From 48bb1164e26d88d15b4200c20dc0f89a66d1f00f Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Fri, 13 Sep 2024 17:59:22 -0400
Subject: [PATCH 1/2] Create python-package-conda.yml

---
 .github/workflows/python-package-conda.yml | 42 ++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
new file mode 100644
index 0000000..cc2a322
--- /dev/null
+++ b/.github/workflows/python-package-conda.yml
@@ -0,0 +1,42 @@
+name: Python Package using Conda
+
+on:
+  push:
+    branches:
+    - main
+    - dev
+    - release/*
+  pull_request:
+    branches:
+    - main
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

From b5153103cb15e77785edd7ac94e8198f83cb8d8a Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Fri, 13 Sep 2024 18:03:21 -0400
Subject: [PATCH 2/2] add env

---
 environment.yml | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..4423fce
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,6 @@
+dependencies:
+  - python=3.11
+  - bioconda::pysam
+  - bioconda::pybedtools
+  - conda-forge::pandas
+  - bioconda::biopython
\ No newline at end of file