Add makefile and CI to check analysis notebooks work

.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/[email protected]
+
+    - name: Setup Conda Environment
+      run: |
+        apt update && apt install -y git make
+        make env
+
+    - name: Test Analysis
+      run: |
+        make test-analysis

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)

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
+}

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