From b8e8a345379a075789c758c0d54103b89c795df1 Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Mon, 29 Apr 2024 17:09:53 +0100
Subject: [PATCH] update testing

---
 .github/workflows/docs.yml    | 54 -----------------------------------
 .github/workflows/testing.yml | 42 +++++++++++++++++++++++++++
 tests/run_test.py             |  3 +-
 3 files changed, 44 insertions(+), 55 deletions(-)
 delete mode 100644 .github/workflows/docs.yml
 create mode 100644 .github/workflows/testing.yml

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
deleted file mode 100644
index 4b8f1f6..0000000
--- a/.github/workflows/docs.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-# Simple workflow for deploying static content to GitHub Pages
-name: Deploy static content to Pages
-
-on:
-  # Runs on pushes targeting the default branch
-  push:
-    branches: ["docs"]
-
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-# Allow one concurrent deployment
-concurrency:
-  group: "pages"
-  cancel-in-progress: true
-
-jobs:
-  # Single deploy job since we're just deploying
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Setup Pages
-        uses: actions/configure-pages@v3
-      - name: build docs
-        uses: actions/setup-python@v4
-        with: 
-          python-version: 3.x
-      - uses: actions/cache@v2
-        with:
-          key: ${{ github.ref }}
-          path: .cache
-      - run: pip install mkdocs-material
-      - run: mkdir docs/build
-      - run: mkdocs build -f docs/config/en/mkdocs.yml
-      - run: mkdocs build -f docs/config/pt/mkdocs.yml
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
-        with:
-          # Upload entire repository
-          path: 'docs/build'
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v1
diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
new file mode 100644
index 0000000..3f301e2
--- /dev/null
+++ b/.github/workflows/testing.yml
@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    defaults:
+      run: 
+        shell: bash -el {0}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+          python-version: 3.8
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: true
+
+    - name: install dependancies
+      run: |
+        mamba create -n test tb-profiler -y
+        
+    - name: Install dependencies
+      run: |
+        conda activate test
+        pip install --force-reinstall .
+    - name: Run tests
+      run: |
+        cd tests
+        mamba install pytest -y
+        pytest -x .
+    
diff --git a/tests/run_test.py b/tests/run_test.py
index 67bccf7..4c341a3 100644
--- a/tests/run_test.py
+++ b/tests/run_test.py
@@ -31,9 +31,10 @@
 ]
 
 db = 'testdb'
+branch = 'who'
 
 def test_db():
-    run_cmd(f"tb-profiler update_tbdb --branch test --prefix {db}")
+    run_cmd(f"tb-profiler update_tbdb --branch {branch} --prefix {db}")
 
 
 def check_assertations(filename):