snk-cli 0.3.3__tar.gz → 0.4.0__tar.gz

{snk_cli-0.3.3 → snk_cli-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.3.3
+Version: 0.4.0
 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-0.3.3 → snk_cli-0.4.0}/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",
@@ -44,13 +45,13 @@ 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-0.4.0}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.3.3"
+__version__ = "0.4.0"

{snk_cli-0.3.3 → snk_cli-0.4.0}/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
 
@@ -52,19 +53,24 @@ 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
             )
         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)
-        self.snakefile = self._find_snakefile()
+        # 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 +128,6 @@ 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 +137,6 @@ 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-0.4.0}/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-0.4.0}/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
 
@@ -42,14 +41,9 @@ 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-0.4.0}/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-0.3.3 → snk_cli-0.4.0}/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-0.4.0}/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-0.4.0}/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-0.3.3 → snk_cli-0.4.0}/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-0.3.3 → snk_cli-0.4.0}/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-0.4.0}/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