From fb0de71a1c5f4a61ca398bcc75c32e38fab0510a Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Thu, 11 Mar 2021 07:19:40 +0100
Subject: [PATCH] Fix tests and add caching
---
.github/workflows/ci.yml | 39 +++++++++++++++++++++++++++++++--------
1 file changed, 31 insertions(+), 8 deletions(-)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a48c87e..7cfbe51 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -38,29 +38,44 @@ jobs:
- integration-two-samples
- integration-target-baits
- integration-bed-coverage
- - integration-restrict_BQSR
+ - integration-restrict-BQSR
- integration-targets-only
- integration-multisample
- steps:
- - uses: actions/checkout@v2
+steps:
+- uses: actions/checkout@v2
- - uses: eWaterCycle/setup-singularity@v6
+ - name: Install singularity
+ uses: eWaterCycle/setup-singularity@v6
with:
singularity-version: 3.6.4
- - uses: conda-incubator/setup-miniconda@v2.0.1
+ - name: Cache conda environment
+ uses: actions/cache@v2
+ env:
+ cache-name: cache-conda-environment
+ # Increase this value to reset the cache without changing
+ # environment.yml
+ cache-number: 0
+ with:
+ path: ~/conda_pkgs_dir
+ key: build-${{ env.cache-name }}-${{ env.cache-number }}-${{ hashFiles('environment.yml') }}
+
+ - name: Install miniconda
+ uses: conda-incubator/setup-miniconda@v2.0.1
# https://github.com/conda-incubator/setup-miniconda.
+ # https://github.com/marketplace/actions/setup-miniconda
with:
activate-environment: hutspot
environment-file: environment.yml
auto-activate-base: false
+ use-only-tar-bz2: true
- name: Run test in conda evironment
# Use --symlink to limit disk usage.
run: >-
- pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} --symlink tests/
+ pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} tests/
- - name: Check job stderr messages in case of failure
+ - name: Check pipeline stderr messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
@@ -68,7 +83,7 @@ jobs:
echo $file; cat $file
done
'
- - name: Check job stdout messages in case of failure
+ - name: Check pipeline stdout messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
@@ -76,3 +91,11 @@ jobs:
echo $file; cat $file
done
'
+ - name: Check all job log files in case of failure
+ if: ${{ failure() }}
+ run: >-
+ bash -c '
+ for file in $(find /tmp/pytest_workflow_*/${{ matrix.test}}/log/ -type f); do
+ echo $file; cat $file
+ done
+ '
--
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