From fd05001edf1435eae03f0e95e57a72d2b286328d Mon Sep 17 00:00:00 2001
From: Magnus Wahlberg <endast@gmail.com>
Date: Tue, 14 Nov 2023 13:40:03 +0100
Subject: [PATCH] add cli tests

---
 assets/images/coverage.svg         |   6 +-
 fake_vcf/__main__.py               |   2 +-
 tests/test_example/test_vcf_cli.py | 108 +++++++++++++++++++++++++++++
 3 files changed, 112 insertions(+), 4 deletions(-)
 create mode 100644 tests/test_example/test_vcf_cli.py

diff --git a/assets/images/coverage.svg b/assets/images/coverage.svg
index 6d68f47..e5db27c 100644
--- a/assets/images/coverage.svg
+++ b/assets/images/coverage.svg
@@ -9,13 +9,13 @@
     </mask>
     <g mask="url(#a)">
         <path fill="#555" d="M0 0h63v20H0z"/>
-        <path fill="#dfb317" d="M63 0h36v20H63z"/>
+        <path fill="#4c1" d="M63 0h36v20H63z"/>
         <path fill="url(#b)" d="M0 0h99v20H0z"/>
     </g>
     <g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,Verdana,Geneva,sans-serif" font-size="11">
         <text x="31.5" y="15" fill="#010101" fill-opacity=".3">coverage</text>
         <text x="31.5" y="14">coverage</text>
-        <text x="80" y="15" fill="#010101" fill-opacity=".3">64%</text>
-        <text x="80" y="14">64%</text>
+        <text x="80" y="15" fill="#010101" fill-opacity=".3">100%</text>
+        <text x="80" y="14">100%</text>
     </g>
 </svg>
diff --git a/fake_vcf/__main__.py b/fake_vcf/__main__.py
index 90a3b0f..938c002 100644
--- a/fake_vcf/__main__.py
+++ b/fake_vcf/__main__.py
@@ -69,4 +69,4 @@ def main(
 
 
 if __name__ == "__main__":
-    app()
+    app()  # pragma: no cover
diff --git a/tests/test_example/test_vcf_cli.py b/tests/test_example/test_vcf_cli.py
new file mode 100644
index 0000000..0c9318f
--- /dev/null
+++ b/tests/test_example/test_vcf_cli.py
@@ -0,0 +1,108 @@
+import pytest
+from typer.testing import CliRunner
+
+from fake_vcf import version
+from fake_vcf.__main__ import app
+from tests.test_example.test_vcf_fake import NR_NON_SAMPLE_COL
+
+runner = CliRunner()
+
+
+def test_app_no_input():
+    result = runner.invoke(app, [])
+    assert result.exit_code == 0
+    assert "source=VCFake" in result.stdout
+
+
+def test_app_no_compression_output(tmp_path):
+    output_file = tmp_path / "example.vcf"
+    result = runner.invoke(app, ["-o", output_file])
+    assert result.exit_code == 0
+    assert output_file.exists()
+    assert "No compression" in result.stdout
+
+
+def test_app_compression(tmp_path):
+    output_file = tmp_path / "example.vcf.gz"
+    result = runner.invoke(app, ["-o", output_file])
+    assert result.exit_code == 0
+    assert output_file.exists()
+    assert "Using compression" in result.stdout
+
+
+def test_app_seed_same(tmp_path):
+    result_1 = runner.invoke(app, ["--seed", "42"])
+    result_2 = runner.invoke(app, ["--seed", "42"])
+    assert result_1.exit_code == 0
+    assert result_2.exit_code == 0
+    assert result_1.stdout == result_2.stdout
+
+
+def test_app_seed_differ(tmp_path):
+    result_1 = runner.invoke(app, ["--seed", "42"])
+    result_2 = runner.invoke(app, ["--seed", "1337"])
+    assert result_1.exit_code == 0
+    assert result_2.exit_code == 0
+    assert result_1.stdout != result_2.stdout
+
+
+def test_app_version(tmp_path):
+    result = runner.invoke(app, ["-v"])
+    assert result.exit_code == 0
+    assert version in result.stdout
+
+
+@pytest.mark.parametrize(
+    ("chr",),
+    [
+        *[(f"chr{c}",) for c in range(1, 22)],
+    ],
+)
+def test_app_chr_flag(chr):
+    result = runner.invoke(app, ["-c", chr])
+    assert result.exit_code == 0
+    assert chr in result.stdout
+
+
+@pytest.mark.parametrize(
+    ("prefix",),
+    [
+        ("BAM",),
+        ("SAM",),
+        ("MAM",),
+        ("wham",),
+        ("tapir",),
+    ],
+)
+def test_app_sample_prefix_flag(prefix):
+    result = runner.invoke(app, ["-p", prefix])
+    assert result.exit_code == 0
+    assert f"{prefix}0000" in result.stdout
+
+
+@pytest.mark.parametrize(
+    ("expected_rows",),
+    [
+        *[(r,) for r in range(1, 100, 10)],
+    ],
+)
+def test_app_nr_rows(expected_rows):
+    result = runner.invoke(app, ["-r", f"{expected_rows}"])
+    row_count = len([r for r in result.stdout.split("\n") if r.startswith("chr1")])
+    assert result.exit_code == 0
+    assert row_count == expected_rows
+
+
+@pytest.mark.parametrize(
+    ("expected_sample_count",),
+    [
+        *[(r,) for r in range(1, 100, 10)],
+    ],
+)
+def test_app_nr_samples(expected_sample_count):
+    result = runner.invoke(app, ["-s", f"{expected_sample_count}"])
+    sample_count = len(
+        [r for r in result.stdout.split("\n") if r.startswith("chr1")][0].split("\t")
+    )
+    assert result.exit_code == 0
+    assert sample_count == expected_sample_count + NR_NON_SAMPLE_COL