comprehensive configure integration test, shared file io commands\

casanovo/casanovo.py

@@ -51,21 +51,13 @@
 click.rich_click.SHOW_ARGUMENTS = True
 
 
-class _SharedParams(click.RichCommand):
-    """Options shared between most Casanovo commands"""
+class _SharedFileIOParams(click.RichCommand):
+    """File IO options shared between most Casanovo commands"""
 
     def __init__(self, *args, **kwargs) -> None:
         """Define shared options."""
         super().__init__(*args, **kwargs)
         self.params += [
-            click.Option(
-                ("-m", "--model"),
-                help="""
-                Either the model weights (.ckpt file) or a URL pointing to the 
-                model weights file. If not provided, Casanovo will try to 
-                download the latest release automatically.
-                """,
-            ),
             click.Option(
                 ("-d", "--output_dir"),
                 help="The destination directory for output files.",
@@ -77,30 +69,44 @@ def __init__(self, *args, **kwargs) -> None:
                 type=click.Path(dir_okay=False),
             ),
             click.Option(
-                ("-c", "--config"),
-                help="""
-                The YAML configuration file overriding the default options.
-                """,
-                type=click.Path(exists=True, dir_okay=False),
+                ("-f", "--force_overwrite"),
+                help="Whether to overwrite output files.",
+                is_flag=True,
+                show_default=True,
+                default=False,
             ),
             click.Option(
                 ("-v", "--verbosity"),
-                help="""
-                Set the verbosity of console logging messages. Log files are
-                always set to 'debug'.
-                """,
+                help=(
+                    "Set the verbosity of console logging messages."
+                    " Log files are always set to 'debug'."
+                ),
                 type=click.Choice(
                     ["debug", "info", "warning", "error"],
                     case_sensitive=False,
                 ),
                 default="info",
             ),
+        ]
+
+
+class _SharedParams(_SharedFileIOParams):
+    """Options shared between main Casanovo commands"""
+
+    def __init__(self, *args, **kwargs) -> None:
+        """Define shared options."""
+        super().__init__(*args, **kwargs)
+        self.params += [
             click.Option(
-                ("-f", "--force_overwrite"),
-                help="Whether to overwrite output files.",
-                is_flag=True,
-                show_default=True,
-                default=False,
+                ("-m", "--model"),
+                help="""Either the model weights (.ckpt file) or a URL pointing to 
+                the model weights file. If not provided, Casanovo will try to 
+                download the latest release automatically.""",
+            ),
+            click.Option(
+                ("-c", "--config"),
+                help="The YAML configuration file overriding the default options.",
+                type=click.Path(exists=True, dir_okay=False),
             ),
         ]
 
@@ -335,38 +341,16 @@ def version() -> None:
     sys.stdout.write("\n".join(versions) + "\n")
 
 
-@main.command()
-@click.option(
-    "-d",
-    "--output_dir",
-    help="The destination directory for log and config file.",
-    type=click.Path(dir_okay=True),
-    required=False,
-)
-@click.option(
-    "-o",
-    "--output_root",
-    help="The root name for log and config file.",
-    type=click.Path(dir_okay=False),
-    required=False,
-)
-@click.option(
-    "-f",
-    "--force_overwrite",
-    help="Whether to overwrite output files.",
-    is_flag=True,
-    show_default=True,
-    default=False,
-)
+@main.command(cls=_SharedFileIOParams)
 def configure(
-    output_dir: str, output_root: str, force_overwrite: bool
+    output_dir: str, output_root: str, verbosity: str, force_overwrite: bool
 ) -> None:
     """Generate a Casanovo configuration file to customize.
 
     The casanovo configuration file is in the YAML format.
     """
     output_path, _ = _setup_output(
-        output_dir, output_root, force_overwrite, "info"
+        output_dir, output_root, force_overwrite, verbosity
     )
     config_fname = output_root if output_root is not None else "casanovo"
     config_fname = Path(config_fname).with_suffix(".yaml")
@@ -375,7 +359,7 @@ def configure(
 
     config_path = str(output_path / config_fname)
     Config.copy_default(config_path)
-    logger.info(f"Wrote {config_path}\n")
+    logger.info(f"Wrote {config_path}")
 
 
 def setup_logging(

tests/test_integration.py

@@ -1,5 +1,6 @@
 import functools
 import subprocess
+import yaml
 from pathlib import Path
 
 import pyteomics.mztab
@@ -215,7 +216,7 @@ def test_train_and_run(
     assert output_filename.is_file()
 
 
-def test_auxilliary_cli(tmp_path, monkeypatch):
+def test_auxilliary_cli(tmp_path, mgf_small, monkeypatch):
     """Test the secondary CLI commands"""
     run = functools.partial(
         CliRunner().invoke, casanovo.main, catch_exceptions=False
@@ -231,5 +232,30 @@ def test_auxilliary_cli(tmp_path, monkeypatch):
     with pytest.raises(FileExistsError):
         run(["configure", "-o", "test.yaml"])
 
+    with open("casanovo.yaml") as f_in:
+        config = yaml.safe_load(f_in)
+
+    config["max_epochs"] = 1
+    config["n_layers"] = 1
+
+    with open("small.yaml", "w") as f_out:
+        yaml.dump(config, f_out)
+
+    train_args = [
+        "train",
+        "--validation_peak_path",
+        str(mgf_small),
+        "--config",
+        "small.yaml",
+        "--output_dir",
+        str(tmp_path),
+        "--output_root",
+        "train",
+        str(mgf_small),
+    ]
+
+    result = run(train_args)
+    assert result.exit_code == 0
+
     res = run("version")
     assert res.output

tests/unit_tests/test_unit.py

@@ -573,7 +573,6 @@ def test_calc_match_score():
 
 
 def test_digest_fasta_cleave(tiny_fasta_file, residues_dict):
-
     # No missed cleavages
     expected_normal = [
         "ATSIPAR",
@@ -1092,7 +1091,6 @@ def test_get_candidates(tiny_fasta_file, residues_dict):
 
 
 def test_get_candidates_isotope_error(tiny_fasta_file, residues_dict):
-
     # Tide isotope error windows for 496.2, 2+:
     # 0: [980.481617, 1000.289326]
     # 1: [979.491114, 999.278813]