From 32e39ea78759504ad86cea28234e3e356fc4f98c Mon Sep 17 00:00:00 2001
From: Michael Blaschek <michael.blaschek@univie.ac.at>
Date: Wed, 1 Dec 2021 11:43:25 +0100
Subject: [PATCH] conda activate function revised!
---
Python/QA-003-Conda-Environment.ipynb | 32 ++++++++++++++++++++---
Python/Your-First-Notebook-onJet_v2.ipynb | 29 +++++++++++++++++---
2 files changed, 54 insertions(+), 7 deletions(-)
diff --git a/Python/QA-003-Conda-Environment.ipynb b/Python/QA-003-Conda-Environment.ipynb
index cc8118b..ecd5845 100644
--- a/Python/QA-003-Conda-Environment.ipynb
+++ b/Python/QA-003-Conda-Environment.ipynb
@@ -259,14 +259,38 @@
"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",
+ "This script is used by `conda init bash` to set the configuration, we simply source (load) it and get the same functionality as we would be using `conda init bash`. **(Do not use `conda init bash`)**\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",
+ "source $(dirname $(which conda))/../etc/profile.d/conda.sh\n",
"# now activating the environment works\n",
"conda activate myenv\n",
+ "```\n",
+ "\n",
+ "#### bash conda_activate function\n",
+ "optionaly you can add this bash function to your `.bashrc` for convenience:\n",
+ "\n",
+ "```bash\n",
+ "conda_activate(){\n",
+ " if ! command -v conda &> /dev/null; then\n",
+ " echo \"Load ana/miniconda module first\"\n",
+ " else\n",
+ " if [ $# -ne 1 ]; then\n",
+ " echo \"usage: conda_activate [env-name]\"\n",
+ " \n",
+ " else\n",
+ " source $(dirname $(which conda))/../etc/profile.d/conda.sh\n",
+ " conda activate $1\n",
+ " fi\n",
+ " fi\n",
+ "}\n",
+ "```\n",
+ "\n",
+ "After your `.bashrc` has been loaded (e.g. logout/login again) you should be able to use\n",
+ "\n",
+ "```bash\n",
+ "module load anaconda3\n",
+ "conda_activate myenv\n",
"```"
]
},
diff --git a/Python/Your-First-Notebook-onJet_v2.ipynb b/Python/Your-First-Notebook-onJet_v2.ipynb
index 5d37966..3105d22 100644
--- a/Python/Your-First-Notebook-onJet_v2.ipynb
+++ b/Python/Your-First-Notebook-onJet_v2.ipynb
@@ -575,13 +575,36 @@
"\n",
"Hint: Checkout the guides on [Gitlab](https://gitlab.phaidra.org/imgw/computer-resources/-/blob/master/Python/QA-003-Conda-Environment.ipynb#Activate-your-conda-environment)\n",
"\n",
- "### Load from the current conda module the BASH functionality (as in activate)\n",
+ "### Load bash conda configuration\n",
+ "This script is used by `conda init bash` to set the configuration, we simply source (load) it and get the same functionality as we would be using `conda init bash`. **(Do not use `conda init bash`)**\n",
"\n",
- "```sh\n",
- "source $(which conda)/../etc/profile.d/conda.sh\n",
+ "```bash\n",
+ "source $(dirname $(which conda))/../etc/profile.d/conda.sh\n",
"# now activating the environment works\n",
"conda activate myenv\n",
"```\n",
+ "optionaly you can add this bash function to your `.bashrc` for convenience:\n",
+ "```bash\n",
+ "conda_activate(){\n",
+ " if ! command -v conda &> /dev/null; then\n",
+ " echo \"Load ana/miniconda module first\"\n",
+ " else\n",
+ " if [ $# -ne 1 ]; then\n",
+ " echo \"usage: conda_activate [env-name]\"\n",
+ " \n",
+ " else\n",
+ " source $(dirname $(which conda))/../etc/profile.d/conda.sh\n",
+ " conda activate $1\n",
+ " fi\n",
+ " fi\n",
+ "}\n",
+ "```\n",
+ "After your `.bashrc` has been loaded (e.g. logout/login again) you should be able to use\n",
+ "\n",
+ "```bash\n",
+ "module load anaconda3\n",
+ "conda_activate myenv\n",
+ "```\n",
"\n",
"### Activate your kernel in your notebooks\n",
"\n",
--
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