From 3082802a77743445fd05614159fc46ad92e077c3 Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Thu, 12 Dec 2024 14:04:30 +0800
Subject: [PATCH] refactor example_worklfow test run into separate script to
 preserve alias

---
 .github/workflows/run_test_example.sh | 8 ++++++++
 .github/workflows/test_example.yml    | 6 +-----
 2 files changed, 9 insertions(+), 5 deletions(-)
 create mode 100755 .github/workflows/run_test_example.sh

diff --git a/.github/workflows/run_test_example.sh b/.github/workflows/run_test_example.sh
new file mode 100755
index 0000000..4f5678f
--- /dev/null
+++ b/.github/workflows/run_test_example.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# alias to a call launching the syri entrypoint from python
+# necessary, as the hacky git install does not install the CLI entrypoints
+alias syri='python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")'
+
+# run using source to preserve alias
+source ../../example/example_workflow.sh
diff --git a/.github/workflows/test_example.yml b/.github/workflows/test_example.yml
index 9f02a71..4ab148c 100644
--- a/.github/workflows/test_example.yml
+++ b/.github/workflows/test_example.yml
@@ -25,8 +25,4 @@ jobs:
       run: |
         $CONDA/bin/conda install -c conda-forge -c bioconda "minimap2"
     - name: Test example_run.sh
-      run: |
-        # alias to a call launching the syri entrypoint from python
-        # necessary, as the hacky git install does not install the CLI entrypoints
-        alias syri='python <(echo "import syri.scripts.syri;syri.scripts.syri.main()")'
-        ./example/example_workflow.sh
+      run: ./.github/workflows/run_test_example.sh