snk-cli 0.3.0__tar.gz → 0.3.2__tar.gz

{snk_cli-0.3.0 → snk_cli-0.3.2}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.3.0
-Project-URL: Documentation, https://github.com/unknown/snk-cli#readme
-Project-URL: Issues, https://github.com/unknown/snk-cli/issues
-Project-URL: Source, https://github.com/unknown/snk-cli
+Version: 0.3.2
+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
 Author-email: Wytamma Wirth <wytamma.wirth@me.com>
 License-Expression: MIT
 License-File: LICENSE.txt
@@ -23,7 +23,7 @@ Requires-Dist: gitpython~=3.1
 Requires-Dist: makefun~=1.15
 Requires-Dist: pulp<2.8
 Requires-Dist: snakemake>=7
-Requires-Dist: typer[all]~=0.9.0
+Requires-Dist: typer[all]~=0.9
 Description-Content-Type: text/markdown
 
 # snk-cli

{snk_cli-0.3.0 → snk_cli-0.3.2}/pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 ]
 dependencies = [
   "snakemake>=7",
-  "typer[all]~=0.9.0",
+  "typer[all]~=0.9",
   "GitPython~=3.1",
   "pulp<2.8",  # Pin pulp <2.8 for snakemake: https://github.com/snakemake/snakemake/issues/2607
   "art~=5.9",
@@ -35,9 +35,9 @@ dependencies = [
 ]
 
 [project.urls]
-Documentation = "https://github.com/unknown/snk-cli#readme"
-Issues = "https://github.com/unknown/snk-cli/issues"
-Source = "https://github.com/unknown/snk-cli"
+Documentation = "https://github.com/wytamma/snk-cli#readme"
+Issues = "https://github.com/wytamma/snk-cli/issues"
+Source = "https://github.com/wytamma/snk-cli"
 
 [tool.hatch.version]
 path = "src/snk_cli/__about__.py"

{snk_cli-0.3.0 → snk_cli-0.3.2}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.3.0"
+__version__ = "0.3.2"

snk_cli-0.3.2/src/snk_cli/subcommands/profile.py

@@ -0,0 +1,110 @@
+import typer
+from snk_cli.dynamic_typer import DynamicTyper
+from ..workflow import Workflow
+from rich.console import Console
+from rich.syntax import Syntax
+from pathlib import Path
+
+
+class ProfileApp(DynamicTyper):
+    def __init__(
+        self,
+        workflow: Workflow,
+    ):
+        self.workflow = workflow
+        self.register_command(self.list, help="List the profiles in the workflow.")
+        self.register_command(self.show, help="Show the contents of a profile.")
+        self.register_command(self.edit, help="Edit the contents of a profile.")
+
+    def list(
+        self,
+        verbose: bool = typer.Option(
+            False, "--verbose", "-v", help="Show profiles as paths."
+        ),
+    ):
+        from rich.console import Console
+        from rich.table import Table
+
+        table = Table("Name", "CMD", show_header=True, show_lines=True)
+        if verbose:
+            table.add_column("Path")
+        for profile in self.workflow.profiles:
+            if verbose:
+                path = str(profile.resolve())
+                table.add_row(
+                    profile.stem,
+                    f"{self.workflow.name} profile show {profile.stem}",
+                    path,
+                )
+            else:
+                table.add_row(
+                    profile.stem, f"{self.workflow.name} profile show {profile.stem}"
+                )
+        console = Console()
+        console.print(table)
+
+    def _get_profile_path(self, name: str) -> Path:
+        profile = [
+            p for p in self.workflow.profiles if p.name == name or p.stem == name
+        ]
+        if not profile:
+            self.error(f"Profile {name} not found!")
+        return profile[0] / "config.yaml"
+
+    def show(
+        self,
+        name: str = typer.Argument(..., help="The name of the profile."),
+        pretty: bool = typer.Option(
+            False, "--pretty", "-p", help="Pretty print the profile."
+        ),
+    ):
+        profile_path = self._get_profile_path(name)
+        profile_file_text = profile_path.read_text()
+        if pretty:
+            syntax = Syntax(profile_file_text, "yaml")
+            console = Console()
+            console.print(syntax)
+        else:
+            typer.echo(profile_file_text)
+
+    def _open_text_editor(self, file_path):
+        """
+        Opens the system's default text editor to edit the specified file.
+
+        Parameters:
+        file_path (str): The path to the file to be edited.
+        """
+        import subprocess
+        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."
+                    )
+        except Exception as e:
+            print(f"An error occurred: {e}")
+
+    def edit(self, name: str = typer.Argument(..., help="The name of the profile.")):
+        profile_path = self._get_profile_path(name)
+        ## open the profile in the system editor
+        self._open_text_editor(profile_path)

{snk_cli-0.3.0 → snk_cli-0.3.2}/src/snk_cli/subcommands/script.py

@@ -113,7 +113,9 @@ class ScriptApp(DynamicTyper):
     ):
         script_path = self._get_script_path(name)
         executor = self._get_executor(script_path.suffix[1:])
-        cmd = [executor, f'"{script_path}"'] + args
+        cmd = [executor, f'"{script_path}"'] 
+        if args:
+            cmd += args
         if env:
             env_path = self._get_conda_env_path(env)
             env = conda_environment_factory(env_path, self.conda_prefix_dir)

snk_cli-0.3.2/tests/test_cli/test_profile.py

@@ -0,0 +1,69 @@
+import pytest
+import subprocess
+import os # noqa: F401
+import platform # noqa: F401
+import typer # noqa: F401
+from pathlib import Path
+from unittest.mock import patch, call
+
+from ..utils import SnkCliRunner
+
+@pytest.fixture
+def mock_platform_system():
+    with patch('platform.system') as mock:
+        yield mock
+
+@pytest.fixture
+def mock_os_startfile():
+    if platform.system() == 'Windows':
+        with patch('os.startfile') as mock:
+            yield mock
+    else:
+        yield None
+
+@pytest.fixture
+def mock_subprocess_call():
+    with patch('subprocess.call') as mock:
+        yield mock
+
+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')
+
+    res = local_runner(["profile", "edit", "slurm"])
+    assert res.exit_code == 0, res.stderr
+    if mock_os_startfile:
+        mock_os_startfile.assert_called_once_with(file_path)
+
+def test_open_text_editor_mac(mock_platform_system, mock_subprocess_call, local_runner: SnkCliRunner):
+    mock_platform_system.return_value = 'Darwin'
+    file_path = Path('tests/data/workflow/workflow/profiles/slurm/config.yaml')
+
+    res = local_runner(["profile", "edit", "slurm"])
+    assert res.exit_code == 0, res.stderr
+    mock_subprocess_call.assert_called_once_with(('open', file_path))
+
+def test_open_text_editor_linux(mock_platform_system, mock_subprocess_call, local_runner: SnkCliRunner):
+    mock_platform_system.return_value = 'Linux'
+    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
+        
+        res = local_runner(["profile", "edit", "slurm"])
+        assert res.exit_code == 0, res.stderr
+        mock_call.assert_has_calls([call(['which', 'nano'], stdout=subprocess.PIPE, stderr=subprocess.PIPE),
+                                    call(['which', 'vim'], stdout=subprocess.PIPE, stderr=subprocess.PIPE),
+                                    call(['which', 'vi'], stdout=subprocess.PIPE, stderr=subprocess.PIPE),
+                                    call(['vi', file_path])])
+
+def test_open_text_editor_no_editor_found(mock_platform_system, mock_subprocess_call, local_runner: SnkCliRunner):
+    mock_platform_system.return_value = 'Linux'
+    
+    with patch('subprocess.call') as mock_call:
+        mock_call.side_effect = [1, 1, 1]  # Mocking 'which' command results: none of the editors found
+
+        with patch('typer.secho') as mock_print:
+            res = local_runner(["profile", "edit", "slurm"])
+            assert res.exit_code == 0, res.stderr
+            mock_print.assert_called_once_with("No suitable text editor found. Please install nano or vim.", fg='red', err=True)

snk_cli-0.3.0/src/snk_cli/subcommands/profile.py

@@ -1,60 +0,0 @@
-import typer
-from snk_cli.dynamic_typer import DynamicTyper
-from ..workflow import Workflow
-from rich.console import Console
-from rich.syntax import Syntax
-from pathlib import Path
-
-
-class ProfileApp(DynamicTyper):
-    def __init__(
-        self,
-        workflow: Workflow,
-    ):
-        self.workflow = workflow
-        self.register_command(self.list, help="List the profiles in the workflow.")
-        self.register_command(
-            self.show, help="Show the contents of a profile."
-        )
-
-    def list(
-        self,
-        verbose: bool = typer.Option(False, "--verbose", "-v", help="Show profiles as paths."), 
-    ):
-        from rich.console import Console
-        from rich.table import Table
-        table = Table("Name", "CMD", show_header=True, show_lines=True)
-        if verbose:
-            table.add_column("Path")
-        for profile in self.workflow.profiles:
-            if verbose:
-                path = str(profile.resolve())
-                table.add_row(profile.stem, f"{self.workflow.name} profile show {profile.stem}", path)
-            else:
-                table.add_row(profile.stem, f"{self.workflow.name} profile show {profile.stem}")
-        console = Console()
-        console.print(table)
-
-
-
-    def _get_profile_path(self, name: str) -> Path:
-        profile = [p for p in self.workflow.profiles if p.name == name or p.stem == name]
-        if not profile:
-            self.error(f"Profile {name} not found!")
-        return profile[0] / "config.yaml"
-    
-    def show(
-        self, 
-        name: str = typer.Argument(..., help="The name of the profile."),
-        pretty: bool = typer.Option(
-            False, "--pretty", "-p", help="Pretty print the profile."
-        ),
-    ):
-        profile_path = self._get_profile_path(name)
-        profile_file_text = profile_path.read_text()
-        if pretty:
-            syntax = Syntax(profile_file_text, "yaml")
-            console = Console()
-            console.print(syntax)
-        else:
-            typer.echo(profile_file_text)