snk-cli 0.3.3__tar.gz → 0.3.4__tar.gz

{snk_cli-0.3.3 → snk_cli-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.3.3
+Version: 0.3.4
 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-0.3.3 → snk_cli-0.3.4}/pyproject.toml

@@ -44,13 +44,13 @@ path = "src/snk_cli/__about__.py"
 
 
 [[tool.hatch.envs.snakemake.matrix]]
-snakemake = ["7.32.4", "8.10.8"]
+snakemake = ["==7.32.4", ">8"]
 
 [tool.hatch.envs.default]
 dependencies = [
   "coverage[toml]>=6.5",
   "pytest",
-  "snakemake=={matrix:snakemake:7.32.4}",
+  "snakemake{matrix:snakemake:==7.32.4}",
 ]
 [tool.hatch.envs.default.scripts]
 test = "pytest {args:tests}"

{snk_cli-0.3.3 → snk_cli-0.3.4}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.3.3"
+__version__ = "0.3.4"

{snk_cli-0.3.3 → snk_cli-0.3.4}/src/snk_cli/cli.py

@@ -15,6 +15,7 @@ from snk_cli.config.config import (
     SnkConfig,
     load_workflow_snakemake_config,
 )
+from snk_cli.config.utils import load_configfile
 from snk_cli.options.utils import build_dynamic_cli_options
 from snk_cli.workflow import Workflow
 
@@ -52,7 +53,7 @@ class CLI(DynamicTyper):
         if workflow_dir_path.is_file():
             workflow_dir_path = workflow_dir_path.parent
         self.workflow = Workflow(path=workflow_dir_path)
-        self.snakemake_config = load_workflow_snakemake_config(workflow_dir_path)
+        
         if snk_config is None:
             self.snk_config = SnkConfig.from_workflow_dir(
                 workflow_dir_path, create_if_not_exists=True
@@ -63,8 +64,17 @@ class CLI(DynamicTyper):
             self.version = self.workflow.version
         else: 
             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)
-        self.snakefile = self._find_snakefile()
+        print(self.options)
+        # try to load the snakefile from the snakemake config
+        snakefile = self.snk_config.snakefile
+        if not snakefile:
+            snakefile = self._find_snakefile()
+        self.snakefile = snakefile
         self.conda_prefix_dir = self.workflow.conda_prefix_dir
         self.singularity_prefix_dir = self.workflow.singularity_prefix_dir
         self.name = self.workflow.name
@@ -122,8 +132,6 @@ class CLI(DynamicTyper):
                 EnvApp(
                     workflow=self.workflow,
                     conda_prefix_dir=self.conda_prefix_dir,
-                    snakemake_config=self.snakemake_config,
-                    snakefile=self.snakefile,
                 ),
                 name="env",
                 help="Access the workflow conda environments.",
@@ -133,8 +141,6 @@ class CLI(DynamicTyper):
                 ScriptApp(
                     workflow=self.workflow,
                     conda_prefix_dir=self.conda_prefix_dir,
-                    snakemake_config=self.snakemake_config,
-                    snakefile=self.snakefile,
                 ),
                 name="script",
                 help="Access the workflow scripts.",

{snk_cli-0.3.3 → snk_cli-0.3.4}/src/snk_cli/config/config.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 from typing import List, Optional
-import snakemake
 from dataclasses import dataclass, field
 from .utils import get_version_from_config, load_configfile
 import yaml
@@ -72,6 +71,8 @@ class SnkConfig:
     skip_missing: bool = False # skip any missing cli options (i.e. those not in the snk file)
     additional_snakemake_args: List[str] = field(default_factory=list)
     commands: List[str] = field(default_factory=lambda: ["run", "script", "env", "profile", "info", "config"])
+    snakefile: Optional[Path] = None
+    configfile: Optional[Path] = None
     cli: dict = field(default_factory=dict)
     _snk_config_path: Path = None
 
@@ -113,6 +114,8 @@ class SnkConfig:
         ]
         snk_config.validate_resources(snk_config.resources)
         snk_config._snk_config_path = snk_config_path
+        snk_config.snakefile = Path(snk_config.snakefile) if snk_config.snakefile else None
+        snk_config.configfile = Path(snk_config.configfile) if snk_config.configfile else None
         return snk_config
   
     @classmethod

{snk_cli-0.3.3 → snk_cli-0.3.4}/src/snk_cli/subcommands/env.py

@@ -42,14 +42,9 @@ class EnvApp(DynamicTyper):
         self,
         workflow: Workflow,
         conda_prefix_dir: Path,
-        snakemake_config,
-        snakefile: Path,
     ):
         self.workflow = workflow
         self.conda_prefix_dir = conda_prefix_dir
-        self.snakemake_config = snakemake_config
-        self.snakefile = snakefile
-        self.configfile = get_config_from_workflow_dir(self.workflow.path)
         self.register_command(self.list, help="List the environments in the workflow.")
         self.register_command(self.show, help="Show the contents of an environment.")
         self.register_command(

{snk_cli-0.3.3 → snk_cli-0.3.4}/src/snk_cli/subcommands/run.py

@@ -197,7 +197,10 @@ class RunApp(DynamicTyper):
             args.append(f"--snakefile={self.snakefile}")
 
         if not configfile:
-            configfile = get_config_from_workflow_dir(self.workflow.path)
+            if self.snk_config.configfile:
+                configfile = self.snk_config.configfile
+            else:
+                configfile = get_config_from_workflow_dir(self.workflow.path)
         if configfile:
             args.append(f"--configfile={configfile}")
 

{snk_cli-0.3.3 → snk_cli-0.3.4}/src/snk_cli/subcommands/script.py

@@ -11,7 +11,6 @@ from ..workflow import Workflow
 from rich.console import Console
 from rich.syntax import Syntax
 from snakemake.deployment.conda import Conda
-from snk_cli.config.config import get_config_from_workflow_dir
 
 
 class ScriptApp(DynamicTyper):
@@ -19,14 +18,9 @@ class ScriptApp(DynamicTyper):
         self,
         workflow: Workflow,
         conda_prefix_dir: Path,
-        snakemake_config,
-        snakefile: Path,
     ):
         self.workflow = workflow
         self.conda_prefix_dir = conda_prefix_dir
-        self.snakemake_config = snakemake_config
-        self.snakefile = snakefile
-        self.configfile = get_config_from_workflow_dir(self.workflow.path)
         self.register_command(self.list, help="List the scripts in the workflow.")
         self.register_command(
             self.show, help="Show the contents of a script."

{snk_cli-0.3.3 → snk_cli-0.3.4}/tests/test_cli/test_run.py

@@ -47,4 +47,4 @@ def test_snakemake_help(local_runner: SnkCliRunner):
 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"]
+    assert res.stdout.startswith("7.32.4") or res.stdout.startswith("8.")

{snk_cli-0.3.3 → snk_cli-0.3.4}/tests/test_cli/test_snk_config.py

@@ -1,6 +1,6 @@
 from snk_cli.config import SnkConfig
 from ..utils import dynamic_runner
-
+from pathlib import Path
 
 def test_skip_missing(tmp_path):
     runner = dynamic_runner({"missing": True}, SnkConfig(skip_missing=True, cli={"visible": {"help": "visible"}}), tmp_path=tmp_path)
@@ -27,3 +27,18 @@ def test_snk_config_commands_run_only(tmp_path):
     assert "script" not in res.stdout, res.stderr
     assert "profile" not in res.stdout, res.stderr
 
+def test_non_standard_snakefile(tmp_path):
+    with open(tmp_path / "Snakefile2", "w") as f:
+        f.write("print('Snakefile2')")
+    runner = dynamic_runner({}, SnkConfig(snakefile=tmp_path / "Snakefile2"), tmp_path=tmp_path)
+    res = runner.invoke(["run"])
+    assert res.exit_code == 0, res.stderr
+    assert "Snakefile2" in res.stdout, res.stderr
+
+def test_non_standard_configfile(tmp_path):
+    with open(tmp_path / "config2.yaml", "w") as f:
+        f.write("value: config2")
+    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