diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index d3e6509d0f00fdb0014fadea8eb1525189c91f86..167a069b9c3d88db7a7442290f78145a5cbd9947 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -180,9 +180,9 @@ build-spack-env-on-runner:
- mkdir -p $CI_PROJECT_DIR/spack_logs/installed $CI_PROJECT_DIR/spack_logs/not_installed
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
- PKG_DIR=$CI_PROJECT_DIR/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0
- - if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" -o -name ".spack_test_results" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
+ - if cd $PKG_DIR; then find . \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- - if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 -name "*.txt" -exec cp --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
+ - if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
# - if [ -d /tmp/spack_tests ]; then mv /tmp/spack_tests $CI_PROJECT_DIR; fi
artifacts:
paths:
@@ -215,9 +215,9 @@ sync-gitlab-spack-instance:
# for succesfully installed packages: keep the spack logs for any package modified during this CI job
# (we use repo.yaml, that is modified at each start of the pipeline, as a reference file)
- PKG_DIR=$SPACK_PATH_GITLAB/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-10.3.0
- - if cd $PKG_DIR; then find . -newer $SPACK_REPO_PATH/repo.yaml \( -name ".spack" -o -name ".spack_test_results" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
+ - if cd $PKG_DIR; then find . -newer $SPACK_REPO_PATH/repo.yaml \( -name ".spack" -o -name ".build" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/installed \;; fi
# for not succesfully installed packages: also keep the spack logs for any packages that failed
- - if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 -name "*.txt" -exec cp --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
+ - if cd /tmp/$(whoami)/spack-stage/; then find . -maxdepth 2 \( -name "*.txt" -o -name ".install_time_tests" \) -exec cp -r --parents "{}" $CI_PROJECT_DIR/spack_logs/not_installed \;; fi
artifacts:
paths:
- spack_logs
diff --git a/packages/wf-brainscales2-demos/package.py b/packages/wf-brainscales2-demos/package.py
index 5acf551cb328cf87a9d2942de1baa612fd044c4d..2b0e7bbb01a51a80869a7f9f5723cee76a9ada67 100644
--- a/packages/wf-brainscales2-demos/package.py
+++ b/packages/wf-brainscales2-demos/package.py
@@ -39,20 +39,30 @@ class WfBrainscales2Demos(Package):
def install(self, spec, prefix):
install_tree(".", join_path(prefix, "notebooks"))
+ def _nbconvert(self, nb, nb_out):
+ jupyter = Executable("jupyter")
+ args = [
+ "nbconvert",
+ "--ExecutePreprocessor.kernel_name=python3",
+ "--execute",
+ "--to",
+ "notebook",
+ nb,
+ "--output",
+ nb_out
+ ]
+ try:
+ # execute notebook and save
+ jupyter(*args)
+ except Exception as e:
+ # if the above fails, re-run notebook to produce output with error
+ jupyter(*(args+["--allow-errors"]))
+ raise
+
def _run_notebooks(self, output_dir):
mkdirp(output_dir)
- # execute notebook and save
- jupyter = Executable("jupyter")
for fn in glob(join_path(prefix, "notebooks", "ts*.ipynb")) + glob(join_path(prefix, "notebooks", "tp*.ipynb")):
- jupyter("nbconvert",
- "--ExecutePreprocessor.kernel_name=python3",
- "--execute",
- "--allow-errors",
- "--to",
- "notebook",
- fn,
- "--output",
- join_path(output_dir, os.path.basename(fn)))
+ self._nbconvert(fn, join_path(output_dir, os.path.basename(fn)))
def _set_collab_things(self):
# enable "EBRAINS lab" mode
@@ -66,7 +76,8 @@ class WfBrainscales2Demos(Package):
def installcheck(self):
self._set_collab_things()
# TODO (ECM): Provide a selection of notebooks that perform local-only tests.
- #self._run_notebooks(join_path(self.prefix, ".spack_test_results"))
+ # self._run_notebooks(join_path(self.stage.path, ".install_time_tests"))
+ # copy_tree(join_path(self.stage.path, ".install_time_tests"), join_path(self.prefix, '.build'))
def test_notebooks(self):
self._set_collab_things()
diff --git a/packages/wf-multi-area-model/package.py b/packages/wf-multi-area-model/package.py
index a19d2e4d626d54d8bfe0875a221c565247ed2244..8544d1422b2e4f51a037fc8e3071ebd95796f53a 100644
--- a/packages/wf-multi-area-model/package.py
+++ b/packages/wf-multi-area-model/package.py
@@ -33,24 +33,35 @@ class WfMultiAreaModel(Package):
def install(self, spec, prefix):
install_tree(".", join_path(prefix, "notebooks"))
- def _run_notebooks(self, output_dir):
- mkdirp(output_dir)
- # execute notebook and save
+ def _nbconvert(self, nb, nb_out):
jupyter = Executable("jupyter")
- jupyter("nbconvert",
+ args = [
+ "nbconvert",
"--ExecutePreprocessor.kernel_name=python3",
"--execute",
- "--allow-errors",
"--to",
"notebook",
- join_path(self.prefix, "notebooks", "multi-area-model.ipynb"),
+ nb,
"--output",
- join_path(output_dir, "multi-area-model.ipynb"))
+ nb_out
+ ]
+ try:
+ # execute notebook and save
+ jupyter(*args)
+ except Exception as e:
+ # if the above fails, re-run notebook to produce output with error
+ jupyter(*(args+["--allow-errors"]))
+ raise
+
+ def _run_notebooks(self, output_dir):
+ mkdirp(output_dir)
+ self._nbconvert(join_path(self.prefix, "notebooks", "multi-area-model.ipynb"), join_path(output_dir, "multi-area-model.ipynb"))
@run_after("install")
@on_package_attributes(run_tests=True)
def installcheck(self):
- self._run_notebooks(join_path(self.prefix, ".spack_test_results"))
+ self._run_notebooks(join_path(self.stage.path, ".install_time_tests"))
+ copy_tree(join_path(self.stage.path, ".install_time_tests"), join_path(self.prefix, '.build'))
def test_notebook(self):
self._run_notebooks(join_path(self.test_suite.stage, self.spec.format("out-{name}-{version}-{hash:7}")))