Merge pull request #86 from Adamtaranto/update_packaging

Update_packaging

Author: martinghunt

.gitignore

@@ -1,3 +1,11 @@
+# Mac stuff
+.DS_Store
+
+# Versioning
+src/pyfastaq/_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
 *.py[cod]
 
 # C extensions

.travis.yml

@@ -1,6 +1,6 @@
 language: python
 python:
-  - "3.4"
+  - "3.8"
 sudo: false
 script:
-  - "python setup.py test"
+  - "pip install . && pytest tests"

MANIFEST.in

@@ -0,0 +1,8 @@
+name: fastaq
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - python 3.12
+  - hatch
+  - pytest

README.md

@@ -0,0 +1,65 @@
+# Build system configuration
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+# Project metadata
+[project]
+name = "pyfastaq"
+description = "Script to manipulate FASTA and FASTQ files, plus API for developers."
+readme="README.md"
+requires-python = ">=3.8"
+license = { text = "GPLv3" }
+authors = [
+    { name = "Martin Hunt", email = "path-help@sanger.ac.uk" },
+]
+
+# The classifiers for the project.
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Programming Language :: Python :: 3 :: Only",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)"
+]
+
+# The dependencies required to install the package.
+dependencies = []
+
+# Dynamic versioning
+dynamic = ["version"]
+
+# Project URLs
+[project.urls]
+homepage = "https://github.com/sanger-pathogens/Fastaq"
+documentation = "https://github.com/sanger-pathogens/Fastaq"
+repository = "https://github.com/sanger-pathogens/Fastaq"
+
+# Command-line script entry point
+[project.scripts]
+fastaq="pyfastaq.app_fastaq:main"
+
+# Hatch build configuration
+[tool.hatch.build]
+source = "src"
+
+# Exclude files and directories from the build
+exclude = [
+    "environment.yml",
+]
+
+# Hatch versioning configuration
+[tool.hatch.version]
+source = "vcs"
+
+# Version control system (VCS) versioning
+[tool.hatch.version.vcs]
+tag-pattern = "v*"  # Git tags starting with 'v' will be used for versioning
+fallback-version = "0.0.0"
+
+# Version file location for VCS
+[tool.hatch.build.hooks.vcs]
+version-file = "src/pyfastaq/_version.py"
+
+# Optional dependencies for testing
+[project.optional-dependencies]
+tests = ["pytest"]

environment.yml

@@ -1,11 +1,4 @@
-from pkg_resources import get_distribution
-
-try:
-    __version__ = get_distribution('pyfastaq').version
-except:
-    __version__ = 'local'
-
-
+from pyfastaq._version import __version__
 
 __all__ = [
     'caf',
@@ -16,4 +9,5 @@
     'intervals',
     'runners'
 ]
+
 from pyfastaq import *

pyproject.toml

@@ -1,5 +1,3 @@
-#!/usr/bin/env python3
-
 import argparse
 import sys
 
@@ -57,16 +55,20 @@ def print_usage_and_exit():
     sys.exit(1)
 
 
-if len(sys.argv) == 1 or sys.argv[1] in ['-h', '-help', '--help']:
-    print_usage_and_exit()
+def main():
+    if len(sys.argv) == 1 or sys.argv[1] in ['-h', '-help', '--help']:
+        print_usage_and_exit()
+
+    task = sys.argv.pop(1)
 
-task = sys.argv.pop(1)
+    if task not in tasks:
+        print('Task "' + task + '" not recognised. Cannot continue.\n', file=sys.stderr)
+        print_usage_and_exit()
 
-if task not in tasks:
-    print('Task "' + task + '" not recognised. Cannot continue.\n', file=sys.stderr)
-    print_usage_and_exit()
 
+    exec('import pyfastaq.runners.' + task)
+    exec('pyfastaq.runners.' + task + '.run("' + tasks[task] + '")')
 
-exec('import pyfastaq.runners.' + task)
-exec('pyfastaq.runners.' + task + '.run("' + tasks[task] + '")')
 
+if __name__ == "__main__":
+    main()