From 522b41ae1ba1de0c195e76f04c985c66c02defcc Mon Sep 17 00:00:00 2001
From: Nicolas <n.kruse@fz-juelich.de>
Date: Mon, 19 Sep 2022 11:31:29 +0000
Subject: [PATCH] changed setup_apps_miniforge to use work-environment.yml

---
 setup_apps_miniforge.sh | 24 +++++++-------------
 work-environment.yml    | 50 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+), 16 deletions(-)
 create mode 100644 work-environment.yml

diff --git a/setup_apps_miniforge.sh b/setup_apps_miniforge.sh
index acd5590..b7db47d 100644
--- a/setup_apps_miniforge.sh
+++ b/setup_apps_miniforge.sh
@@ -82,16 +82,15 @@ ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh
 
 mkdir -p /opt/conda/envs/
 
-/opt/conda/bin/conda create --prefix /opt/conda/envs/default_python python=3.7 ipykernel --yes
-/opt/conda/envs/default_python/bin/python -m ipykernel install --prefix /usr/local/ --name 'python3' --display-name "Python (default)"
-
-
-#install ofen used python packages for default environment
-/opt/conda/bin/conda install h5py tqdm pandas pillow matplotlib ipympl matplotlib pandas numpy --yes -n default_python
-/opt/conda/bin/conda install cantera --channel cantera --yes -n default_python
-
-#remove ipykernel for base enviroment:
+#remove existing environment and ipykernel:
 #jupyter kernelspec remove python3
+#/opt/conda/bin/conda env remove -p /opt/conda/envs/default_python
+
+#setup default conda environment
+/opt/conda/bin/conda env create --prefix /opt/conda/envs/default_python -f work-environment.yml
+
+#setup kernel for using the enviroment in jupyter lab
+/opt/conda/envs/default_python/bin/python -m ipykernel install --prefix /usr/local/ --name 'python3' --display-name "Python (default)"
 
 
 #users have to setup their kernel like this:
@@ -99,15 +98,9 @@ mkdir -p /opt/conda/envs/
 #conda create ipykernel --name mypersonal_enviroment
 #python -m ipykernel install --user --name mypersonal_enviroment --display-name "Python My Env"
 
-
-#conda install --yes jupyterhub jupyterlab notebook configurable-http-proxy jupyterlab-git jupyter-server-proxy
-#jupyter labextension install jupyter-matplotlib
-
 #echo "Install Tensorflow..."
 #conda install --yes tensorflow-gpu -c conda-forge
 
-#echo "Install common Python libs..."
-#conda install --yes h5py tqdm pandas ipywidgets pillow matplotlib ipympl opencv-python
 
 #Other tools:
 
@@ -130,7 +123,6 @@ mkdir -p /opt/conda/envs/
 
 echo "Start JupyterHub..."
 systemctl start jupyterhub.service
-#sudo systemctl restart jupyterhub
 
 echo ""
 echo "Setup successfully finished"
diff --git a/work-environment.yml b/work-environment.yml
new file mode 100644
index 0000000..32ab35b
--- /dev/null
+++ b/work-environment.yml
@@ -0,0 +1,50 @@
+name: work
+channels:
+  - cantera
+  - conda-forge
+  - nodefaults
+  - bioconda #required for nmrglue (on anaconda.org)
+dependencies:
+  - python
+  - matplotlib
+  - numpy
+  - pandas
+  - pytables
+  - nptdms # for Labview TDMS files
+  - openpyxl  # read/write excel files
+  - snappy # for now, fixes dependency error of pytables  
+  - scipy
+  - scikit-learn
+  - spyder
+  - pillow
+  - notebook
+  - jupyterthemes
+  - jupyter_contrib_nbextensions
+  - jupyter_nbextensions_configurator
+  - nbconvert
+  - nbdime
+  - ipypublish
+  - jupyter-book>=0.12.1
+  - sqlalchemy~=1.3.12  # for jupyter-cache - try to update later...
+#  - pyppeteer
+  - cantera
+  - h5py  
+  - cvxpy
+  - jupyterlab
+  - jupyterlab-git
+  - pip
+  - pip:
+    - impedance
+    - emd
+    - pyschedule
+    - pulp==2.0
+    - ProcessScheduler
+  - rise
+  - plotly
+  - tqdm #easy to use progress bar: tqdm(iterable)
+  - odfpy #open OpenDocument spread sheed files with pandas
+  - psycopg2 #PostgreSQL adapter
+  - nmrglue #working with NMR data in Python
+  - jupyter_pivottablejs
+#  - blaze #blaze -> python[version='2.7.*|3.5.*|3.6.*'] (Your python: python=3.7)
+  - ipykernel
\ No newline at end of file