Make `conda env update --prune` ignore history specs. #9614

tarcisioe · 2020-01-17T21:07:06Z

This is supposed to solve #7279. The idea here is that if we are pruning we must use only the specs coming from environment.yml and ignore the history. Regression tests have also been added.

Resolves #7279

cla-bot · 2020-01-17T21:07:08Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

nicoddemus · 2020-01-20T10:43:22Z

Great work @tarcisioe! Fixing --prune means we can upgrade our conda version at @ESSS. 👍

tests/core/test_solve.py

cla-bot · 2020-01-20T21:13:48Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

tarcisioe · 2020-01-21T16:02:22Z

@marcelotrevisani @msarahan I have submitted my CLA (twice, actually), is anything else needed for the bot to see it? Maybe it needs to be updated in .cla-signers?

tarcisioe · 2020-01-21T16:07:17Z

Also, I believe appveyor/pr wasn't broken by my change, and I'm not too sure about what's happened in circleci conda-build. Should I do something about those?

marcelotrevisani · 2020-01-22T05:48:25Z

@marcelotrevisani @msarahan I have submitted my CLA (twice, actually), is anything else needed for the bot to see it? Maybe it needs to be updated in .cla-signers?

Hi @tarcisioe , this process has a manual part lets say. @msarahan has to review and approve it. It seems to be a legal process which they cannot avoid.

marcelotrevisani · 2020-01-22T05:49:24Z

tests/core/test_solve.py

@@ -363,6 +363,170 @@ def test_prune_1(tmpdir):
        assert convert_to_dist_str(link_precs) == link_order


+def test_update_prune_1(tmpdir):


Thanks for the tests! :)

marcelotrevisani · 2020-01-22T14:09:24Z

@cla-bot check

cla-bot · 2020-01-22T14:09:25Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

cla-bot · 2020-01-22T14:09:27Z

The cla-bot has been summoned, and re-checked this pull request!

kahing · 2020-02-06T23:27:38Z

what's the status of this? does the maintainer agree that this is the right fix?

kahing · 2020-02-07T00:18:22Z

I tried to manually apply this patch to 4.8.2 and the steps in #7279 (comment) is still broken

tarcisioe · 2020-02-07T20:18:27Z

@kahing It hasn't been reviewed yet by the maintainers. I will try to reproduce the steps you posted and investigate.

tarcisioe · 2020-02-07T22:05:08Z

Well, shame on me I guess. I developed this patch on top of 4.7.x and trusted my regression tests. They are indeed still passing, so something else reintroduced the issue. I went through the major tags rebasing my patch onto them:

4.7.9 was ok
4.8.0 was ok
4.8.1 stopped working

So I made a script that applied my patch and tested, and got the change that ended up nullifying my fix with git bisect. It was commit 03d22d4. I will work on matching my fix to what was intended on that commit now.

cla-bot · 2020-02-07T23:57:59Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

tarcisioe · 2020-02-08T00:00:09Z

@kahing it's now rebased on master and when pruning the option "freeze-installed" is ignored (which was making packages that should otherwise be pruned be kept). I'm unsure if that is the best solution, but it basically reverts prune to the previous behaviour. Another regression test was added.

kalefranz · 2020-02-20T21:09:03Z

Thanks for contributing this PR, and apologies for the delay in review. We're undergoing some changes in the Conda team right now, but it's our plan to be spending considerably more resources directly on Conda soon.

In particular for this PR, does this PR change the behavior of conda install --prune or conda update --prune?

tarcisioe · 2020-02-23T02:37:39Z

@kalefranz It shouldn't. What it does is:

When prune is enabled, history is not included in the specs (since that ends up including every package in the spec and therefore avoids any package being pruned).
Disables FREEZE_INSTALLED when pruning. This was done mostly because I wasn't able to make both things work properly together, but I considered it reasonable since the change that introduced that modifier as a default (03d22d4) was made in between 4.8.0 and 4.8.1, when prune was already not working.

Therefore, --prune --freeze-installed will ignore --freeze-installed, but I am unsure if those flags ever worked together.

Also, no issues with the delay, I am aware of the size of conda as a project and how much work you guys have. I'm the one to thank you for the maintenance!

cla-bot · 2020-03-17T21:13:35Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

cla-bot · 2020-03-24T16:29:24Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

prusse-martin · 2020-03-30T20:15:27Z

The current state can trigger an error due the missing installed specs.

cla-bot · 2020-06-24T20:33:28Z

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cla-bot · 2020-06-25T18:14:25Z

We require contributors to sign our Contributor License Agreement, and we don't have one on file for @tarcisioe. In order for us to review and merge your code, please e-sign the PDF at https://conda.io/en/latest/contributing.html#conda-contributor-license-agreement. We then need to manually verify your signature. We will ping the bot to refresh the PR status when we have confirmed your signature.

beeankha · 2023-08-18T18:22:10Z

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conda/core/solve.py

tests/core/test_solve.py

conda/core/solve.py

Co-authored-by: Ken Odegard <kodegard@anaconda.com>

kenodegard

Looks like it is passing 🎉, just need the news snippet and then this will be good to go

jaimergp

TIL that --prune is only enabled in conda env. I had the impression that it was a general flag (and the code in solve.py does not check for the subcommand used), but it's not exposed in any other CLI. 🤷

For that reason, I'd change the PR title to "Make conda env update --prune ignore history specs"? Although the tests seem to be general and could be extended to conda update if the CLI was updated.

news/9614-prune-ignores-history-specs

* start branch * trigger ci * port logic from conda/conda#9614 * deselect a couple tests (accelerate and libmamba do not get along) * add news * Apply suggestions from code review * Alternative logic for solver creation tasks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix tests/core/test_solve.py::test_auto_update_conda * some progress with pins (but not quite there yet) * Increase timeouts in CI env setup * allow uninstall by default only on removals * handle prune * avoid crash * cleanup * only lock the installed spec * pre-commit * add SolverInputState.always_update helper mapping * allow uninstall of conflicts * use always_update list for simplicity * not update-all if pinned * explain pins if involved in errors * re-enable original test_neutering_of_historic_specs * bump minimum required conda and libmamba versions * fix tests/core/test_solve.py::test_force_remove_1 and tests/core/test_solve.py::test_pinned_1 * Re-enable tests that are failing * Require libmambapy >= 1.5.1 * pre-commit * amend news * Update __init__.py * fix test_neutering_of_historic_specs * consider 1.5.1 in warnings too * pre-commit * adjust test * remove comment * fix json serialization * xfail in 1.5.1 too * catch RuntimeError for the whole 1.5.x series * xfail test_explicit * fix test_pinned_1 * lock installed name-only pinned packages * do not add installed channels to list if --override-channels in use * add adjusted variant for test_priority * always define lock * explain some deselected tests * adjust test_install_features * xfail test_export * pre-commit --------- Co-authored-by: Jannis Leidel <jannis@leidel.info> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Chris Ostrouchov <chris.ostrouchov@gmail.com>

tarcisioe requested a review from a team as a code owner January 17, 2020 21:07

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tarcisioe force-pushed the ignore-history-on-prune branch from 8be1767 to c7451e2 Compare February 7, 2020 23:57

tarcisioe force-pushed the ignore-history-on-prune branch from 01502fc to c7451e2 Compare March 24, 2020 16:29

prusse-martin force-pushed the ignore-history-on-prune branch from c7451e2 to 463c94c Compare June 24, 2020 20:33

prusse-martin force-pushed the ignore-history-on-prune branch from 463c94c to 2ae84f0 Compare June 25, 2020 18:14

prusse-martin force-pushed the ignore-history-on-prune branch from 2ae84f0 to 7bd6701 Compare July 6, 2020 16:35

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Co-authored-by: Ken Odegard <kodegard@anaconda.com>

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beeankha changed the title ~~Make update --prune ignore history specs.~~ Make update --prune ignore history specs. Aug 18, 2023

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beeankha changed the title ~~Make update --prune ignore history specs.~~ Make conda env update --prune ignore history specs. Aug 21, 2023

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Merge branch 'main' into ignore-history-on-prune

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beeankha merged commit 9c7af40 into conda:main Aug 22, 2023
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This was referenced Aug 24, 2023

add subcommand plugin for repoquery conda/conda-libmamba-solver#258

Merged

Investigate errors with new --prune tests conda/conda-libmamba-solver#267

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jaimergp added a commit to conda/conda-libmamba-solver that referenced this pull request Aug 25, 2023

port logic from conda/conda#9614

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AlbertDeFusco mentioned this pull request Aug 25, 2023

Add / remove packages commands conda-incubator/conda-project#112

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AlbertDeFusco mentioned this pull request Sep 6, 2023

Removing dependencies from an existing lock file conda/conda-lock#196

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jezdez mentioned this pull request Sep 26, 2023

Release 23.9.x #13080

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nicoddemus deleted the ignore-history-on-prune branch November 7, 2023 13:02

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Make `conda env update --prune` ignore history specs. #9614

Make `conda env update --prune` ignore history specs. #9614

tarcisioe commented Jan 17, 2020 •

edited by kenodegard

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		@@ -363,6 +363,170 @@ def test_prune_1(tmpdir):
		assert convert_to_dist_str(link_precs) == link_order


		def test_update_prune_1(tmpdir):

Make conda env update --prune ignore history specs. #9614

Make conda env update --prune ignore history specs. #9614

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Make `conda env update --prune` ignore history specs. #9614

Make `conda env update --prune` ignore history specs. #9614

tarcisioe commented Jan 17, 2020 •

edited by kenodegard

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