[med-svn] [Git][med-team/python-pyspoa][master] 5 commits: New upstream version 0.0.9
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Thu Jun 15 17:07:18 BST 2023
Nilesh Patra pushed to branch master at Debian Med / python-pyspoa
Commits:
0762d5f8 by Nilesh Patra at 2023-06-15T21:28:05+05:30
New upstream version 0.0.9
- - - - -
32880a73 by Nilesh Patra at 2023-06-15T21:28:05+05:30
Update upstream source from tag 'upstream/0.0.9'
Update to upstream version '0.0.9'
with Debian dir 3de48b33dc91abab8335a26369130b66ef3ea319
- - - - -
245a04a2 by Nilesh Patra at 2023-06-15T21:28:08+05:30
Bump Standards-Version to 4.6.2 (no changes needed)
- - - - -
ae0a0082 by Nilesh Patra at 2023-06-15T21:30:42+05:30
Update adjust-spoa-lib.patch
- - - - -
1e0abd87 by Nilesh Patra at 2023-06-15T21:30:57+05:30
Upload to unstable
- - - - -
12 changed files:
- − .github/workflows/build-wheels.sh
- − .github/workflows/publish.yml
- − .github/workflows/test.yml
- Makefile
- README.md
- + build.py
- debian/changelog
- debian/control
- debian/patches/adjust-spoa-lib.patch
- + pyproject.toml
- − requirements.txt
- setup.py
Changes:
=====================================
.github/workflows/build-wheels.sh deleted
=====================================
@@ -1,18 +0,0 @@
-#!/bin/bash
-set -e -x
-
-for PYBIN in /opt/python/cp3[6789]*/bin; do
- rm -rf venv3
- "${PYBIN}/python3" -m venv venv3
- source venv3/bin/activate
- python3 -m pip install cmake==3.18.4
- python3 -m pip install -r requirements.txt
- make test
- "${PYBIN}/python3" setup.py bdist_wheel
- make clean
- deactivate
-done
-
-for wheel in dist/*.whl; do
- auditwheel repair "${wheel}"
-done
=====================================
.github/workflows/publish.yml deleted
=====================================
@@ -1,45 +0,0 @@
-name: publish-pyspao
-
-on:
- push:
- tags:
- - 'v*'
-
-jobs:
-
- linux-wheels:
- runs-on: ubuntu-latest
- container: quay.io/pypa/manylinux2010_x86_64
- steps:
- - uses: actions/checkout at v1
- - name: Build wheels
- run: |
- git submodule update --init --recursive
- bash .github/workflows/build-wheels.sh
- - uses: actions/upload-artifact at v1
- with:
- name: linux-wheels
- path: wheelhouse/
-
- osx-wheels:
- runs-on: macos-latest
- strategy:
- matrix:
- python-version: [3.6, 3.7, 3.8, 3.9]
- steps:
- - uses: actions/checkout at v1
- - uses: actions/setup-python at v1
- with:
- python-version: ${{ matrix.python-version }}
- - name: Build wheels
- run: |
- git submodule update --init --recursive
- python3 -m venv venv3
- source venv3/bin/activate
- python3 -m pip install -r requirements.txt
- make test
- python3 setup.py bdist_wheel
- - uses: actions/upload-artifact at v1
- with:
- name: osx-${{ matrix.python-version }}-wheel
- path: dist/
=====================================
.github/workflows/test.yml deleted
=====================================
@@ -1,52 +0,0 @@
-name: test-pyspoa
-
-on: [push]
-
-jobs:
-
- test:
- strategy:
- matrix:
- os: [ubuntu-latest, macos-latest]
- runs-on: ${{ matrix.os }}
- steps:
- - uses: actions/checkout at v1
- - uses: actions/setup-python at v1
- with:
- python-version: '3.9'
- - name: Test ${{ matrix.os }} binding
- run: |
- git submodule update --init --recursive
- python3 -m venv venv3
- source venv3/bin/activate
- python3 -m pip install -r requirements.txt
- make test
-
- linux-wheels:
- runs-on: ubuntu-latest
- container: quay.io/pypa/manylinux2010_x86_64
- steps:
- - uses: actions/checkout at v1
- - name: Build wheels
- run: |
- git submodule update --init --recursive
- bash .github/workflows/build-wheels.sh
-
- osx-wheels:
- runs-on: macos-latest
- strategy:
- matrix:
- python-version: [3.6, 3.7, 3.8, 3.9]
- steps:
- - uses: actions/checkout at v1
- - uses: actions/setup-python at v1
- with:
- python-version: ${{ matrix.python-version }}
- - name: Build wheels
- run: |
- git submodule update --init --recursive
- python3 -m venv venv3
- source venv3/bin/activate
- python3 -m pip install -r requirements.txt
- make test
- python3 setup.py bdist_wheel
=====================================
Makefile
=====================================
@@ -1,9 +1,13 @@
build:
- python3 setup.py develop
+ pip wheel . -w dist
-test: build
+install: build
+ pip install dist/pyspoa*.whl
+
+test: install
python3 tests/test_pyspoa.py
clean:
- rm -rf src/build build tmp *~
+ rm -rf src/build build tmp var *~ *.whl __pycache__
python setup.py clean
+ pip uninstall -y pyspoa
=====================================
README.md
=====================================
@@ -33,7 +33,6 @@ $ git clone --recursive https://github.com/nanoporetech/pyspoa.git
$ cd pyspoa
$ python3 -m venv pyspoa
$ source pyspoa/bin/activate
-(pyspoa) $ pip install -r requirements.txt
(pyspoa) $ make build
```
=====================================
build.py
=====================================
@@ -0,0 +1,13 @@
+import os
+from shutil import rmtree
+from subprocess import run
+
+if __name__ == "__main__":
+ bdir = "src/build"
+ rmtree(bdir, ignore_errors=True)
+ os.makedirs(bdir)
+ run([
+ "cmake", "-D", "spoa_optimize_for_portability=ON", "-D", "CMAKE_BUILD_TYPE=Release",
+ "-D", "CMAKE_CXX_FLAGS='-I ../vendor/cereal/include/ -fPIC '", "..",
+ ], cwd=bdir)
+ run("make", cwd=bdir)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+python-pyspoa (0.0.9-1) unstable; urgency=medium
+
+ * New upstream version 0.0.9
+ * Bump Standards-Version to 4.6.2 (no changes needed)
+ * Update adjust-spoa-lib.patch
+
+ -- Nilesh Patra <nilesh at debian.org> Thu, 15 Jun 2023 21:30:48 +0530
+
python-pyspoa (0.0.8-3) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends:
python3-setuptools,
libspoa-dev,
python3-pybind11
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-pyspoa
Vcs-Git: https://salsa.debian.org/med-team/python-pyspoa.git
Homepage: https://github.com/nanoporetech/pyspoa
=====================================
debian/patches/adjust-spoa-lib.patch
=====================================
@@ -4,7 +4,18 @@ Forwarded: not-needed
Last-Update: 2021-07-10
--- a/setup.py
+++ b/setup.py
-@@ -101,7 +101,7 @@
+@@ -58,10 +58,6 @@
+ bdir = "src/build"
+ rmtree(bdir, ignore_errors=True)
+ os.makedirs(bdir)
+- run([
+- "cmake", "-D", "spoa_optimize_for_portability=ON", "-D", "CMAKE_BUILD_TYPE=Release",
+- "-D", "CMAKE_CXX_FLAGS='-I ../vendor/cereal/include/ -fPIC '", "..",
+- ], cwd=bdir)
+ run("make", cwd=bdir)
+
+
+@@ -113,7 +109,7 @@
],
language='c++',
extra_objects=[
@@ -13,28 +24,6 @@ Last-Update: 2021-07-10
],
),
-@@ -117,10 +117,6 @@
- bdir = "src/build"
- rmtree(bdir, ignore_errors=True)
- os.makedirs(bdir)
-- run([
-- "cmake", "-D", "spoa_optimize_for_portability=ON", "-D", "CMAKE_BUILD_TYPE=Release",
-- "-D", "CMAKE_CXX_FLAGS='-I ../vendor/cereal/include/ -fPIC '", "..",
-- ], cwd=bdir)
- run("make", cwd=bdir)
- install.run(self)
-
-@@ -135,8 +131,8 @@
- long_description=long_description,
- long_description_content_type='text/markdown',
- ext_modules=ext_modules,
-- install_requires=['pybind11>=2.4', 'cmake==3.18.4'],
-- setup_requires=['pybind11>=2.4', 'cmake==3.18.4'],
-+ install_requires=['pybind11>=2.4'],
-+ setup_requires=['pybind11>=2.4'],
- cmdclass={
- 'build_ext': BuildExt,
- 'develop': build_spoa,
--- a/pyspoa.cpp
+++ b/pyspoa.cpp
@@ -1,4 +1,4 @@
=====================================
pyproject.toml
=====================================
@@ -0,0 +1,3 @@
+[build-system]
+requires = ["cmake", "pybind11", "setuptools", "wheel", "scikit-build"]
+build-backend = "setuptools.build_meta"
=====================================
requirements.txt deleted
=====================================
@@ -1,5 +0,0 @@
-wheel>=0.34.1
-pybind11>=2.4
-auditwheel>=3.1.0
-scikit-build==0.11.1
-
=====================================
setup.py
=====================================
@@ -1,12 +1,12 @@
import os
import sys
-import setuptools
from shutil import rmtree
from subprocess import run
-from setuptools import setup, Extension
-from setuptools.command.build_ext import build_ext
+import setuptools
+from setuptools import setup, Extension
from setuptools.command.install import install
+from setuptools.command.build_ext import build_ext
class get_pybind_include(object):
@@ -54,6 +54,17 @@ def cpp_flag(compiler):
raise RuntimeError('Unsupported compiler -- at least C++11 support is needed!')
+def build_spoa():
+ bdir = "src/build"
+ rmtree(bdir, ignore_errors=True)
+ os.makedirs(bdir)
+ run([
+ "cmake", "-D", "spoa_optimize_for_portability=ON", "-D", "CMAKE_BUILD_TYPE=Release",
+ "-D", "CMAKE_CXX_FLAGS='-I ../vendor/cereal/include/ -fPIC '", "..",
+ ], cwd=bdir)
+ run("make", cwd=bdir)
+
+
class BuildExt(build_ext):
"""
A custom build extension for adding compiler-specific options.
@@ -73,6 +84,7 @@ class BuildExt(build_ext):
l_opts['unix'] += darwin_opts
def build_extensions(self):
+ build_spoa()
ct = self.compiler.compiler_type
opts = self.c_opts.get(ct, [])
link_opts = self.l_opts.get(ct, [])
@@ -112,22 +124,10 @@ with open('README.md', encoding='utf-8') as f:
long_description = f.read()
-class build_spoa(install):
- def run(self):
- bdir = "src/build"
- rmtree(bdir, ignore_errors=True)
- os.makedirs(bdir)
- run([
- "cmake", "-D", "spoa_optimize_for_portability=ON", "-D", "CMAKE_BUILD_TYPE=Release",
- "-D", "CMAKE_CXX_FLAGS='-I ../vendor/cereal/include/ -fPIC '", "..",
- ], cwd=bdir)
- run("make", cwd=bdir)
- install.run(self)
-
setup(
name='pyspoa',
- version='0.0.8',
+ version='0.0.9',
author='Oxford Nanoporetech Technologies, Ltd.',
author_email='support at nanoporetech.com',
url='https://github.com/nanoporetech/pyspoa',
@@ -135,12 +135,8 @@ setup(
long_description=long_description,
long_description_content_type='text/markdown',
ext_modules=ext_modules,
- install_requires=['pybind11>=2.4', 'cmake==3.18.4'],
- setup_requires=['pybind11>=2.4', 'cmake==3.18.4'],
cmdclass={
'build_ext': BuildExt,
- 'develop': build_spoa,
- 'install': build_spoa,
},
zip_safe=False,
)
View it on GitLab: https://salsa.debian.org/med-team/python-pyspoa/-/compare/c15130f173ffbd4bda10a1113ae65d23369682b5...1e0abd87506adc84a879b3d4c6aadf1fdeffadd1
--
View it on GitLab: https://salsa.debian.org/med-team/python-pyspoa/-/compare/c15130f173ffbd4bda10a1113ae65d23369682b5...1e0abd87506adc84a879b3d4c6aadf1fdeffadd1
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