From 41fda1a9f52d56578a76f8bf185db86da2128a0e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 9 Feb 2022 15:25:21 +0100
Subject: [PATCH] Use cache
---
.github/workflows/lint.yml | 39 ++++++++++++++++++++++++++++++++++----
1 file changed, 35 insertions(+), 4 deletions(-)
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b22d072..3386241 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -19,15 +19,46 @@ jobs:
- uses: actions/checkout@v2.3.4
with:
submodules: recursive
+
+ - name: Set cache date
+ run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
+
+ - name: Cache conda packages
+ uses: actions/cache@v2.1.7
+ env:
+ # Increase this value to manually invalidate the cache
+ CACHE_NUMBER: 0
+ with:
+ path: ~/conda_pkgs_dir
+ key:
+ ${{runner.os}}-conda-${{ env.CACHE_NUMBER }}-${env.date}-${{ hashFiles('.github/lint-environment.yml') }}
+
+ - name: Cache conda environment
+ uses: actions/cache@v2.1.7
+ env:
+ # Increase this value to manually invalidate the cache
+ CACHE_NUMBER: 0
+ with:
+ path: /usr/share/miniconda/envs/biowdl-lint
+ key:
+ ${{runner.os}}-biowdl-lint-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/lint-environment.yml') }}
+ id: env_cache
+
- name: install miniconda
- uses: conda-incubator/setup-miniconda@v2.0.1
+ uses: conda-incubator/setup-miniconda@v2.1.1
with:
+ miniforge-variant: Mambaforge
+ miniforge-version: latest
+ use-mamba: true
channels: conda-forge,bioconda,defaults
channel-priority: strict
- installer-url: https://github.com/conda-forge/miniforge/releases/download/4.11.0-0/Mambaforge-4.11.0-0-Linux-x86_64.sh
- # Conda-incubator uses 'test' environment by default.
- - name: install requirements
+ auto-activate-base: false
+ activate-environment: biowdl-lint
+
+ - name: Update test environment
run: mamba install -n test cromwell miniwdl wdl-aid
+ if: steps.env_cache.outputs.cache-hit != 'true'
+
- name: run womtool validate
run: |
bash -c '
--
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