Merge pull request #2 from pythonhealthdatascience/dev

amyheather · web-flow · commit d998f4dee2f1 · 2026-01-09T12:04:41.000Z
Dev
diff --git a/.Rprofile b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/.github/workflows/docker_quarto.yaml b/.github/workflows/docker_quarto.yaml
@@ -0,0 +1,89 @@
+name: Publish docker on GHCR, then render and deploy quarto on GitHub pages
+
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+    inputs:
+      force_docker_build:
+        description: 'Force Docker build (skip change detection)'
+        required: true
+        type: boolean
+        default: false
+      skip_docker_build:
+        description: 'Skip Docker build (use last built image)'
+        required: true
+        type: boolean
+        default: false
+
+jobs:
+  publish-docker:
+    name: Publish docker
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Check if Docker build needed
+        id: changes
+        uses: dorny/paths-filter@v3
+        with:
+          filters: |
+            docker:
+              - 'Dockerfile'
+              - 'environment.yaml'
+              - 'renv.lock'
+              - 'renv/**'
+
+      - name: Login to GitHub Container Registry
+        if: >
+          (!inputs.skip_docker_build) &&
+          (inputs.force_docker_build || steps.changes.outputs.docker == 'true')
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build the Docker image
+        if: >
+          (!inputs.skip_docker_build) &&
+          (inputs.force_docker_build || steps.changes.outputs.docker == 'true')
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          tags: |
+            ghcr.io/pythonhealthdatascience/hdruk_tests:latest
+          push: true
+  
+  build-deploy:
+    runs-on: ubuntu-latest
+    needs: [publish-docker]
+    container:
+      image: ghcr.io/pythonhealthdatascience/hdruk_tests:latest
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+      packages: read
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Configure Git safe directory
+        run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+
+      - name: Render and publish to GitHub pages
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
 /.quarto/
 **/*.quarto_ipynb
-_site/
+_site/
+.Rproj.user
+.Renviron
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,6 @@
+Title: hdruk_tests
+Imports:
+    knitr
+    reticulate
+    rmarkdown
+    testthat
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,81 @@
+FROM ubuntu:24.04
+
+# Non-interactive and locale
+ENV DEBIAN_FRONTEND=noninteractive
+
+# System dependencies (R 4.4+ from CRAN, wget, etc.)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        wget \
+        ca-certificates \
+        gnupg \
+        software-properties-common \
+        dirmngr \
+        locales \
+        git && \
+    locale-gen en_GB.UTF-8 && \
+    rm -rf /var/lib/apt/lists/*
+
+ENV LANG=en_GB.UTF-8
+ENV LC_ALL=en_GB.UTF-8
+
+# Add CRAN repo for R >= 4.4 on Ubuntu 24.04 (noble)
+RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | \
+        gpg --dearmor -o /usr/share/keyrings/r-project.gpg && \
+    echo "deb [signed-by=/usr/share/keyrings/r-project.gpg] https://cloud.r-project.org/bin/linux/ubuntu noble-cran40/" \
+        > /etc/apt/sources.list.d/r-project.list && \
+    apt-get update && \
+    apt-get install -y --no-install-recommends \
+        r-base \
+        r-base-dev && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Quarto CLI
+RUN wget -qO /tmp/quarto.deb https://quarto.org/download/latest/quarto-linux-amd64.deb && \
+    apt-get update && \
+    apt-get install -y /tmp/quarto.deb && \
+    rm /tmp/quarto.deb && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install Miniconda
+ENV CONDA_DIR=/opt/conda
+RUN wget -qO /tmp/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash /tmp/miniconda.sh -b -p "$CONDA_DIR" && \
+    rm /tmp/miniconda.sh
+ENV PATH="$CONDA_DIR/bin:${PATH}"
+
+# Configure conda for non-interactive use and faster solving
+RUN conda config --system --set always_yes yes && \
+    conda config --system --set changeps1 no
+
+# Accept Anaconda ToS for required channels in non-interactive builds
+RUN conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main && \
+    conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
+
+# Copy project
+WORKDIR /workspace
+COPY . /workspace
+
+# Remove .Renviron if it was copied (to avoid hardcoded host paths)
+RUN rm -f /workspace/.Renviron
+
+# Create the conda environment
+RUN conda env create -f environment.yaml
+
+# Make the environment active by default
+ENV CONDA_DEFAULT_ENV=hdruk_tests
+ENV PATH="/opt/conda/envs/hdruk_tests/bin:${PATH}"
+RUN echo "conda activate hdruk_tests" >> /root/.bashrc
+
+# R: set renv path and restore packages
+ENV RENV_PATHS_LIBRARY=/workspace/renv/library
+
+# Install renv and restore R packages
+RUN Rscript -e "install.packages('renv', repos = 'https://cloud.r-project.org')" && \
+    Rscript -e "renv::restore()"
+
+# Set conda environment as default for reticulate
+ENV RETICULATE_PYTHON=/opt/conda/envs/hdruk_tests/bin/python
+
+# Default command
+CMD ["/bin/bash"]
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
-# HDR UK Futures RSE Testing Course Materials
+# HDR UK Futures RSE: Testing in Research Workflows
 
-This repository contains code behind our website with materials for the 'Testing' module on HDR UK's RSE001 <a href='https://hdruklearn.org/courses/course-v1:HDRUK+RSE001+2024' target ='_blank'>Research Software Engineering training course</a>. It was developed as part of the <a href='https://pythonhealthdatascience.github.io/stars/' target='_blank'>STARS project</a>."
+This repository contains code behind our website with materials for the 'Testing in Research Workflows' module on HDR UK's RSE001 <a href='https://hdruklearn.org/courses/course-v1:HDRUK+RSE001+2024' target ='_blank'>Research Software Engineering training course</a>. It was developed as part of the <a href='https://pythonhealthdatascience.github.io/stars/' target='_blank'>STARS project</a>.
     
 You can view the website here: <https://pythonhealthdatascience.github.io/hdruk_tests/>
 
diff --git a/_quarto.yml b/_quarto.yml
@@ -2,7 +2,7 @@ project:
   type: website
 
 website:
-  title: "Testing Course Materials"
+  title: "Testing in Research Workflows"
   favicon: images/futures.png
   page-navigation: true
   navbar:
@@ -11,7 +11,7 @@ website:
   announcement:
     dismissable: false
     icon: info-circle
-    content: "This site contains materials for the 'Testing' module on HDR UK's RSE001 <a href='https://hdruklearn.org/courses/course-v1:HDRUK+RSE001+2024' target ='_blank'>Research Software Engineering training course</a>. It was developed as part of the <a href='https://pythonhealthdatascience.github.io/stars/' target='_blank'>STARS project</a>."
+    content: "This site contains materials for the testing module on HDR UK's RSE001 <a href='https://hdruklearn.org/courses/course-v1:HDRUK+RSE001+2024' target ='_blank'>Research Software Engineering training course</a>. It was developed as part of the <a href='https://pythonhealthdatascience.github.io/stars/' target='_blank'>STARS project</a>."
     position: below-navbar
   sidebar:
     contents:
diff --git a/environment.yaml b/environment.yaml
@@ -0,0 +1,6 @@
+name: hdruk_tests
+channels:
+  - conda-forge
+dependencies:
+  - pytest=9.0.2
+  - python=3.14
diff --git a/hdruk_tests.Rproj b/hdruk_tests.Rproj
@@ -0,0 +1,14 @@
+Version: 1.0
+ProjectId: 3b6708d0-59ad-4b5f-a7b1-9f9769eaa5b0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
diff --git a/images/website_screenshot.png b/images/website_screenshot.png
diff --git a/pages/write_basic_test.qmd b/pages/write_basic_test.qmd
@@ -2,4 +2,56 @@
 title: "How to write a basic test"
 ---
 
-<!-- How to write a basic test (showing a simple code example on screen, in Python pytest and R testthat - with all continuing examples shown in both languages too). -->
+```{r}
+#| include: false
+library(reticulate)
+use_condaenv("hdruk_tests", required = TRUE)
+```
+
+<br>
+
+Automated tests check that code behaves as expected by running small, focused checks called tests. Each test sets up some values, runs code, and then uses an assertion or expectation to confirm the result.
+
+## Python
+
+A popular framework for testing in python is **pytest**.
+
+In pytest, each test is a function containing an `assert` statement to check a condition. If an assertion fails, pytest will return an error message explaining what went wrong.
+
+Test are typically stored in a `tests/` folder in files whose names start with `test_`. These are automatically discovered and run by pytest.
+
+Here's an example of a simple test:
+
+```{python}
+import pytest
+
+
+def test_positive():
+    """
+    Confirm that the number is positive.
+    """
+    number = 5
+    assert number > 0, "The number should be positive"
+```
+
+## R
+
+A popular framework for testing in R is **testthat**.
+
+Tests are created with `test_that()` and built around expectations like `expect_true()`, `expect_false()`, `expect_equal()`, `expect_error()`, and others (see [package index](https://testthat.r-lib.org/reference/index.html) for more).
+
+Tests are stored in `tests/testthat/` in files starting with `test_`. These are automatically discovered and run by testthat.
+
+Here's an example of a simple test:
+
+```{r}
+#| output: false
+library(testthat)
+```
+
+```{r}
+test_that("Confirm that the number is positive", {
+  number <- 5L
+  expect_gt(number, 0L)
+})
+```
diff --git a/renv.lock b/renv.lock
diff --git a/renv/.gitignore b/renv/.gitignore
diff --git a/renv/activate.R b/renv/activate.R
diff --git a/renv/settings.json b/renv/settings.json
