Pre-install

Author: krystophny

.github/workflows/main.yml

@@ -43,6 +43,63 @@ jobs:
             python3-pip \
             python3-venv
 
+          apt-get install -y -q --no-install-recommends \
+            procps \
+            nano \
+            vim \
+            htop \
+            ncdu \
+            less \
+            gdb \
+            cmake-curses-gui
+
+          apt-get install -y -q --no-install-recommends \
+            pkg-config \
+            libsuitesparse-dev \
+            libopenblas-dev \
+            libsuperlu-dev \
+            libhdf5-dev \
+            libhdf5-openmpi-dev \
+            libnetcdf-dev \
+            libnetcdff-dev \
+            libfftw3-dev \
+            libgsl-dev \
+            libopenmpi-dev \
+            libscalapack-openmpi-dev \
+            libpcre3-dev \
+            libreadline-dev \
+            h5utils \
+            hdf5-tools \
+            netcdf-bin
+
+          apt-get install -y -q --no-install-recommends \
+            python3-wheel python3-setuptools \
+            # Shell and file formats
+            python3-ipython jupyter python3-sphinx python3-matplotlib \
+            python3-openpyxl python3-xlrd python3-h5py python3-netcdf4 \
+            # Scientific computing
+            python3-sympy python3-uncertainties python3-numpy python3-scipy \
+            python3-numba \
+            # Statistics
+            python3-pandas python3-sklearn python3-torch \
+            # For OMFIT
+            python3-boto3 python3-lmfit python3-configobj python3-dill \
+            python3-pyodbc python3-pyotp \
+            # Misc
+            fortran-language-server python3-tqdm python3-pytest \
+            python3-mpi4py python3-skbuild
+
+          mkdir -p /opt/venv
+          python3 -m venv --system-site-packages /opt/venv/plasma
+          python -m pip install pylance black f90wrap
+
+          echo 'export PATH=$HOME/bin:$PATH' >> ~/.bashrc && \
+          echo 'export LD_LIBRARY_PATH=$HOME/bin:$LD_LIBRARY_PATH' >> ~/.bashrc && \
+          echo 'export STELLOPT_PATH="/src/STELLOPT"' >> ~/.bashrc && \
+          echo 'export MACHINE="ubuntu"' >> ~/.bashrc && \
+          echo 'export OMPI_ALLOW_RUN_AS_ROOT=1' >> ~/.bashrc && \
+          echo 'export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1' >> ~/.bashrc && \
+          echo '. /opt/venv/plasma/bin/activate' >> ~/.bashrc
 
       - name: Initialize Gitlab access token
         run: |
@@ -52,7 +109,7 @@ jobs:
       - name: libneo
         run: |
           git clone https://github.com/itpplasma/libneo.git
-      
+
       - name: NEO-2
         run: |
           git clone https://github.com/itpplasma/NEO-2.git
@@ -83,5 +140,3 @@ jobs:
       - name: KIM
         run: |
           git clone https://gitlab.tugraz.at/plasma/codes/MEPHIT.git
-
-