Meta-ticket: improve conda setup

[tobiasdiez]

• Conda: Add primecountpy #33330: primecountpy is not installed in the conda env because it is not listed in environment.yml
• conda-forge-standard: Runtime error in sage.libs.giac #33056: giac installed via conda is not usable and leads to many doctest failures
• Fix for rename of conda e-antic package to libeantic #33358: fix for downgrades in src/environment-optional.yml
• Fixes for the conda-for-Sage-developers installation method, add GH Actions workflow #30845: Fix the conda-for-Sage-developers installation method, add GH Actions workflow
• Updated https://wiki.sagemath.org/Conda to match Fixes for the conda-for-Sage-developers installation method, add GH Actions workflow #30845
  • use configure --prefix=$CONDA_PREFIX
  • use configure --with-system-...=force
  • use conda for all python dependencies instead of relying on pip -r requirements.txt
• add more details on conda-based installations of Sage #33426 Migrate documentation from wiki https://wiki.sagemath.org/Conda to developer and installation docs
• Update build/pkgs/matplotlib/install-requires.txt and distros/conda.txt #33642 Update build/pkgs/matplotlib/install-requires.txt
• More updates for installation and developer guides #33088 More updates for installation and developer guides
• Add pip packages to conda environments, add missing conda.txt files #33613 Pip package git_trac_command, add pip packages to conda environments
• On WSL, gc and thus ecl are not found, as discussed at #30845 comment:152
• Make sure conda installs only python packages that are satisfying the version constraints specified in install_requires. Notably, ptyprocess, iniconfig, sphinx, pytest, rpy2 are currently reinstalled by pip. Also add --no-dependencies to pip install in the conda ci workflow. This is Conda config does not respect constraints in install_requires #35074.

Fix remaining tests that fail:

• sage distutils classes

File "src/sage/interfaces/sage0.py", line 208, in sage.interfaces.sage0.Sage.cputime
Failed example:
    sage0.cputime()     # random output
Exception raised:
    Traceback (most recent call last):
      File "/home/runner/work/sage/sage/src/sage/doctest/forker.py", line 695, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/runner/work/sage/sage/src/sage/doctest/forker.py", line 1093, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.interfaces.sage0.Sage.cputime[0]>", line 1, in <module>
        sage0.cputime()     # random output
      File "/home/runner/work/sage/sage/src/sage/interfaces/sage0.py", line 219, in cputime
        return float(s)
    ValueError: could not convert string to float: 'iniconda/envs/sage-build/lib/python3.8/site-packages/setuptools/_distutils/version.py:351: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.\n  other = LooseVersion(other)\n1.60718'

• conda: 3d graphics do not show #34298: threejs path

 File "src/sage/repl/ipython_kernel/install.py", line 127, in sage.repl.ipython_kernel.install.SageKernelSpec.use_local_threejs
Failed example:
    os.path.isdir(threejs)
Expected:
    True
Got:
    False

CC: @isuruf @dimpase @saraedum @mkoeppe @slel

Component: build

Issue created by migration from https://trac.sagemath.org/ticket/33331

[isuruf]

comment:4

The correct version of rpy2, scipy, sphinx among other packages is not installed in the conda env, so add version constraints in the corresponding conda.txt files

@tobiasdiez, is this fixed by #33358 too?

[tobiasdiez]

comment:5

Replying to @isuruf:

The correct version of rpy2, scipy, sphinx among other packages is not installed in the conda env, so add version constraints in the corresponding conda.txt files

@tobiasdiez, is this fixed by #33358 too?

Nope, still present. See e.g. output of https://pipelines.actions.githubusercontent.com/wUvxDab7ZCURYAl3HeSwsAoJVAdvXg6u4iTbsP5NChUqrJ4TKs/_apis/pipelines/1/runs/9243/signedlogcontent/3?urlExpires=2022-02-17T12%3A02%3A43.1351322Z&urlSigningMethod=HMACV1&urlSignature=ildfTJhaQ2KGVywf69MDFQSVOl7GTONDSdIOurIphKI%3D

Conda is installing rpy2 v3.4.5, while sagelib install requires specify <3.4,>=3.3. Thus pip will download an older version. I think it should be enough to specify the same upper constraint (for the few python packages that have one) in the distros/conda.txt.

[dimpase]

comment:12

in ​https://wiki.sagemath.org/Conda there is a confusing mix of conda and mamba commands. Can they all be mamba?

[slel]

comment:13

I think after running mamba init you can
always use mamba instead of conda.

[slel]

comment:14

I followed the "Conda for Sage developers"
section of the Conda page on the Sage wiki.

I noticed it downgrades the openssl version from 3.0.0 to 1.1.1l.
Can that be fixed?

[slel]

comment:15

Using src/environment-optional.yml
downgrades a few more packages:

• boost-cpp from 1.77.0 to 1.74.0
• cmake from 3.22.3 to 3.21.3
• ncursesfrom 6.3 to 6.2
• python from 3.10.2 to 3.8.12
• singular from 4.2.1.p3 to 4.2.0.p3
• sqlite from 3.37.1 to 3.37.0

[mkoeppe]

comment:16

Did you use the branch of #30845?

[mkoeppe]

comment:17

Replying to @dimpase:

in ​https://wiki.sagemath.org/Conda there is a confusing mix of conda and mamba commands. Can they all be mamba?

They can, but I'm not sure if it would be an improvement to this documentation.
I have added a comment to the step "conda install mamba", please take a look

[slel]

comment:19

Replying to @mkoeppe:

Did you use the branch of #30845?

Oops, I had not used that branch.
Using it, only openssl gets downgraded,

• whether using src/environment.yml
• or using src/environment-optional.yml

This is on macOS 11.6.5 Big Sur.

[tobiasdiez]

Everything is done here, so let's close this.