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Add TC test run to CI #195

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Sep 20, 2023
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Disable snakemake run
  • Loading branch information
eu9ene committed Sep 15, 2023
commit b61e25699fc78a862d3af6cc20870aeb70d9f209
76 changes: 38 additions & 38 deletions taskcluster/ci/tests/kind.yml
Original file line number Diff line number Diff line change
Expand Up @@ -47,44 +47,44 @@ tasks:
make dry-run &&
make test-dry-run

snakemake-run:
# Ensure that the snakemake workflow is still executing correctly, even though
# taskcluster is the preferred execution environment.
worker-type: b-linux-v100-gpu
worker:
max-run-time: 86400
env:
CUDA_DIR: fetches/cuda-toolkit
CUDNN_DIR: fetches/cuda-toolkit
run-on-tasks-for: ["github-pull-request"]
artifacts:
- name: public/build
path: artifacts
type: directory
fetches:
toolchain:
- cuda-toolkit
run:
command:
- bash
- -c
- >-
echo "Setting environment variables" &&
mkdir artifacts &&
export CONDA_PATH=artifacts/mambaforge &&
export SNAKEMAKE_OUTPUT_CACHE=artifacts/mambaforge &&
export REPORTS=artifacts/reports &&
export MODELS=artifacts/models &&
export PROFILE=tc-test &&
export CONFIG=configs/config.ci.yml &&

echo "Install necessary dependencies" &&
make conda &&
make snakemake &&
make git-modules &&

echo "Start the run" &&
make run
# snakemake-run:
# # Ensure that the snakemake workflow is still executing correctly, even though
# # taskcluster is the preferred execution environment.
# worker-type: b-linux-v100-gpu
# worker:
# max-run-time: 86400
# env:
# CUDA_DIR: fetches/cuda-toolkit
# CUDNN_DIR: fetches/cuda-toolkit
# run-on-tasks-for: ["github-pull-request"]
# artifacts:
# - name: public/build
# path: artifacts
# type: directory
# fetches:
# toolchain:
# - cuda-toolkit
# run:
# command:
# - bash
# - -c
# - >-
# echo "Setting environment variables" &&
# mkdir artifacts &&
# export CONDA_PATH=artifacts/mambaforge &&
# export SNAKEMAKE_OUTPUT_CACHE=artifacts/mambaforge &&
# export REPORTS=artifacts/reports &&
# export MODELS=artifacts/models &&
# export PROFILE=tc-test &&
# export CONFIG=configs/config.ci.yml &&
#
# echo "Install necessary dependencies" &&
# make conda &&
# make snakemake &&
# make git-modules &&
#
# echo "Start the run" &&
# make run

black:
# Run python's black formatter, which formats python files.
Expand Down