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fix kb-sdk #210

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merged 10 commits into from
Jul 30, 2024
Merged

fix kb-sdk #210

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dbe8032
initiate gc_content, dna_size, and md5
Xiangs18 Jun 27, 2024
e37d861
fix kb-sdk test
Xiangs18 Jul 20, 2024
ca4dfd6
retry kb-sdk test
Xiangs18 Jul 22, 2024
d4bc8a3
update kb-sdk tag ver
Xiangs18 Jul 22, 2024
6422469
remove code
Xiangs18 Jul 23, 2024
c680d55
rerun kb-sdk test after new images registered
Xiangs18 Jul 27, 2024
ae56d06
set the constructor to dev
Xiangs18 Jul 27, 2024
facdafe
add dev in _PROV_SUBACTION_VERSION_PATTERN
Xiangs18 Jul 27, 2024
ab4923a
revert service version back to release
Xiangs18 Jul 30, 2024
674cb8f
revert service version
Xiangs18 Jul 30, 2024
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19 changes: 2 additions & 17 deletions .github/workflows/kb_sdk_test.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,26 +16,13 @@ jobs:
if: "!contains(github.event.head_commit.message, 'skip ci')"
uses: actions/checkout@v2

- name: Check out Actions CI files
if: "!contains(github.event.head_commit.message, 'skip ci')"
uses: actions/checkout@v2
with:
repository: 'kbaseapps/kb_sdk_actions'
path: 'kb_sdk_actions'


- name: Set up test environment
if: "!contains(github.event.head_commit.message, 'skip ci')"
shell: bash
env:
KBASE_TEST_TOKEN: ${{ secrets.KBASE_CI_TOKEN }}
run: |
# Verify kb_sdk_actions clone worked
test -f "$HOME/kb_sdk_actions/bin/kb-sdk" && echo "CI files cloned"
# Pull kb-sdk & create startup script
docker pull kbase/kb-sdk

sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/make_testdir && echo "Created test_local"
sh scripts/GHA/make_testdir && echo "Created test_local"
test -f "test_local/test.cfg" && echo "Confirmed config exists"

- name: Configure authentication
Expand All @@ -55,10 +42,8 @@ jobs:
- name: Run tests
if: "!contains(github.event.head_commit.message, 'skip ci')"
shell: bash
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
run: |
sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test
sh scripts/GHA/kb-sdk test --verbose

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
Expand Down
12 changes: 12 additions & 0 deletions scripts/GHA/kb-sdk
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
#!/bin/sh

# TODO may want to make the image an env var or argument

# See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/kb-sdk for source

# Cache the group for the docker file
if [ ! -e $HOME/.kbsdk.cache ] ; then
docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache
fi

exec docker run -i --rm -v $HOME:$HOME -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 $@
16 changes: 16 additions & 0 deletions scripts/GHA/make_testdir
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
#!/bin/sh

# TODO may want to make the image an env var or argument

# See https://github.com/kbaseapps/kb_sdk_actions/blob/master/bin/make_testdir for source

# Disable the default `return 1` when creating `test_local`
set +e

# Cache the group for the docker file
if [ ! -e $HOME/.kbsdk.cache ] ; then
docker run -i -v /var/run/docker.sock:/var/run/docker.sock --entrypoint ls ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 -l /var/run/docker.sock|awk '{print $4}' > $HOME/.kbsdk.cache
fi

exec docker run -i --rm -v $HOME:$HOME -u $(id -u) -w $(pwd) -v /var/run/docker.sock:/var/run/docker.sock -e DUSER=$USER -e DSHELL=$SHELL --group-add $(cat $HOME/.kbsdk.cache) ghcr.io/kbase/kb_sdk_patch-develop:br-0.0.4-rc-1 test
exit
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