14 user friendly installation (#12)

Author: krystophny

.gitlab-ci.yml

@@ -1,11 +1,5 @@
 image: ghcr.io/itpplasma/devel-tex
 
-workflow:
-  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
-    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" && $CI_MERGE_REQUEST_TARGET_BRANCH_NAME == "main"'
-    - if: $CI_PIPELINE_SOURCE == "web"
-
 variables:
   GIT_HTTPS: "true"
 
@@ -124,7 +118,7 @@ kim:
     - set_branch
     - clone_gitlab kim
     - cd kim
-    - ../scripts/checkout_branch.sh $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME
+    - ../scripts/checkout_branch.sh $CI_COMMIT_REF_NAME
     - mkdir build
     - cd build
     - cmake .. -DCMAKE_Fortran_FLAGS=-I/usr/include/hdf5/serial
@@ -145,7 +139,10 @@ neo2-job:
     - source activate.sh
     - pushd external; install_package fgsl 1.6.0; popd
     - clone_github NEO-2
-    - scripts/setup/neo2.sh
+    - cd NEO-2
+    - ../scripts/checkout_branch.sh $CI_COMMIT_REF_NAME
+    - make
+    - cd python; pip install -e .
   artifacts:
     paths:
       - NEO-2/
@@ -176,7 +173,7 @@ simple:
     - source activate.sh
     - clone_github SIMPLE
     - cd SIMPLE
-    - ../scripts/checkout_branch.sh $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME
+    - ../scripts/checkout_branch.sh $CI_COMMIT_REF_NAME
     - make
   artifacts:
     paths:
@@ -191,7 +188,7 @@ gorilla:
     - set_branch
     - clone_github GORILLA
     - cd GORILLA
-    - ../scripts/checkout_branch.sh $CI_MERGE_REQUEST_SOURCE_BRANCH_NAME
+    - ../scripts/checkout_branch.sh $CI_COMMIT_REF_NAME
     - ./build.sh
   artifacts:
     paths:

README.md

@@ -5,7 +5,7 @@ to setup development and use of internal and external codes. Our development
 environment is Visual Studio Code, and we strongly recommend GitHub Copilot
 there and in the [CLI](https://docs.github.com/en/copilot/github-copilot-in-the-cli/setting-up-github-copilot-in-the-cli).
 
-CODE is based around our standard Debian bookworm system at ITPcp and provides 
+CODE is based around our standard Debian bookworm system at ITPcp and provides
 
 - Setup scripts `scripts/setup/...`
 - Quality-of-life shell commands via `scripts/util.sh`
@@ -42,19 +42,19 @@ Then open the directory in VS Code with
 
     code code
 
-When asked to initialize the devcontainer, remove the message. 
+When asked to initialize the devcontainer, remove the message.
 Run the setup script manually with
 
-    source scripts/setup.sh
+    scripts/setup.sh
 
 The setup will install external dependencies and create and activate
 a Python virtual environment in the hidden `.venv` directory.
 
-If you work outside a container, also manually put a line
+If you work outside a container, also manually run
 
     source /path/to/code/activate.sh
 
-in your bashrc.
+and put this line in your bashrc.
 
 
 ## Testing
@@ -64,5 +64,3 @@ Integration tests are run by
     pytest tests/
 
 This will perform all the tests in `tests/` and its subfolders.
-
-

images/devel/Dockerfile

@@ -26,8 +26,3 @@ COPY scripts/setup/debian/octave.sh /tmp/setup_octave.sh
 RUN apt-get update -y && bash /tmp/setup_octave.sh && \
 	apt-get clean && rm -rf /var/cache/apt/* && \
 	rm -rf /var/lib/apt/lists/* && rm -rf /tmp/*
-
-# Prepare required packages for venv
-COPY requirements.txt .
-RUN python3 -m pip install -r requirements.txt --break-system-packages && \
-	python3 -m pip cache purge

modules/mars/2022

@@ -2,7 +2,7 @@
 
 module-whatis "MARS (2022)"
 
-prereq nvhpc/24.5
+prereq nvhpc/24.1
 
 setenv       MARSHOME        $env(CODE)/external/MARS/MarsQ_2022
 prepend-path PATH            $env(MARSHOME)

requirements.txt

@@ -1,7 +1,7 @@
 # Basics
 wheel
 pip
-setuptools<65  # For f90wrap
+setuptools
 jupyterlab
 notebook
 ipython
@@ -80,7 +80,3 @@ Shapely
 importlib-metadata
 freeqdsk
 freegs
-
-# Simsopt
-simsopt
-booz-xform

scripts/setup.sh

@@ -1,19 +1,20 @@
 #!/bin/bash
 
+set -e
+
 SCRIPTPATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
 export CODE=$SCRIPTPATH/..
-export GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=accept-new" 
+export GIT_SSH_COMMAND="ssh -o StrictHostKeyChecking=accept-new"
 
-source $CODE/scripts/setup/venv.sh
-source $CODE/activate.sh
+$CODE/scripts/setup/venv.sh
+source $CODE/.venv/bin/activate
 
 pushd $CODE/external
-$CODE/scripts/setup/fgsl.sh
+    $CODE/scripts/setup/fgsl.sh
+    $CODE/scripts/setup/triangle.sh
 popd
 
 pushd $CODE
-source $CODE/scripts/setup/libneo.sh
+    $CODE/scripts/setup/libneo.sh
 popd
-
-source $CODE/activate.sh

scripts/setup/archlinux.sh

@@ -72,7 +72,8 @@ pacman -S --noconfirm --needed \
     pugixml \
     zstd \
     cppzmq \
-    util-linux
+    util-linux \
+    graphviz
 
 # The following packages need to be installed from the AUR:
 # - metis

scripts/setup/debian/libs.sh

@@ -29,4 +29,5 @@ apt-get install -y -q --no-install-recommends \
     slepc-dev \
     h5utils \
     hdf5-tools \
-    netcdf-bin
+    netcdf-bin \
+    graphviz

scripts/setup/libneo.sh

@@ -1,6 +1,9 @@
 #!/bin/bash
 
 set -e
+
+source $CODE/scripts/util.sh
+
 echo "Building and installing 'efit_to_boozer'..."
 if [ ! -d "efit_to_boozer" ] ; then
     echo "Cloning 'efit_to_boozer'..."

scripts/setup/mac.sh

@@ -8,7 +8,7 @@ eval "$(/usr/local/bin/brew shellenv)"
 brew install gcc make cmake ninja [email protected] [email protected]
 brew install autoconf automake autogen
 brew install openblas suitesparse metis
-brew install hdf5 netcdf netcdf-fortran fftw
+brew install hdf5 netcdf netcdf-fortran fftw graphviz
 brew install --cask orbstack devpod visual-studio-code
 
 sudo ln -s /Applications/OrbStack.app/Contents/MacOS/xbin/docker /usr/local/bin/docker

scripts/setup/mars.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 set -e
-module load nvhpc/24.5
+module load nvhpc/24.1
 git clone [email protected]:plasma/codes/mars.git MARS
 cd MARS/MarsQ_2022
 make

scripts/setup/neo2.sh

@@ -19,4 +19,4 @@ source .venv/bin/activate
 python -m pip install --upgrade pip
 python -m pip install --upgrade meson
 python -m pip install --upgrade ninja
-python -m pip install -r requirements.txt
+python -m pip install --upgrade -r requirements.txt

scripts/setup/venv.sh

@@ -14,6 +14,8 @@ alias vscode='code $CODE'
 set_branch() {
     if [ -n "$CI_MERGE_REQUEST_SOURCE_BRANCH_NAME" ]; then
         export CODE_BRANCH=$CI_MERGE_REQUEST_SOURCE_BRANCH_NAME
+    elif [ -n "$CI_COMMIT_REF_NAME" ]; then
+        export CODE_BRANCH=$CI_COMMIT_REF_NAME
     else
         pushd $CODE
         export CODE_BRANCH=$(git branch --show-current)