From 830e1bf380e33b3b17cd6481fc84e53325ad5966 Mon Sep 17 00:00:00 2001
From: Athanasios Karmas <karmas@athenarc.gr>
Date: Mon, 13 Dec 2021 18:17:12 +0000
Subject: [PATCH] release v0.1 hotfix to include clb-nb-utils package enable
user to install packages with pip and start JupyterLab kernel with the
default profile
---
create_JupyterLab_kernel.sh | 7 ++++++-
packages/clb-nb-utils/package.py | 12 ++++++++++++
spack.yaml | 2 ++
3 files changed, 20 insertions(+), 1 deletion(-)
create mode 100644 packages/clb-nb-utils/package.py
diff --git a/create_JupyterLab_kernel.sh b/create_JupyterLab_kernel.sh
index 6f21c9ea..eef8e777 100644
--- a/create_JupyterLab_kernel.sh
+++ b/create_JupyterLab_kernel.sh
@@ -20,7 +20,12 @@ spack repo add /srv/$INSTALLATION_ROOT/ebrains-spack-builds
#spack env activate $SPACKIFIED_ENV
module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-broadwell/
+module use /srv/$INSTALLATION_ROOT/spack/share/spack/modules/linux-centos7-x86_64/
source /srv/$INSTALLATION_ROOT/spack/var/spack/environments/$SPACKIFIED_ENV/loads
+# add also user's .local python3.8 packages to allow package installation at runtime
+# by the user using pip
+export PYTHONPATH=$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages
+export PATH=$PATH:/opt/app-root/src/.local/bin
# capture the env after spack activation
cd /opt/app-root/src
@@ -49,7 +54,7 @@ chmod +x $LAB_KERNEL_PATH/bin/env.sh
mkdir $LAB_KERNEL_PATH/spack_python_kernel_release_20210930
cat <<EOF >$LAB_KERNEL_PATH/spack_python_kernel_release_20210930/kernel.json
{
- "argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}"],
+ "argv": ["$LAB_KERNEL_PATH/bin/env.sh", "{connection_file}", "--profile=default"],
"display_name": "EBRAINS_release_v0.1_202109",
"name": "spack_python_kernel_release_20210930",
"language": "python"
diff --git a/packages/clb-nb-utils/package.py b/packages/clb-nb-utils/package.py
new file mode 100644
index 00000000..d8f8452c
--- /dev/null
+++ b/packages/clb-nb-utils/package.py
@@ -0,0 +1,12 @@
+from spack import *
+
+# Usage
+# from clb_nb_utils import oauth
+# oauth.get_token()
+class ClbNbUtils(PythonPackage):
+ url = 'https://github.com/HumanBrainProject/clb-nb-utils/archive/refs/heads/master.zip'
+ maintainers = ['akarmas']
+ version('0.1.0','aa079ed0a8c4806db4657a6e7b534f4d')
+ depends_on('python@3.8:', type=('build','run'))
+ depends_on('py-setuptools', type=('build','run'))
+ depends_on('py-requests', type=('build','run'))
diff --git a/spack.yaml b/spack.yaml
index 451e6a54..3a7f3609 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -7,6 +7,8 @@ spack:
- py-ipython %gcc@10.3.0
- py-ipykernel %gcc@10.3.0
- py-notebook %gcc@10.3.0
+ # Collab utils
+ - clb-nb-utils@0.1.0 %gcc@10.3.0
# General
- py-pip %gcc@10.3.0
- py-numpy %gcc@10.3.0
--
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