From fdaf1c8879c8088dd9025788c336197b7bd152e5 Mon Sep 17 00:00:00 2001
From: finlayclark <s1629668@ed.ac.uk>
Date: Thu, 6 Jun 2024 11:33:43 +0100
Subject: [PATCH] Add makefile and CI to check analysis notebooks work

---
 .github/workflows/ci.yaml | 27 +++++++++++++++++++++++++++
 Makefile                  | 14 ++++++++++++++
 analysis/print.ipynb      | 20 ++++++++++++++++++++
 devtools/envs/base.yaml   | 21 +++++++++++++++++++++
 4 files changed, 82 insertions(+)
 create mode 100644 .github/workflows/ci.yaml
 create mode 100644 Makefile
 create mode 100644 analysis/print.ipynb
 create mode 100644 devtools/envs/base.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..0a8ca2b
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,27 @@
+name: CI
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push: { branches: [ "main" ] }
+  pull_request: { branches: [ "main" ] }
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    container: condaforge/mambaforge:latest
+
+    steps:
+    - uses: actions/checkout@v3.3.0
+
+    - name: Setup Conda Environment
+      run: |
+        apt update && apt install -y git make
+        make env
+
+    - name: Test Analysis
+      run: |
+        make test-analysis
\ No newline at end of file
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..39d5e1b
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,14 @@
+PACKAGE_NAME  := a3fe_reproduce
+CONDA_ENV_RUN := conda run --no-capture-output --name $(PACKAGE_NAME)
+
+ANALYSIS_NBS := $(wildcard analysis/*.ipynb)
+
+.PHONY: env test-analysis
+
+env:
+	mamba create     --name $(PACKAGE_NAME)
+	mamba env update --name $(PACKAGE_NAME) --file devtools/envs/base.yaml
+	$(CONDA_ENV_RUN) pip install --no-build-isolation --no-deps git+https://github.com/michellab/a3fe.git
+
+test-analysis:
+	$(CONDA_ENV_RUN) jupyter nbconvert --to notebook --execute $(ANALYSIS_NBS)
diff --git a/analysis/print.ipynb b/analysis/print.ipynb
new file mode 100644
index 0000000..7543806
--- /dev/null
+++ b/analysis/print.ipynb
@@ -0,0 +1,20 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!echo \"Hello make world!\""
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml
new file mode 100644
index 0000000..691279f
--- /dev/null
+++ b/devtools/envs/base.yaml
@@ -0,0 +1,21 @@
+name: a3fe_reproduce
+
+channels:
+  - conda-forge
+  - "openbiosim/label/dev"
+
+dependencies:
+    # Base depends
+  - arviz
+  - pandas
+  - python
+  - pip
+  - numpy
+  - matplotlib
+  - scipy
+  - ipython
+  - pymbar<4
+  - ambertools
+  - biosimspace>2023.4
+  - numpydoc
+  - pydantic
\ No newline at end of file