snk-cli 0.5.1__tar.gz → 0.5.3__tar.gz

{snk_cli-0.5.1 → snk_cli-0.5.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.5.1
+Version: 0.5.3
 Project-URL: Documentation, https://github.com/wytamma/snk-cli#readme
 Project-URL: Issues, https://github.com/wytamma/snk-cli/issues
 Project-URL: Source, https://github.com/wytamma/snk-cli

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.5.1"
+__version__ = "0.5.3"

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/cli.py

@@ -259,5 +259,5 @@ class CLI(DynamicTyper):
         info_dict["conda_prefix_dir"] = str(self.conda_prefix_dir)
         info_dict["singularity_prefix_dir"] = str(self.singularity_prefix_dir)
         info_dict["workflow_dir_path"] = str(self.workflow.path)
-        typer.echo(json.dumps(info_dict, indent=2))
+        self.echo(json.dumps(info_dict, indent=2))
 

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/config/config.py

@@ -205,6 +205,17 @@ class SnkConfig:
           >>> snk_config.to_yaml(Path("snk.yaml"))
         """
         config_dict = {k: v for k, v in vars(self).items() if not k.startswith("_")}
+        def convert_paths(data):
+            if isinstance(data, dict):
+                return {key: convert_paths(value) for key, value in data.items()}
+            elif isinstance(data, list):
+                return [convert_paths(item) for item in data]
+            elif isinstance(data, Path):
+                return str(data)
+            return data
+        
+        config_dict = convert_paths(config_dict)
+
         with open(path, "w") as f:
             yaml.dump(config_dict, f)
 

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/dynamic_typer.py

@@ -152,7 +152,7 @@ class DynamicTyper:
         if option.type is Enum or option.choices:
             if not option.choices:
                 raise ValueError(f"Enum type {option.name} requires choices to be defined.")
-            annotation_type = Enum(f'{option.name}Enum', {e: e for e in option.choices})
+            annotation_type = Enum(f'{option.name}', {str(e): str(e) for e in option.choices})
             if default:
               try:
                 default = annotation_type(default)

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/subcommands/config.py

@@ -66,4 +66,4 @@ class ConfigApp(DynamicTyper):
             console = Console()
             console.print(syntax)
         else:
-            typer.echo(yaml_str)
+            self.echo(yaml_str)

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/subcommands/env.py

@@ -106,7 +106,7 @@ class EnvApp(DynamicTyper):
             console = Console()
             console.print(syntax)
         else:
-            typer.echo(env_file_text)
+            self.echo(env_file_text)
 
     def run(
         self,

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/subcommands/profile.py

@@ -65,7 +65,7 @@ class ProfileApp(DynamicTyper):
             console = Console()
             console.print(syntax)
         else:
-            typer.echo(profile_file_text)
+            self.echo(profile_file_text)
 
     def _open_text_editor(self, file_path):
         """

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/subcommands/run.py

@@ -213,10 +213,9 @@ class RunApp(DynamicTyper):
         # Set up conda frontend
         conda_found = check_command_available("conda")
         if not conda_found and verbose:
-            typer.secho(
+            self.log(
                 "Conda not found! Install conda to use environments.\n",
-                fg=typer.colors.MAGENTA,
-                err=True,
+                color=typer.colors.MAGENTA,
             )
 
         if conda_found and self.snk_config.conda and not no_conda:
@@ -228,10 +227,9 @@ class RunApp(DynamicTyper):
             )
             if not check_command_available("mamba"):
                 if verbose:
-                    typer.secho(
+                    self.log(
                         "Could not find mamba, using conda instead...",
-                        fg=typer.colors.MAGENTA,
-                        err=True,
+                        color=typer.colors.MAGENTA,
                     )
                 args.append("--conda-frontend=conda")
             else:
@@ -260,7 +258,7 @@ class RunApp(DynamicTyper):
         if configs:
             args.extend(["--config", *configs])
         if verbose:
-            typer.secho(f"snakemake {' '.join(args)}\n", fg=typer.colors.MAGENTA, err=True)
+            self.log(f"snakemake {' '.join(args)}\n", color=typer.colors.MAGENTA)
         if not keep_snakemake and Path(".snakemake").exists():
             keep_snakemake = True
         try:
@@ -281,7 +279,7 @@ class RunApp(DynamicTyper):
                 if status:
                     sys.exit(status)
         if not keep_snakemake and Path(".snakemake").exists():
-            typer.secho("Cleaning up '.snakemake' folder... use --keep-snakemake to keep.", fg=typer.colors.YELLOW, err=True)
+            self.log("Cleaning up '.snakemake' folder... use --keep-snakemake to keep.")
             shutil.rmtree(".snakemake")
 
     def _save_dag(self, snakemake_args: List[str], filename: Path):
@@ -320,11 +318,10 @@ class RunApp(DynamicTyper):
             )
             with open(filename, "w") as output_file:
                 if self.verbose:
-                    typer.secho(f"Saving dag to {filename}", fg=typer.colors.MAGENTA, err=True)
+                    self.log(f"Saving dag to {filename}", color=typer.colors.MAGENTA)
                 subprocess.run(["cat"], stdin=dot_process.stdout, stdout=output_file)
         except (subprocess.CalledProcessError, FileNotFoundError):
-            typer.echo("dot command not found!", fg=typer.colors.RED, err=True)
-            raise typer.Exit(1)
+            self.error("Graphviz `dot` command not found! Please install.", exit=True)
 
     @contextmanager
     def _copy_resources(
@@ -355,10 +352,9 @@ class RunApp(DynamicTyper):
 
         def copy_resource(src: Path, dst: Path, symlink: bool = False):
             if self.verbose:
-                typer.secho(
+                self.log(
                     f"  - Copying resource '{src}' to '{dst}'",
-                    fg=typer.colors.MAGENTA,
-                    err=True,
+                    color=typer.colors.MAGENTA,
                 )
             target_is_directory = src.is_dir()
             if symlink:
@@ -380,10 +376,9 @@ class RunApp(DynamicTyper):
         if resources_folder.exists():
             resources.insert(0, Path("resources"))
         if self.verbose and resources:
-            typer.secho(
+            self.log(
                 f"Copying {len(resources)} resources to working directory...",
-                fg=typer.colors.MAGENTA,
-                err=True,
+                color=typer.colors.MAGENTA
             )
         try:
             for resource in resources:
@@ -394,10 +389,9 @@ class RunApp(DynamicTyper):
                     copy_resource(abs_path, destination, symlink=symlink_resources)
                     copied_resources.append(destination)
                 elif self.verbose:
-                    typer.secho(
+                    self.log(
                         f"  - Resource '{resource.name}' already exists! Skipping...",
-                        fg=typer.colors.MAGENTA,
-                        err=True,
+                        color=typer.colors.MAGENTA,
                     )
             yield
         finally:
@@ -406,10 +400,9 @@ class RunApp(DynamicTyper):
             for copied_resource in copied_resources:
                 if copied_resource.exists():
                     if self.verbose:
-                        typer.secho(
+                        self.log(
                             f"Deleting '{copied_resource.name}' resource...",
-                            fg=typer.colors.MAGENTA,
-                            err=True,
+                            color=typer.colors.MAGENTA,
                         )
                     remove_resource(copied_resource)
 

{snk_cli-0.5.1 → snk_cli-0.5.3}/src/snk_cli/subcommands/script.py

@@ -79,7 +79,7 @@ class ScriptApp(DynamicTyper):
             console = Console()
             console.print(code)
         else:
-            typer.echo(code)
+            self.echo(code)
 
     def _get_executor(self, suffix: str) -> str:
         if suffix == "py":

snk_cli-0.5.3/tests/test_SnkConfig.py

@@ -0,0 +1,125 @@
+import pytest
+from snk_cli.config.config import SnkConfig
+
+
+def test_snk_config_creation():
+    snk_config = SnkConfig()
+    assert snk_config.tagline == "A Snakemake workflow CLI generated with Snk"
+    assert snk_config.font == "small"
+    assert snk_config.resources == []
+    assert snk_config.cli == {}
+    assert snk_config.symlink_resources is False
+    assert snk_config.version is None
+    assert snk_config.skip_missing is False
+
+
+def test_validate_resources_with_existing_files(tmp_path):
+    resources = [tmp_path / "file1", tmp_path / "file2"]
+    for resource in resources:
+        resource.touch()
+    snk_config = SnkConfig()
+    # Should not raise an exception
+    snk_config.validate_resources(resources)
+
+
+def test_validate_resources_with_missing_files(tmp_path):
+    resources = [tmp_path / "file1", tmp_path / "missing_file"]
+    resources[0].touch()
+    snk_config = SnkConfig()
+    with pytest.raises(FileNotFoundError):
+        snk_config.validate_resources(resources)
+
+
+def test_add_resources(tmp_path):
+    resources = [tmp_path / "file1", tmp_path / "file2"]
+    for resource in resources:
+        resource.touch()
+    snk_config = SnkConfig()
+    snk_config.add_resources(resources)
+    assert len(snk_config.resources) == 2
+
+
+def test_from_path_with_existing_file(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    config_file.touch()
+    config_file.write_text("logo: test_logo")
+    snk_config = SnkConfig.from_path(config_file)
+    assert snk_config._snk_config_path == config_file
+
+def test_missing_file(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    with pytest.raises(FileNotFoundError):
+        SnkConfig.from_path(config_file)
+
+def test_empty_file(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    config_file.touch()
+    with pytest.raises(ValueError):
+        SnkConfig.from_path(config_file)
+
+def test_invalid_yaml(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    config_file.touch()
+    config_file.write_text("logo: test_logo\ninvalid_yaml")
+    with pytest.raises(Exception):
+        SnkConfig.from_path(config_file)
+
+def test_from_dir_with_existing_file(tmp_path):
+    config_file = tmp_path / ".snk"
+    config_file.touch()
+    config_file.write_text("logo: test_logo")
+    # catch warning 
+    with pytest.warns(DeprecationWarning):
+        snk_config = SnkConfig.from_workflow_dir(tmp_path)
+    assert snk_config._snk_config_path == config_file
+
+
+def test_from_path_with_missing_file(tmp_path):
+    config_file = tmp_path / "missing_file.yaml"
+    # assert it raises FileNotFoundError
+    with pytest.raises(FileNotFoundError):
+        SnkConfig.from_path(config_file)
+
+
+def test_to_yaml(tmp_path):
+    snk_config = SnkConfig(art="test_art", logo="test_logo")
+    yaml_file = tmp_path / "snk.yaml"
+    snk_config.to_yaml(yaml_file)
+    assert yaml_file.exists()
+
+
+def test_save(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    snk_config = SnkConfig(_snk_config_path=config_file)
+    snk_config.art = "new_art"
+    snk_config.save()
+    saved_snk_config = SnkConfig.from_path(config_file)
+    assert saved_snk_config.art == "new_art"
+
+
+def test_version_from_about_file(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    about_file = tmp_path / "__about__.py"
+    about_file.touch()
+    about_file.write_text("__version__ = '0.0.1'")
+    config_file.write_text("version: __about__.py")
+    snk_config = SnkConfig.from_path(config_file)
+    assert snk_config.version == "0.0.1"
+
+def test_version_from_about_file_with_missing_file(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    about_file = tmp_path / "__about__.py"
+    config_file.write_text("version: __about__.py")
+    with pytest.raises(FileNotFoundError):
+        SnkConfig.from_path(config_file)
+
+def test_paths_are_written_as_strings(tmp_path):
+    config_file = tmp_path / "snk.yaml"
+    snk_config = SnkConfig(snakefile=tmp_path / "snakefile", resources=[tmp_path / "file1", tmp_path / "file2"])
+    snk_config.to_yaml(config_file)
+    with open(config_file) as f:
+        config = f.read()
+    print(config)
+    assert f"snakefile: {tmp_path / 'snakefile'}" in config
+    assert f"- {tmp_path / 'file1'}" in config
+    assert f"- {tmp_path / 'file2'}" in config

{snk_cli-0.5.1 → snk_cli-0.5.3}/tests/test_cli/test_validate.py

@@ -24,6 +24,12 @@ import pytest
         {"example": {"type": "bool"}},
         {"example": True}
     ),
+    # timestamp
+    (
+        {"example": "2021-01-01T00:00:00"},
+        {"example": {"type": "str"}},
+        {"example": "2021-01-01T00:00:00"}
+    ),
     # None
     (
         {"example": None},