From 575c45d5c02598d178f3d06f55ccb4c593906622 Mon Sep 17 00:00:00 2001
From: Nezar Abdennur <nabdennur@gmail.com>
Date: Sun, 12 Mar 2023 00:35:10 -0500
Subject: [PATCH] Re-incorporate libkent into package build process

---
 MANIFEST.in    | 10 +++---
 Makefile       | 12 +++-----
 pyproject.toml | 22 +++----------
 setup.py       | 84 ++++++++++++++++++++++++++++++++++++--------------
 src/makefile   | 14 ++++++---
 5 files changed, 85 insertions(+), 57 deletions(-)

diff --git a/MANIFEST.in b/MANIFEST.in
index ebc6036..25e48dd 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,13 +1,13 @@
 include LICENSE
 include README.md
 include Makefile
-graft tests
-graft include
+include bbi/cbbi.pyx
+include bbi/cbbi.pxd
 graft src
+graft include
+graft tests
 
-global-include *.pyx
-global-include *.pxd
-
+recursive-exclude venv *
 global-exclude __pycache__/*
 global-exclude *.o
 global-exclude *.a
diff --git a/Makefile b/Makefile
index 55b9f11..5c74e0d 100644
--- a/Makefile
+++ b/Makefile
@@ -5,26 +5,24 @@ UNAME_S := $(shell uname -s)
 
 ifeq (${MACHTYPE},)
 	MACHTYPE:=$(shell uname -m)
-#    $(info MACHTYPE was empty, set to: ${MACHTYPE})
-endif
-ifneq (,$(findstring -,$(MACHTYPE)))
-#    $(info MACHTYPE has - sign ${MACHTYPE})
-	MACHTYPE:=$(shell uname -m)
-#    $(info MACHTYPE has - sign set to: ${MACHTYPE})
 endif
 export MACHTYPE
 
 export CC ?= gcc
 export COPTS=-g -pthread -fPIC -static
 export CFLAGS=-Wall $(shell pkg-config --static --cflags-only-other openssl zlib libpng)
+export DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -DUSE_SSL
 export LDFLAGS=-L${current_dir}/src/${MACHTYPE} $(shell pkg-config --static --libs openssl zlib libpng)
 export INC=-I${current_dir}/include $(shell pkg-config --static --cflags-only-I openssl zlib libpng)
-export DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE} -DUSE_SSL
 # pass through COREDUMP
 ifneq (${COREDUMP},)
 	DEFS+=-DCOREDUMP
 endif
 
+# Append values to CFLAGS and LDFLAGS
+CFLAGS += $(shell echo $$CFLAGS)
+LDFLAGS += $(shell echo $$LDFLAGS)
+
 
 all: build
 
diff --git a/pyproject.toml b/pyproject.toml
index c49682a..ad0585b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,27 +71,15 @@ repository = "https://github.com/nvictus/pybbi"
 [tool.cibuildwheel]
 build = ["cp38-*", "cp39-*", "cp310-*", "cp311-*"]
 skip = "*-musllinux*"
-
+build-verbosity = 3
 
 [tool.cibuildwheel.linux]
 archs = ["x86_64", "aarch64"]
 before-all = "yum install -y gcc make zlib-devel openssl-devel libpng-devel"
-before-build = "make build-ucsc"
-
-[tools.cibuildwheel.linux.environment]
-LDFLAGS = "-Wl,--no-as-needed"
 
 
 [tool.cibuildwheel.macos]
-archs = ["x86_64"]
-before-all = "brew install pkg-config openssl libpng"
-before-build = "make build-ucsc"
-
-[tool.cibuildwheel.macos.environment]
-LDFLAGS = "-L/usr/local/opt/openssl/lib -L/opt/homebrew/opt/openssl/lib"
-CPPFLAGS = "-I/usr/local/opt/openssl/include -I/opt/homebrew/opt/openssl/include"
-PATH = "/usr/local/opt/openssl/bin:/opt/homebrew/opt/openssl/bin:$PATH"
-PKG_CONFIG_PATH = "/usr/local/opt/openssl/lib/pkgconfig:/opt/homebrew/opt/openssl/lib/pkgconfig:$PKG_CONFIG_PATH"
-C_INCLUDE_PATH = "/usr/local/include/libpng:/usr/local/opt/openssl/include:$C_INCLUDE_PATH"
-BLDSHARED = 'gcc -bundle -undefined dynamic_lookup -arch x86_64 -g'
-LDSHARED = 'gcc -bundle -undefined dynamic_lookup -arch x86_64 -g'
+archs = ["x86_64"]  # "arm64" is not yet supported by GitHub Actions (Needs M1 runner)
+before-all = """
+brew install pkg-config openssl libpng  # -> /usr/local (x86_64)
+"""
diff --git a/setup.py b/setup.py
index 7e1ba7b..2b847fb 100644
--- a/setup.py
+++ b/setup.py
@@ -1,29 +1,71 @@
 import os
-import os.path
 import pathlib
+import subprocess
 import sys
 
-import numpy
-import pkgconfig
-from Cython.Build import cythonize
-from Cython.Distutils.build_ext import new_build_ext as cython_build_ext
 from setuptools import Extension, setup
 
-ARCH = os.uname().machine
+# Determine architecture for build; defaults to machine architecture.
+# cibuildwheel sets ARCHFLAGS on macos runners
+# user can also set ARCH to override
+MACHINE_ARCH = os.uname().machine
+if sys.platform == "darwin" and "ARCHFLAGS" in os.environ:
+    ARCH = os.environ["ARCHFLAGS"].split()[-1]
+elif "ARCH" in os.environ:
+    ARCH = os.environ["ARCH"]
+else:
+    ARCH = MACHINE_ARCH
 
-deps = {}
-if "sdist" not in sys.argv:
+
+if "sdist" in sys.argv:
+    # Skip compilation when building a source distribution
+    setup()
+
+else:
+    import numpy
+    import pkgconfig
+    from Cython.Build import cythonize
+    from Cython.Distutils.build_ext import new_build_ext as cython_build_ext
+
+    # 1. Compile the UCSC library (libkent.a)
+    # Pass the target architecture to the makefile
+    os.environ["MACHTYPE"] = ARCH
+
+    # Platform and architecture-specific flags
+    if sys.platform == "darwin":
+        brew_optdir = None
+        if ARCH.startswith("arm"):
+            brew_optdir = "/opt/homebrew/opt"
+        else:
+            brew_optdir = "/usr/local/opt"
+        os.environ["CFLAGS"] = f"-arch {ARCH}"
+        if brew_optdir is not None:
+            os.environ["LDFLAGS"] = f"-L{brew_optdir}/openssl/lib {os.environ.get('LDFLAGS', '')}"
+            os.environ["C_INCLUDE_PATH"] = f"{brew_optdir}/openssl/include:{brew_optdir}/libpng/include:{os.environ.get('C_INCLUDE_PATH', '')}"
+            os.environ["PKG_CONFIG_PATH"] = f"{brew_optdir}/openssl/lib/pkgconfig:{os.environ.get('PKG_CONFIG_PATH', '')}"
+
+    # Parse pkg-config dependencies
+    # This will let us know if something is missing
     deps = pkgconfig.parse("zlib openssl libpng")
 
+    # Build the UCSC library
     if not pathlib.Path("src", ARCH, "libkent.a").exists():
-        raise RuntimeError(
-            f"src/{ARCH}/libkent.a not found. "
-            "Please run `make build-ucsc`."
-        )
+        subprocess.run(["make", "clean-ucsc"])
+        ret = subprocess.run(["make", "build-ucsc"], check=True)
+        if ret.returncode != 0:
+            raise RuntimeError("Failed to build UCSC library.")
 
 
-def get_extension_modules():
-    ext_modules = [
+    # 2. Compile cython extension module, link to libkent and other dependencies
+    # Platform and architecture-specific linker flags
+    if sys.platform == "darwin":
+        os.environ["BLDSHARED"] = f'gcc -bundle -undefined dynamic_lookup -arch {ARCH} -g'
+        os.environ["LDSHARED"] = f'gcc -bundle -undefined dynamic_lookup -arch {ARCH} -g'
+    elif sys.platform == "linux":
+        os.environ["LDFLAGS"] = f"-Wl,--no-as-needed {os.environ.get('LDFLAGS', '')}"
+    
+    # Configure and cythonize pyx to C extension module
+    ext_modules = cythonize([
         Extension(
             name="bbi.cbbi",
             sources=[os.path.join("bbi", "cbbi.pyx")],
@@ -39,14 +81,10 @@ def get_extension_modules():
             + deps.pop("include_dirs", []),
             **deps,
         ),
-    ]
-    if "sdist" in sys.argv:
-        return ext_modules
-    else:
-        return cythonize(ext_modules)
+    ])
 
 
-setup(
-    ext_modules=get_extension_modules(),
-    build_ext=cython_build_ext,
-)
+    setup(
+        ext_modules=ext_modules,
+        build_ext=cython_build_ext,
+    )
diff --git a/src/makefile b/src/makefile
index e57a9e3..1513e94 100644
--- a/src/makefile
+++ b/src/makefile
@@ -54,17 +54,21 @@ $(MACHTYPE)/libkent.a: $(O) $(MACHTYPE)
 $(MACHTYPE):
 	mkdir $(MACHTYPE)
 
+.PHONY: all
+all: $(MACHTYPE)/libkent.a
+
+%.o: %.c
+	${CC} ${COPTS} ${CFLAGS} ${DEFS} ${LDFLAGS} ${INC} -o $@ -c $<
+
+.PHONY: test
 test:
 	cd tests && ${MAKE} test
 
+.PHONY: clean
 clean:
 	rm -f ${O} $(MACHTYPE)/libkent.a
 	cd tests && ${MAKE} clean
 
+.PHONY: tags
 tags:
 	etags ../inc/*.h ../lib/*.h ../lib/*.c  ../hg/inc/*.h ../hg/lib/*.h ../hg/lib/*.c ../hg/hgTracks/*.c ../hg/hgc/*.c ../hg/hgTrackUi/*.c
-
-%.o: %.c
-	${CC} ${COPTS} ${CFLAGS} ${DEFS} ${LDFLAGS} ${INC} -o $@ -c $<
-
-all: $(MACHTYPE)/libkent.a
\ No newline at end of file