Merge branch 'main' into clean

Author: krystophny

scripts/checkout_branch.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 BRANCH_NAME="${1:-main}" # Default branch name is "main"
 

scripts/clone_all.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 GITHUB_REPOS="libneo spline BOOZER_MAGFIE SIMPLE GORILLA GORILLA_APPLETS NEO-2 NEO-RT MEPHIT KAMEL"
 

scripts/docker_build_push_all.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 $CODE/images/base/cross_build_push.sh
 $CODE/images/devel/cross_build_push.sh
 $CODE/images/devel-tex/cross_build_push.sh

scripts/machines/init_viper.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 module load gcc/14
 module load openmpi/4.1

scripts/machines/setup_viper.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 source $CODE/machines/init_viper.sh
 

scripts/reset.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 cd $( dirname "${BASH_SOURCE[0]}" )
 

scripts/setup.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 

scripts/setup/archlinux.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # Update the system
 pacman -Syu --noconfirm
@@ -28,8 +28,6 @@ pacman -S --noconfirm --needed \
     gettext \
     bash-completion
 
-#!/bin/bash
-
 # Install additional tools (skip already installed ones)
 pacman -S --noconfirm --needed \
     procps-ng \
@@ -50,8 +48,6 @@ pacman -S --noconfirm --needed \
     gdb \
     findutils
 
-#!/bin/bash
-
 # Install development libraries (skip already installed ones)
 pacman -S --noconfirm --needed \
     pkgconf \
@@ -89,13 +85,9 @@ pacman -S --noconfirm --needed \
 # Use yay or another AUR helper to install these:
 # yay -S metis parmetis scotch petsc slepc scalapack triangle-bin hdf5-cpp-fortran netcdf-fortran
 
-#!/bin/bash
-
 # Install Octave and gnuplot (skip already installed ones)
 pacman -S --noconfirm --needed octave gnuplot
 
-#!/bin/bash
-
 # Install TeX Live and related tools (skip already installed ones)
 pacman -S --noconfirm --needed \
     texlive-core \
@@ -123,8 +115,6 @@ if [ -n "$(ls /tmp/fmt* 2>/dev/null)" ]; then
   cat /tmp/fmt*
 fi
 
-#!/bin/bash
-
 # Install fonts (skip already installed ones)
 pacman -S --noconfirm --needed \
     texlive-fontsextra \

scripts/setup/chease.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 if [ ! -d "CHEASE" ] ; then

scripts/setup/compiler_intel.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 echo "Setting up Intel compiler..."
 
 # download the key to system keyring
@@ -29,7 +29,7 @@ then
             echo $MOD_FILE
             echo -e 'g/^module-whatis \"Version:/d\nw\nq' |      sudo ed $MOD_FILE
             echo -e 'g/^module-whatis \"Dependencies:/d\nw\nq' | sudo ed $MOD_FILE
-            echo -e 'g/^module-whatis \"URL:/d\nw\nq' |          sudo ed $MOD_FILE 
+            echo -e 'g/^module-whatis \"URL:/d\nw\nq' |          sudo ed $MOD_FILE
         done
     else
         echo "## ENVIRONMENT Modules - where is the config directory?"

scripts/setup/compiler_nvidia.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 echo "Setting up NVIDIA compiler..."
 

scripts/setup/debian.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -e
 
 # src: https://stackoverflow.com/a/246128/16527499

scripts/setup/debian/base.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt-get install -y -q --no-install-recommends \
     file \

scripts/setup/debian/desktop.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt install i3 fuse nextcloud-desktop gnupg fonts-noto-color-emoji
 

scripts/setup/debian/fonts.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt-get install -y -q --no-install-recommends \
     texlive-fonts-recommended \

scripts/setup/debian/interactive.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt-get install -y -q --no-install-recommends \
     procps \

scripts/setup/debian/libs.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt-get install -y -q --no-install-recommends \
     pkg-config \

scripts/setup/debian/octave.sh

@@ -1,3 +1,3 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt-get install -y -q --no-install-recommends octave gnuplot

scripts/setup/debian/texlive.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 apt-get install -y -q --no-install-recommends \
     texlive-latex-base \

scripts/setup/devcontainer.sh

@@ -1,4 +1,4 @@
-#/bin/bash
+#!/usr/bin/env bash
 
 export GIT_HTTPS=1
 export CODE_TEMPLATE=/usr/local/src/code_template

scripts/setup/fgsl.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 if [ ! -d "fgsl-1.6.0" ] ; then
     echo "Fetching and building FGSL..."

scripts/setup/focus.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # https://princetonuniversity.github.io/FOCUS/
 #

scripts/setup/gpec.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 echo "Setting up GPEC..."
 echo "Upstream code access: https://princetonuniversity.github.io/GPEC/developers.html"

scripts/setup/gvec.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 echo "Setting up GVEC..."
 

scripts/setup/kamel.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 cd external
 echo "Building Slatec..."
 mkdir slatec

scripts/setup/lazygit.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 install_lazygit() {
     if ! command -v lazygit &>/dev/null; then

scripts/setup/lfortran.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 sudo --validate || exit 1
 sudo apt update && sudo apt install -y --no-install-recommends llvm-dev

scripts/setup/libneo.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 

scripts/setup/mac.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
 

scripts/setup/mars.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 module load nvhpc/24.1

scripts/setup/mephit.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 source /etc/profile.d/modules.sh

scripts/setup/mfem.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 if [ ! -d "mfem-4.7" ] ; then
     echo "Fetching and building MFEM..."

scripts/setup/neort.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 set -e
 echo "Building and installing NEO-RT..."
@@ -32,4 +32,4 @@ pushd build
 cmake ..
 make
 popd
-popd
+popd

scripts/setup/netcdf.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 export FFLAGS=-fPIC
 export CFLAGS=-fPIC

scripts/setup/nodejs.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # installs nvm (Node Version Manager)
 curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.7/install.sh | bash
@@ -15,4 +15,3 @@ node -v # should print `v20.15.0`
 
 # verifies the right NPM version is in the environment
 npm -v # should print `10.7.0`
-

scripts/setup/omfit.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 echo "Setting up OMFIT..."
 echo "Requires personal Git access to OMFIT repository."

scripts/setup/omfit/init_conda.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 # Manually deactivate any existing venv
 if [[ -n "$VIRTUAL_ENV" ]]; then

scripts/setup/sbgeom.sh

@@ -1,5 +1,5 @@
 
-#!/bin/bash
+#!/usr/bin/env bash
 #
 # Setup for SBGeom - A simple package for creating blanket geometries
 # derived from Fourier Surfaces. Package author: Timo Bogaarts, TU Eindhoven

scripts/setup/simsopt.sh

@@ -1,5 +1,5 @@
 
-#!/bin/bash
+#!/usr/bin/env bash
 
 if [ ! -d "simsopt" ] ; then
     echo "Fetching and building simsopt..."

scripts/setup/stellopt.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 if [ ! -d "STELLOPT" ] ; then
     echo "Fetching and building STELLOPT..."

scripts/setup/triangle.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 CC=${CC:-gcc}
 

scripts/setup/venv.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 if command -v python3 &> /dev/null; then
     PYTHON=$(command -v python3)

scripts/setup/vmec2000.sh

@@ -1,5 +1,5 @@
 
-#!/bin/bash
+#!/usr/bin/env bash
 
 if [ ! -d "VMEC2000" ] ; then
     echo "Fetching and building VMEC2000..."

scripts/templates/condor_script/exec_test.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
 echo -e "\nExecutable: $0   "
 echo -e "Job number  : $1 \n"

shell.nix

@@ -0,0 +1,37 @@
+with (import <nixpkgs> {});
+mkShell {
+  buildInputs = [
+    # Base
+    curl
+    wget
+    git
+    openssh
+    cmake
+    ninja
+    gcc
+    gfortran
+    mpi
+
+    # Libs
+    openblas
+    suitesparse
+    hdf5
+    hdf5-fortran
+    netcdf
+    netcdffortran
+    fftw
+
+    # Interactive
+    coreutils
+    which
+    less
+    vim
+    lazygit
+  ];
+
+  shellHook = ''
+    export CC=gcc
+    export CXX=g++
+    export FC=gfortran
+  '';
+}