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Add pip packages to conda environments, add missing conda.txt files #33613

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mkoeppe opened this issue Mar 31, 2022 · 76 comments
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Add pip packages to conda environments, add missing conda.txt files #33613

mkoeppe opened this issue Mar 31, 2022 · 76 comments
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c: porting p: major / 3 t: enhancement
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sage-9.8

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@mkoeppe
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mkoeppe commented Mar 31, 2022

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 mkoeppe added this to the sage-9.6 milestone Mar 31, 2022
@mkoeppe mkoeppe changed the title gitpod: Install sage-trac-command gitpod: Install git-trac-command Mar 31, 2022
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mkoeppe commented Mar 31, 2022

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: [email protected]: 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
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comment:4

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

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mkoeppe commented Mar 31, 2022

Dependencies: #33589

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mkoeppe commented Mar 31, 2022

comment:5

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

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mkoeppe commented Mar 31, 2022

Branch: u/mkoeppe/gitpod__install_git_trac_command

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mkoeppe commented Mar 31, 2022

Author: Matthias Koeppe

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mkoeppe commented Mar 31, 2022

Last 10 new commits:

a5d10a2Fix typo
4950bcfAdd fallback to github mirror
c235eadDisable pushing to github
40d1e23Always disable pushing to origin
89591c4Remove wrong trac from prebuild
3d450f3Update docs
e9035aeSilence semi-expected errors during (pre)build
8432e1dMerge #33589
8aaaf07build/pkgs/python3/distros/debian.txt: New
eacd393docker/.gitpod.Dockerfile: Install pip for system python, install git-trac-command

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mkoeppe commented Mar 31, 2022

Commit: eacd393

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sagetrac-git mannequin commented Mar 31, 2022

Changed commit from eacd393 to 3f71861

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sagetrac-git mannequin commented Mar 31, 2022

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

3f71861docker/.gitpod.Dockerfile: hardcode python3-pip

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sagetrac-git mannequin commented Mar 31, 2022

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

866a833docker/.gitpod.Dockerfile: Run apt-get update first

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sagetrac-git mannequin commented Mar 31, 2022

Changed commit from 3f71861 to 866a833

@mkoeppe mkoeppe modified the milestones: sage-9.6, sage-9.7 Apr 17, 2022
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@mkoeppe mkoeppe changed the title gitpod: Install git-trac-command Script package git_trac_command May 16, 2022
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mkoeppe commented May 16, 2022

Changed dependencies from #33589 to #33740, #33851

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mkoeppe commented May 16, 2022

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

@mkoeppe mkoeppe changed the title Script package git_trac_command Pip package git_trac_command May 16, 2022
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sagetrac-git mannequin commented May 16, 2022

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

ccbc21abootstrap, bootstrap-conda, src/doc/bootstrap: Use build/bin/sage-package directly
4560895src/doc/Makefile: Remove explicit use of SAGE_ROOT and the top-level sage script
7759f3cGenerate en/reference/repl/options.txt at build time, not bootstrap time
58ab878bootstrap-conda: Fix typo, generate->generating to match messages from bootstrap
12ea8cebuild/pkgs/_develop/distros: Add packages providing gpgconf
238b7bbbuild/pkgs/_develop/distros: Add packages providing ssh
01a126cMerge #33851
a74ccaabuild/pkgs/git_trac_command: New
e28f6d9build/pkgs/_develop/dependencies: Add git_trac_command
d2b8c4ebootstrap-conda: Also generate pip: lines

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sagetrac-git mannequin commented May 16, 2022

Changed commit from 866a833 to d2b8c4e

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sagetrac-git mannequin commented May 17, 2022

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

ffde371bootstrap-conda: Do not include packages that declare SAGERUNTIME as a dependency

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sagetrac-git mannequin commented May 17, 2022

Changed commit from d2b8c4e to ffde371

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sagetrac-git mannequin commented Aug 6, 2022

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

6d06720build/pkgs: Add even more distros/conda.txt files (fixup)

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sagetrac-git mannequin commented Aug 6, 2022

Changed commit from 1c47261 to 6d06720

@mkoeppe mkoeppe changed the title Pip package git_trac_command, add pip packages to conda environments Pip package git_trac_command, add pip packages to conda environments, add missing conda.txt files Aug 6, 2022
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mkoeppe commented Aug 24, 2022

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

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sagetrac-git mannequin commented Aug 24, 2022

Changed commit from 6d06720 to 175a758

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sagetrac-git mannequin commented Aug 24, 2022

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

3f6660bbootstrap-conda: Write an additional comment
04045d3build/pkgs/_develop/dependencies: Add pytest, pytest_xdist
0856a00bootstrap-conda: Write an additional comment (fixup)
8f17c11bootstrap-conda: Rewrite using fewer redirects
15598c5build/pkgs/_develop/distros: Add packages providing gpgconf
eab7c56build/pkgs/_develop/distros: Add packages providing ssh
6592b38README.md: All developers should install _bootstrap packages
2e96172src/doc/bootstrap: Generate *-develop.txt
c96c7c5src/doc/en/installation/source.rst: Include *-develop.txt and *-recommended.txt
175a758Merge #33851

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sagetrac-git mannequin commented Aug 24, 2022

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

6dfc583build/pkgs/_develop/dependencies: Add git_trac_command

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sagetrac-git mannequin commented Aug 24, 2022

Changed commit from 175a758 to 6dfc583

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sagetrac-git mannequin commented Sep 12, 2022

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

d90b64cRevert "build/pkgs/git_trac_command: New"

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sagetrac-git mannequin commented Sep 12, 2022

Changed commit from 6dfc583 to d90b64c

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@mkoeppe mkoeppe changed the title Pip package git_trac_command, add pip packages to conda environments, add missing conda.txt files Add pip packages to conda environments, add missing conda.txt files Sep 12, 2022
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sagetrac-git mannequin commented Sep 12, 2022

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

0e4a696Merge tag '9.7.rc1' into t/33613/gitpod__install_git_trac_command

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sagetrac-git mannequin commented Sep 12, 2022

Changed commit from d90b64c to 0e4a696

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mkoeppe commented Sep 12, 2022

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

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dimpase commented Sep 16, 2022

Reviewer: Dima Pasechnik

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dimpase commented Sep 16, 2022

comment:62

this should be merged soon.

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mkoeppe commented Sep 16, 2022

comment:63

Thank you!

@mkoeppe mkoeppe modified the milestones: sage-9.7, sage-9.8 Sep 19, 2022
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vbraun commented Sep 20, 2022

Changed branch from u/mkoeppe/gitpod__install_git_trac_command to 0e4a696

@vbraun vbraun closed this as completed in 700a1f5 Sep 20, 2022
@tobiasdiez tobiasdiez mentioned this issue Jan 29, 2023
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