Merge pull request #7 from beardymcjohnface/dev

Move utils to separate package

.github/workflows/python-app.yml

@@ -34,7 +34,7 @@ jobs:
     strategy:
       matrix:
         os: [macos-12, ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
       - uses: "actions/checkout@v3"

README.md

@@ -1,9 +1,12 @@
 # Snaketool
 
-[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![](https://img.shields.io/static/v1?label=Citation&message=PlosCompBiol&color=blue)](https://doi.org/10.1371/journal.pcbi.1010705)
+[![](https://img.shields.io/static/v1?label=Licence&message=MIT&color=black)](https://opensource.org/license/mit/)
 ![GitHub last commit](https://img.shields.io/github/last-commit/beardymcjohnface/snaketool)
 [![CI](https://github.com/beardymcjohnface/Snaketool/actions/workflows/python-app.yml/badge.svg)](https://github.com/beardymcjohnface/Snaketool/actions/workflows/python-app.yml)
 
+---
+
 [Cookiecutter](https://github.com/cookiecutter/cookiecutter) profile for making a Snakemake-based bioinformatics tool.
 
 __See [Nektool](https://github.com/beardymcjohnface/Nektool) for a NextFlow-based template__
@@ -63,7 +66,6 @@ And here's what you get:
 │   ├── my_snaketool.CITATION
 │   ├── my_snaketool.LICENSE
 │   ├── my_snaketool.VERSION
-│   ├── util.py
 │   └── workflow
 │       └── Snakefile
 ├── README.md

cookiecutter.json

@@ -9,7 +9,7 @@
   "project_version": "0.1.0",
   "citation_doi": "",
   "license": ["MIT license", "BSD license", "ISC License (ISCL)", "Apache Software License", "GNU General Public License v3 (GPLv3)", "Other/Proprietary License"],
-  "min_python_version": ">=3.7",
+  "min_python_version": ">=3.9",
   "snakemake_version": ">=7.14.0",
   "pyyaml_version": ">=6.0",
   "click_version": ">=8.1.3"

{{cookiecutter.project_slug}}/setup.py

@@ -32,9 +32,9 @@ def get_data_files():
     "Natural Language :: English",
     "Operating System :: POSIX :: Linux",
     "Operating System :: MacOS :: MacOS X",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 
@@ -52,6 +52,7 @@ def get_data_files():
     data_files=get_data_files(),
     py_modules=["{{cookiecutter.project_slug}}"],
     install_requires=[
+        "snaketool-utils>=0.0.2",
         "snakemake{{cookiecutter.snakemake_version}}",
         "pyyaml{{cookiecutter.pyyaml_version}}",
         "Click{{cookiecutter.click_version}}",

{{cookiecutter.project_slug}}/{{cookiecutter.project_slug}}/__main__.py

@@ -8,15 +8,33 @@
 import os
 import click
 
-from .util import (
-    snake_base,
-    get_version,
-    default_to_output,
-    copy_config,
-    run_snakemake,
-    OrderedCommands,
-    print_citation,
-)
+from snaketool_utils.cli_utils import OrderedCommands, run_snakemake, copy_config, echo_click
+
+
+def snake_base(rel_path):
+    """Get the filepath to a Snaketool system file (relative to __main__.py)"""
+    return os.path.join(os.path.dirname(os.path.realpath(__file__)), rel_path)
+
+
+def get_version():
+    """Read and print the version from the version file"""
+    with open(snake_base("{{cookiecutter.project_slug}}.VERSION"), "r") as f:
+        version = f.readline()
+    return version
+
+
+def print_citation():
+    """Read and print the Citation information from the citation file"""
+    with open(snake_base("{{cookiecutter.project_slug}}.CITATION"), "r") as f:
+        for line in f:
+            echo_click(line)
+
+
+def default_to_output(ctx, param, value):
+    """Callback for click options; places value in output directory unless specified"""
+    if param.default == value:
+        return os.path.join(ctx.params["output"], value)
+    return value
 
 
 def common_options(func):
@@ -122,12 +140,17 @@ def cli():
 def run(_input, output, log, **kwargs):
     """Run {{cookiecutter.project_name}}"""
     # Config to add or update in configfile
-    merge_config = {"input": _input, "output": output, "log": log}
+    merge_config = {
+        "input": _input,
+        "output": output,
+        "log": log
+    }
 
     # run!
     run_snakemake(
         # Full path to Snakefile
         snakefile_path=snake_base(os.path.join("workflow", "Snakefile")),
+        system_config=snake_base(os.path.join("config", "config.yaml")),
         merge_config=merge_config,
         log=log,
         **kwargs
@@ -138,7 +161,7 @@ def run(_input, output, log, **kwargs):
 @common_options
 def config(configfile, **kwargs):
     """Copy the system default config file"""
-    copy_config(configfile)
+    copy_config(configfile, system_config=snake_base(os.path.join("config", "config.yaml")))
 
 
 @click.command()