Initial commit

Daniel-Mietchen · Nov 19, 2019 · 37c291df373a98f7a0d53cb1a251d7e39c99f43a · 37c291d
commit 37c291df373a98f7a0d53cb1a251d7e39c99f43a
Unified Split

Showing with 471 additions and 0 deletions.

+19 −0 .github/workflows/validate.yml

+433 −0 Alignment viewing and filtering.ipynb

+18 −0 README.md

+1 −0 requirements.txt
diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml
@@ -0,0 +1,19 @@
+name: Validation
+on: push
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1
+      - uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install dependencies
+        run: |
+          python -m pip install -q --upgrade pip
+          python -m pip install -q numpy
+          python -m pip install -q -r requirements.txt
+          python -m pip install -q jupyter
+      - name: Validate
+        run: |
+          jupyter nbconvert --execute *.ipynb
diff --git a/Alignment viewing and filtering.ipynb b/Alignment viewing and filtering.ipynb
diff --git a/README.md b/README.md
@@ -0,0 +1,18 @@
+# Jupyter CI
+
+This repository demonstrates automated verification of a [Jupyter](http://jupyter.org/) notebook. Whenever the `.ipynb` file is updated it is executed by [GitLab Actions](https://github.com/features/actions). Any errors are automatically emailed to the author and clearly indicated by the following badge: ![build status](https://github.com/mwoodbri/jupyter-ci/workflows/Validation/badge.svg)
+
+The provided example is a lightly modified version of the "Alignment viewing and filtering" recipe from [The scikit-bio cookbook](http://nbviewer.jupyter.org/github/biocore/scikit-bio-cookbook/blob/master/Index.ipynb).
+
+To use your own notebook:
+
+1. Clone this repository
+2. Replace the notebook
+3. Add any additional dependencies to `requirements.txt`
+4. Check in your changes and push to GitLab
+
+You'll then receive an email indicating whether the notebook could be executed and the badge will update accordingly.
+
+This approach was inspired by an [investigation of data science reproducibility](https://markwoodbridge.com/2017/03/05/jupyter-reproducible-science.html) for Open Data Day 2017.
+
+This repository is a port of [jupyter-ci](https://gitlab.com/mwoodbri/jupyter-ci/) from GitLab CI to GitHub Actions.
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1 @@
+scikit-bio==0.5.1