From 75de514799802d708b6fe88bef0a63db6a0fbbd4 Mon Sep 17 00:00:00 2001
From: Ronak Shah <shahr2@mskcc.org>
Date: Fri, 6 Sep 2024 11:01:24 -0400
Subject: [PATCH] Updating for workflows

---
 .github/workflows/test_bam_collapsing.yaml |  3 +++
 tox.ini                                    | 16 ++++++++--------
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test_bam_collapsing.yaml b/.github/workflows/test_bam_collapsing.yaml
index 113540d..9efc11b 100644
--- a/.github/workflows/test_bam_collapsing.yaml
+++ b/.github/workflows/test_bam_collapsing.yaml
@@ -38,6 +38,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install tox tox-gh-actions
+      - name: Install Test data 
+        run: |
+          bash get_test_data.sh
       - name: Test with tox
         id: run-tox
         run: tox -vv
diff --git a/tox.ini b/tox.ini
index 3889ce9..c377778 100644
--- a/tox.ini
+++ b/tox.ini
@@ -30,11 +30,11 @@ deps =
 
 passenv = {gh-actions,pytest}
 
-whitelist_externals =
-    wget
-    chmod
-    tar
-    goodls
-commands_pre = ./get_test_data.sh
-commands =
-    py.test --capture=sys --basetemp={envtmpdir} tests
+passenv = {gh-actions,pytest}
+# allowlist_externals= /bin/bash
+# install data 
+# commands_pre = bash install_data.sh
+# install testing framework
+deps = -r ./requirements.txt
+# run the tests
+commands = pytest