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ntsynt: support python 3.13 #1934

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ntsynt: support python 3.13 #1934

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14 changes: 7 additions & 7 deletions Formula/ntsynt.rb
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
class Ntsynt < Formula

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GitHub Actions / build-bottles (macos-15)

No bottle built for ntsynt! 

ntsynt has unbottled dependencies, so a bottle will not be built.
include Language::Python::Virtualenv
include Language::Python::Shebang
# cite Coombe_2024: "https://doi.org/10.1101/2024.02.07.579356"
Expand All @@ -23,7 +23,7 @@
depends_on "rust" => :build
depends_on "pigz" => :test
depends_on "bedtools"
depends_on "btllib"
depends_on "brewsci/bio/btllib"
depends_on "cbc"
depends_on "certifi"
depends_on "cython"
Expand All @@ -32,7 +32,7 @@
depends_on "libyaml"
depends_on "numpy"
depends_on "openssl@3"
depends_on "python@3.12"
depends_on "python@3.13"
depends_on "samtools"
depends_on "seqtk"
depends_on "xz"
Expand Down Expand Up @@ -327,10 +327,10 @@
end

def python3
which("python3.12")
which("python3.13")
end

def install

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GitHub Actions / build-bottles (macos-14)

`brew install --verbose --formula --build-bottle brewsci/bio/ntsynt` failed on macOS Sonoma (14) on Apple Silicon! 


  running build_ext
  building 'immutables._map' extension
  creating build/temp.macosx-14.0-arm64-cpython-313/immutables
  clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk -DNDEBUG=1 -I/opt/homebrew/Cellar/ntsynt/1.0.2/libexec/include -I/opt/homebrew/opt/[email protected]/Frameworks/Python.framework/Versions/3.13/include/python3.13 -c immutables/_map.c -o build/temp.macosx-14.0-arm64-cpython-313/immutables/_map.o -O2 -std=c99 -fsigned-char -Wall -Wsign-compare -Wconversion
  immutables/_map.c:1287:12: error: call to undeclared function '_PyLong_Format'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
      tmp2 = _PyLong_Format(tmp1, 2);
             ^
  immutables/_map.c:1287:10: error: incompatible integer to pointer conversion assigning to 'PyObject *' (aka 'struct _object *') from 'int' [-Wint-conversion]
      tmp2 = _PyLong_Format(tmp1, 2);
           ^ ~~~~~~~~~~~~~~~~~~~~~~~
  2 errors generated.
  error: command '/opt/homebrew/Library/Homebrew/shims/mac/super/clang' failed with exit code 1
  error: subprocess-exited-with-error
  
  × Building wheel for immutables (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /opt/homebrew/Cellar/ntsynt/1.0.2/libexec/bin/python /opt/homebrew/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /private/tmp/tmp12s_h5qm
  cwd: /private/tmp/ntsynt--immutables-20241020-19378-xlps5r/immutables-0.20
  Building wheel for immutables (pyproject.toml): finished with status 'error'
  ERROR: Failed building wheel for immutables
Failed to build immutables
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (immutables)

==> Formula
Tap: brewsci/bio
Path: /opt/homebrew/Library/Taps/brewsci/homebrew-bio/Formula/ntsynt.rb
==> Configuration
HOMEBREW_VERSION: 4.4.1-62-g6f17b06
ORIGIN: https://github.com/Homebrew/brew
HEAD: 6f17b0644771e0a1d7c15ac72471dae2ef87314a
Last commit: 30 hours ago
Core tap HEAD: 401c8d52044a0b63680b73c7ebf5cdcca19351b6
Core tap last commit: 6 days ago
Core tap JSON: 20 Oct 00:09 UTC
Core cask tap HEAD: c0fd9d20c432ea2470b6f46415cce46ced667348
Core cask tap last commit: 6 days ago
Core cask tap JSON: 20 Oct 00:09 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_BOOTSNAP: set
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: [email protected]
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 3
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.3.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.3.5/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 15.0.0 build 1500
Git: 2.39.3 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 14.7-arm64
CLT: 16.0.0.0.1.1724870825
Xcode: 15.4 => /Applications/Xcode_15.4.app/Contents/Developer
Rosetta 2: false
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j3
CMAKE_PREFIX_PATH: /opt/homebrew/opt/readline:/opt/homebrew/opt/sqlite:/opt/homebrew/opt/libomp:/opt/homebrew/opt/openblas:/opt/homebrew/opt/cython:/opt/homebrew
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH:

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GitHub Actions / build-bottles (macos-13)

`brew install --verbose --formula --build-bottle brewsci/bio/ntsynt` failed on macOS Ventura (13)! 


  running build_ext
  building 'immutables._map' extension
  creating build/temp.macosx-13.0-x86_64-cpython-313/immutables
  clang -fno-strict-overflow -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk -DNDEBUG=1 -I/usr/local/Cellar/ntsynt/1.0.2/libexec/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.13/include/python3.13 -c immutables/_map.c -o build/temp.macosx-13.0-x86_64-cpython-313/immutables/_map.o -O2 -std=c99 -fsigned-char -Wall -Wsign-compare -Wconversion
  immutables/_map.c:1287:12: error: call to undeclared function '_PyLong_Format'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
      tmp2 = _PyLong_Format(tmp1, 2);
             ^
  1 error generated.
  error: command '/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang' failed with exit code 1
  error: subprocess-exited-with-error
  
  × Building wheel for immutables (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  full command: /usr/local/Cellar/ntsynt/1.0.2/libexec/bin/python /usr/local/lib/python3.13/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /private/tmp/tmp0glunhlz
  cwd: /private/tmp/ntsynt--immutables-20241020-26547-6sqvr2/immutables-0.20
  Building wheel for immutables (pyproject.toml): finished with status 'error'
  ERROR: Failed building wheel for immutables
Failed to build immutables
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (immutables)

==> Formula
Tap: brewsci/bio
Path: /usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio/Formula/ntsynt.rb
==> Configuration
HOMEBREW_VERSION: 4.4.1-62-g6f17b06
ORIGIN: https://github.com/Homebrew/brew
HEAD: 6f17b0644771e0a1d7c15ac72471dae2ef87314a
Last commit: 30 hours ago
Core tap HEAD: 677c31e0d35d336bec94d43ef2a1c427e441cfbc
Core tap last commit: 11 days ago
Core tap JSON: 20 Oct 00:09 UTC
Core cask tap HEAD: 7259460b60aa1ad0803a5f714fb8f8afe6c6aeb0
Core cask tap last commit: 11 days ago
Core cask tap JSON: 20 Oct 00:09 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_BOOTSNAP: set
HOMEBREW_CACHE: /Users/runner/Library/Caches/Homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_CURL_PATH: /usr/bin/curl
HOMEBREW_FAIL_LOG_LINES: 150
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_GIT_EMAIL: [email protected]
HOMEBREW_GIT_NAME: BrewTestBot
HOMEBREW_GIT_PATH: /usr/bin/git
HOMEBREW_LOGS: /Users/runner/work/homebrew-bio/homebrew-bio/logs
HOMEBREW_MAKE_JOBS: 4
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_EMOJI: set
HOMEBREW_NO_ENV_HINTS: set
HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: set
HOMEBREW_NO_INSTALL_CLEANUP: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.3.5 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.5/bin/ruby
CPU: quad-core 64-bit ivybridge
Clang: 15.0.0 build 1500
Git: 2.39.3 => /usr/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 13.7-x86_64
CLT: 14.3.1.0.1.1683849156
Xcode: 15.2 => /Applications/Xcode_15.2.app/Contents/Developer
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local/opt/readline:/usr/local/opt/sqlite:/usr/local/opt/libomp:/usr/local/opt/openblas:/usr/local/opt/cython:/usr/local
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX13.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /usr/local/opt/[email protected]/Frameworks
PKG_CONFIG_PATH: /usr/local/opt/xz/lib/pkgconfig:/usr/local/opt/mpdecimal/lib/pkgconfig:/usr/local/opt/openssl@3/lib/pkgconfig:/usr/local/opt/readline/lib/pkgconfig:/usr/local/opt/sqlite/lib/pkgconfig:/usr/local/opt/pyth
venv = virtualenv_create(libexec, python3)
venv.pip_install resources
# Remove the bundled CBC solver (Ref: homebrew-core/Formula/snakemake.rb)
Expand All @@ -344,20 +344,20 @@
inreplace "bin/meson.build", "install_dir : 'bin'", "install_dir : 'libexec'"
inreplace "scripts/install-ntjoin", "${MESON_INSTALL_PREFIX}/bin",
"${MESON_INSTALL_PREFIX}/libexec"
# pkg_resources is deprecated in Python 3.12
inreplace libexec/"lib/python3.12/site-packages/wrapt/importer.py" do |s|
# pkg_resources is deprecated in Python 3.13
inreplace libexec/"lib/python3.13/site-packages/wrapt/importer.py" do |s|
s.gsub! "import pkg_resources",
"group_entry_points = importlib.metadata.entry_points().get(group, [])"
s.gsub! "pkg_resources.iter_entry_points(group=group)",
"group_entry_points"
end
inreplace libexec/"lib/python3.12/site-packages/ncls/__init__.py" do |s|
inreplace libexec/"lib/python3.13/site-packages/ncls/__init__.py" do |s|
s.gsub! "import pkg_resources",
"import importlib.metadata"
s.gsub! "pkg_resources.get_distribution(\"ncls\").version",
"importlib.metadata.version(\"ncls\")"
end
inreplace libexec/"lib/python3.12/site-packages/stopit/__init__.py" do |s|
inreplace libexec/"lib/python3.13/site-packages/stopit/__init__.py" do |s|
s.gsub! "import pkg_resources",
"import importlib.metadata"
s.gsub! "pkg_resources.get_distribution(__name__).version",
Expand Down
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