📝 write-the mkdocs

.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

README.md

@@ -1 +1,3 @@
 # snk-cli
+
+The dynamic CLI from [snk](https://snk.wytamma.com/). 

docs/env.md

@@ -0,0 +1,109 @@
+---
+title: Environments
+---
+
+# The CLI env command 
+
+The `env` subcommand in the `workflow` tool allows you to access and manage the conda environments used within the workflow. This guide provides an overview of the available options and commands for working with workflow environments.
+
+## Options
+
+- `--help`, `-h`: Show the help message and exit.
+
+## Commands
+
+The `env` subcommand provides several commands to manage the workflows conda environments.
+
+### `list`
+
+List the environments in the workflow.
+
+```bash
+workflow env list [OPTIONS]
+```
+
+### `activate`
+
+Activate a workflow conda environment.
+
+```bash
+workflow env activate [OPTIONS] ENV_NAME
+```
+
+- `ENV_NAME`: Name of the environment to activate.
+
+This command activates the specified conda environment within the workflow.
+
+### `create`
+
+This command creates all the conda environments specified in the `envs` dir.
+
+A Snakemake workflow that uses a lot of conda envs can take a long time to install as each env is created sequentially. Running `workflow env create` will create all the conda envs in parallel (up to `--workers` at a time, defaults to number of cores).
+
+```bash
+workflow env create [OPTIONS] [NAME]
+```
+
+Individual conda envs can be create with `workflow env create ENV_NAME`.
+
+
+### `remove`
+
+Delete all conda environments.
+
+```bash
+workflow env remove [OPTIONS]
+```
+
+This command deletes all the conda environments in the workflow.
+
+### `run`
+
+The `env run` command in the `workflow` tool allows you to run a command within one of the workflow environments.
+
+#### Arguments
+
+- `cmd`: The command to run in the environment. This argument is required.
+
+#### Options
+
+- `--env`, `-e`: The name of the environment in which to run the command.
+- `--help`, `-h`: Show the help message and exit.
+
+#### Usage
+
+To run a command in one of the workflow environments, use the following command format:
+
+```bash
+workflow env run --env ENV_NAME CMD...
+```
+
+- `CMD...`: The command and its arguments to execute within the specified environment.
+
+Make sure to replace `ENV_NAME` with the actual name of the desired environment, and `CMD...` with the command you want to run.
+
+#### Example
+
+Here's an example command that demonstrates the usage of `workflow env run`:
+
+```bash
+workflow env run -e my_environment "python script.py --input input_file.txt --output output_file.txt"
+```
+
+This command runs the `python script.py --input input_file.txt --output output_file.txt` command within the `my_environment` environment in the workflow. Adjust the command and environment name according to your specific use case.
+
+
+- `ENV_NAME`: Name of the environment in which to run the command.
+- `COMMAND [ARGS]...`: The command and its arguments to execute within the specified environment.
+
+This command runs the provided command within the specified conda environment in the workflow.
+
+### `show`
+
+Show the environments config file contents.
+
+```bash
+workflow env show [OPTIONS]
+```
+
+This command displays the contents of the environments configuration file used in the workflow.

docs/index.md

@@ -0,0 +1,19 @@
+---
+title: Home
+---
+# snk-cli
+
+The dynamic CLI from [snk](https://snk.wytamma.com/). 
+
+# The Dynamically Generated Snk CLI
+
+The primary feature of Snk is dynamic CLI generation. Many aspects of this CLI can be configure though the [Snk config file](/snk_config_file/). 
+
+The CLI provides several commands for interacting with the workflow including 
+
+- config - Access the workflow configuration.
+- [env](/CLI/env/) - Access the workflow conda environments.
+- [script](/CLI/script/) - Access the workflow scripts.
+- info - Display information about the workflow.
+- profile - Access the workflow profiles.
+- run - Run the Snakemake workflow.

docs/reference/cli.md

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

docs/reference/config.md

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

docs/reference/dynamic_typer.md

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

docs/reference/options.md

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

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
+

docs/reference/testing.md

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

docs/reference/utils.md

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

docs/reference/validate.md

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

docs/reference/workflow.md

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

docs/script.md

@@ -0,0 +1,41 @@
+---
+title: Scripts
+---
+
+# Script Commands
+
+The `script` commands allow you to interact with the workflow scripts. Scripts must be located in the `scripts` directory of the workflow.
+
+## List
+
+The list command will list all scripts in the workflow.
+
+```bash
+snk script list
+```
+
+## Show
+
+The show command will display the contents of a script.
+
+```bash
+snk script show hello.py
+```
+
+## Run
+
+The run command will run a script.
+
+```bash
+snk script run hello.py
+```
+
+!!! note
+    The executor used to run the script is determined by the suffix of the script file. For example, a script named `hello.py` will be run using the `python` executor.
+
+Use the `--env` option to specify the environment to run the script in.
+
+```bash
+snk script run --env python hello.py
+```
+

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

src/snk_cli/cli.py

@@ -58,10 +58,10 @@ def __init__(self, workflow_dir_path: Path = None, *, pipeline_dir_path: Path =
             )
         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