From 1f5f8bde77a87471ee15431b6f4ae09a2db7e11b Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Wed, 24 Apr 2024 16:54:50 +0200
Subject: [PATCH] added unit tests

---
 .github/workflows/unit-tests.yml | 60 ++++++++++++++++++++++++++++++++
 tests/test_assembly_finder.py    | 55 +++++++++++++++++++++++++++++
 2 files changed, 115 insertions(+)
 create mode 100644 .github/workflows/unit-tests.yml
 create mode 100644 tests/test_assembly_finder.py

diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
new file mode 100644
index 0000000..419a1a0
--- /dev/null
+++ b/.github/workflows/unit-tests.yml
@@ -0,0 +1,60 @@
+name: Tests
+
+on:
+  push:
+    branches: ["main"]
+    paths:
+      - ".github/workflows/unit-tests.yaml"
+      - "tests/**"
+      - "assembly_finder/**"
+      - "setup.py"
+  pull_request:
+    branches: ["main"]
+    paths:
+      - ".github/workflows/unit-tests.yaml"
+      - "tests/**"
+      - "assembly_finder/**"
+      - "setup.py"
+
+permissions:
+  contents: read
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          miniforge-version: "latest"
+          miniforge-variant: Mambaforge
+          use-mamba: true
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+          activate-environment: assembly_finder
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: "Test and generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest coverage
+          python -m pip install .
+          coverage run -m pytest
diff --git a/tests/test_assembly_finder.py b/tests/test_assembly_finder.py
new file mode 100644
index 0000000..2f23cf1
--- /dev/null
+++ b/tests/test_assembly_finder.py
@@ -0,0 +1,55 @@
+import subprocess
+from pathlib import Path
+import pytest
+import shutil
+import os
+
+
+@pytest.fixture(scope="session")
+def tmp_dir(tmpdir_factory):
+    return tmpdir_factory.mktemp("tmp")
+
+
+test_data_path = Path("assembly_finder/test_data")
+outdir = Path("test_out")
+
+
+def remove_directory(dir_path):
+    if os.path.exists(dir_path):
+        shutil.rmtree(dir_path)
+
+
+def exec_command(cmnd, stdout=subprocess.PIPE, stderr=subprocess.PIPE):
+    """executes shell command and returns stdout if completes exit code 0
+    Parameters
+    ----------
+    cmnd : str
+      shell command to be executed
+    stdout, stderr : streams
+      Default value (PIPE) intercepts process output, setting to None
+      blocks this."""
+
+    proc = subprocess.Popen(cmnd, shell=True, stdout=stdout, stderr=stderr)
+    out, err = proc.communicate()
+    if proc.returncode != 0:
+        raise RuntimeError(f"FAILED: {cmnd}\n{err}")
+    return out.decode("utf8") if out is not None else None
+
+
+def test_cli():
+    exec_command("assembly_finder -h")
+    exec_command("assembly_finder -v")
+
+
+def test_taxons():
+    """download genomes from taxons"""
+    exec_command(f"assembly_finder -i {test_data_path}/taxons.tsv --output {outdir}")
+    remove_directory(outdir)
+
+
+def test_accessions():
+    """download genomes from accessions"""
+    exec_command(
+        f"assembly_finder -i {test_data_path}/accessions.txt --accession --output {outdir}"
+    )
+    remove_directory(outdir)