap because the command 'gap -r -b -p -T -E -m 64m  /Users/jpalmier/Desktop/Sage/sage_builds/TESTING/sage-9.5.beta6/src/sage/ext_data/gap/sage.g' failed: The command was not found or was not executable: gap.

I haven't looked at all of the failures to see what else is there.

@tobiasdiez
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comment:485

Thanks for testing!

Some failing tests are to be expected since pipenv is rather different to the existing way to use sage (as part of sage-the-distribution). But I think for the modularization effort this ticket gives a helpful testcase how sage performs in a "pip-installable" environment.

I also had problems with gap (for the github action) and fixed it by manually setting the SAEG_LOCAL env variable. I guess there is potential for improvement as follow-up tickets but I'm not the right person to work on this as I'm not familiar with these parts of sage.

@mkoeppe
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mkoeppe commented Dec 18, 2021

comment:486

Stalled in needs_review or needs_info; likely won't make it into Sage 9.5.

@mkoeppe mkoeppe modified the milestones: sage-9.5, sage-9.6 Dec 18, 2021
@sagetrac-git
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sagetrac-git mannequin commented Jan 3, 2022

Changed commit from 0b0437f to c736e0c

@sagetrac-git
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sagetrac-git mannequin commented Jan 3, 2022

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

c736e0cMerge branch 'develop' of https://github.com/sagemath/sage into public/build/inplace

@mkoeppe mkoeppe modified the milestones: sage-9.6, sage-9.7 Apr 2, 2022
@mkoeppe mkoeppe modified the milestones: sage-9.7, sage-9.8 Sep 19, 2022
@dimpase
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dimpase commented Dec 4, 2022

comment:490

needs a rebase

@mkoeppe
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mkoeppe commented Feb 12, 2023

Branch has merge conflicts

@mkoeppe mkoeppe removed this from the sage-10.0 milestone Mar 16, 2023
@mkoeppe mkoeppe closed this as not planned Won't fix, can't repro, duplicate, stale Jul 27, 2024
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