#29415 closed enhancement (fixed)
tox.ini: Add environment local-conda
Reported by: | mkoeppe | Owned by: | |
---|---|---|---|
Priority: | major | Milestone: | sage-9.1 |
Component: | porting | Keywords: | |
Cc: | dimpase, jhpalmieri, isuruf, saraedum, gh-kliem | Merged in: | |
Authors: | Matthias Koeppe | Reviewers: | Isuru Fernando |
Report Upstream: | N/A | Work issues: | |
Branch: | a61c48e (Commits, GitHub, GitLab) | Commit: | |
Dependencies: | #29087 | Stopgaps: |
Description (last modified by )
This environment creates an isolated conda installation within the tox environment directory,
similar to local-homebrew
.
To run:
MAKE="make -j8" tox -e local-conda-forge-standard MAKE="make -j8" tox -e local-conda-forge-minimal
Attachments (2)
Change History (31)
comment:1 Changed 2 years ago by
- Branch set to u/mkoeppe/tox_ini__add_environment_local_conda
comment:2 Changed 2 years ago by
- Commit set to 36e1c9afe2379c243d02bd348adb75c720247f78
- Description modified (diff)
- Status changed from new to needs_review
comment:3 Changed 2 years ago by
- Dependencies changed from #29104 to #29087
comment:4 Changed 2 years ago by
- Description modified (diff)
comment:5 Changed 2 years ago by
- Commit changed from 36e1c9afe2379c243d02bd348adb75c720247f78 to a71ec3fd7bb082a8f6006ff542da34d46fa846fd
Branch pushed to git repo; I updated commit sha1. New commits:
a71ec3f | Use conda-install --yes --quiet
|
comment:6 Changed 2 years ago by
- Commit changed from a71ec3fd7bb082a8f6006ff542da34d46fa846fd to 354cf90635e94587435c75e237a3d6ef8c806e06
comment:7 Changed 2 years ago by
Rebased on 9.1.beta9+#29087
comment:8 Changed 2 years ago by
Needs testing, in particular on Linux
comment:9 Changed 2 years ago by
I end up with a C++ error in Singular
libtool: compile: /home/dimpase/sage/.tox/local-conda-forge-standard/conda/bin/x86_64-conda_cos6-linux-gnu-c++ -DHAVE_CONFIG_H -I. -I. ./../.. -I. -I../../.. -I../../.. -I../../../libpolys -I../../../libpolys -I/home/dimpase/sage/.tox/local-conda-forge-standard/local/var/tmp/sage/build/singular-4.1.1p2.p0/src -I/home/dimpase/sage/.tox/local-conda-forge-standard/local/var/tmp/sage/build/singular-4.1.1p2.p0/src/factory/include -I/home/dimpase/sage/.tox/local-conda-forge-standard/local/var/tmp/sage/build/singular-4.1.1p2.p0/src -I/home/dimpase/sage/.tox/local-conda-forge-standard/local/var/tmp/sage/build/singular-4.1.1p2.p0/src -pthread -DDYNAMIC_VERSION -DGMPRATIONAL -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/dimpase/sage/.tox/local-conda-forge-standard/conda/include -O2 -g -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dimpase/sage/.tox/local-conda-forge-standard/conda/include -fno-common -g0 -O3 -Wno-unused-function -Wno-trigraphs -Wno-unused-parameter -Wunknown-pragmas -Wno-unused-variable -fomit-frame-pointer -fwrapv -fvisibility=default -finline-functions -fno-exceptions -fno-threadsafe-statics -fno-enforce-eh-specs -fconserve-space -funroll-loops -fno-delete-null-pointer-checks -fno-rtti -fexceptions -frtti -c groebnerCone.cc -fPIC -DPIC -o .libs/gfanlib_la-groebnerCone.o groebnerCone.cc:428:58: error: no 'bool groebnerCone::pointsOutwards(gfan::ZVector) const' member function declared in class 'groebnerCone' bool groebnerCone::pointsOutwards(const gfan::ZVector w) const ^~~~~ groebnerCone.cc: In member function 'groebnerCones groebnerCone::tropicalNeighbours() const': groebnerCone.cc:449:13: error: 'pointsOutwards' was not declared in this scope if (pointsOutwards(ray[j])) ^~~~~~~~~~~~~~ make[9]: *** [Makefile:726: gfanlib_la-groebnerCone.lo] Error 1
this is on Debian, and might be due to using gfan from the system.
comment:10 follow-up: ↓ 18 Changed 2 years ago by
This is fixed in singular 4.1.2. https://github.com/Singular/Sources/commit/80a9ffc773542e3329935e5377f6906628be16e6
A workaround is to do export CPPFLAGS="$CPPFLAGS -UNDEBUG"
in Singular build script.
comment:11 follow-up: ↓ 12 Changed 2 years ago by
should we upgrade Sage's singular?
comment:12 in reply to: ↑ 11 Changed 2 years ago by
comment:13 follow-up: ↓ 29 Changed 2 years ago by
I also see a failure (testing with #29417):
local-conda-forge-macos-standard
:[dochtml] from sage.symbolic.all import * [dochtml] File "/Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/all.py", line 3, in <module> [dochtml] from sage.libs.pynac.pynac import I [dochtml] File "sage/symbolic/expression.pxd", line 4, in init sage.libs.pynac.pynac (build/cythonized/sage/libs/pynac/pynac.cpp:30411) [dochtml] File "sage/symbolic/expression.pyx", line 160, in init sage.symbolic.expression (build/cythonized/sage/symbolic/expression.cpp:75349) [dochtml] ImportError: dlopen(/Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so, 2): Symbol not found: __ZN5GiNaC9containerINSt3__16vectorEEC2ERKNS2_INS_2exENS1_9allocatorIS4_EEEEb [dochtml] Referenced from: /Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so [dochtml] Expected in: flat namespace [dochtml] in /Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so
(this is with #29404 -- should take another look)
comment:14 Changed 2 years ago by
In any case, the present ticket is about adding the testing framework for local-conda, which appears to work. Needs review.
comment:15 Changed 2 years ago by
- Cc gh-kliem added
comment:16 follow-up: ↓ 17 Changed 2 years ago by
Shameless plug. Use miniforge instead of miniconda?
comment:17 in reply to: ↑ 16 ; follow-up: ↓ 19 Changed 2 years ago by
Replying to isuruf:
Shameless plug. Use miniforge instead of miniconda?
Just tried it and it behaves a bit different from miniconda:
local-macos-conda-forge-standard-python2 run-test-pre: commands[6] | bash -c '/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-macos-conda-forge-standard-python2/conda/bin/conda update -n base --yes conda' Traceback (most recent call last): File "/Users/mkoeppe/s/sage/sage-rebasing/worktree-algebraic-2018-spring/.tox/local-macos-conda-forge-standard-python2/conda/bin/conda", line 12, in <module> from conda.cli import main ModuleNotFoundError: No module named 'conda'
Do I need to activate the environment before using that?
comment:18 in reply to: ↑ 10 Changed 2 years ago by
Replying to isuruf:
This is fixed in singular 4.1.2. https://github.com/Singular/Sources/commit/80a9ffc773542e3329935e5377f6906628be16e6
A workaround is to do
export CPPFLAGS="$CPPFLAGS -UNDEBUG"
in Singular build script.
Because the singular upgrade (#25993) will not be ready for 9.1, I have opened #29438 for this
comment:19 in reply to: ↑ 17 Changed 2 years ago by
Replying to mkoeppe:
Do I need to activate the environment before using that?
Yes, but even miniconda needs activation.
comment:20 Changed 2 years ago by
- Commit changed from 354cf90635e94587435c75e237a3d6ef8c806e06 to a61c48e04b0c463b02fb47903454a94133b3a560
Changed 2 years ago by
Changed 2 years ago by
comment:21 Changed 2 years ago by
I guess it works in the way that it doesn't work.
* package: openblas-0.3.6.p0 last build time: Apr 1 10:54 log file: /srv/public/kliem/sage/logs/pkgs/openblas-0.3.6.p0.log build directory: /srv/public/kliem/sage/.tox/local-conda-forge-standard/local/var/tmp/sage/build/openblas-0.3.6.p0 * package: singular-4.1.1p2.p0 last build time: Apr 1 11:00 log file: /srv/public/kliem/sage/logs/pkgs/singular-4.1.1p2.p0.log build directory: /srv/public/kliem/sage/.tox/local-conda-forge-standard/local/var/tmp/sage/build/singular-4.1.1p2.p0
I attached the logs.
comment:22 Changed 2 years ago by
Singular might need the fix proposed by Isuru above
comment:23 Changed 2 years ago by
I'm not sure that I understand.
At least this here did not fix the problem.
+++ b/build/pkgs/singular/spkg-install.in @@ -19,6 +19,7 @@ else fi export CFLAGS CXXFLAGS +export CPPFLAGS="$CPPFLAGS -UNDEBUG" remove_old_version()
Now openblas, tachyon, m4ri, givaro, ecm, python3, giac, singular fail to install.
comment:24 Changed 2 years ago by
Singular fixes - please on #29438, not here
comment:25 Changed 2 years ago by
This ticket is about adding the testing environment for conda, not fixing everything that may be broken in the conda build
comment:26 Changed 2 years ago by
- Reviewers set to Isuru Fernando
- Status changed from needs_review to positive_review
comment:27 Changed 2 years ago by
Thank you.
comment:28 Changed 2 years ago by
- Branch changed from u/mkoeppe/tox_ini__add_environment_local_conda to a61c48e04b0c463b02fb47903454a94133b3a560
- Resolution set to fixed
- Status changed from positive_review to closed
comment:29 in reply to: ↑ 13 Changed 2 years ago by
- Commit a61c48e04b0c463b02fb47903454a94133b3a560 deleted
Replying to mkoeppe:
I also see a failure (testing with #29417):
local-conda-forge-macos-standard
:[dochtml] from sage.symbolic.all import * [dochtml] File "/Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/all.py", line 3, in <module> [dochtml] from sage.libs.pynac.pynac import I [dochtml] File "sage/symbolic/expression.pxd", line 4, in init sage.libs.pynac.pynac (build/cythonized/sage/libs/pynac/pynac.cpp:30411) [dochtml] File "sage/symbolic/expression.pyx", line 160, in init sage.symbolic.expression (build/cythonized/sage/symbolic/expression.cpp:75349) [dochtml] ImportError: dlopen(/Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so, 2): Symbol not found: __ZN5GiNaC9containerINSt3__16vectorEEC2ERKNS2_INS_2exENS1_9allocatorIS4_EEEEb [dochtml] Referenced from: /Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so [dochtml] Expected in: flat namespace [dochtml] in /Users/runner/runners/2.165.2/work/sage/sage/.tox/local-conda-forge-macos-standard/local/lib/python3.7/site-packages/sage/symbolic/ring.cpython-37m-darwin.so(this is with #29404 -- should take another look)
This is now #29574
Last 10 new commits:
Reorder systems so debian-sid comes after other debians
tox.ini [ubuntu-focal]: Use IGNORE_MISSING_SYSTEM_PACKAGES=yes because of libpython3.7-dev
Merge tag '9.1.beta8' into t/29354/tox_ini__add_slackware_environments
Add slackware package info
Fixup packages
build/bin/sage-guess-package-system, build/bin/sage-print-system-package-command: Handle slackware too
build/bin/sage-spkg: Show equivalent system packages for ALL distros
Merge branch 't/29354/tox_ini__add_slackware_environments' into t/29087/CI-gh-actions-tox-configure-build
tox.ini: Add local-conda environments
tox.yml: Add local-conda-forge