snk-cli 0.0.1__tar.gz → 0.1.1__tar.gz

snk_cli-0.1.1/.github/workflows/mkdocs.yml

@@ -0,0 +1,23 @@
+
+name: mkdocs 
+on:
+  push:
+    branches:
+      - master 
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - uses: actions/cache@v2
+        with:
+          key: ${{ github.ref }}
+          path: .cache
+      - run: pip install "mkdocstrings==0.22.0" "mkdocstrings-python==1.3.*" "mkdocs-material"
+      - run: mkdocs gh-deploy --force

{snk_cli-0.0.1 → snk_cli-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: snk-cli
-Version: 0.0.1
+Version: 0.1.1
 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
@@ -27,3 +27,8 @@ Requires-Dist: typer[all]~=0.9.0
 Description-Content-Type: text/markdown
 
 # snk-cli
+[![PyPI - Version](https://img.shields.io/pypi/v/snk-cli.svg)](https://pypi.org/project/snk-cli)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/snk-cli.svg)](https://pypi.org/project/snk-cli)
+[![write-the - docs](https://badgen.net/badge/write-the/docs/blue?icon=https://raw.githubusercontent.com/Wytamma/write-the/master/images/write-the-icon.svg)](https://write-the.wytamma.com/)
+
+Used internally by [snk](https://snk.wytamma.com/) to generate dynamic [snakemake](https://snakemake.github.io/) CLIs. You can use `snk-cli` to build self contained snakemake tools. See here for more details -> [https://snk.wytamma.com/workflow_packages](https://snk.wytamma.com/workflow_packages/)

snk_cli-0.1.1/README.md

@@ -0,0 +1,6 @@
+# snk-cli
+[![PyPI - Version](https://img.shields.io/pypi/v/snk-cli.svg)](https://pypi.org/project/snk-cli)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/snk-cli.svg)](https://pypi.org/project/snk-cli)
+[![write-the - docs](https://badgen.net/badge/write-the/docs/blue?icon=https://raw.githubusercontent.com/Wytamma/write-the/master/images/write-the-icon.svg)](https://write-the.wytamma.com/)
+
+Used internally by [snk](https://snk.wytamma.com/) to generate dynamic [snakemake](https://snakemake.github.io/) CLIs. You can use `snk-cli` to build self contained snakemake tools. See here for more details -> [https://snk.wytamma.com/workflow_packages](https://snk.wytamma.com/workflow_packages/)

snk_cli-0.1.1/docs/index.md

@@ -0,0 +1,8 @@
+---
+title: Home
+---
+# snk-cli
+
+The dynamic CLI from [snk](https://snk.wytamma.com/). 
+
+This site primary holds the reference docs for snk-cli 

snk_cli-0.1.1/docs/reference/cli.md

@@ -0,0 +1,2 @@
+::: src.snk_cli.cli
+

snk_cli-0.1.1/docs/reference/config.md

@@ -0,0 +1,4 @@
+::: src.snk_cli.config.config
+
+::: src.snk_cli.config.utils
+

snk_cli-0.1.1/docs/reference/dynamic_typer.md

@@ -0,0 +1,2 @@
+::: src.snk_cli.dynamic_typer
+

snk_cli-0.1.1/docs/reference/options.md

@@ -0,0 +1,4 @@
+::: src.snk_cli.options.option
+
+::: src.snk_cli.options.utils
+

snk_cli-0.1.1/docs/reference/subcommands.md

@@ -0,0 +1,12 @@
+::: src.snk_cli.subcommands.run
+
+::: src.snk_cli.subcommands.config
+
+::: src.snk_cli.subcommands.env
+
+::: src.snk_cli.subcommands.profile
+
+::: src.snk_cli.subcommands.utils
+
+::: src.snk_cli.subcommands.script
+

snk_cli-0.1.1/docs/reference/testing.md

@@ -0,0 +1,2 @@
+::: src.snk_cli.testing
+

snk_cli-0.1.1/docs/reference/utils.md

@@ -0,0 +1,2 @@
+::: src.snk_cli.utils
+

snk_cli-0.1.1/docs/reference/validate.md

@@ -0,0 +1,2 @@
+::: src.snk_cli.validate
+

snk_cli-0.1.1/docs/reference/workflow.md

@@ -0,0 +1,2 @@
+::: src.snk_cli.workflow
+

snk_cli-0.1.1/mkdocs.yml

@@ -0,0 +1,44 @@
+
+site_name: snk_cli
+# repo_url: https://github.com/wytamma/write-the
+
+theme:
+  name: "material"
+  # homepage: https://write-the.wytamma.com
+  # logo: assets/logo.png
+  # favicon: images/favicon.png
+  palette: 
+    - scheme: default
+      toggle:
+        icon: material/brightness-7 
+        name: Switch to dark mode
+    - scheme: slate
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+  features:
+    - toc.follow
+    - content.action.edit
+
+extra:
+  social:
+    - icon: fontawesome/solid/robot
+      link: https://github.com/Wytamma/write-the
+      name: Generated with write-the
+
+plugins:
+- search
+- mkdocstrings:
+    handlers:
+      python:
+        options:
+          docstring_style: "google"
+
+markdown_extensions:
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences

{snk_cli-0.0.1 → snk_cli-0.1.1}/src/snk_cli/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Wytamma Wirth <wytamma.wirth@me.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.0.1"
+__version__ = "0.1.1"

{snk_cli-0.0.1 → snk_cli-0.1.1}/src/snk_cli/cli.py

@@ -24,10 +24,13 @@ from snk_cli.workflow import Workflow
 class CLI(DynamicTyper):
     """
     Constructor for the dynamic Snk CLI class.
+
     Args:
       workflow_dir_path (Path): Path to the workflow directory.
+
     Side Effects:
       Initializes the CLI class.
+
     Examples:
       >>> CLI(Path('/path/to/workflow'))
     """
@@ -58,10 +61,10 @@ class CLI(DynamicTyper):
             )
         else:
             self.snk_config = snk_config
-        if self.snk_config.version:
-            self.version = self.snk_config.version
-        else: 
+        if self.workflow.version:
             self.version = self.workflow.version
+        else: 
+            self.version = self.snk_config.version
         self.options = build_dynamic_cli_options(self.snakemake_config, self.snk_config)
         self.snakefile = self._find_snakefile()
         self.conda_prefix_dir = self.workflow.conda_prefix_dir
@@ -88,31 +91,35 @@ class CLI(DynamicTyper):
             invoke_without_command=True,
             context_settings={"help_option_names": ["-h", "--help"]},
         )
-        self.register_command(self.info, help="Show information about the workflow.")
-
-        run_app = RunApp(
-            conda_prefix_dir=self.conda_prefix_dir,
-            snk_config=self.snk_config,
-            singularity_prefix_dir=self.singularity_prefix_dir,
-            snakefile=self.snakefile,
-            workflow=self.workflow,
-            verbose=self.verbose,
-            logo=self.logo,
-            dynamic_run_options=self.options,
-        )
+
         # Subcommands
-        self.register_command(
-            run_app,
-            name="run",
-        )
-        self.register_command(
-            ConfigApp(
+        if "info" in self.snk_config.commands:
+            self.register_command(self.info, help="Show information about the workflow.")
+
+        if "run" in self.snk_config.commands:
+            run_app = RunApp(
+                conda_prefix_dir=self.conda_prefix_dir,
+                snk_config=self.snk_config,
+                singularity_prefix_dir=self.singularity_prefix_dir,
+                snakefile=self.snakefile,
                 workflow=self.workflow,
-                options=self.options,
-            ),
-            name="config",
-        )
-        if self.workflow.environments:
+                verbose=self.verbose,
+                logo=self.logo,
+                dynamic_run_options=self.options,
+            )
+            self.register_command(
+                run_app,
+                name="run",
+            )
+        if "config" in self.snk_config.commands:
+            self.register_command(
+                ConfigApp(
+                    workflow=self.workflow,
+                    options=self.options,
+                ),
+                name="config",
+            )
+        if self.workflow.environments and "env" in self.snk_config.commands:
             self.register_group(
                 EnvApp(
                     workflow=self.workflow,
@@ -123,7 +130,7 @@ class CLI(DynamicTyper):
                 name="env",
                 help="Access the workflow conda environments.",
             )
-        if self.workflow.scripts:
+        if self.workflow.scripts and "script" in self.snk_config.commands:
             self.register_group(
                 ScriptApp(
                     workflow=self.workflow,
@@ -134,7 +141,7 @@ class CLI(DynamicTyper):
                 name="script",
                 help="Access the workflow scripts.",
             )
-        if self.workflow.profiles:
+        if self.workflow.profiles and "profile" in self.snk_config.commands:
             self.register_group(
                 ProfileApp(
                     workflow=self.workflow,
@@ -185,10 +192,14 @@ class CLI(DynamicTyper):
     ):
         """
         Create a logo for the CLI.
+
         Args:
-          font (str): The font to use for the logo.
+          tagline (str, optional): The tagline to include in the logo. Defaults to "A Snakemake workflow CLI generated with snk".
+          font (str, optional): The font to use for the logo. Defaults to "small".
+
         Returns:
           str: The logo.
+
         Examples:
           >>> CLI._create_logo()
         """
@@ -203,8 +214,13 @@ class CLI(DynamicTyper):
     def _find_snakefile(self):
         """
         Search possible snakefile locations.
+
         Returns:
           Path: The path to the snakefile.
+
+        Raises:
+          FileNotFoundError: If the snakefile is not found.
+
         Examples:
           >>> CLI._find_snakefile()
         """
@@ -216,8 +232,10 @@ class CLI(DynamicTyper):
     def info(self):
         """
         Display information about current workflow install.
+
         Returns:
           str: A JSON string containing information about the current workflow install.
+
         Examples:
           >>> CLI.info()
         """

{snk_cli-0.0.1 → snk_cli-0.1.1}/src/snk_cli/config/config.py

@@ -7,18 +7,58 @@ import yaml
 
 
 class SnkConfigError(Exception):
-    """Base class for all SNK config exceptions"""
+    """
+    Base class for all SNK config exceptions.
+    """
 
 class InvalidSnkConfigError(SnkConfigError, ValueError):
-    """Thrown if the given SNK config appears to have an invalid format."""
+    """
+    Thrown if the given SNK config appears to have an invalid format.
+    """
 
 class MissingSnkConfigError(SnkConfigError, FileNotFoundError):
-    """Thrown if the given SNK config file cannot be found."""
+    """
+    Thrown if the given SNK config file cannot be found.
+    """
 
 @dataclass
 class SnkConfig:
     """
     A dataclass for storing Snakemake workflow configuration.
+
+    Attributes:
+      art (str, optional): The art to display in the CLI. Defaults to None.
+      logo (str, optional): The logo to display in the CLI. Defaults to None.
+      tagline (str): The tagline to display in the CLI. Defaults to "A Snakemake workflow CLI generated with Snk".
+      font (str): The font size for the CLI. Defaults to "small".
+      version (Optional[str], optional): The version of the workflow. Defaults to None.
+      conda (bool): Whether to use conda for managing environments. Defaults to True.
+      resources (List[Path]): List of paths to additional resources. Defaults to an empty list.
+      symlink_resources (bool): Whether to symlink resources instead of copying them. Defaults to False.
+      skip_missing (bool): Whether to skip missing CLI options. Defaults to False.
+      additional_snakemake_args (List[str]): List of additional Snakemake command-line arguments. Defaults to an empty list.
+      commands (List[str]): List of subcommands to include in the CLI. Defaults to ["run", "script", "env", "profile", "info", "config"].
+      cli (dict): Dictionary of CLI options and their values. Defaults to an empty dictionary.
+      _snk_config_path (Path): The path to the SNK config file. Defaults to None.
+
+    Methods:
+      from_path(snk_config_path: Path) -> SnkConfig:
+        Load and validate Snk config from file.
+
+      from_workflow_dir(workflow_dir_path: Path, create_if_not_exists: bool = False) -> SnkConfig:
+        Load and validate SNK config from workflow directory.
+
+      validate_resources(resources: List[Path]) -> None:
+        Validate resources.
+
+      add_resources(resources: List[Path], workflow_dir_path: Path = None) -> None:
+        Add resources to the SNK config.
+
+      to_yaml(path: Path) -> None:
+        Write SNK config to YAML file.
+
+      save() -> None:
+        Save SNK config.
     """
 
     art: str = None
@@ -28,10 +68,11 @@ class SnkConfig:
     version: Optional[str] = None
     conda: bool = True
     resources: List[Path] = field(default_factory=list)
+    symlink_resources: bool = False
     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"])
     cli: dict = field(default_factory=dict)
-    symlink_resources: bool = False
     _snk_config_path: Path = None
 
     @classmethod

{snk_cli-0.0.1 → snk_cli-0.1.1}/src/snk_cli/config/utils.py

@@ -3,17 +3,24 @@ from snakemake import load_configfile
 
 def get_version_from_config(config_path: Path, config_dict: dict = None) -> str:
     """
-    Get the version from config. If dict not provided, load from file.
-    If the version is a path to a __about__ file, load the version from the file.
-    Path must be relative to the config file.
+    Get the version from the config file or config dictionary.
+
     Args:
       config_path (Path): Path to the config file.
-      config_dict (dict): Config dict.
+      config_dict (dict, optional): Config dictionary. Defaults to None.
+
     Returns:
-      str: Version.
+      str: The version.
+
+    Raises:
+      FileNotFoundError: If the version file (__about__.py) is not found.
+      KeyError: If the __version__ key is not found in the version file.
+
     Examples:
-      >>> get_version_from_config_dict({"version": "0.1.0"})
+      >>> get_version_from_config(Path("config.yaml"))
       '0.1.0'
+      >>> get_version_from_config(Path("config.yaml"), {"version": "0.2.0"})
+      '0.2.0'
     """
     if not config_dict:
         config_dict = load_configfile(config_path)

{snk_cli-0.0.1 → snk_cli-0.1.1}/src/snk_cli/dynamic_typer.py

@@ -10,27 +10,41 @@ import sys
 class DynamicTyper:
     app: typer.Typer
 
-    def __init_subclass__(cls, **kwargs):
-        super().__init_subclass__(**kwargs)
-        cls.app = typer.Typer()
+    def __init__(self):
+        self.app = typer.Typer()
 
     def __call__(self):
         """
         Invoke the CLI.
+
         Side Effects:
           Invokes the CLI.
+
         Examples:
           >>> CLI(Path('/path/to/workflow'))()
         """
-        self.app()
+        self._set_app()
+
+    def _set_app(self):
+        """
+        Set the app attribute.
+
+        Side Effects:
+          Sets the app attribute to a Typer object.
+        """
+        if not hasattr(self, "app"):
+          self.app = typer.Typer()
 
     def register_default_command(self, command: Callable, **command_kwargs) -> None:
         """
         Register a default command to the CLI.
+
         Args:
           command (Callable): The command to register.
+
         Side Effects:
           Registers the command to the CLI.
+
         Examples:
           >>> CLI.register_default_command(my_command)
         """
@@ -65,13 +79,19 @@ class DynamicTyper:
     ) -> None:
         """
         Register a command to the CLI.
+
         Args:
           command (Callable): The command to register.
+          dynamic_options (List[Option], optional): A list of dynamic options to add to the command.
+
         Side Effects:
           Registers the command to the CLI.
+
         Examples:
           >>> CLI.register_command(my_command)
+          >>> CLI.register_command(my_command, dynamic_options=[option1, option2])
         """
+        self._set_app()
         if dynamic_options is not None:
             command = self.add_dynamic_options(command, dynamic_options)
         if isinstance(command, DynamicTyper):
@@ -82,34 +102,45 @@ class DynamicTyper:
     def register_callback(self, command: Callable, **command_kwargs) -> None:
         """
         Register a callback to the CLI.
+
         Args:
           command (Callable): The callback to register.
+
         Side Effects:
           Registers the callback to the CLI.
+
         Examples:
           >>> CLI.register_callback(my_callback)
         """
+        self._set_app()
         self.app.callback(**command_kwargs)(command)
 
     def register_group(self, group: "DynamicTyper", **command_kwargs) -> None:
         """
-        Register a subcommand group group to the CLI.
+        Register a subcommand group to the CLI.
+
         Args:
           group (DynamicTyper): The subcommand group to register.
+
         Side Effects:
           Registers the subcommand group to the CLI.
+
         Examples:
-          >>> CLI.register_app(my_group)
+          >>> CLI.register_group(my_group)
         """
+        self._set_app()
         self.app.add_typer(group.app, **command_kwargs)
 
     def _create_cli_parameter(self, option: Option):
         """
         Creates a parameter for a CLI option.
+
         Args:
           option (Option): An Option object containing the option's name, type, required status, default value, and help message.
+
         Returns:
           Parameter: A parameter object for the CLI option.
+
         Examples:
           >>> option = Option(name='foo', type='int', required=True, default=0, help='A number')
           >>> create_cli_parameter(option)
@@ -131,8 +162,10 @@ class DynamicTyper:
     def check_if_option_passed_via_command_line(self, option: Option):
         """
         Check if an option is passed via the command line.
+
         Args:
           option (Option): An Option object containing the option's name, type, required status, default value, and help message.
+
         Returns:
           bool: Whether the option is passed via the command line.
         """
@@ -148,15 +181,17 @@ class DynamicTyper:
     def add_dynamic_options(self, func: Callable, options: List[Option]):
         """
         Function to add dynamic options to a command.
+
         Args:
-          command (Callable): The command to which the dynamic options should be added.
-          options (List[dict]): A list of dictionaries containing the option's name, type, required status, default value, and help message.
+          func (Callable): The command to which the dynamic options should be added.
+          options (List[Option]): A list of Option objects containing the options to add.
+
         Returns:
           Callable: A function with the dynamic options added.
+
         Examples:
-          >>> my_func = add_dynamic_options_to_function(my_func, [{'name': 'foo', 'type': 'int', 'required': True, 'default': 0, 'help': 'A number'}])
+          >>> my_func = add_dynamic_options_to_function(my_func, [option1, option2])
           >>> my_func
-          <function my_func at 0x7f8f9f9f9f90>
         """
         func_sig = signature(func)
         params = list(func_sig.parameters.values())
@@ -168,13 +203,16 @@ class DynamicTyper:
         def func_wrapper(*args, **kwargs):
             """
             Wraps a function with dynamic options.
+
             Args:
-                *args: Variable length argument list.
-                **kwargs: Arbitrary keyword arguments.
+              *args: Variable length argument list.
+              **kwargs: Arbitrary keyword arguments.
+
             Returns:
-                Callable: A wrapped function with the dynamic options added.
+              Callable: A wrapped function with the dynamic options added.
+
             Notes:
-                This function is used in the `add_dynamic_options_to_function` function.
+              This function is used in the `add_dynamic_options_to_function` function.
             """
             flat_config = None
 
@@ -216,6 +254,7 @@ class DynamicTyper:
     def error(self, msg, exit=True):
         """
         Logs an error message (red) and exits (optional).
+
         Args:
           msg (str): The error message to log.
           exit (bool): Whether to exit after logging the error message.
@@ -227,6 +266,7 @@ class DynamicTyper:
     def success(self, msg):
         """
         Logs a success message (green).
+
         Args:
           msg (str): The success message to log.
         """
@@ -235,14 +275,18 @@ class DynamicTyper:
     def log(self, msg, color="yellow", stderr=True):
         """
         Logs a message (yellow).
+
         Args:
           msg (str): The message to log.
+          color (str, optional): The color of the log message. Defaults to "yellow".
+          stderr (bool, optional): Whether to log the message to stderr. Defaults to True.
         """
         typer.secho(msg, fg=color, err=stderr)
 
     def echo(self, msg):
         """
         Prints a message.
+
         Args:
           msg (str): The message to print.
         """

{snk_cli-0.0.1 → snk_cli-0.1.1}/src/snk_cli/options/utils.py

@@ -37,13 +37,16 @@ def create_option_from_annotation(
 ) -> Option:
     """
     Create an Option object from a given annotation.
+
     Args:
-      annotation_key: The key in the annotations.
-      annotation_values: The dictionary of annotation values.
-      default_values: default value from config.
+      annotation_key (str): The key in the annotations.
+      annotation_values (dict): The dictionary of annotation values.
+      default_values (dict): Default value from config.
+      from_annotation (bool, optional): Whether the option is from an annotation. Defaults to False.
+
     Returns:
-      An Option object.
-    """    
+      Option: An Option object.
+    """
     config_default = default_values.get(annotation_key, None)
 
     default = annotation_values.get(f"{annotation_key}:default", config_default)
@@ -83,9 +86,11 @@ def build_dynamic_cli_options(
 ) -> List[dict]:
     """
     Builds a list of options from a snakemake config and a snk config.
+
     Args:
       snakemake_config (dict): A snakemake config.
       snk_config (SnkConfig): A snk config.
+
     Returns:
       List[dict]: A list of options.
     """