Merge pull request #8 from scientificcomputing/dokken/conda

Use conda for all actions

Author: jorgensd

.github/actions/install-dependencies/action.yml

@@ -1,22 +1,40 @@
 name: Install dependencies
 
+inputs:
+  python-version:
+    description: Python version to install
+    required: true
+    type: string
+    default: "3.10"
 
 runs:
   using: composite
   steps:
-      - name: Install and upgrade pip
-        shell: bash -el {0}
-        run: |
-          apt-get update
-          apt-get install -y python3-pip
-          python3 -m pip install -U pip
+    - name: Setup conda-forge
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          activate-environment: mpi-tutorial
+          python-version: ${{ inputs.python-version }}
+          use-mamba: true
+          environment-file: environment.yml
+
+    # - name: Prepare cache
+    #   shell: bash -el {0}
+    #   run: |
+    #     if [[ $CONDA != /opt/conda ]]; then
+    #       mkdir -p /opt/conda/
+    #       ln -s $CONDA/envs /opt/conda/envs
+    #     fi
+    #     echo CONDA=$CONDA
+    #     mamba env list
+        
+    # - name: Environment cache
+    #   uses: actions/cache@v3
+    #   with:
+    #     path: /opt/conda/envs/mpi-tutorial
+    #     key: env-conda-mpi-tutorial-${{ inputs.python-version }}-${{ hashFiles('.github/actions/install-dependencies/*') }}
+    #   id: cache
 
-      - name: Install MPICH
-        shell: bash -el {0}
-        run: |
-          apt-get install -y libmpich-dev
 
-      - name: Install requirements
-        shell: bash -el {0}
-        run: |
-          python3 -m pip install -r requirements.txt

.github/workflows/build_docs.yml

@@ -12,7 +12,6 @@ env:
 jobs:
   build-book:
     runs-on: ubuntu-latest
-    container: ubuntu:22.04
 
     steps:
 
@@ -21,14 +20,9 @@ jobs:
       - name: Install common packages
         uses: ./.github/actions/install-dependencies
 
-      - name: Install book deps
-        run:
-          python3 -m pip install -r requirements.txt
-
       - name: Build the book
         run: 
-          jupyter-book build . -W
-
+          conda run -n mpi-tutorial jupyter-book build . -W
       - uses: actions/upload-artifact@v3
         with:
           name: documentation

Dockerfile

@@ -8,9 +8,13 @@ Welcome to this tutorial (in development)
 2. Clone the repository (or fork) and create a new branch with `git checkout -b github-username/feature-description`
 3. Create a compatible working environment, for instance by building the project docker-image.
 ```bash
-docker build -t local_docker_file -f Dockerfile .
+docker build -t local_docker_file -f docker/Dockerfile .
 docker run -ti -v $(pwd):/root/shared -w /root/shared --name=tutorialmpi local_docker_file
 ```
+You can also use conda to build your environment
+```bash
+conda env update --file environment.yml --name name-of-your-env
+```
 4. Create an `.ipynb` in the [notebooks](./notebooks/) folder, or modify the existing notebooks. If a new notebook has been created, add it to the appropriate section of [_toc.yml](_toc.yml).
 5. Make sure the webpage builds correctly by calling `jupyter book build -W .` from the root of the repository. You can inspect the webpage locally by opening [_build/html/index.html](_build/html/index.html) with the web-browser of your choice.
 6. Make a [pull-request](https://github.com/scientificcomputing/mpi-tutorial/compare) to the main branch of this repo.

README.md

@@ -8,8 +8,8 @@ logo: logo.png
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: cache
-
+  execute_notebooks: force
+  timeout: 1800
 
 # Information about where the book exists on the web
 repository:

_config.yml

@@ -0,0 +1,19 @@
+FROM condaforge/mambaforge 
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install ssh (missing dependency to run conda envs)
+RUN apt-get update && \
+    apt-get install -y ssh build-essential
+
+# Upgrade mamba
+RUN mamba upgrade -y mamba
+
+# Copy environment and requirements files into docker env
+COPY environment.yml .
+
+# Update environment file with new environment name
+RUN mamba env update --file environment.yml --name dockerenv
+SHELL ["mamba", "run", "-n", "dockerenv", "/bin/bash", "-c"]
+
+RUN echo "source activate dockerenv" > ~/.bashrc

docker/Dockerfile

@@ -0,0 +1,9 @@
+name: mpi-tutorial
+channels:
+  - conda-forge
+dependencies:
+  - mpich
+  - ipyparallel
+  - jupyter-book
+  - mpi4py
+  - autopep8