From 7805b04905bf8ef37851289f32a18630fc5d974c Mon Sep 17 00:00:00 2001
From: Eleni Mathioulaki <emathioulaki@athenarc.gr>
Date: Wed, 6 Sep 2023 18:56:40 +0200
Subject: [PATCH] use notebook as test for multi-area-model workflow package
---
.gitlab-ci.yml | 3 ++-
packages/wf-multi-area-model/package.py | 24 +++++++++++++++++++++---
spack.yaml | 2 +-
3 files changed, 24 insertions(+), 5 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 59ec4499..7f765299 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -207,7 +207,7 @@ build-spack-env-on-runner:
- |
# succesfully installed packages: keep the spack logs for any package modified during this CI job
SPACK_PACKAGES_DIR=$SPACK_DEV_PATH/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0
- if cp --parents $SPACK_PACKAGES_DIR/*/.spack/*.txt ./; then
+ if cp --parents $SPACK_PACKAGES_DIR/*/.spack/*.txt $SPACK_PACKAGES_DIR/*/.spack_test_results/* ./; then
mv .$SPACK_PACKAGES_DIR spack_logs/installed
else
echo "No packages installed, so no logs to collect"
@@ -290,6 +290,7 @@ sync-gitlab-spack-instance:
# (we use repo.yaml, that is modified at each start of the pipeline, as a reference file)
SPACK_PACKAGES_DIR=$SPACK_PATH/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0
if find $SPACK_PACKAGES_DIR/*/.spack/*.txt -newer $SPACK_REPO_PATH/repo.yaml -exec cp --parents -r "{}" ./ \;; then
+ cp --parents -r $SPACK_PACKAGES_DIR/*/.spack_test_results/* ./
mv .$SPACK_PACKAGES_DIR spack_logs/installed
else
echo "No packages installed, so no logs to collect"
diff --git a/packages/wf-multi-area-model/package.py b/packages/wf-multi-area-model/package.py
index 4458d123..0020b1de 100644
--- a/packages/wf-multi-area-model/package.py
+++ b/packages/wf-multi-area-model/package.py
@@ -6,15 +6,33 @@
from spack import *
-class WfMultiAreaModel(BundlePackage):
+class WfMultiAreaModel(Package):
"""Meta-package to collect all dependencies of the Multi-Area-Model."""
homepage="https://inm-6.github.io/multi-area-model/"
- git = "https://github.com/INM-6/multi-area-model"
+ #git = "https://github.com/INM-6/multi-area-model"
+ git = "https://github.com/terhorstd/multi-area-model"
maintainer = ["terhorstd"]
- version("0.1")
+ version("master", branch="master")
+ version("ebrains", branch="lab.ebrains.eu")
depends_on("py-nested-dict")
depends_on("py-dicthash")
+ depends_on("py-matplotlib")
+ depends_on("py-numpy")
+ depends_on("py-scipy")
+ depends_on("py-future")
+ depends_on("nest")
+ depends_on("py-notebook", type="test")
+ def install(self, spec, prefix):
+ # sanity_check_prefix requires something in the install directory
+ mkdirp(prefix + "/.spack_test_results")
+
+ @run_after("install")
+ @on_package_attributes(run_tests=True)
+ def installcheck(self):
+ # execute notebook and save
+ jupyter = Executable("jupyter")
+ jupyter("nbconvert", "--ExecutePreprocessor.kernel_name=python3", "--execute", "--allow-errors", "--to", "notebook", "multi-area-model.ipynb", "--output", prefix+"/.spack_test_results/multi-area-model.ipynb")
diff --git a/spack.yaml b/spack.yaml
index 89e7eec2..4a859257 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -62,7 +62,7 @@ spack:
- wf-biobb
- wf-brainscales2-demos
- wf-uq-akar4@0.1
- - wf-multi-area-model@0.1
+ - wf-multi-area-model@ebrains
#- py-cerebstats
#- py-cerebunit
#- py-morphounit@1.0.4
--
GitLab