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GHA fix #204

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merged 18 commits into from
Jan 4, 2024
Merged

GHA fix #204

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9b5d557
fix GHA
Xiangs18 Jan 2, 2024
a7277cc
make GHA pass
Xiangs18 Jan 3, 2024
11804d8
run a single test
Xiangs18 Jan 3, 2024
6f37527
fix cp error
Xiangs18 Jan 3, 2024
92dbda4
rm another cp error
Xiangs18 Jan 3, 2024
12223b3
clean up
Xiangs18 Jan 3, 2024
aa72b2b
GHA should fail
Xiangs18 Jan 3, 2024
8245f23
add return_code
Xiangs18 Jan 3, 2024
0c5271f
add echo check
Xiangs18 Jan 3, 2024
713bd17
change to 22601
Xiangs18 Jan 3, 2024
1386f50
add cat command to help debug
Xiangs18 Jan 3, 2024
4c70d2d
cat in test_dir
Xiangs18 Jan 3, 2024
d3ef695
add $
Xiangs18 Jan 4, 2024
a780c83
change to test_dir
Xiangs18 Jan 4, 2024
67f6b19
add exitcode logic
Xiangs18 Jan 4, 2024
5022d9b
test run
Xiangs18 Jan 4, 2024
f9857e8
if test passes, GHA passes
Xiangs18 Jan 4, 2024
9d805fe
if test fails, GHA fails
Xiangs18 Jan 4, 2024
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6 changes: 5 additions & 1 deletion .github/workflows/kb_sdk_test.yaml
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Expand Up @@ -54,4 +54,8 @@ jobs:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
run: |
sh $GITHUB_WORKSPACE/kb_sdk_actions/bin/kb-sdk test
bash <(curl -s https://codecov.io/bash)

- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
with:
fail_ci_if_error: true
1 change: 0 additions & 1 deletion Makefile
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Expand Up @@ -51,7 +51,6 @@ build-test-script:
echo 'export PYTHONPATH=$$script_dir/../$(LIB_DIR):$$PATH:$$PYTHONPATH' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'cd $$script_dir/../$(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'python -m nose --with-coverage --cover-package=$(SERVICE_CAPS) --cover-html --cover-html-dir=/kb/module/work/test_coverage --cover-xml --cover-xml-file=/kb/module/work/test_coverage/coverage.xml --nocapture --nologcapture .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'cp /kb/module/.coveragerc .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
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Why are this and the other line dealing with .coveragerc not needed?

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  1. this file does not exist: https://github.com/kbaseapps/GenomeFileUtil/actions/runs/7404244710/job/20145462822#step:6:1100
  2. Upload coverage to Codecov step works fine without it

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Interesting, it looks like when coverage was added to this repo no one added a coveragerc but did add the line: 8005699

echo 'cp .coverage /kb/module/work/' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'mkdir -p /kb/module/work/kb/module/lib/' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
echo 'cp -R /kb/module/lib/$(SERVICE_CAPS)/ /kb/module/work/kb/module/lib/' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
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3 changes: 2 additions & 1 deletion scripts/run_tests_within_container.sh
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Expand Up @@ -9,7 +9,8 @@ export TEST_PATH=.

cd $script_dir/../test
python -m nose --with-coverage --cover-package=GenomeFileUtil --cover-html --cover-html-dir=/kb/module/work/test_coverage --cover-xml --cover-xml-file=/kb/module/work/test_coverage/coverage.xml --nocapture --nologcapture $TEST_PATH
cp /kb/module/.coveragerc .
returncode=$?
if [ $returncode != 0 ]; then exit $returncode; fi
cp .coverage /kb/module/work/
mkdir -p /kb/module/work/kb/module/lib/
cp -R /kb/module/lib/GenomeFileUtil/ /kb/module/work/kb/module/lib/P
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