From 0ba2842225ba7dc1ffe85c124323046d2aca5793 Mon Sep 17 00:00:00 2001
From: Oliver Schwengers <oliver.schwengers@computational.bio.uni-giessen.de>
Date: Tue, 18 Jan 2022 17:34:09 +0100
Subject: [PATCH] Create ci.yaml

---
 .github/workflows/ci.yaml | 45 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 .github/workflows/ci.yaml

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..0528c76
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,45 @@
+name: CI (Conda/PyTest)
+on:
+  push:
+    paths-ignore:
+      - 'README.md'
+  pull_request:
+    types:
+      - opened
+    paths-ignore:
+      - 'README.md'
+jobs:
+  build:
+    name: test (${{ matrix.os }}, ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.8]
+    steps:
+    - uses: actions/checkout@v2
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-update-conda: false
+        python-version: ${{ matrix.python-version }}
+        miniconda-version: "latest"
+        mamba-version: "*"
+        channels: conda-forge,bioconda
+        channel-priority: true
+        auto-activate-base: false
+        environment-file: environment.yml
+        activate-environment: deepsig
+    - name: Conda info
+      run: |
+        conda info
+        conda list
+        conda config --show
+        printenv | sort
+    - name: Install DeepSig
+      run: python -m pip install --no-deps .
+    - name: Run Test
+      run: deepsig -f testdata/test-prok.faa --organism gramn --outf test --outfmt gff3 --threads 1