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feat: simplify unify containers#959

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daler wants to merge 147 commits intomasterbioconda/bioconda-utils:masterfrom simplify-unify-containersbioconda/bioconda-utils:simplify-unify-containersCopy head branch name to clipboard

+4,295-78

Commits

Commits on Feb 9, 2024

• initial migration of container infra from bioconda-containers

  daler

  committed
  172ffa5

• first draft of build script

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  committed
  40cee01

Commits on Feb 11, 2024

• rename/reorganize

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  committed
  d68171b

• parameterize busybox image to copy from

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  acb1d84

• git checkout parameterized branch

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  988ee01

• parameterize busybox image

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  a4801a5

• depend on passed-in conda/mamba versions

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  committed
  de2635b

• first round of refactoring build-images.yml

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  committed
  5a00ef3

• move generic build to top, and adjust workflow

  daler

  committed
  8fb2257

Commits on Feb 12, 2024

• split out base-debian into an independent job

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  e9864ba

• factor out archs

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  9ffeda8

• add build-env and create-env

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  c7ac9b1

• try using branch name for now

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  8ffc3ea

Commits on Feb 13, 2024

• fix path

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  a971e5d

• rm redundant if clause

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  976f350

• parameterize create-env test to use local images

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  5d3acc7

• check for existing tags

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  e368e39

• allow missing repository on quay.io if configured

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  bbbd9d3

• add ARG for next FROM context

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  36d2fc6

• add build script for local testing (may be moved later)

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  03c2472

• add docs

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  b7a6f4a

• parameterize archs

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  3ff8d68

• rm manifests by default before building locally

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  b580a38

• add switches to build each container

  daler

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  cfd7b85

Commits on Feb 15, 2024

• fix arg

  daler

  committed
  073c3df

• use python (which will come from conda-forge)

  Show description for 33e6ff4
  daler

  committed
  33e6ff4

Commits on Feb 17, 2024

• improve comments in build.sh

  daler

  committed
  0475a92

• warn -> error

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  fd21947

• move test build-args closer to actual test

  daler

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  7399905

• clean up buildah inspect output

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  committed
  be2b3f0

• overhaul how tests are run, plus notes & comments

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  324d8ee

• warn -> error in workflow

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  06b138c

• rm build docker container from prev workflow

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  3f62390

• first attempt at pushing base-debian

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  315604e

• for now always try pushing

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  5f91c86

• hard code registry like bioconda-containers

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  8b019bb

• add comments and ids to workflow

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  072c987

• start support for logging

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  committed
  8e26443

• attempt to control github actions via log

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  c545c66

• mess with conditionals

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  f8783f4

• single-quote to match others

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  66926b4

• no env var

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  55919a1

• now try version bump

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  7b15c02

• more conditional

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  2aec81c

• enable builds and pushes for other containers

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  b4d4cbf

• swap out registry depending on if tag exists

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  5298c43

• do registry swap for create-env

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  250b47b

• lots o' comments

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  ac3d8aa

• TIL GHA expressions work in comments

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  daddbd4

• missing will now become error

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  bbecba3

• bump just base version to test behavior

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  59d8b30

• explicitly specify (single) tag, and add to bioconda-utils version

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  860adc0

Commits on Feb 18, 2024

• be better about tags

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  14c43c5

• fix tags

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  0d6602e

• add "base" to base version

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  9b62f67

• add base prefix to upload steps

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  f9b8720

• bump version to ensure 'latest' tags get pushed

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  ab41890

• move pushes to end

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  efe0154

• runs-on

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  64226bf

• don't depend on test

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  ece22a2

• fix job outputs

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  1b28410

• better message when tag exists

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  9bcd6c7

• comments cleanup

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  bd16b6a

• add test before push

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  1ffb34d

• typo

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  9a02abc

• typo

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  b39c87c

• keep recipes in work dir

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  b654430

• activate env in test

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  f47c2de

• eval hook

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  cb8157d

• include output for bioconda-utils version in job

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  3166fbd

• fix names

  daler

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  a428b4b

• bump version for end-to-end testing

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  aedd032

• don't use "localhost" as registry for docker

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  26325e9

• registry includes the slash

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  ec3704c

Commits on Feb 19, 2024

• convert back to steps rather than jobs

  Show description for 56b1fe2
  daler

  committed
  56b1fe2

• need to podman push images to docker-daemon so docker can use

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  81aca27

• update build.sh for local tests

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  committed
  15c1954

• comments and cleanup

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  committed
  01122df

• tags need bioconda-utils version

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  bd90014

• use correct output

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  7d6f5c8

• attempt pushing to docker-daemon

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  7ce9bd1

• disable some jobs so we can do some container pushing tests

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  8b7b1ff

• try pushing to ghcr.io

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  dc4514a

• rm push to docker daemon

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  6a177d2

• login to ghcr

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  3188ea3

• test pull from ghcr

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  39ab36a

• yaml syntax

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  93cb439

• try building everything and pushing/pulling to/from ghcr.io

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  ce45345

• re-enable build-others job

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  9967d44

• get bioconda-utils version from step output

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  c4554f7

Commits on Feb 20, 2024

• get bioconda-utils version from build-other job

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  73aef1c

• aaaand use right output

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  2ce4b8c

• push the right image

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  c5eb650

• add additional label to tie to bioconda-utils

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  f45e2ff

• fix label

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  e9c6b7f

• new version number to see if ghcr will make public

  daler

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  c8cb13e

• ensure all tags are pulled

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  e291d36

• ensure latest manifest is pushed in the first place

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  8c42d0f

• use job-level tag

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  00f458e

• use jobs not steps

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  a0554c4

Commits on Feb 22, 2024

• typo in missing argument handling

  daler

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  ce17266

• re-enable library tests

  daler

  committed
  59ef090

Commits on Feb 27, 2024

• create & store local version of locale

  Show description for dbc13b7
  daler

  committed
  dbc13b7

• overhaul how everything is configured

  daler

  committed
  4c89ac7

• cleanup

  daler

  committed
  2c16506

• copied bioconda-utils version expected to be already checked out

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  9b40495

• simplify creating requirements

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  d5d3560

• first pass overhauling simplified & unified builds GH Actions

  daler

  committed
  fed48a4

• Merge branch 'master' into simplify-unify-containers

  daler

  authored
  6f5cc43

• reenable

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  committed
  fb25c5a

• disable main tests

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  committed
  b3b2ccb

• fix job names

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  committed
  00f52a7

• move ghcr login back to main workflow

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  f889d09

• log in to and use ghcr.io, not localhost registry

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  8ff41e1

Commits on Feb 28, 2024

• don't use localhost

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  4713899

• disable test for now

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  f9c3216

• manifest push

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  d6bf0e6

• be explicit about base vs bioconda tags

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  1242b9a

• still need TAG for build.sh

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  e55d5fa

Commits on Mar 2, 2024

• add function to move manifests from ghcr to quay.io

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  committed
  552488b

• don't use "latest"

  daler

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  54ed243

• re-enable tests

  daler

  committed
  628ab79

• back to podman

  daler

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  5a959ac

• fix path

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  committed
  699b55f

• fix path

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  committed
  f30738f

• still need to clone repo for versions.sh

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  committed
  d4b8557

• now try moving from ghcr to quay

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  committed
  edeea83

• login to quay

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  e998ce7

• use right creds

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  0dc9242

• re-enable orig tests

  daler

  committed
  589df6b

Commits on Mar 17, 2024

• Merge branch 'master' into simplify-unify-containers

  daler

  authored
  9f334e6

Commits on Mar 19, 2024

• Merge branch 'master' into simplify-unify-containers

  daler

  authored
  a0e057f

Commits on Aug 10, 2024

• A round of comments and documentation

  daler

  committed
  59d5325

• Merge branch 'master' into simplify-unify-containers

  daler

  committed
  9732c2b

Commits on Aug 11, 2024

• fix image tag

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  committed
  5d534ef

• temporarily disable full tests

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  committed
  1f97cf2

• first try at enabling docker tests for just-built containers

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  committed
  523acf3

• consider env var for build image

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  5ad8842

• use utils, not recipes, for test

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  9195c9e

• rm mamba from images

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  f311612

• bump version to trigger container build

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  3983859

• be more clear about passing image name to mulled

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  committed
  4a0b20d

• Revert "rm mamba from images"

  Show description for cf71d12
  daler

  committed
  cf71d12

• try reverting truststore removal

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  committed
  46cf321

Commits on Aug 12, 2024

• another attempt at removing mamba

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  committed
  c946860

• use new name for image sent to mulled

  daler

  committed
  9b4c928

Commits on Aug 13, 2024

• use matched branch on bioconda-common

  Show description for af16e9a
  daler

  committed
  af16e9a