rdkit_chem 2025.09.3.13 → 2025.09.3.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4ead3b69c8da6f0fddb3a5fe01f5a8d6b50045831e09b041f3a41c77bd06c592
-  data.tar.gz: 6198fa63ccdece161d05392f179a1c25241707680e79ec16e98de72367bc449c
+  metadata.gz: 5fde0a4b5dbefb09dade31e754b66bea9dbbe816cdf0a5e21bc3ab397cfb1d14
+  data.tar.gz: 91ada719794c6beb08034004dc4e85121c47618a4745a43dac28ba0eb0575db3
 SHA512:
-  metadata.gz: 5d552f59f51878f3e521d80ce47c82fd8bcb387cf0fff12f5fe07edb5efe55761a9167cbbaf8189de04fc3ecfcb87d389f68ab6f118b2bef675367bdc135ec72
-  data.tar.gz: 78ae51ccc565f8d70738184b8138efb80f43f50a4a092ab830232c085c9ec06e524b81de3acf285916e5237ceba6063a2a6c24dcb3f606435df9f84b93ed5bd5
+  metadata.gz: 5f156318e8e0657fb96ef9b12ce8f24e0303e5dc9a87e914d11b2d68735fb430c593cb4b594ed94c7dd384ca3a8c4e8090d96975bae7ab6d2c21b4e0aef44016
+  data.tar.gz: b257e8c96af48d2545a82f9516938dd65ce74ac0334efba87fa2237efdac4c484031791d7ead4c96d4e4e091b1d217c1489436a9eb0a17dff529881fd83af0cf

data/Rakefile

@@ -30,8 +30,8 @@ task :build do
   sh 'gem build rdkit_chem.gemspec'
 end
 
-desc 'Build pre-compiled gem for current platform'
-task :build_native do
+desc 'Stage native libraries for current Ruby version (used by CI)'
+task :stage_native do
   ext_so = File.join(NATIVE_DIR, 'RDKitChem.so')
   ext_bundle = File.join(NATIVE_DIR, 'RDKitChem.bundle')
 
@@ -44,7 +44,7 @@ task :build_native do
   ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
   target_dir = "lib/rdkit_chem/#{ruby_version}"
 
-  puts "Packaging pre-compiled gem for Ruby #{ruby_version}..."
+  puts "Staging native libraries for Ruby #{ruby_version} to #{target_dir}..."
 
   # Create target directory
   FileUtils.mkdir_p(target_dir)
@@ -52,7 +52,7 @@ task :build_native do
   # Copy native extension and all shared libraries
   # Linux: *.so*, macOS: *.bundle and *.dylib
   lib_patterns = ["#{NATIVE_DIR}/*.so*", "#{NATIVE_DIR}/*.bundle", "#{NATIVE_DIR}/*.dylib"]
-  
+
   lib_patterns.each do |pattern|
     Dir.glob(pattern).each do |lib|
       # Skip symlinks first pass, copy only real files
@@ -63,7 +63,6 @@ task :build_native do
   end
 
   # Also copy symlinks (they're needed for library resolution)
-  # This includes both .so -> .so.1 and .so.1 -> .so.1.version symlinks
   lib_patterns.each do |pattern|
     Dir.glob(pattern).each do |lib|
       next unless File.symlink?(lib)
@@ -74,17 +73,59 @@ task :build_native do
     end
   end
 
+  puts "Staged #{Dir.glob("#{target_dir}/*").count} files for Ruby #{ruby_version}"
+end
+
+desc 'Build pre-compiled gem for current platform (single Ruby version)'
+task :build_native do
+  Rake::Task['stage_native'].invoke
+
   # Build the platform-specific gem
   ENV['RDKIT_PRECOMPILED'] = '1'
   sh 'gem build rdkit_chem.gemspec'
   ENV.delete('RDKIT_PRECOMPILED')
 
-  # Clean up
-  FileUtils.rm_rf(target_dir)
+  # Clean up staged files
+  ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
+  FileUtils.rm_rf("lib/rdkit_chem/#{ruby_version}")
 
   puts "\nBuilt: rdkit_chem-#{VERSION}-#{Gem::Platform.local}.gem"
 end
 
+desc 'Build fat gem containing all staged Ruby versions'
+task :build_fat_gem do
+  staged_dirs = Dir.glob('lib/rdkit_chem/*.0').select { |d| File.directory?(d) }
+
+  if staged_dirs.empty?
+    abort "ERROR: No staged Ruby versions found in lib/rdkit_chem/\n" \
+          "Run 'rake stage_native' for each Ruby version first."
+  end
+
+  puts "Building fat gem with Ruby versions: #{staged_dirs.map { |d| File.basename(d) }.join(', ')}"
+
+  # Verify each staged directory has the extension
+  staged_dirs.each do |dir|
+    unless File.exist?(File.join(dir, 'RDKitChem.so')) || File.exist?(File.join(dir, 'RDKitChem.bundle'))
+      abort "ERROR: #{dir} missing RDKitChem.{so,bundle}"
+    end
+  end
+
+  # Build the platform-specific gem
+  ENV['RDKIT_PRECOMPILED'] = '1'
+  sh 'gem build rdkit_chem.gemspec'
+  ENV.delete('RDKIT_PRECOMPILED')
+
+  puts "\nBuilt fat gem: rdkit_chem-#{VERSION}-#{Gem::Platform.local}.gem"
+  puts "Contains Ruby versions: #{staged_dirs.map { |d| File.basename(d) }.join(', ')}"
+end
+
+desc 'Clean staged native libraries'
+task :clean_staged do
+  Dir.glob('lib/rdkit_chem/*.0').each do |dir|
+    FileUtils.rm_rf(dir, verbose: true)
+  end
+end
+
 desc 'Bundle system libraries (Boost) into native directory'
 task :bundle_system_libs do
   so_file = File.join(NATIVE_DIR, 'RDKitChem.so')
@@ -247,10 +288,7 @@ end
 desc 'Clean build artifacts'
 task :clean do
   FileUtils.rm_f(Dir.glob('*.gem'))
-  FileUtils.rm_rf('lib/rdkit_chem/3.0')
-  FileUtils.rm_rf('lib/rdkit_chem/3.1')
-  FileUtils.rm_rf('lib/rdkit_chem/3.2')
-  FileUtils.rm_rf('lib/rdkit_chem/3.3')
+  Rake::Task['clean_staged'].invoke
 end
 
 task default: :test

data/lib/rdkit_chem/version.rb

@@ -2,5 +2,5 @@
 
 module RDKitChem
   VERSION = '2025.09.3'
-  GEMVERSION = "#{VERSION}.13"
+  GEMVERSION = "#{VERSION}.14"
 end

data/lib/rdkit_chem.rb

@@ -3,31 +3,34 @@
 require 'rdkit_chem/version'
 
 # Try to load the native extension from multiple possible locations:
-# 1. Pre-compiled gem: lib/rdkit_chem/<ruby_version>/RDKitChem.so
-# 2. Source-compiled gem: rdkit_chem/lib/RDKitChem.so (legacy location)
+# 1. Pre-compiled gem: lib/rdkit_chem/<ruby_version>/RDKitChem.so (fat gem with all Ruby versions)
+# 2. Source-compiled gem: rdkit_chem/lib/RDKitChem.so (development/legacy location)
 
 def find_rdkit_native_extension
   ruby_version = "#{RUBY_VERSION.split('.')[0..1].join('.')}.0"
   base_dir = File.expand_path('rdkit_chem', __dir__)
 
-  # Location 1: Pre-compiled gem - exact Ruby version match
+  # Location 1: Pre-compiled gem - exact Ruby version match (fat gem)
   precompiled_path = File.join(base_dir, ruby_version)
   return precompiled_path if File.directory?(precompiled_path) && has_native_extension?(precompiled_path)
 
-  # Location 2: Pre-compiled gem - any available Ruby version (fallback)
-  # This handles cases where gem was built with different Ruby minor version
-  if File.directory?(base_dir)
-    Dir.glob(File.join(base_dir, '*.0')).sort.reverse.each do |version_dir|
-      return version_dir if has_native_extension?(version_dir)
-    end
-  end
-
-  # Location 3: Source-compiled gem (legacy rdkit_chem/lib/)
+  # Location 2: Source-compiled gem (development build at rdkit_chem/lib/)
   source_compiled_path = File.expand_path('../rdkit_chem/lib', __dir__)
   return source_compiled_path if has_native_extension?(source_compiled_path)
 
-  raise LoadError, 'Cannot find RDKitChem native extension. ' \
-                   "Searched in:\n  - #{precompiled_path}\n  - #{base_dir}/*.0\n  - #{source_compiled_path}"
+  # List available Ruby versions for better error message
+  available_versions = Dir.glob(File.join(base_dir, '*.0'))
+                          .select { |d| has_native_extension?(d) }
+                          .map { |d| File.basename(d) }
+
+  error_msg = "Cannot find RDKitChem native extension for Ruby #{ruby_version}.\n"
+  error_msg += "Searched in:\n  - #{precompiled_path}\n  - #{source_compiled_path}\n"
+  if available_versions.any?
+    error_msg += "Available versions in gem: #{available_versions.join(', ')}\n"
+    error_msg += 'You may need to install a newer version of rdkit_chem gem.'
+  end
+
+  raise LoadError, error_msg
 end
 
 def has_native_extension?(dir)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rdkit_chem
 version: !ruby/object:Gem::Version
-  version: 2025.09.3.13
+  version: 2025.09.3.14
 platform: ruby
 authors:
 - An Nguyen
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2026-01-22 00:00:00.000000000 Z
+date: 2026-01-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake