Merge branch 'fix-wf-tests' into 'master'

fix wf notebook tests

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!453

.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

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()

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}")))