snk-cli 0.2.1__tar.gz → 0.3.1__tar.gz

{snk_cli-0.2.1 → snk_cli-0.3.1}/.github/workflows/tests.yml

@@ -11,7 +11,7 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: "conda-incubator/setup-miniconda@v2"
@@ -22,6 +22,9 @@ jobs:
           channels: conda-forge,bioconda,defaults
           channel-priority: strict
           auto-update-conda: true
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11' 
       - uses: actions/cache@v2
         with:
           key: ${{ github.ref }}

{snk_cli-0.2.1 → snk_cli-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.2.1
+Version: 0.3.1
 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
@@ -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-0.2.1 → snk_cli-0.3.1}/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",

{snk_cli-0.2.1 → snk_cli-0.3.1}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.2.1"
+__version__ = "0.3.1"

{snk_cli-0.2.1 → snk_cli-0.3.1}/src/snk_cli/dynamic_typer.py

@@ -11,7 +11,7 @@ class DynamicTyper:
     app: typer.Typer
 
     def __init__(self):
-        self.app = typer.Typer()
+        self.app = typer.Typer(add_completion=False)
 
     def __call__(self):
         """
@@ -33,7 +33,7 @@ class DynamicTyper:
           Sets the app attribute to a Typer object.
         """
         if not hasattr(self, "app"):
-          self.app = typer.Typer()
+          self.app = typer.Typer(add_completion=False)
 
     def register_default_command(self, command: Callable, **command_kwargs) -> None:
         """

{snk_cli-0.2.1 → snk_cli-0.3.1}/src/snk_cli/subcommands/env.py

@@ -80,7 +80,7 @@ class EnvApp(DynamicTyper):
                 cmd = f"{self.workflow.name} env activate {env.stem}"
             else:
                 address = ""
-                cmd = f"{self.workflow.name} env show {env.stem}"
+                cmd = f"{self.workflow.name} env create {env.stem}"
             table.add_row(
                 env.stem, cmd, address
             )
@@ -153,7 +153,7 @@ class EnvApp(DynamicTyper):
     def create(
             self, 
             names: Optional[List[str]] = typer.Argument(None, help="The names of the environments to create. If not provided, all environments will be created."),
-            max_workers: int = typer.Option(get_num_cores(), "--workers", "-w", help="Max number of envs to create in parallel.")
+            max_workers: int = typer.Option(1, "--workers", "-w", help="Max number of envs to create in parallel.")
         ):
         if names:
             env_paths = [self._get_conda_env_path(name) for name in names]

{snk_cli-0.2.1 → snk_cli-0.3.1}/src/snk_cli/subcommands/script.py

@@ -50,7 +50,7 @@ class ScriptApp(DynamicTyper):
         table = Table("Name", "CMD", "File", show_header=True, show_lines=True)
         for script in self.workflow.scripts:
             # address relative to cwd
-            table.add_row(script.stem, f"{self.workflow.name} script show {script.stem}", str(script.resolve()) if verbose else script.name)
+            table.add_row(script.stem, f"{self.workflow.name} script run {script.stem} --env ...", str(script.resolve()) if verbose else script.name)
         console = Console()
         console.print(table)
 
@@ -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-0.2.1/tests/data/workflow/workflow/envs/python.yml → snk_cli-0.3.1/tests/data/workflow/workflow/envs/wget.yml

@@ -2,4 +2,4 @@ channels:
   - bioconda                                                                                                                                                                
   - conda-forge                                                                                                                                                             
 dependencies:                                                                                                                                                               
-  - python=3.9
+  - wget

{snk_cli-0.2.1 → snk_cli-0.3.1}/tests/test_cli/test_subcommands.py

@@ -6,12 +6,12 @@ import pytest
     (["script", "show", "hello.py"], ["print('hello world')"], []),
     (["profile", "list"], ["slurm"], []),
     (["profile", "show", "slurm"], ["cluster"], []),
-    (["env", "list"], ["python"], []),
-    (["env", "show", "python"], ["python"], []),
+    (["env", "list"], ["wget"], []),
+    (["env", "show", "wget"], ["wget"], []),
     (["env", "create"], ["All conda environments created!"], []),
-    (["env", "create", "python"], ["Created environment python!"], []),
-    (["env", "run", "python", "which python"], ["bin/python"], []),
-    (["env", "activate", "python"], [], ["Activating python environment...", "Exiting python environment..."]),
+    (["env", "create", "wget"], ["Created environment wget!"], []),
+    (["env", "run", "wget", "which wget"], [".conda"], []),
+    (["env", "activate", "wget"], [], ["Activating wget environment...", "Exiting wget environment..."]),
     (["env", "remove", "-f"], ["Deleted"], []),
     (["info"], ["name", "version", "snakefile", "conda_prefix_dir", "singularity_prefix_dir", "workflow_dir_path"], []),
 ])

{snk_cli-0.2.1 → snk_cli-0.3.1}/tests/test_conda_env.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 
 def test_conda_env(tmp_path):
-    env = conda_environment_factory("tests/data/workflow/workflow/envs/python.yml", tmp_path)
+    env = conda_environment_factory("tests/data/workflow/workflow/envs/wget.yml", tmp_path)
     assert isinstance(env, Env)
     assert not Path(env.address).exists()
     env.create()