Updating for workflows

.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

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