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fix: cleaned up and rewritten execution backend structure, (fixing #1475
, #860, #1007, #1008) (PR #1491)
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johanneskoester committed Mar 21, 2022
1 parent 12d6f67 commit e87cc979bea0567e1cd97722d385f472857df83c
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Showing 16 changed files with 486 additions and 503 deletions.
@@ -114,18 +114,19 @@ jobs:
echo CONTAINER_IMAGE=snakemake/snakemake:$GITHUB_SHA >> $GITHUB_ENV
# TODO reactivate in April (we have no free resources left this month)
# - name: Test Kubernetes execution
# if: env.GCP_AVAILABLE
# env:
# CI: true
# run: |
# # activate conda env
# export PATH="/usr/share/miniconda/bin:$PATH"
# source activate snakemake

# pytest -s -v -x tests/test_kubernetes.py

- name: Test AWS execution
- name: Test Kubernetes execution
if: env.GCP_AVAILABLE
env:
CI: true
run: |
# activate conda env
export PATH="/usr/share/miniconda/bin:$PATH"
source activate snakemake
pytest -s -v -x tests/test_kubernetes.py
# TODO temporarily deactivate and fix in separate PR.
- name: Test Tibanna (AWS) execution
if: env.AWS_AVAILABLE
env:
CI: true
@@ -134,16 +135,16 @@ jobs:
export PATH="/usr/share/miniconda/bin:$PATH"
source activate snakemake
pytest -v -x tests/test_tibanna.py
# pytest -v -x -s tests/test_tibanna.py

# TODO reactivate in April (we have no free resources left this month)
# - name: Test Google Life Sciences Executor
# if: env.GCP_AVAILABLE
# run: |
# # activate conda env
# export PATH="/usr/share/miniconda/bin:$PATH"
# source activate snakemake
# pytest -s -v -x tests/test_google_lifesciences.py
- name: Test Google Life Sciences Executor
if: env.GCP_AVAILABLE
run: |
# activate conda env
export PATH="/usr/share/miniconda/bin:$PATH"
source activate snakemake
pytest -s -v -x tests/test_google_lifesciences.py
- name: Test GA4GH TES executor
run: |
@@ -436,6 +436,9 @@ def snakemake(
# clean up all previously recorded jobids.
shell.cleanup()
else:
if default_resources is None:
# use full default resources if in cluster or cloud mode
default_resources = DefaultResources(mode="full")
if edit_notebook:
raise WorkflowError(
"Notebook edit mode is only allowed with local execution."
@@ -599,6 +602,7 @@ def snakemake(
check_envvars=not lint, # for linting, we do not need to check whether requested envvars exist
all_temp=all_temp,
local_groupid=local_groupid,
keep_metadata=keep_metadata,
latency_wait=latency_wait,
)
success = True
@@ -800,7 +804,6 @@ def snakemake(
export_cwl=export_cwl,
batch=batch,
keepincomplete=keep_incomplete,
keepmetadata=keep_metadata,
)

except BrokenPipeError:

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