chore: Update dependencies and build configuration

.github/workflows/release.yml

@@ -180,20 +180,6 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: Install Dependencies
-        env:
-          HOMEBREW_NO_AUTO_UPDATE: 1
-          HOMEBREW_NO_INSTALL_CLEANUP: 1 # Do not run brew cleanup automatically.
-          HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: 1 # Do not automatically update packages.
-        run: |
-          # brew install openssl@3
-          # mkdir -p /usr/local/include
-          # mkdir -p /usr/local/lib
-          ln -sf  $(brew --prefix openssl)/include/openssl /usr/include/openssl
-          ln -sf  $(brew --prefix openssl)/lib/*a /usr/lib/
-          ln -sf  $(brew --prefix openssl)/lib/*dylib /usr/lib/
-          ls $(brew --prefix openssl)/include
-
       - name: Install poetry
         uses: snok/install-poetry@v1
         with:

build.py

@@ -160,25 +160,33 @@ def find_available_library(lib_name: str, *, ignores=[]):
     return Path(lib_path).parent, header_path
 
 
-# def find_openssl_libs():
-#     openssl_dir = subprocess.getoutput('openssl version -d')
-#     openssl_dir = openssl_dir.replace('OPENSSLDIR: "', '').replace('"', '').strip()
+def find_openssl_libs_header():
+    from shutil import which
+    import platform
 
-#     lib_paths = [f"{openssl_dir}/lib"]
-#     head_paths = [f"{openssl_dir}/include"]
+    current_platform = platform.system().lower()
 
+    lib_paths = []
+    head_paths = []
 
-#     if not Path(lib_paths[0]).exists():
-#         print(f"Cannot find openssl lib in {lib_paths[0]}")
-#     else:
-#         print(f"Find openssl lib_paths: {lib_paths}")
+    if current_platform == "darwin" and which("brew"):
+        openssl_dir = subprocess.getoutput('brew --prefix openssl')
 
-#     if not Path(head_paths[0]).exists():
-#         print(f"Cannot find openssl include in {head_paths[0]}")
-#     else:
-#         print(f"Find openssl include: {head_paths}")
+        lib_paths.append(f"{openssl_dir}/lib")
+        head_paths.append(f"{openssl_dir}/include")
+
+        if not Path(lib_paths[0]).exists():
+            print(f"Cannot find openssl lib in {lib_paths[0]}")
+        else:
+            print(f"Find openssl lib_paths: {lib_paths}")
+
+        if not Path(head_paths[0]).exists():
+            print(f"Cannot find openssl include in {head_paths[0]}")
+        else:
+            print(f"Find openssl include: {head_paths}")
+
+    return lib_paths, head_paths
 
-#     return lib_paths, head_paths
 
 def _extra_compile_args_for_libpxblat():
     return [
@@ -214,12 +222,12 @@ def _extra_compile_args_for_pxblat():
 ParallelCompile(f"{get_thread_count()}").install()
 
 
-# openssl_lib, openssl_include = find_openssl_libs()
+openssl_lib, openssl_include = find_openssl_libs_header()
 
 extra_compile_args = ["-pthread"]
 hidden_visibility_args = []
-include_dirs: list[str] = []
-library_dirs: list[str] = []
+include_dirs: list[str] = [] + openssl_include
+library_dirs: list[str] = [] + openssl_lib
 python_module_link_args = []
 base_library_link_args: list[str] = []
 external_libraries = [

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pxblat"
-version = "1.1.17"
+version = "1.1.18"
 description = "A native python binding for blat suite"
 authors = ["Yangyang Li <yangyang.li@northwestern.edu>"]
 homepage = "https://github.com/ylab-hi/pxblat"