Add pip packages to conda environments, add missing conda.txt files

[mkoeppe]

We have a number of pip-installable optional packages, for which there is no conda package.

Here we add a mechanism to add such packages using a pip: line
in src/environment-optional.yml and src/environment-dev.yml (#33740).

We also add lots of conda.txt files.

To test, follow the instructions in https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental
using src/environment-optional.yml or src/environment-dev.yml

(A use case for the pip line in src/environment-dev.yml is #34524: Pip package git_trac_command.)

CC: @tobiasdiez @dimpase @isuruf @saraedum @slel @yuan-zhou

Component: porting

Author: Matthias Koeppe

Branch/Commit: 0e4a696

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/33613

[mkoeppe]

comment:3

(Without #33589) I also get

(sage-sh) gitpod@sagemath-sagetracmirror-72wwexpcfmb:sagetrac-mirror$ git trac checkout 33608
Loading ticket #33608...
Checking out Trac #33608 remote branch u/klee/33608 -> local branch t/33608/33608...
Traceback (most recent call last):
    STDERR: Warning: Permanently added the ECDSA host key for IP address '104.197.143.230' to the list of known hosts.
    STDERR: Load key "/home/gitpod/.ssh/id_rsa": invalid format
    STDERR: git@trac.sagemath.org: Permission denied (publickey).
    STDERR: fatal: Could not read from remote repository.
    STDERR: 
    STDERR: Please make sure you have the correct access rights
    STDERR: and the repository exists.

[tobiasdiez]

comment:4

Did you followed the steps outlined in sage's gitpod docs to add the ssh key?

[mkoeppe]

Dependencies: #33589

[mkoeppe]

comment:5

No. In #33589 we should make sure that fetching can be done without these steps.

[mkoeppe]

Branch: u/mkoeppe/gitpod__install_git_trac_command

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

Last 10 new commits:

a5d10a2	Fix typo
4950bcf	Add fallback to github mirror
c235ead	Disable pushing to github
40d1e23	Always disable pushing to origin
89591c4	Remove wrong trac from prebuild
3d450f3	Update docs
e9035ae	Silence semi-expected errors during (pre)build
8432e1d	Merge #33589
8aaaf07	build/pkgs/python3/distros/debian.txt: New
eacd393	docker/.gitpod.Dockerfile: Install pip for system python, install git-trac-command

[mkoeppe]

Commit: eacd393

[sagetrac-git]

Changed commit from eacd393 to 3f71861

[sagetrac-git]

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

3f71861

docker/.gitpod.Dockerfile: hardcode python3-pip

[sagetrac-git]

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

866a833

docker/.gitpod.Dockerfile: Run apt-get update first

[sagetrac-git]

Changed commit from 3f71861 to 866a833

[mkoeppe]

Changed dependencies from #33589 to #33740, #33851

[mkoeppe]

Changed dependencies from #33740, #33851 to #33740, #33822, #33851

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. Last 10 new commits:

ccbc21a	bootstrap, bootstrap-conda, src/doc/bootstrap: Use build/bin/sage-package directly
4560895	src/doc/Makefile: Remove explicit use of SAGE_ROOT and the top-level sage script
7759f3c	Generate en/reference/repl/options.txt at build time, not bootstrap time
58ab878	bootstrap-conda: Fix typo, generate->generating to match messages from bootstrap
12ea8ce	build/pkgs/_develop/distros: Add packages providing gpgconf
238b7bb	build/pkgs/_develop/distros: Add packages providing ssh
01a126c	Merge #33851
a74ccaa	build/pkgs/git_trac_command: New
e28f6d9	build/pkgs/_develop/dependencies: Add git_trac_command
d2b8c4e	bootstrap-conda: Also generate pip: lines

[sagetrac-git]

Changed commit from 866a833 to d2b8c4e

[sagetrac-git]

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

ffde371

bootstrap-conda: Do not include packages that declare SAGERUNTIME as a dependency

[sagetrac-git]

Changed commit from d2b8c4e to ffde371

[mkoeppe]

Changed dependencies from #34263, #34274 to #34263, #34274, #33851

[sagetrac-git]

Changed commit from 6d06720 to 175a758

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

3f6660b	bootstrap-conda: Write an additional comment
04045d3	build/pkgs/_develop/dependencies: Add pytest, pytest_xdist
0856a00	bootstrap-conda: Write an additional comment (fixup)
8f17c11	bootstrap-conda: Rewrite using fewer redirects
15598c5	build/pkgs/_develop/distros: Add packages providing gpgconf
eab7c56	build/pkgs/_develop/distros: Add packages providing ssh
6592b38	README.md: All developers should install _bootstrap packages
2e96172	src/doc/bootstrap: Generate *-develop.txt
c96c7c5	src/doc/en/installation/source.rst: Include *-develop.txt and *-recommended.txt
175a758	Merge #33851

[sagetrac-git]

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

6dfc583

build/pkgs/_develop/dependencies: Add git_trac_command

[sagetrac-git]

Changed commit from 175a758 to 6dfc583

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

d90b64c

Revert "build/pkgs/git_trac_command: New"

[sagetrac-git]

Changed commit from 6dfc583 to d90b64c

[sagetrac-git]

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

0e4a696

Merge tag '9.7.rc1' into t/33613/gitpod__install_git_trac_command

[sagetrac-git]

Changed commit from d90b64c to 0e4a696

[mkoeppe]

Changed dependencies from #34263, #34274, #33851 to none

[dimpase]

Reviewer: Dima Pasechnik

[dimpase]

comment:62

this should be merged soon.

[mkoeppe]

comment:63

Thank you!

[vbraun]

Changed branch from u/mkoeppe/gitpod__install_git_trac_command to 0e4a696