From cab0ddccd51518a719137e8d13586ae293af7cf0 Mon Sep 17 00:00:00 2001
From: Brad Macdonald <bwm03570@gmail.com>
Date: Mon, 8 Jan 2024 10:17:49 -0700
Subject: [PATCH] updates CI to test

---
 .github/workflows/ci.yml | 23 ++++++++++-------------
 tox.ini                  | 20 ++++++++++----------
 2 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6a0de0f..108675d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -80,26 +80,23 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
-      # - uses: actions/download-artifact@v3
-      #   with: {name: python-distribution-files, path: dist/}
-      # - name: Install tox-gh plugin
-      #   run: python -m pip install tox-gh>=1.2
-      # - name: Setup test suite
-      #   run: tox -vv --notest
-      - name: Install pipenv
-        run: python -m pip install pipenv
+      - uses: actions/download-artifact@v3
+        with: {name: python-distribution-files, path: dist/}
+      - name: Install tox-gh plugin
+        run: python -m pip install tox-gh>=1.2
+      - name: Setup test suite
+        run: tox -vv --notest
       - name: Install dependencies
-        run: pipenv install -d
+        run: ./dev_setup.sh {{{ matrix.python }}}
       - name: Run tests
         env:
           # New variables should match a `passenv` pattern under `[testenv]` in tox.ini
           SEVENBRIDGES_CONNECTION_URI: ${{ secrets.SEVENBRIDGES_CONNECTION_URI }}
           NEXTFLOWTOWER_CONNECTION_URI: ${{ secrets.NEXTFLOWTOWER_CONNECTION_URI }}
           SYNAPSE_CONNECTION_URI: ${{ secrets.SYNAPSE_CONNECTION_URI }}
-        run: pipenv run pytest -vvv
-          # >-
-          #   tox --installpkg '${{ needs.prepare.outputs.wheel-path }}'
-          #   -- -rFEx --durations 10 --color yes
+        run: >-
+            tox --installpkg '${{ needs.prepare.outputs.wheel-path }}'
+            -- -rFEx --durations 10 --color yes
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
diff --git a/tox.ini b/tox.ini
index 8a4d7c2..d775021 100644
--- a/tox.ini
+++ b/tox.ini
@@ -94,13 +94,13 @@ commands =
     python -m twine upload {posargs:--repository {env:TWINE_REPOSITORY:testpypi}} dist/*
 
 
-[testenv:pipenv]
-description =
-    Refresh the Pipfile.lock file based on the latest dependencies in setup.cfg
-skip_install = True
-changedir = {toxinidir}
-setenv =
-    PIPENV_IGNORE_VIRTUALENVS = 1
-deps = pipenv
-commands =
-    pipenv install --dev --ignore-pipfile
+; [testenv:pipenv]
+; description =
+;     Set up the python virtual environment and install dependencies using pip
+; skip_install = True
+; changedir = {toxinidir}
+; setenv =
+;     PIPENV_IGNORE_VIRTUALENVS = 1
+; deps = pip
+; commands =
+;     ./dev_setup.sh