Update installation instructions in README.md

Removed outdated installation videotutorials and consolidated installation instructions.

Author: alexvakimov

README.md

@@ -27,259 +27,9 @@ Not maintained for long time, but may still contain some useful info on some top
   hasn't been used for a while - use the Slack workspace instead
 
 
-## Installation Videotutorials (as of 5/16/2022)
+## Installation 
 
-* [Installing WSL2](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=02184b70-7745-4eb4-a776-ae92014c652a&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)
-
-* [Installing WSL2: After reboot](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=972aef79-e235-4a90-9ce1-ae92014d34db&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)
-
-* [Installing Ubuntu on Windows 11](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=31a63536-f333-4242-9b56-ae92015ece64&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)
-
-* [Creating Conda environment for Libra](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=d6ada23e-7e16-4b7a-b290-ae920188627c&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)
-
-* [Installing Libra](https://ub.hosted.panopto.com/Panopto/Pages/Embed.aspx?id=7f8dd8c4-9f58-4ca0-a8cb-ae930166b7ec&autoplay=false&offerviewer=true&showtitle=true&showbrand=true&captions=false&interactivity=all)
-
-## Installation (as of after 3/23/2023)
-
-### 1. Install miniconda (for Python 3.9) and activate Conda
-
-#### 1.1 Download and install
-
-    mkdir Conda
-    cd Conda/
-    wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh .
-    sh ./Miniconda3-py39_4.12.0-Linux-x86_64.sh -b -u -p <install_dir>
-
-  Here, 
-
-  * the `-b` option will accept the license agreement and will skip all the prompts
-  * the `-u` option will tell the installer to do all the needed updates
-  * the `-p` option followed by the installation directory path (will be created), tells
-     the installed where to install the package.
-
-  Test it is working by doing:
-
-    which conda
-
-
-#### 1.2 Update the conda
-
-  Actually, let's not do this:
-
-    conda update -n base -c defaults conda
-
-
-#### 1.3 Activate the environment
-
-  Add the following line to you `.bashrc` or `.bash_profile` scripts:
-
-    eval "$(<path to bin/conda> shell.bash hook)"
-
-  For instance, 
-
-    eval "$(/projects/academic/cyberwksp21/SOFTWARE/Conda/bin/conda shell.bash hook)"
-
-  Restart your terminal or reload the `.bashrc` script:
-
-    source ~/.bashrc
-
-
-  When you do this, your command line should show up the (base) in front, indicating that
-  the base environment is ready
-
-  Test it is working by doing:
-
-    which conda
-
-
-
-### 2. Create the environment equipped with all Libra needs 
-
-#### 2.1 Create the `libra` environment 
-
-  In fact, you can call it whatever you like:
-
-    conda create -n libra python=3.7
-
-#### 2.2 Activate this environment
-
-    conda activate libra
-
-This is very important step - when activated, all the installs will go into that folder. 
-
-**In case you mess up with an environment**, you can remove it with:
-
-    conda remove --name libra --all
-
-
-#### 2.3 Now, equip your environment with the required packages
-
-Do this **one by one, and in this order**, (should not matter too much, but who knows...)
-
-    > To automate the below procedures, you can use `-y` option to accept prompts (sometimes this will override)
-    > previous packages/conflicts, so be careful
-    > 
-    > You can also use `-q` to get rid of all the messages to the output, although i'd keep it to keep track of what's going on
-
-
-First let's install the most general packages:
-
-    conda install -y -c conda-forge numpy scipy matplotlib imageio
-
-
-Next, all what we actually need:
-
-    conda install -y conda-build make
-    conda install -y anaconda::py-boost
-    conda install -y -c conda-forge gcc_linux-64=12.2.0 gxx_linux-64=12.2.0 cmake=3.24.2 python-devtools llvm-openmp
-    conda install -y -c conda-forge/label/gcc7 eigen mpfr
-    conda install -y -c psi4/label/dev libint2=2.7.1
-    conda install -y -c anaconda h5py gmp
-
-Install Jupyter Lab or traditional Jupyter notebook as explainted [here](https://jupyter.org/install):
-
-    pip install -U jupyterlab
-
-    or 
-
-    pip install -U notebook
-
-
-Install py3Dmol for viewing molecular structures:
-
-    pip install -U py3Dmol
-
-
-Installation instruction of Scikit-learn from its official website:
-
-    pip install -U scikit-learn
-
- 
-    >
-    >  YES - IT GOT SMALLER AND MORE COMPACT !
-    >
-
-Install PyTorch - since the current versions of Libra have a growing number of 
-functions/modules written with PyTorch. The general instructions can be found [here](https://pytorch.org/get-started/locally/)
-
-As a simple (most common case, peraps), we install PyTorch for CPU on Linux with:
-
-    pip install -U torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
-
-or
-
-    conda install pytorch cpuonly -c pytorch
-    
-
-### 3. Download and build Libra
-
-#### 3.1 Get it from the GitHub and choose the right branch
-
-  Clone the repo from the GitHub
-
-    git clone https://github.com/Quantum-Dynamics-Hub/libra-code.git libra
-
-  and switch to the correct branch or tag - usually, it would be `devel` branch
-
-    cd libra
-    git checkout devel
-
-#### 3.2 Create the build directory and make the Makefiles
-
-   Then in the `libra` directory, create the build directory:
-
-    mkdir _build
-    cd _build
-    cmake ../
-
-#### 3.3 Compile the package
-    
-    make -j4
-
-
-### 4. Make it ready to use
-
-   Add the following exports to your `.bash_profile` file
-
-    export PYTHONPATH=<path to the ppackage>/libra/_build/src:$PYTHONPATH
-
-
-   Restart the terminal or source the bash profile and activate libra conda environment
-
-    source .bash_profile 
-    conda activate libra
-    
-   And you should be ready to use Libra.
-
-
-## Useful notes:
-
-### 1. 2/15/2025 (from Liz Stippell):
-
-Notes on making Libra if you have python v3.7+ installed anywhere on your system (Linux):
-Although the libra environment is made with python 3.7, during the `cmake ../` step it will search for any python, 
-including versions outside of the libra environment. (Ex: my system kept finding python v3.9 in my 
-Miniconda here: `/path/to/Conda/Miniconda3/include/python3.9` instead of searching within the libra 
-environment: `/path/to/Conda/Miniconda3/envs/libra` )
-
-To avoid this issue, you can add the following lines in the CMakeLists.txt file in your libra source code directory around line 44:
-
-"""
-set(Python3_ROOT_DIR "/path/to/Conda/Miniconda3/envs/libra")
-set(Python3_EXECUTABLE "/path/to/Conda/Miniconda3/envs/libra/bin/python3")
-set(Python3_LIBRARY "/path/to/Conda/Miniconda3/envs/libra/lib/libpython3.7m.so")
-set(Python3_INCLUDE_DIR "/path/to/Conda/Miniconda3/envs/libra/include/python3.7m")
-FIND_PACKAGE(Python3 3.6 REQUIRED COMPONENTS Development)
-"""
-
-This will force the make to search within the libra environment in the specified locations where you know the files exist. 
-
-
-### 2. 4/17/2025 (Alexey Akimov)
-
-A good way to setup the conda environment to have Boost and Python version consistent is this:
-
-
-    conda install -c conda-forge boost=1.82 python=3.10
-
-
-### 3. 4/17/2025 (Alexey Akimov)
-
-Another useful recipe for setting up jupyter notebook specific to a selected Conda environment:
-
-Step 1: Activate the environment
-
-    conda activate libra
-
-
-Step 2: Install ipykernel and register the kernel
-
-
-    conda install ipykernel
-    python -m ipykernel install --user --name=libra --display-name "Python (libra)"
-
-
-Now, in Jupyter, you'll see a new kernel called "Python (libra)". Select that in your notebook.
-
-### 4. 7/31/2025 (from Daeho Han)
-
-Here are some installationinstructions from **Daeho Han** that may be used as a good revised summary of the above
-installation instructions:
-
-    conda create -n libra
-    conda install -c conda-forge boost=1.82 python=3.10
-    conda install -y -c conda-forge numpy scipy matplotlib imageio
-
-    conda install -y conda-build make
-    conda install -y -c conda-forge gcc_linux-64=12.2.0 gxx_linux-64=12.2.0 cmake=3.24.2 python-devtools llvm-openmp
-    conda install -y -c conda-forge/label/gcc7 eigen mpfr
-    conda install -y -c psi4/label/dev libint2=2.7.1
-    conda install -y -c anaconda h5py gmp
-
-    pip install -U jupyterlab
-    pip install -U py3Dmol
-    pip install -U scikit-learn
-    pip install -U torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
+Please see [here](INSTALLATION.md)
 
 ## Developers and Contributors