Fixes for the conda-for-Sage-developers installation method, add GH Actions workflow

[mkoeppe]

Add github action workflow that checks the build of sage in a conda environment, completely bypassing the installation of any sage package. This is based on the steps outlined at https://wiki.sagemath.org/Conda.

This also tests that the generated src/environment*.yml files work correctly. (See documentation added in #28745)

Run: https://github.com/sagemath/sagetrac-mirror/actions/workflows/ci-conda.yml

Fixes:

• Conda: Add primecountpy #33330: primecountpy is not installed in the conda env because its not listed in environment.yml
• environment-optional: lcalc 1 is installed and then not recognized / leads to error

building 'sage.libs.lcalc.lcalc_Lfunction' extension
    cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
    In file included from sage/libs/lcalc/lcalc_Lfunction.cpp:740:
    sage/libs/lcalc/lcalc_sage.h:1:10: fatal error: lcalc/L.h: No such file or directory
        1 | #include "lcalc/L.h"
          |          ^~~~~~~~~~~
    compilation terminated.

• environment-optional: probably related, pari 2.11.4 is installed by conda instead of the newest 2.13.2. This version is then rejected by configure as being too old.
• Disable conda distro information for gdb because it is broken on macOS.
• Add conda distro information for lrcalc_python
• Filter out conda-specific ld warnings in doctests
• In the feature test for sage_spkg, check whether any Sage packages are actually installed
• Include an upper version bound for ptyprocess in sagemath-standard's install-requires

Follow-ups: See Meta-ticket #33331

Depends on #33358
Depends on #33330
Depends on #33361
Depends on #33141

CC: @isuruf @tobiasdiez @dimpase @saraedum

Component: build

Keywords: sd111

Author: Tobias Diez, Matthias Koeppe

Branch/Commit: 93fce5a

Reviewer: Matthias Koeppe, Dima Pasechnik, Tobias Diez

Issue created by migration from https://trac.sagemath.org/ticket/30845

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1 +1,2 @@
+This would also test that the generated `environment*.yml` files work correctly.
 

[mkoeppe]

comment:3

Hoping we can make progress on this ticket this week - https://wiki.sagemath.org/days111

[mkoeppe]

Changed keywords from none to sd111

[mkoeppe]

Description changed:

--- 
+++ 
@@ -1,2 +1 @@
-This would also test that the generated `environment*.yml` files work correctly.
-
+This would also test that the generated `environment*.yml` files work correctly. (See documentation added in #28745 and https://wiki.sagemath.org/Conda)

[tobiasdiez]

comment:7

Something like https://github.com/tobiasdiez/sage/blob/public/build/conda_gh/.github/workflows/ci-conda.yml?

This currently fails with

configure: creating ./config.status
config.status: creating build/make/Makefile-auto
config.status: creating build/make/Makefile
config.status: creating src/bin/sage-env-config
config.status: creating src/bin/sage-src-env-config
config.status: creating build/bin/sage-build-env-config
config.status: creating build/pkgs/sage_conf/src/sage_conf.py
config.status: creating build/pkgs/sage_conf/src/setup.cfg
config.status: executing depfiles commands
config.status: executing mkdirs commands
config.status: creating directory /home/runner/work/sage/sage/logs/pkgs
config.status: creating directory 
mkdir: cannot create directory '': No such file or directory
config.status: error: could not create 
Error: Process completed with exit code 1.

https://github.com/tobiasdiez/sage/runs/1594237745?check_suite_focus=true
Any idea what could be the reason and how to fix it?

[tobiasdiez]

Commit: 9af4614

[tobiasdiez]

Author: Tobias Diez

[tobiasdiez]

New commits:

c68d262	Add first version of workflow
9af4614	Try with sudo (why is this needed now?!)

[tobiasdiez]

Branch: public/build/conda_gh

[sagetrac-git]

Changed commit from 9af4614 to a178b56

[sagetrac-git]

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

5ac74ee	Try with conda-incubator
a178b56	Run in the conda shell

[sagetrac-git]

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

199886c	Install more conda dependencies
10de3f5	Fix conda env name
86411b8	Remove unnececesary install of conda dep

[sagetrac-git]

Changed commit from a178b56 to 86411b8

[tobiasdiez]

comment:11

Managed to fix the above error, just to be stuck two lines further down:

configure: creating ./config.status
config.status: creating build/make/Makefile-auto
config.status: creating build/make/Makefile
config.status: creating src/bin/sage-env-config
config.status: creating src/bin/sage-src-env-config
config.status: creating build/bin/sage-build-env-config
config.status: creating build/pkgs/sage_conf/src/sage_conf.py
config.status: creating build/pkgs/sage_conf/src/setup.cfg
config.status: executing depfiles commands
config.status: executing broken-gcc commands
config.status: executing mkdirs commands
config.status: creating directory /home/runner/work/sage/sage/logs/pkgs
config.status: creating directory /usr/share/miniconda/envs/sage-build
config.status: creating directory /usr/share/miniconda/envs/sage-build/bin
config.status: creating directory /usr/share/miniconda/envs/sage-build/etc
config.status: creating directory /usr/share/miniconda/envs/sage-build/include
config.status: creating directory /usr/share/miniconda/envs/sage-build/lib
config.status: creating directory /usr/share/miniconda/envs/sage-build/lib/pkgconfig
config.status: creating directory /usr/share/miniconda/envs/sage-build/share
config.status: creating directory /usr/share/miniconda/envs/sage-build/var/lib/sage/installed
config.status: error: Cannot perform incremental update, run "make distclean && make"
config.status: /usr/share/miniconda/envs/sage-build/lib64 is not a symlink, see Trac #19782
Error: Process completed with exit code 1.

https://github.com/tobiasdiez/sage/runs/1594601374?check_suite_focus=true

[tobiasdiez]

comment:12

Found a hack that fixed it by removing the lib64 folder. It only contained libcc1.so (not sure where/how this is needed).