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 -- GitLab