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feat: Unify containers #953

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172ffa5
initial migration of container infra from bioconda-containers
daler Feb 9, 2024
40cee01
first draft of build script
daler Feb 9, 2024
d68171b
rename/reorganize
daler Feb 11, 2024
acb1d84
parameterize busybox image to copy from
daler Feb 11, 2024
988ee01
git checkout parameterized branch
daler Feb 11, 2024
a4801a5
parameterize busybox image
daler Feb 11, 2024
de2635b
depend on passed-in conda/mamba versions
daler Feb 11, 2024
5a00ef3
first round of refactoring build-images.yml
daler Feb 11, 2024
8fb2257
move generic build to top, and adjust workflow
daler Feb 11, 2024
e9864ba
split out base-debian into an independent job
daler Feb 12, 2024
9ffeda8
factor out archs
daler Feb 12, 2024
c7ac9b1
add build-env and create-env
daler Feb 12, 2024
8ffc3ea
try using branch name for now
daler Feb 12, 2024
a971e5d
fix path
daler Feb 13, 2024
976f350
rm redundant if clause
daler Feb 13, 2024
5d3acc7
parameterize create-env test to use local images
daler Feb 13, 2024
e368e39
check for existing tags
daler Feb 13, 2024
bbbd9d3
allow missing repository on quay.io if configured
daler Feb 13, 2024
36d2fc6
add ARG for next FROM context
daler Feb 13, 2024
03c2472
add build script for local testing (may be moved later)
daler Feb 13, 2024
b7a6f4a
add docs
daler Feb 13, 2024
3ff8d68
parameterize archs
daler Feb 13, 2024
b580a38
rm manifests by default before building locally
daler Feb 13, 2024
cfd7b85
add switches to build each container
daler Feb 13, 2024
073c3df
fix arg
daler Feb 15, 2024
33e6ff4
use python (which will come from conda-forge)
daler Feb 15, 2024
0475a92
improve comments in build.sh
daler Feb 17, 2024
fd21947
warn -> error
daler Feb 17, 2024
7399905
move test build-args closer to actual test
daler Feb 17, 2024
be2b3f0
clean up buildah inspect output
daler Feb 17, 2024
324d8ee
overhaul how tests are run, plus notes & comments
daler Feb 17, 2024
06b138c
warn -> error in workflow
daler Feb 17, 2024
3f62390
rm build docker container from prev workflow
daler Feb 17, 2024
315604e
first attempt at pushing base-debian
daler Feb 17, 2024
5f91c86
for now always try pushing
daler Feb 17, 2024
8b019bb
hard code registry like bioconda-containers
daler Feb 17, 2024
072c987
add comments and ids to workflow
daler Feb 17, 2024
8e26443
start support for logging
daler Feb 17, 2024
c545c66
attempt to control github actions via log
daler Feb 17, 2024
f8783f4
mess with conditionals
daler Feb 17, 2024
66926b4
single-quote to match others
daler Feb 17, 2024
55919a1
no env var
daler Feb 17, 2024
7b15c02
now try version bump
daler Feb 17, 2024
2aec81c
more conditional
daler Feb 17, 2024
b4d4cbf
enable builds and pushes for other containers
daler Feb 17, 2024
5298c43
swap out registry depending on if tag exists
daler Feb 17, 2024
250b47b
do registry swap for create-env
daler Feb 17, 2024
ac3d8aa
lots o' comments
daler Feb 17, 2024
daddbd4
TIL GHA expressions work in comments
daler Feb 17, 2024
bbecba3
missing will now become error
daler Feb 17, 2024
59d8b30
bump just base version to test behavior
daler Feb 17, 2024
860adc0
explicitly specify (single) tag, and add to bioconda-utils version
daler Feb 17, 2024
14c43c5
be better about tags
daler Feb 18, 2024
0d6602e
fix tags
daler Feb 18, 2024
9b62f67
add "base" to base version
daler Feb 18, 2024
f9b8720
add base prefix to upload steps
daler Feb 18, 2024
ab41890
bump version to ensure 'latest' tags get pushed
daler Feb 18, 2024
efe0154
move pushes to end
daler Feb 18, 2024
64226bf
runs-on
daler Feb 18, 2024
ece22a2
don't depend on test
daler Feb 18, 2024
1b28410
fix job outputs
daler Feb 18, 2024
9bcd6c7
better message when tag exists
daler Feb 18, 2024
bd16b6a
comments cleanup
daler Feb 18, 2024
1ffb34d
add test before push
daler Feb 18, 2024
9a02abc
typo
daler Feb 18, 2024
b39c87c
typo
daler Feb 18, 2024
b654430
keep recipes in work dir
daler Feb 18, 2024
f47c2de
activate env in test
daler Feb 18, 2024
cb8157d
eval hook
daler Feb 18, 2024
3166fbd
include output for bioconda-utils version in job
daler Feb 18, 2024
a428b4b
fix names
daler Feb 18, 2024
aedd032
bump version for end-to-end testing
daler Feb 18, 2024
26325e9
don't use "localhost" as registry for docker
daler Feb 18, 2024
ec3704c
registry includes the slash
daler Feb 18, 2024
56b1fe2
convert back to steps rather than jobs
daler Feb 19, 2024
81aca27
need to podman push images to docker-daemon so docker can use
daler Feb 19, 2024
15c1954
update build.sh for local tests
daler Feb 19, 2024
01122df
comments and cleanup
daler Feb 19, 2024
bd90014
tags need bioconda-utils version
daler Feb 19, 2024
7d6f5c8
use correct output
daler Feb 19, 2024
7ce9bd1
attempt pushing to docker-daemon
daler Feb 19, 2024
8b7b1ff
disable some jobs so we can do some container pushing tests
daler Feb 19, 2024
dc4514a
try pushing to ghcr.io
daler Feb 19, 2024
6a177d2
rm push to docker daemon
daler Feb 19, 2024
3188ea3
login to ghcr
daler Feb 19, 2024
39ab36a
test pull from ghcr
daler Feb 19, 2024
93cb439
yaml syntax
daler Feb 19, 2024
ce45345
try building everything and pushing/pulling to/from ghcr.io
daler Feb 19, 2024
9967d44
re-enable build-others job
daler Feb 19, 2024
c4554f7
get bioconda-utils version from step output
daler Feb 19, 2024
73aef1c
get bioconda-utils version from build-other job
daler Feb 20, 2024
2ce4b8c
aaaand use right output
daler Feb 20, 2024
c5eb650
push the right image
daler Feb 20, 2024
f45e2ff
add additional label to tie to bioconda-utils
daler Feb 20, 2024
e9c6b7f
fix label
daler Feb 20, 2024
c8cb13e
new version number to see if ghcr will make public
daler Feb 20, 2024
e291d36
ensure all tags are pulled
daler Feb 20, 2024
8c42d0f
ensure latest manifest is pushed in the first place
daler Feb 20, 2024
00f458e
use job-level tag
daler Feb 20, 2024
a0554c4
use jobs not steps
daler Feb 20, 2024
ce17266
typo in missing argument handling
daler Feb 22, 2024
59ef090
re-enable library tests
daler Feb 22, 2024
25f1135
support env var configuration of images to use
daler Feb 23, 2024
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11 changes: 4 additions & 7 deletions .github/workflows/GithubActionTests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -33,15 +33,12 @@ jobs:
conda activate bioconda
python setup.py install

- name: Build docker container
run: |
docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info -a && conda list'
docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./

- name: Run tests '${{ matrix.py_test_marker }}'
run: |
export MULLED_CONDA_IMAGE="quay.io/bioconda/create-env:latest"
export DEFAULT_BASE_IMAGE="quay.io/bioconda/base-glibc-busybox-bash:latest"
export DEFAULT_EXTENDED_BASE_IMAGE="quay.io/bioconda/base-glibc-debian-bash:latest"
export DOCKER_BASE_IMAGE="quay.io/bioconda/bioconda-utils-build-env-cos7:latest"
eval "$(conda shell.bash hook)"
conda activate bioconda
if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
Expand Down
63 changes: 0 additions & 63 deletions .github/workflows/build-image.yml

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