From 5e8708b48b7fc3c18a6874df8a5bedd889bfab82 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jens=20Henrik=20G=C3=B6bbert?= <goebbert1@jwlogin10.juwels>
Date: Fri, 31 Mar 2023 17:30:37 +0200
Subject: [PATCH] update conda howto

---
 03-HowTos/Create_JupyterKernel_conda.ipynb | 33 +++++++++++++---------
 1 file changed, 19 insertions(+), 14 deletions(-)

diff --git a/03-HowTos/Create_JupyterKernel_conda.ipynb b/03-HowTos/Create_JupyterKernel_conda.ipynb
index 9560d7c..76100b7 100644
--- a/03-HowTos/Create_JupyterKernel_conda.ipynb
+++ b/03-HowTos/Create_JupyterKernel_conda.ipynb
@@ -56,7 +56,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Selectable **CONDA_TARGET_DIR** path for the central conda installation, should be in the project filesystem"
+    "Selectable **CONDA_ENV** name, will be used to specify the environment name\n",
+    "  - must be lowercase"
    ]
   },
   {
@@ -65,15 +66,17 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "export CONDA_TARGET_DIR=${HOME}/PROJECT_training2005/testdir/miniconda3"
+    "CONDA_ENV=my_condaenv\n",
+    "\n",
+    "export CONDA_ENV=$(echo \"${CONDA_ENV}\" | awk '{print tolower($0)}')\n",
+    "echo ${CONDA_ENV} # double check"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Selectable **CONDA_ENV** name, will be used to specify the environment name\n",
-    "  - must be lowercase"
+    "Selectable **CONDA_TARGET_DIR** path for the central conda installation, should be in the project filesystem"
    ]
   },
   {
@@ -82,10 +85,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "CONDA_ENV=my_env\n",
-    "\n",
-    "export CONDA_ENV=$(echo \"${CONDA_ENV}\" | awk '{print tolower($0)}')\n",
-    "echo ${CONDA_ENV} # double check"
+    "export CONDA_TARGET_DIR=${PROJECT}/${USER}/miniconda3/${CONDA_ENV}"
    ]
   },
   {
@@ -133,7 +133,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mkdir -p ${CONDA_TARGET_DIR}"
+    "mkdir -p ${CONDA_TARGET_DIR}\n",
+    "echo ${CONDA_TARGET_DIR}"
    ]
   },
   {
@@ -158,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "${CONDA_TARGET_DIR}/bin/conda init bash"
+    "${CONDA_TARGET_DIR}/bin/conda init --no-rc bash"
    ]
   },
   {
@@ -198,7 +199,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "${CONDA_TARGET_DIR}/bin/conda create -n ${CONDA_ENV} -y python=3.6.8 ipykernel"
+    "${CONDA_TARGET_DIR}/bin/conda create -n ${CONDA_ENV} -y python=3.10.4 ipykernel"
    ]
   },
   {
@@ -230,7 +231,7 @@
     "source '\"${CONDA_TARGET_DIR}\"'/bin/activate '\"${CONDA_ENV}\"'\n",
     "    \n",
     "# Ensure python packages installed in conda are always prefered, not necessary if module purge is used\n",
-    "export PYTHONPATH=${CONDA_PREFIX}/lib/python3.6/site-packages:${PYTHONPATH}\n",
+    "export PYTHONPATH=${CONDA_PREFIX}/lib/python3.10/site-packages:${PYTHONPATH}\n",
     "    \n",
     "exec python -m ipykernel $@' > ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh"
    ]
@@ -241,7 +242,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "chmod +x ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh"
+    "chmod +x ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh\n",
+    "echo ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh"
    ]
   },
   {
@@ -288,7 +290,10 @@
     "  \"{connection_file}\"\n",
     " ],\n",
     " \"display_name\": \"conda_'\"${CONDA_ENV}\"'\",\n",
-    " \"language\": \"python\"\n",
+    " \"language\": \"python\",\n",
+    " \"metadata\": {\n",
+    "   \"debugger\": true\n",
+    "  }\n",
     "}' > $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}/kernel.json"
    ]
   },
-- 
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