Updated conda environment

Python/QA-003-Conda-Environment.ipynb

@@ -4,7 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Setting up a user environment with conda\n"
+    "# Setting up a user environment\n",
+    "\n",
+    "Topics\n",
+    "* Setup a user environment [using conda](#using-conda)\n",
+    "    - [Add user environment to notebook kernels](#add-the-new-environment-to-your-active-kernels)\n",
+    "    - [Activate your conda environment](#activate-your-conda-environment)\n",
+    "* Setup a user environment [using venv](#using-virtual-environment)\n",
+    "* Include `PATH` in [Notebook Kernel](#add-path-to-your-user-environment)\n"
    ]
   },
   {
@@ -26,6 +33,13 @@
     "!module list"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Using conda"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -231,6 +245,31 @@
     "!~/.conda/envs/myenv/bin/python -m ipykernel install --user --name MYENV --display-name \"Py3.7\""
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Activate your conda environment\n",
+    "Conda Environments need to be added to the `PATH` to work well. So there is an `activate` function for these conda environments.\n",
+    "\n",
+    "However, running\n",
+    "```bash\n",
+    "conda init bash\n",
+    "```\n",
+    "will edit your `.bashrc` and that is not nice, especially when you might move to another module. \n",
+    "**Therefore this is not recommended to do.**\n",
+    "\n",
+    "In order to use your environment in a shell script or on a slurm job, try the following:\n",
+    "\n",
+    "Load the shell setup script located in the conda source tree (`${CONDA_ROOT}/etc/profile.d/conda.sh`) and activate your environment:\n",
+    "```bash\n",
+    "# Load from the current conda module the BASH functionality (as in activate)\n",
+    "source $(which conda)/../etc/profile.d/conda.sh\n",
+    "# now activating the environment works\n",
+    "conda activate myenv\n",
+    "```"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 5,
@@ -255,7 +294,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Custom Environment Python Environment"
+    "## Using virtual environment"
    ]
   },
   {
@@ -351,6 +390,34 @@
     "!jupyter kernelspec list"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add PATH to your user environment\n",
+    "\n",
+    "In order to get full access to all tools installed in your local environment, add it to your `PATH`.\n",
+    "\n",
+    "Open your `kernel.json` file located `/jetfs/home/mblaschek/.local/share/jupyter/kernels/myenv/kernel.json`:\n",
+    "```json\n",
+    "{\n",
+    "    \"argv\": [\n",
+    "        \"/jetfs/home/mblaschek/.conda/envs/myenv/bin/python\",\n",
+    "        \"-m\",\n",
+    "        \"ipykernel_launcher\",\n",
+    "        \"-f\",\n",
+    "        \"{connection_file}\"\n",
+    "    ],\n",
+    "    \"env\" : {\n",
+    "        \"PATH\": \"/jetfs/home/mblaschek/.conda/envs/myenv/bin/:${PATH}\",\n",
+    "        \"LD_LIBRARY_PATH\": \"/jetfs/home/mblaschek/.conda/envs/myenv/lib:${LD_LIBRARY_PATH}\"\n",
+    "    },\n",
+    "    \"display_name\": \"MYENV\",\n",
+    "    \"language\": \"python\"\n",
+    "}\n",
+    "```"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -361,7 +428,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Miniconda3 (4.8.2)",
+   "display_name": "Anaconda3 (2020.07)",
    "language": "python",
    "name": "python3"
   },
@@ -375,7 +442,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.1"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,