Merge pull request ccsb-scripps#340 from rwxayheee/test_workflow

Upgrade actions/download-artifact to v4; Explicitly Check PEP 440 Compliance; Fix Workflows, Makefiles, and Boost Usage

.github/workflows/compile-binaries.yaml

@@ -23,7 +23,7 @@ on:
 
 jobs:
   compile_binaries:
-    name: Build wheels on ${{ matrix.os }}
+    name: Compile binaries on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -33,6 +33,9 @@ jobs:
           - os: ubuntu-latest
             arch: aarch64
           - os: macos-latest
+            arch: x86_64
+          - os: macos-latest
+            arch: aarch64
           - os: windows-latest
 
     steps:
@@ -61,8 +64,6 @@ jobs:
           run: |
             cd /vina/build/linux/release
             make
-            mv vina vina-${{ matrix.arch }}
-            mv vina_split vina_split-${{ matrix.arch }}
       - name: Compile Vina for macOS
         if: matrix.os == 'macos-latest'
         run: |
@@ -80,13 +81,8 @@ jobs:
           .\compile.bat
         shell: powershell
       - name: Upload artifacts for inspection
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: binaries
+          name: binaries-${{ matrix.os }}${{ matrix.arch }}
           path: |
-            ./**/release/vina
-            ./**/release/vina-${{ matrix.arch }}
-            ./**/release/vina_split
-            ./**/release/vina_split-${{ matrix.arch }}
-            ./**/release/vina.exe
-            ./**/release/vina_split.exe
+            ./**/release/vina*

.github/workflows/pypi-build.yml

@@ -27,7 +27,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        include:
+          - os: ubuntu-latest
+            arch: x86_64
 
     steps:
       - name: Checkout
@@ -61,13 +63,17 @@ jobs:
         env:
           CIBW_SKIP: pp*
           CIBW_ARCHS: auto64
-          CIBW_ARCHS_LINUX: auto64 aarch64
+          CIBW_ARCHS_LINUX: ${{ matrix.arch }}
           CIBW_BEFORE_BUILD: |
             pip install --upgrade pip setuptools
           CIBW_BEFORE_ALL_MACOS: |
             brew install boost swig
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
           CIBW_BEFORE_ALL_LINUX: |
+            sed -i s/mirror.centos.org/vault.centos.org/g /etc/yum.repos.d/*.repo 
+            sed -i s/^#.*baseurl=http/baseurl=http/g /etc/yum.repos.d/*.repo 
+            sed -i s/^mirrorlist=http/#mirrorlist=http/g /etc/yum.repos.d/*.repo
+            yum clean all && yum -y update 
             yum install -y wget python-devel pcre-devel
             # Install SWIG
             wget https://downloads.sourceforge.net/swig/swig-4.0.2.tar.gz
@@ -87,9 +93,9 @@ jobs:
             rm -rf boost_1_*
             rm -rf swig-4*
       - name: Upload artifacts for inspection
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: wheels
           path: ./wheelhouse/*.whl
 
   build_sdist:
@@ -117,9 +123,9 @@ jobs:
           cd ./build/python
           python setup.py sdist
       - name: Upload artifacts for inspection
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: sdist
           path: ./build/python/dist/*.tar.gz
 
   upload_pypi:
@@ -139,7 +145,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip setuptools twine
       - name: Download artifacts
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: ./dist

build/linux/release/Makefile

@@ -1,4 +1,4 @@
-BASE=/usr/local
+BASE=/usr
 BOOST_VERSION=
 BOOST_INCLUDE = $(BASE)/include
 C_PLATFORM=-static -pthread

build/mac/release/Makefile

@@ -1,4 +1,4 @@
-BASE=/usr/local
+BASE=$(shell brew --prefix)
 BOOST_VERSION=
 BOOST_INCLUDE = $(BASE)/include
 C_PLATFORM=-pthread

build/python/pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools>=50.3", "wheel"]
+requires = ["setuptools>=50.3", "wheel", "packaging"]
 build-backend = "setuptools.build_meta"

build/python/setup.py

@@ -19,7 +19,7 @@
 from distutils.util import convert_path
 from distutils.sysconfig import customize_compiler
 from distutils.ccompiler import show_compilers
-
+from packaging.version import Version, InvalidVersion
 
 # Path to the directory that contains this setup.py file.
 base_dir = os.path.abspath(os.path.dirname(__file__))
@@ -53,13 +53,25 @@ def find_version():
     3. __init__.py (as failback)
 
     """
+
+    def is_compliant(version_str):
+        try:
+            # Attempt to parse the version string using packaging's Version class
+            Version(version_str)
+            return True
+        except InvalidVersion:
+            # If parsing fails, the version is not PEP 440 compliant
+            print(f"{version_str} is not PEP 440 compliant")
+            return False
+
     version_file = os.path.join(base_dir, 'vina', 'version.py')
     if os.path.isfile(version_file):
         with open(version_file) as f:
             version = f.read().strip()
 
         print('Version found: %s (from version.py)' % version)
-        return version
+        if is_compliant(version):
+            return version
 
     try:
         git_output = subprocess.check_output(['git', 'describe', '--abbrev=7', '--dirty=@mod', '--always', '--tags'])
@@ -70,7 +82,8 @@ def find_version():
         version = git_output.replace('-', '.dev', 1).replace('@', '-', 1).replace('-', '+', 1).replace('-','')
 
         print('Version found %s (from git describe)' % version)
-        return version
+        if is_compliant(version):
+            return version
     except:
         pass
 

src/lib/vina.h

@@ -33,9 +33,7 @@
 #include <boost/log/trivial.hpp>
 #include <boost/log/expressions.hpp>
 #include <boost/program_options.hpp>
-#include <boost/filesystem/fstream.hpp>
-#include <boost/filesystem/exception.hpp>
-#include <boost/filesystem/convenience.hpp> // filesystem::basename
+#include <boost/filesystem.hpp>
 #include <boost/thread/thread.hpp> // hardware_concurrency // FIXME rm ?
 #include <boost/algorithm/string.hpp>
 //#include <openbabel/mol.h>

src/split/split.cpp

@@ -28,9 +28,7 @@
 #include <fstream> //  getline?
 #include <cmath> // for ceila
 #include <boost/program_options.hpp>
-#include <boost/filesystem/fstream.hpp>
-#include <boost/filesystem/exception.hpp>
-#include <boost/filesystem/convenience.hpp> // filesystem::basename
+#include <boost/filesystem.hpp>
 
 #include "file.h"
 #include "parse_error.h"