snk-cli 0.2.0__tar.gz → 0.3.0__tar.gz

{snk_cli-0.2.0 → snk_cli-0.3.0}/.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-0.2.0 → snk_cli-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.2.0
+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

{snk_cli-0.2.0 → snk_cli-0.3.0}/pyproject.toml

@@ -46,16 +46,11 @@ path = "src/snk_cli/__about__.py"
 [[tool.hatch.envs.snakemake.matrix]]
 snakemake = ["7.32.4", "8.10.8"]
 
-[tool.hatch.snakemake.test]
-dependencies = [
-  "coverage[toml]>=6.5",
-  "pytest",
-  "snakemake=={matrix:snakemake}"]
-
 [tool.hatch.envs.default]
 dependencies = [
   "coverage[toml]>=6.5",
   "pytest",
+  "snakemake=={matrix:snakemake:7.32.4}",
 ]
 [tool.hatch.envs.default.scripts]
 test = "pytest {args:tests}"

{snk_cli-0.2.0 → snk_cli-0.3.0}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.2.0"
+__version__ = "0.3.0"

{snk_cli-0.2.0 → snk_cli-0.3.0}/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-0.2.0 → snk_cli-0.3.0}/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-0.2.0 → snk_cli-0.3.0}/src/snk_cli/subcommands/run.py

@@ -65,9 +65,7 @@ class RunApp(DynamicTyper):
           >>> RunApp._print_snakemake_help(True)
         """
         if value:
-            import snakemake
-
-            snakemake.main("-h")
+            execute_snakemake("-h")
 
     def run(
         self,

{snk_cli-0.2.0 → snk_cli-0.3.0}/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)
 

snk_cli-0.2.0/tests/data/workflow/workflow/envs/python.yml → snk_cli-0.3.0/tests/data/workflow/workflow/envs/wget.yml

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

{snk_cli-0.2.0 → snk_cli-0.3.0}/tests/test_cli/test_run.py

@@ -39,3 +39,12 @@ def test_run_with_config(tmp_path):
     assert res.exit_code == 0, res.stderr
     assert "cli" in res.stdout, res.stderr
 
+def test_snakemake_help(local_runner: SnkCliRunner):
+    res = local_runner(["run", "-hs"])
+    assert res.exit_code == 0, res.stderr
+    assert "snakemake" in res.stdout
+
+def test_snakemake_version(local_runner: SnkCliRunner):
+    res = local_runner(["run", "--snake-v"])
+    assert res.exit_code == 0, res.stderr
+    assert res.stdout in ["7.32.4\n", "8.10.8\n"]

{snk_cli-0.2.0 → snk_cli-0.3.0}/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-0.2.0 → snk_cli-0.3.0}/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()