snk-cli 0.3.4__tar.gz → 0.5.0__tar.gz

{snk_cli-0.3.4 → snk_cli-0.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.3.4
+Version: 0.5.0
 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
@@ -19,11 +19,12 @@ Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Python: >=3.8
 Requires-Dist: art~=5.9
 Requires-Dist: datrie>=0.8.2
-Requires-Dist: gitpython~=3.1
 Requires-Dist: makefun~=1.15
 Requires-Dist: pulp<2.8
+Requires-Dist: rich>=10.11.0
+Requires-Dist: shellingham>=1.3.0
 Requires-Dist: snakemake>=7
-Requires-Dist: typer[all]~=0.9
+Requires-Dist: typer~=0.9
 Description-Content-Type: text/markdown
 
 # snk-cli

{snk_cli-0.3.4 → snk_cli-0.5.0}/pyproject.toml

@@ -26,8 +26,9 @@ classifiers = [
 ]
 dependencies = [
   "snakemake>=7",
-  "typer[all]~=0.9",
-  "GitPython~=3.1",
+  "typer~=0.9",
+  "shellingham >=1.3.0",
+  "rich >=10.11.0",
   "pulp<2.8",  # Pin pulp <2.8 for snakemake: https://github.com/snakemake/snakemake/issues/2607
   "art~=5.9",
   "makefun~=1.15",

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.3.4"
+__version__ = "0.5.0"

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/cli.py

@@ -60,16 +60,12 @@ class CLI(DynamicTyper):
             )
         else:
             self.snk_config = snk_config
-        if self.workflow.version:
-            self.version = self.workflow.version
-        else: 
-            self.version = self.snk_config.version
+        self.version = self.snk_config.version
         if self.snk_config.configfile:
              self.snakemake_config = load_configfile(self.snk_config.configfile)
         else:
             self.snakemake_config = load_workflow_snakemake_config(workflow_dir_path)
         self.options = build_dynamic_cli_options(self.snakemake_config, self.snk_config)
-        print(self.options)
         # try to load the snakefile from the snakemake config
         snakefile = self.snk_config.snakefile
         if not snakefile:

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/dynamic_typer.py

@@ -2,6 +2,7 @@ import typer
 from typing import List, Callable
 from inspect import signature, Parameter
 from makefun import with_signature
+from enum import Enum
 
 from .options import Option
 import sys
@@ -146,17 +147,25 @@ class DynamicTyper:
           >>> create_cli_parameter(option)
           Parameter('foo', kind=Parameter.POSITIONAL_OR_KEYWORD, default=typer.Option(..., help='[CONFIG] A number'), annotation=int)
         """
+        annotation_type = option.type
+        default = option.default
+        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('DynamicEnum', {e: e for e in option.choices})
+            if default:
+              default = annotation_type(default)
         return Parameter(
             option.name,
             kind=Parameter.POSITIONAL_OR_KEYWORD,
             default=typer.Option(
-                ... if option.required else option.default,
+                ... if option.required else default,
                 *[option.flag, option.short_flag] if option.short else [],
                 help=f"{option.help}",
                 rich_help_panel="Workflow Configuration",
                 hidden=option.hidden,
             ),
-            annotation=option.type,
+            annotation=annotation_type,
         )
 
     def check_if_option_passed_via_command_line(self, option: Option):

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/options/option.py

@@ -16,3 +16,4 @@ class Option:
     short_flag: Optional[str]
     hidden: bool = False
     from_annotation: bool = False
+    choices: Optional[list] = None

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/options/utils.py

@@ -1,8 +1,9 @@
-from typing import List, Any
+from typing import List
 from ..config.config import SnkConfig
 from ..utils import get_default_type, flatten
 from .option import Option
 from pathlib import Path
+from enum import Enum
 
 types = {
     "int": int,
@@ -17,6 +18,7 @@ types = {
     "list[str]": List[str],
     "list[path]": List[Path],
     "list[int]": List[int],
+    "enum": Enum,
 }
 
 def get_keys_from_annotation(annotations):
@@ -78,6 +80,7 @@ def create_option_from_annotation(
         short_flag=f"-{short}" if short else None,
         hidden=hidden,
         from_annotation=from_annotation,
+        choices=annotation_values.get(f"{annotation_key}:choices", None),
     )
 
 

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/subcommands/env.py

@@ -11,8 +11,7 @@ from snk_cli.conda import conda_environment_factory
 from ..workflow import Workflow
 from rich.console import Console
 from rich.syntax import Syntax
-from snakemake.deployment.conda import Conda, Env, CreateCondaEnvironmentException
-from snk_cli.config.config import get_config_from_workflow_dir
+from snakemake.deployment.conda import Conda, CreateCondaEnvironmentException
 
 from concurrent.futures import ProcessPoolExecutor
 

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/subcommands/profile.py

@@ -78,31 +78,28 @@ class ProfileApp(DynamicTyper):
         import os
         import platform
 
-        try:
-            if platform.system() == "Windows":
-                os.startfile(file_path)
-            elif platform.system() == "Darwin":  # macOS
-                subprocess.call(("open", file_path))
-            else:  # Linux and other Unix-like systems
-                editors = ["nano", "vim", "vi"]
-                editor = None
-                for e in editors:
-                    if (
-                        subprocess.call(
-                            ["which", e], stdout=subprocess.PIPE, stderr=subprocess.PIPE
-                        )
-                        == 0
-                    ):
-                        editor = e
-                        break
-                if editor:
-                    subprocess.call([editor, file_path])
-                else:
-                    self.error(
-                        "No suitable text editor found. Please install nano or vim."
+        if platform.system() == "Windows":
+            os.startfile(file_path)
+        elif platform.system() == "Darwin":  # macOS
+            subprocess.call(("open", file_path))
+        else:  # Linux and other Unix-like systems
+            editors = ["nano", "vim", "vi"]
+            editor = None
+            for e in editors:
+                if (
+                    subprocess.call(
+                        ["which", e], stdout=subprocess.PIPE, stderr=subprocess.PIPE
                     )
-        except Exception as e:
-            print(f"An error occurred: {e}")
+                    == 0
+                ):
+                    editor = e
+                    break
+            if editor:
+                subprocess.call([editor, file_path])
+            else:
+                self.error(
+                    "No suitable text editor found. Please install nano or vim."
+                )
 
     def edit(self, name: str = typer.Argument(..., help="The name of the profile.")):
         profile_path = self._get_profile_path(name)

{snk_cli-0.3.4 → snk_cli-0.5.0}/src/snk_cli/workflow.py

@@ -1,7 +1,6 @@
 from pathlib import Path
 import sys
 from typing import Optional
-from git import Repo, InvalidGitRepositoryError
 import importlib.util
 import os
 
@@ -30,61 +29,8 @@ class Workflow:
         """
         self.path = path
         self.editable = self.check_is_editable()
-        if self.editable:  # editable mode
-            self.repo = None
-        else:
-            try:
-                self.repo = Repo(path)
-            except InvalidGitRepositoryError:
-                self.repo = None
         self.name = self.path.name
 
-
-    @property
-    def tag(self):
-        """
-        Gets the tag of the workflow.
-
-        Returns:
-          str: The tag of the workflow, or None if no tag is found.
-        """
-        try:
-            tag = self.repo.git.describe(["--tags", "--exact-match"])
-        except Exception:
-            tag = None
-        return tag
-    
-    @property
-    def commit(self):
-        """
-        Gets the commit SHA of the workflow.
-
-        Returns:
-          str: The commit SHA of the workflow.
-        """
-        try:
-            sha = self.repo.head.object.hexsha
-            commit = self.repo.git.rev_parse(sha, short=8)
-        except Exception:
-           commit = None
-        return commit
-
-    @property
-    def version(self):
-        """
-        Gets the version of the workflow.
-
-        Returns:
-          str: The version of the workflow, or None if no version is found.
-        """
-        if self.repo is None:
-            return None
-        if self.tag:
-            version = self.tag
-        else:
-            version = self.commit
-        return version
-
     @property
     def executable(self):
         """

{snk_cli-0.3.4 → snk_cli-0.5.0}/tests/data/workflow/snk.yaml

@@ -9,6 +9,8 @@ cli:
     type: bool
   null_annotation:
     default: null
+  enum:
+    choices: [a, b, c]
   test:
     another:
       test:

{snk_cli-0.3.4 → snk_cli-0.5.0}/tests/test_cli/test_dynamic_options.py

@@ -35,9 +35,42 @@ def test_create_option_from_annotation(
     assert option.default == "default_value"
     assert option.updated is False
     assert option.help == "Test help"
-    assert option.type == str
+    assert option.type is str
     assert option.required is True
 
+def test_create_option_from_annotation_with_short(
+    default_annotation_values, default_default_values
+):
+    default_annotation_values["test:short"] = "t"
+
+    option = create_option_from_annotation(
+        "test", default_annotation_values, default_default_values
+    )
+
+    assert option.short == "t"
+
+def test_create_option_from_annotation_with_hidden(
+    default_annotation_values, default_default_values
+):
+    default_annotation_values["test:hidden"] = True
+
+    option = create_option_from_annotation(
+        "test", default_annotation_values, default_default_values
+    )
+
+    assert option.hidden is True
+
+def test_create_option_from_annotation_with_enums(
+    default_annotation_values, default_default_values
+):
+    default_annotation_values["test:choices"] = ["a", "b", "c"]
+
+    option = create_option_from_annotation(
+        "test", default_annotation_values, default_default_values
+    )
+
+    assert option.choices == ["a", "b", "c"]
+
 
 @pytest.fixture
 def default_snakemake_config():

{snk_cli-0.3.4 → snk_cli-0.5.0}/tests/test_cli/test_profile.py

@@ -15,7 +15,8 @@ def mock_platform_system():
 
 @pytest.fixture
 def mock_os_startfile():
-    if platform.system() == 'Windows':
+    # Only patch os.startfile if the platform is Windows
+    if hasattr(os, 'startfile'):
         with patch('os.startfile') as mock:
             yield mock
     else:
@@ -26,6 +27,7 @@ def mock_subprocess_call():
     with patch('subprocess.call') as mock:
         yield mock
 
+@pytest.mark.skipif(platform.system() != 'Windows', reason="Requires Windows")
 def test_open_text_editor_windows(mock_platform_system, mock_os_startfile, local_runner: SnkCliRunner):
     mock_platform_system.return_value = 'Windows'
     file_path = Path('tests/data/workflow/workflow/profiles/slurm/config.yaml')
@@ -48,7 +50,7 @@ def test_open_text_editor_linux(mock_platform_system, mock_subprocess_call, loca
     file_path = Path('tests/data/workflow/workflow/profiles/slurm/config.yaml')
     
     with patch('subprocess.call') as mock_call:
-        mock_call.side_effect = [1, 1, 0]  # Mocking 'which' command results: nano not found, vim not found, vi found
+        mock_call.side_effect = [1, 1, 0, 0]  # Mocking 'which' command results: nano not found, vim not found, vi found
         
         res = local_runner(["profile", "edit", "slurm"])
         assert res.exit_code == 0, res.stderr
@@ -65,5 +67,5 @@ def test_open_text_editor_no_editor_found(mock_platform_system, mock_subprocess_
 
         with patch('typer.secho') as mock_print:
             res = local_runner(["profile", "edit", "slurm"])
-            assert res.exit_code == 0, res.stderr
+            assert res.exit_code == 1, res.stderr
             mock_print.assert_called_once_with("No suitable text editor found. Please install nano or vim.", fg='red', err=True)

{snk_cli-0.3.4 → snk_cli-0.5.0}/tests/test_cli/test_snk_config.py

@@ -41,4 +41,11 @@ def test_non_standard_configfile(tmp_path):
     runner = dynamic_runner({}, SnkConfig(configfile=tmp_path / "config2.yaml"), tmp_path=tmp_path)
     res = runner.invoke(["run"])
     assert res.exit_code == 0, res.stderr
-    assert "config2" in res.stdout, res.stderr
+    assert "config2" in res.stdout, res.stderr
+
+def test_snk_config_with_enums(tmp_path):
+    runner = dynamic_runner({}, SnkConfig(cli={"test": {"choices": ["enum1", "enum2"], "type": "enum"}}), tmp_path=tmp_path)
+    res = runner.invoke(["run", "--help"])
+    assert res.exit_code == 0, res.stderr
+    assert "enum1" in res.stdout, res.stderr
+    assert "enum2" in res.stdout, res.stderr