From 6367f43708b31917943986b778e4e9df2bc4bb52 Mon Sep 17 00:00:00 2001
From: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Tue, 17 Dec 2024 10:34:30 +0900
Subject: [PATCH 1/4] Coot 1.1.11 rev. 1
---
Formula/coot.rb | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/Formula/coot.rb b/Formula/coot.rb
index 0f80af494..f0706a0ef 100644
--- a/Formula/coot.rb
+++ b/Formula/coot.rb
@@ -4,6 +4,7 @@ class Coot < Formula
url "https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.11.tar.gz"
sha256 "6fd2b5a2d1bad5bdeebdb030b552b800df28c0c03608334fe69725379da8eec0"
license any_of: ["GPL-3.0-only", "LGPL-3.0-only", "GPL-2.0-or-later"]
+ revision 1
bottle do
root_url "https://ghcr.io/v2/brewsci/bio"
@@ -107,6 +108,7 @@ def install
--with-enhanced-ligand-tools
--with-boost=#{boost_prefix}
--with-boost-libdir=#{boost_prefix}/lib
+ --with-coordgen=#{Formula["coordgen"].opt_prefix}
--with-gemmi=#{Formula["gemmi"].opt_prefix}
--with-glm=#{Formula["glm"].opt_prefix}
--with-rdkit-prefix=#{rdkit_prefix}
@@ -117,12 +119,6 @@ def install
]
ENV.append_to_cflags "-fPIC" if OS.linux?
- # Use libcoordgen instead of RDKitcoordgen
- inreplace "configure", "RDKitcoordgen", "coordgen"
- # patch
- inreplace "src/key-bindings.cc",
- "PyObject *result_py = PyEval_CallObject(function_py, arg_list);",
- "PyObject *result_py = PyObject_Call(function_py, arg_list, nullptr);"
system "./configure", *args
system "make"
ENV.deparallelize { system "make", "install" }
From 73b8504a64ed42ce807e9354adf66a3e5782341c Mon Sep 17 00:00:00 2001
From: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Tue, 17 Dec 2024 14:29:25 +0900
Subject: [PATCH 2/4] coot 1.1.11 Rev.1
---
Formula/coot.rb | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/Formula/coot.rb b/Formula/coot.rb
index f0706a0ef..5e7b4e11e 100644
--- a/Formula/coot.rb
+++ b/Formula/coot.rb
@@ -52,7 +52,7 @@ class Coot < Formula
depends_on "pango"
depends_on "py3cairo"
depends_on "pygobject3"
- depends_on "python@3.13"
+ depends_on "python@3.12"
depends_on "rdkit"
depends_on "sqlite"
@@ -75,7 +75,7 @@ class Coot < Formula
end
def python3
- "python3.13"
+ "python3.12"
end
def install
@@ -99,7 +99,7 @@ def install
# Set Boost, RDKit, and FFTW2 root
boost_prefix = Formula["boost"].opt_prefix
- boost_python_lib = "boost_python312-mt"
+ boost_python_lib = "boost_python312"
rdkit_prefix = Formula["rdkit"].opt_prefix
fftw2_prefix = Formula["clipper4coot"].opt_prefix/"fftw2"
@@ -108,7 +108,6 @@ def install
--with-enhanced-ligand-tools
--with-boost=#{boost_prefix}
--with-boost-libdir=#{boost_prefix}/lib
- --with-coordgen=#{Formula["coordgen"].opt_prefix}
--with-gemmi=#{Formula["gemmi"].opt_prefix}
--with-glm=#{Formula["glm"].opt_prefix}
--with-rdkit-prefix=#{rdkit_prefix}
@@ -116,6 +115,7 @@ def install
--with-backward
--with-libdw
BOOST_PYTHON_LIB=#{boost_python_lib}
+ PYTHON=#{python3}
]
ENV.append_to_cflags "-fPIC" if OS.linux?
From 8b895c9c122b8fc070a313a8d1c7bd5df5359a22 Mon Sep 17 00:00:00 2001
From: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Tue, 17 Dec 2024 14:47:09 +0900
Subject: [PATCH 3/4] coot 1.1.11 Rev.1
---
Formula/coot.rb | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Formula/coot.rb b/Formula/coot.rb
index 5e7b4e11e..c4ce7c37f 100644
--- a/Formula/coot.rb
+++ b/Formula/coot.rb
@@ -29,7 +29,6 @@ class Coot < Formula
depends_on "boost-python3"
depends_on "brewsci/bio/clipper4coot"
depends_on "brewsci/bio/gemmi"
- depends_on "brewsci/bio/gtk4@4.14"
depends_on "brewsci/bio/libccp4"
depends_on "brewsci/bio/mmdb2"
depends_on "brewsci/bio/raster3d"
@@ -44,6 +43,7 @@ class Coot < Formula
depends_on "gmp"
depends_on "graphene"
depends_on "gsl"
+ depends_on "gtk4"
depends_on "harfbuzz"
depends_on "libepoxy"
depends_on "libpng"
From 96285648c573a7e19ee0ed6c76e930657122cc8b Mon Sep 17 00:00:00 2001
From: Yoshitaka Moriwaki <virgospica93@gmail.com>
Date: Tue, 17 Dec 2024 14:58:29 +0900
Subject: [PATCH 4/4] coot 1.1.11 Rev.1
---
Formula/gtk4@4.14.rb | 119 -------------------------------------------
1 file changed, 119 deletions(-)
delete mode 100644 Formula/gtk4@4.14.rb
diff --git a/Formula/gtk4@4.14.rb b/Formula/gtk4@4.14.rb
deleted file mode 100644
index 45d1133c7..000000000
--- a/Formula/gtk4@4.14.rb
+++ /dev/null
@@ -1,119 +0,0 @@
-class Gtk4AT414 < Formula
- desc "Toolkit for creating graphical user interfaces"
- homepage "https://gtk.org/"
- url "https://download.gnome.org/sources/gtk/4.14/gtk-4.14.5.tar.xz"
- sha256 "5547f2b9f006b133993e070b87c17804e051efda3913feaca1108fa2be41e24d"
- license "LGPL-2.1-or-later"
-
- livecheck do
- url :stable
- regex(/gtk[._-](4\.([0-8]\d*?)?[02468](?:\.\d+)*?)\.t/i)
- end
-
- bottle do
- root_url "https://ghcr.io/v2/brewsci/bio"
- sha256 arm64_sequoia: "0f7ad6845e7f25b6d69bd185b5dd586a344a743029324a8a695ebb05fc809b74"
- sha256 arm64_sonoma: "8b5db42d59a9296b73b11b8d98803f4432f9ee2c17805ccc3de839c340338296"
- sha256 ventura: "59178fac56566748b4e0ea8c1aaba45eca62638b91bef29f93affcbcdc8535d3"
- sha256 x86_64_linux: "ac87b20522507f8b766a1c0854116ef96e376977713112683cdf816e5e808643"
- end
-
- keg_only "provided by Homebrew core"
-
- depends_on "docbook" => :build
- depends_on "docbook-xsl" => :build
- depends_on "docutils" => :build
- depends_on "gettext" => :build
- depends_on "gobject-introspection" => :build
- depends_on "meson" => :build
- depends_on "ninja" => :build
- depends_on "pkg-config" => [:build, :test]
- depends_on "sassc" => :build
- depends_on "cairo"
- depends_on "fontconfig"
- depends_on "fribidi"
- depends_on "gdk-pixbuf"
- depends_on "glib"
- depends_on "graphene"
- depends_on "harfbuzz"
- depends_on "hicolor-icon-theme"
- depends_on "jpeg-turbo"
- depends_on "libepoxy"
- depends_on "libpng"
- depends_on "libtiff"
- depends_on "pango"
-
- uses_from_macos "libxslt" => :build # for xsltproc
- uses_from_macos "cups"
-
- on_macos do
- depends_on "gettext"
- end
-
- on_linux do
- depends_on "libx11"
- depends_on "libxcursor"
- depends_on "libxdamage"
- depends_on "libxext"
- depends_on "libxfixes"
- depends_on "libxi"
- depends_on "libxinerama"
- depends_on "libxkbcommon"
- depends_on "libxrandr"
- depends_on "wayland"
- end
-
- def install
- args = %w[
- -Dgtk_doc=false
- -Dman-pages=true
- -Dintrospection=enabled
- -Dbuild-examples=false
- -Dbuild-tests=false
- -Dmedia-gstreamer=disabled
- -Dvulkan=disabled
- ]
-
- if OS.mac?
- args << "-Dx11-backend=false"
- args << "-Dmacos-backend=true"
- args << "-Dprint-cups=disabled" if MacOS.version <= :mojave
- end
-
- # ensure that we don't run the meson post install script
- ENV["DESTDIR"] = "/"
-
- # Find our docbook catalog
- ENV["XML_CATALOG_FILES"] = "#{etc}/xml/catalog"
-
- # Disable asserts and cast checks explicitly
- ENV.append "CPPFLAGS", "-DG_DISABLE_ASSERT -DG_DISABLE_CAST_CHECKS"
-
- system "meson", "setup", "build", *args, *std_meson_args
- system "meson", "compile", "-C", "build", "--verbose"
- system "meson", "install", "-C", "build"
- end
-
- def post_install
- system "#{Formula["glib"].opt_bin}/glib-compile-schemas", "#{HOMEBREW_PREFIX}/share/glib-2.0/schemas"
- system bin/"gtk4-update-icon-cache", "-f", "-t", "#{HOMEBREW_PREFIX}/share/icons/hicolor"
- system "#{Formula["glib"].opt_bin}/gio-querymodules", "#{HOMEBREW_PREFIX}/lib/gtk-4.0/4.0.0/printbackends"
- end
-
- test do
- (testpath/"test.c").write <<~EOS
- #include <gtk/gtk.h>
-
- int main(int argc, char *argv[]) {
- gtk_disable_setlocale();
- return 0;
- }
- EOS
-
- flags = shell_output("#{Formula["pkg-config"].opt_bin}/pkg-config --cflags --libs gtk4").strip.split
- system ENV.cc, "test.c", "-o", "test", *flags
- system "./test"
- # include a version check for the pkg-config files
- assert_match version.to_s, shell_output("cat #{lib}/pkgconfig/gtk4.pc").strip
- end
-end