Merge pull request #8 from erizmr/5_upgrade_movement

Update Movement and set up CI test workflow

.github/workflows/test_warpmesh.yml

@@ -5,6 +5,8 @@ on:
     branches:
       - main
 
+  pull_request:
+
 jobs:
   test-warpmesh:
     name: Test WarpMesh
@@ -14,24 +16,29 @@ jobs:
       options: --user root
     steps:
       - uses: actions/checkout@v3
-      - name: Install movement
+      - name: Install Movement
         run: |
-          git clone https://github.com/pyroteus/movement.git
+          . /home/firedrake/firedrake/bin/activate
+          git clone https://github.com/mesh-adaptation/movement.git
           cd movement
-          pip install -e .
-      - name: Install warpmesh
+          python3 -m pip install -e .
+      - name: Install PyTorch
         run: |
           . /home/firedrake/firedrake/bin/activate
-          pwd
-          pip install -e .
-      - name: install warpmesh dependencies
+          python3 -m pip install torch --index-url https://download.pytorch.org/whl/cpu
+      - name: Install PyTorch3d
         run: |
           . /home/firedrake/firedrake/bin/activate
-          pip install -r requirements.txt
-      - name: test warpmesh
+          python3 -m pip install 'git+https://github.com/facebookresearch/pytorch3d.git'
+      - name: Install other WarpMesh dependencies
         run: |
           . /home/firedrake/firedrake/bin/activate
-          cd ./tests
-          python -m pytest ./test* -v
-          
-
+          python3 -m pip install -r requirements.txt
+      - name: Install WarpMesh
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python3 -m pip install -e .
+      - name: Run WarpMesh test suite
+        run: |
+          . /home/firedrake/firedrake/bin/activate
+          python3 -m pytest tests/test* -v

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "install/movement"]
 	path = install/movement
-	url = https://github.com/pyroteus/movement.git
+	url = https://github.com/mesh-adaptation/movement.git
 

README.md

@@ -24,14 +24,14 @@ Just navigate to **project root** folder, open terminaland execute the `install/
 sh ./install/install.sh
 ```
 
-This will install [firedrake](https://www.firedrakeproject.org/download.html) and [movement](https://github.com/pyroteus/movement) under `install` folder, as well as the `WarpMesh` package.
+This will install [firedrake](https://www.firedrakeproject.org/download.html) and [movement](https://github.com/mesh-adaptation/movement) under `install` folder, as well as the `WarpMesh` package.
 
 
 ### The hard way (in case the easy way did not went well or you want to challenge yourself):
 
 1. The mesh generation relies on firedrake, which is a python package. To install firedrake, please follow the instructions on [firedrakeproject.org](https://www.firedrakeproject.org/download.html).
 
-2. The movement of the mesh is implemented by `pyroteus/movement`, install it in the firedrake venv. To install, run `pip install -e .` in the `pyroteus/movement` directory. Here is a link to that repo: [pyroteus/movement](https://github.com/pyroteus/movement).
+2. The movement of the mesh is implemented by `mesh-adaptation/movement`, install it in the firedrake venv. To install, run `pip install -e .` in the `mesh-adaptation/movement` directory. Here is a link to that repo: [mesh-adaptation/movement](https://github.com/mesh-adaptation/movement).
 
 3. Use the venv provided by firedrake to install the dependencies of this project. The venv is located at `~/firedrakevenv/bin/activate`. To activate the venv, run `source ~/firedrakevenv/bin/activate`. Then run `pip install -r requirements.txt` to install the dependencies.
 

install/install.sh

@@ -2,59 +2,54 @@
 
 # This script will install necessary packages for the project
 
-function yellow_log(){
-  local DATE_N=`date "+%Y-%m-%d %H:%M:%S"`
+function yellow_log() {
+  local DATE_N=$(date "+%Y-%m-%d %H:%M:%S")
   local color="\033[33m"
   echo -e "$DATE_N$color $*  \033[0m"
 }
 
-function green_log(){
-  local DATE_N=`date "+%Y-%m-%d %H:%M:%S"`
+function green_log() {
+  local DATE_N=$(date "+%Y-%m-%d %H:%M:%S")
   local color="\033[32m"
   echo -e "$DATE_N$color $*  \033[0m"
 }
 
 yellow_log "Please deactivate conda enviroment before running this script, otherwise it will fail."
 
-# Download pyroteus/movement package.
-green_log "Start downloading movement..."
+# Download mesh-adaptation/movement package.
+green_log "Start downloading Movement..."
 
-if [ -d ./install/movement ]
-then
-yellow_log "movement dir exists, abort downloading"
+if [ -d ./install/movement ]; then
+  yellow_log "Movement dir exists, abort downloading"
 fi
 
-if [ ! -d ./install/movement ]
-then
-yellow_log "movement does not exist, start downloading movement"
-git submodule add https://github.com/pyroteus/movement.git install/movement
+if [ ! -d ./install/movement ]; then
+  yellow_log "Movement does not exist, start downloading Movement"
+  git submodule add https://github.com/mesh-adaptation/movement.git install/movement
 fi
 
-
 # Download & install firedrake
 cd ./install
 
 # If previous file exists
-if [ -d ./firedrake ]
-then
-green_log "The directory has existed, nothing to be done"
+if [ -d ./firedrake ]; then
+  green_log "The directory has existed, nothing to be done"
 fi
 
-if [ ! -d ./firedrake ]
-then
-curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
-python3 firedrake-install --disable-ssh
-green_log "firedrake has been installed"
+if [ ! -d ./firedrake ]; then
+  curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
+  python3 firedrake-install --disable-ssh
+  green_log "Firedrake has been installed"
 fi
 
-# activate firedrake enviroment
+# Activate Firedrake enviroment
 . ./firedrake/bin/activate
 
-# Install movement
+# Install Movement
 cd movement
 pip install -e .
 
-# Install warpmesh
+# Install WarpMesh
 cd ../..
 pip install -r requirements.txt
 pip install -e .

requirements.txt

@@ -1,4 +1,4 @@
-numpy >= 1.13.0
+numpy
 pandas
 meshio
 matplotlib
@@ -7,9 +7,10 @@ pytest
 pytest-timeout
 jupyter
 ipython
-torch == 1.13.1
-torch_geometric == 2.5.3
-torch_sparse == 0.6.18
+seaborn
+torch
+torch_geometric
+torch_sparse
 tensorboardX
 torch_scatter
 rich
@@ -18,4 +19,4 @@ ipython
 pep8
 sphinx
 einops
-gmsh
+gmsh