V2.0.1 dev (#43)

* Switch to using pyproject.toml (#42)

* Switch to using pyproject.toml

* Include numpy headers

* Start using github actions

* Fix linter errors

* Use pylint for github actions

* Run pylint first

* use defined environments on github

* Fix call windows issue

* Try to run coveralls

* Run on pull requests

* Upload coverage results in parallel jobs

* Bump version number

.github/workflows/tox-test.yml

@@ -0,0 +1,40 @@
+name: Python package
+
+on: ["push", "pull_request"]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9",]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+      - name: Test with tox
+        run: tox --skip-missing-interpreters
+      - name: Coveralls Parallel
+        uses: coverallsapp/github-action@v2
+        with:
+          flag-name: run-${{ join(matrix.*, '-') }}
+          parallel: true
+
+  finish:
+    needs: test
+    if: ${{ always() }}
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@v2
+      with:
+        parallel-finished: true
+        carryforward: "run-3.8,run-3.9"

.pylintrc

@@ -353,4 +353,4 @@ analyse-fallback-blocks=no
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
-overgeneral-exceptions=Exception
+overgeneral-exceptions=builtins.Exception

CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.0.1] - 2023-06-13
+
+### Changed
+- Move to pyproject.toml packaging for compatibility with newer PIP versions
+- Fixed incorrect parameter name in gamtools call_windows
+
 ## [2.0.0] - 2022
 ### Added
 - Allow the doit dependencies database to be reset

MANIFEST.in

@@ -2,4 +2,4 @@ include README.md
 include lib/gamtools/tests/*.py
 include lib/gamtools/data/examples/*
 include lib/gamtools/data/scripts/*
-exclude lib/gamtools/*.pyx
+include lib/gamtools/*.pyx

lib/gamtools/call_windows.py

@@ -420,4 +420,4 @@ def threshold_from_args(args):
 
     threshold_file(args.coverage_file, args.output_file,
                    args.fitting_folder, args.details_file,
-                   args.fitting_function, args.min_reads)
+                   args.fitting_function, args.min_read_threshold)

lib/gamtools/resolution.py

@@ -39,6 +39,9 @@
 from . import segregation
 
 
+class SliceException(Exception):
+    """Exception class for errors related to SLICE"""
+
 def segregation_info(segregation_table, skip_chroms):
     """
     Given a segregation table, retrieve the number of tubes,
@@ -57,10 +60,10 @@ def segregation_info(segregation_table, skip_chroms):
 
     bin_sizes = segregation_windows['size'].value_counts()
     frequent_sizes = [size for (size, freq)
-                      in (bin_sizes / bin_sizes.sum()).iteritems()
+                      in (bin_sizes / bin_sizes.sum()).items()
                       if freq > 0.95]
     if not frequent_sizes:
-        raise Exception('SLICE requires windows of even sizes')
+        raise SliceException('SLICE requires windows of even sizes')
     window_size = frequent_sizes[0]
 
     return genome_size, window_size

pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel", "Cython", "numpy"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "gamtools"
+version = "2.0.1"
+authors = [
+    { name="Rob Beagrie", email="rob@beagrie.co.uk"}
+]
+description = "A package containing some utilities for analyzing GAM data."
+license = { file = "LICENSE" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: Apache Software License"
+]
+dependencies = [
+    "numpy",
+    "scipy",
+    "pandas",
+    "wrapit>=0.3.0",
+    "pytest",
+    "doit==0.29.0; python_version<'3.0'",
+    "mock; python_version<'3.0'",
+    "doit>=0.30.0; python_version>='3.0'"
+]
+
+[project.urls]
+"Homepage" = "https://gam.tools"
+
+[project.scripts]
+gamtools = 'gamtools.main:main'
+create_empty_bedgraph = 'gamtools.utils:empty_bedgraph_from_cmdline'
+
+[tool.setuptools]
+packages = ['gamtools', 'gamtools.qc']
+include-package-data = true
+package-dir = {"" = "lib"}

setup.py

@@ -1,86 +1,16 @@
-import os
-import sys
-from setuptools import setup, Extension
-from setuptools.command.sdist import sdist
-from setuptools.command.build_ext import build_ext
-
-class CustomBuildExtCommand(build_ext):
-    """Customized setuptools build_ext command - checks numpy is installed."""
-    def run(self):
-
-        # Check numpy is installed before trying to find the location
-        # of numpy headers
-
-        try:
-            import numpy
-        except ImportError:
-            raise ImportError('numpy need to be installed before GAMtools can be '
-                              'compiled. Try installing with "pip install numpy" '
-                              'before installing GAMtools.')
-
-        self.include_dirs.append(numpy.get_include())
-
-        build_ext.run(self)
-
-class custom_cythonize_sdist(sdist):
-    def run(self):
-        # Make sure the compiled Cython files in the distribution are up-to-date
-        from Cython.Build import cythonize
-        cythonize([
-                   "lib/gamtools/cosegregation_internal.pyx",
-                   "lib/gamtools/mirnylib_numutils_internal.pyx",
-        ], language_level = "3")
-        sdist.run(self)
-
-# Utility function to read the README file.
-# Used for the long_description.  It's nice, because now 1) we have a top level
-# README file and 2) it's easier to type in the README file than to put a raw
-# string in below ...
-def read(fname):
-    return open(os.path.join(os.path.dirname(__file__), fname)).read()
-
+from setuptools import Extension, setup
+from Cython.Build import cythonize
+import numpy
+
+extensions = [
+    Extension('gamtools.cosegregation_internal',
+        ["lib/gamtools/cosegregation_internal.pyx"],
+              include_dirs=[numpy.get_include()]),
+    Extension('gamtools.mirnylib_numutils_internal',
+        ["lib/gamtools/mirnylib_numutils_internal.pyx"],
+              include_dirs=[numpy.get_include()]),
+	   ]
+
 setup(
-    name = "gamtools",
-    version = "2.0.0",
-    author = "Rob Beagrie",
-    author_email = "rob@beagrie.co.uk",
-    url = "https://gam.tools",
-    description = ("A package containing some utilities for analyzing GAM data."),
-    license = "Apache2.0",
-    package_dir = {'': 'lib'},
-    packages=['gamtools', 'gamtools.qc'],
-    ext_modules = [Extension('gamtools.cosegregation_internal',
-                   ["lib/gamtools/cosegregation_internal.c"]),
-                   Extension('gamtools.mirnylib_numutils_internal',
-                      ["lib/gamtools/mirnylib_numutils_internal.c"],),
-                   ],
-    cmdclass = {
-      'sdist': custom_cythonize_sdist,
-      'build_ext': CustomBuildExtCommand,
-    },
-    install_requires=[
-      'numpy',
-      'scipy',
-      'pandas',
-      'wrapit>=0.3.0',
-      'pytest'],
-    extras_require={
-      ':python_version<"3.0"': ['doit==0.29.0'],
-      ':python_version>="3.0"': ['doit==0.30.0'],
-      ':python_version<"3.0"': ['mock'],
-    },
-    entry_points = {
-                    'console_scripts': [
-                        'gamtools = gamtools.main:main',
-                        'create_empty_bedgraph = gamtools.utils:empty_bedgraph_from_cmdline',
-                    ]
-                   },
-    long_description=read('README.md'),
-    include_package_data=True,
-    classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Intended Audience :: Science/Research",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "License :: OSI Approved :: Apache Software License",
-    ],
+    ext_modules = cythonize(extensions, language_level = "3"),
 )

tox.ini

@@ -4,22 +4,19 @@
 # and then run "tox" from this directory.
 
 [tox]
-envlist = py{38,39}-pandas{12,13}, pylint, docs
+envlist = pylint, py{38,39}-pandas{12,13}, docs
 
 [testenv]
 deps =
-    pytest-cov
     pandas12: pandas>=1.2,<1.3
     pandas13: pandas>=1.3,<1.4
+    pytest-cov
 commands =
     pytest --cov=gamtools --cov-report xml -m "not dependencies"
-    pytest -m "not dependencies"
 
 [testenv:pylint]
 deps =
     pylint
-basepython =
-    python3.9
 commands =
     pylint gamtools --rcfile={toxinidir}/.pylintrc
 
@@ -32,16 +29,3 @@ deps=
     sphinx_rtd_theme
 commands=
     sphinx-build -W -b html -d {envtmpdir}/doctrees .  {envtmpdir}/html
-
-[testenv:coverage]
-deps =
-    pytest-cov
-basepython =
-  python3.9
-commands=
-    pytest --cov=gamtools -m "not dependencies"
-
-[travis]
-python =
-    3.8: py38
-    3.9: py39, docs, pylint