✅ add pair type tests

tests/data/workflow/snk.yaml

@@ -9,6 +9,10 @@ cli:
     type: bool
   null_annotation:
     default: null
+  KeyValuePair:
+    default: ["key", "value"]
+    help: A key-value pair
+    type: pair 
   enum:
     choices: [a, b, c]
   test:

tests/test_cli/test_validate.py

@@ -73,6 +73,18 @@
         {"example": {"type": "list[path]"}},
         {"example": [Path("1"), Path("2")]}
     ),
+    # pair type
+    (
+        {"example": ["1", "2"]},
+        {"example": {"type": "pair[int, int]"}},
+        {"example": [1, 2]}   
+    ),
+    # choices
+    (
+        {"example": "a"},
+        {"example": {"type": "str", "choices": ["a", "b"]}},
+        {"example": "a"}
+    ),
     # nested dictionary
     (
         {"example": {"nested": "1"}},

tests/test_types.py

@@ -0,0 +1,142 @@
+# integration tests for the annotation types from the snk config, snakemake config, and the command line interface
+
+import pytest
+from .utils import dynamic_runner
+from snk_cli.config import SnkConfig
+
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # str
+    (
+        {"example": "1"},
+        {"example": {"type": "str"}},
+        ["--example", "1"],
+        "{'example': '1'}"
+    )])
+def test_str(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # int
+    (
+        {"example": "1"},
+        {"example": {"type": "int"}},
+        ["--example", "1"],
+        "{'example': 1}"
+    )])
+def test_int(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # float
+    (
+        {"example": "1"},
+        {"example": {"type": "float"}},
+        ["--example", "1"],
+        "{'example': 1.0}"
+    )])
+def test_float(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # bool
+    (
+        {"example": "1"},
+        {"example": {"type": "bool"}},
+        ["--example"],
+        "{'example': True}"
+    )])
+def test_bool(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # path
+    (
+        {"example": "file"},
+        {"example": {"type": "path"}},
+        ["--example", "file"],
+        "{'example': 'file'}"
+    )])
+def test_path(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # list
+    (
+        {"example": [1,2,3]},
+        {"example": {"type": "list"}},
+        ["--example", "1", "--example", "2", "--example", "3"],
+        "{'example': ['1', '2', '3']}"
+    )])
+def test_list(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr
+
+@pytest.mark.parametrize("snakemake_config,annotations,cli_args,expected", [
+    # pair
+    (
+        {"example": [1, 2]},
+        {"example": {"type": "pair"}},
+        ["--example", "1", "2"],
+        "{'example': ['1', '2']}"
+    ),
+    (
+        {"example": [1, 2]},
+        {"example": {"type": "pair[int, int]"}},
+        ["--example", "1", "2"],
+        "{'example': [1, 2]}"
+    ),
+    (
+        {"example": ["1", "2"]},
+        {"example": {"type": "pair[float, float]"}},
+        ["--example", "1", "2"],
+        "{'example': [1.0, 2.0]}"
+    ),
+    (
+        {"example": ["1", "2"]},
+        {"example": {"type": "pair[str, str]"}},
+        ["--example", "1", "2"],
+        "{'example': ['1', '2']}"
+    ),
+    (
+        {"example": ["1", "2"]},
+        {"example": {"type": "pair[str, int]"}},
+        ["--example", "1", "2"],
+        "{'example': ['1', 2]}"
+    ),
+    (
+        {"example": ["1", "2"]},
+        {"example": {"type": "pair[int, str]"}},
+        ["--example", "1", "2"],
+        "{'example': [1, '2']}"
+    )
+])
+def test_pair(snakemake_config, annotations, cli_args, expected):
+    snk_config = SnkConfig(cli=annotations)
+    runner = dynamic_runner(snakemake_config, snk_config)
+    res = runner.invoke(["run"] + cli_args)
+    assert res.exit_code == 0, res.stderr
+    assert expected in res.stdout, res.stderr