From b95b3d5958bff55a07a2dd47fd5e5597f1fa3fec Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Mon, 15 Jan 2024 02:56:53 +0100
Subject: [PATCH] wip

---
 .github/workflows/ci.yml | 31 +++++++++++++++----------------
 tests/test_apps.py       |  2 +-
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 07186fa..bfbcfc1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,32 +16,31 @@ jobs:
           - '3.12'
 
     steps:
-      - name: Install Python via conda.
-        uses: s-weigand/setup-conda@v1
+      - name: Install Python
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
+          python-version: "${{ matrix.python-version }}"
+
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           lfs: true
-      - name: Install mamba.
-        run: conda install -y mamba
+
       - name: Install test dependencies via pip
         run: pip install -r requirements/test_black.txt
+
+      - name: Lint
+        run: make lint
+
       - name: Run tests
-        run: pytest
-      - name: Create text report
-        run: coverage report
-      - name: Create XML report for codacy
-        run: coverage xml
+        run: |
+          make test
+          coverage report
+          coverage xml
+
       - name: Upload Python coverage reports to Codecov
         uses: codecov/codecov-action@v3
         with:
           flags: python
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      - name: Check style with black
-        run: make black-check
-      - name: Check style with flake8
-        run: flake8 .
diff --git a/tests/test_apps.py b/tests/test_apps.py
index 9afc7cc..638a726 100644
--- a/tests/test_apps.py
+++ b/tests/test_apps.py
@@ -7,7 +7,7 @@
 from typer.testing import CliRunner
 
 from altamisa.apps import isatab2dot, isatab2isatab, isatab_validate
-from altamisa.exceptions import IsaException, IsaWarning
+from altamisa.exceptions import IsaWarning
 
 runner = CliRunner()