From 156b9984e05245e8d082bba9ee43808a0b7273a8 Mon Sep 17 00:00:00 2001 From: Benjamin Demaille Date: Tue, 7 Jul 2026 05:18:26 +0200 Subject: [PATCH 1/5] tigmint 1.2.10 Co-authored-by: Claude Opus 4.8 (1M context) --- Formula/tigmint.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Formula/tigmint.rb b/Formula/tigmint.rb index 3c39318a2..2a08d3efd 100644 --- a/Formula/tigmint.rb +++ b/Formula/tigmint.rb @@ -2,8 +2,8 @@ class Tigmint < Formula # cite Jackman_2018: "https://doi.org/10.1186/s12859-018-2425-6" desc "Correct misassemblies using linked or long reads" homepage "https://bcgsc.github.io/tigmint/" - url "https://github.com/bcgsc/tigmint/releases/download/v1.2.5/tigmint-1.2.5.tar.gz" - sha256 "15a56748f19732462c0445fe9df2f737a4bf8caa97dbc0fe6e943e3fd1c6b5f0" + url "https://github.com/bcgsc/tigmint/releases/download/v1.2.10/tigmint-1.2.10.tar.gz" + sha256 "8e7b5d424ff69d5da7b117bef9996463b02205078ce0fb6e3074ca6c9933efa9" license "GPL-3.0-only" head "https://github.com/bcgsc/tigmint.git" From b998d5dc0143dd8a846b42452177dc91e8e77e5a Mon Sep 17 00:00:00 2001 From: Benjamin Demaille Date: Tue, 7 Jul 2026 05:48:27 +0200 Subject: [PATCH 2/5] tigmint: specify head branch (audit) Co-authored-by: Claude Opus 4.8 (1M context) --- Formula/tigmint.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Formula/tigmint.rb b/Formula/tigmint.rb index 2a08d3efd..48e2c48bb 100644 --- a/Formula/tigmint.rb +++ b/Formula/tigmint.rb @@ -5,7 +5,7 @@ class Tigmint < Formula url "https://github.com/bcgsc/tigmint/releases/download/v1.2.10/tigmint-1.2.10.tar.gz" sha256 "8e7b5d424ff69d5da7b117bef9996463b02205078ce0fb6e3074ca6c9933efa9" license "GPL-3.0-only" - head "https://github.com/bcgsc/tigmint.git" + head "https://github.com/bcgsc/tigmint.git", branch: "master" bottle do root_url "https://ghcr.io/v2/brewsci/bio" From bfa4367eacf8b97804d892734ce678b72061b4fa Mon Sep 17 00:00:00 2001 From: Benjamin Demaille Date: Fri, 10 Jul 2026 23:15:48 +0200 Subject: [PATCH 3/5] tigmint: use Homebrew btllib instead of unsatisfiable pip pin Co-authored-by: Claude Opus 4.8 (1M context) --- Formula/tigmint.rb | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/Formula/tigmint.rb b/Formula/tigmint.rb index 48e2c48bb..abb218d18 100644 --- a/Formula/tigmint.rb +++ b/Formula/tigmint.rb @@ -1,4 +1,6 @@ class Tigmint < Formula + include Language::Python::Shebang + # cite Jackman_2018: "https://doi.org/10.1186/s12859-018-2425-6" desc "Correct misassemblies using linked or long reads" homepage "https://bcgsc.github.io/tigmint/" @@ -14,24 +16,34 @@ class Tigmint < Formula end depends_on "bedtools" + depends_on "btllib" depends_on "minimap2" depends_on "numpy" - depends_on "python@3.9" + depends_on "python@3.14" depends_on "samtools" def install ENV.prepend_path "PATH", libexec/"bin" - xy = Language::Python.major_minor_version "python3" + python = formula_opt_bin("python@3.14")/"python3.14" + xy = Language::Python.major_minor_version python ENV.prepend_path "PYTHONPATH", libexec/"lib/python#{xy}/site-packages" - inreplace "bin/tigmint-cut", "/usr/bin/env python3", Formula["python@3.9"].bin/"python3.9" - inreplace "bin/tigmint_molecule.py", "/usr/bin/env python3", Formula["python@3.9"].bin/"python3.9" - inreplace "bin/tigmint_molecule_paf.py", "/usr/bin/env python3", Formula["python@3.9"].bin/"python3.9" - system "pip3", "install", "--prefix=#{libexec}", "-r", "requirements.txt", "--no-binary=pysam" + # btllib is provided by Homebrew (its PyPI pin is unsatisfiable on modern + # Python) and numpy comes from the numpy formula; drop both from the pip list. + inreplace "requirements.txt" do |s| + s.gsub!(/^btllib\b.*\n/, "") + s.gsub!(/^numpy\b.*\n/, "") + end + system python, "-m", "pip", "install", "--prefix=#{libexec}", + "-r", "requirements.txt", "--no-binary=pysam" bin.install Dir["bin/*"] + rewrite_shebang python_shebang_rewrite_info(python), *bin.children system "make", "-C", "src" libexec_src = Pathname.new("#{libexec}/src") libexec_src.install "src/long-to-linked-pe" - bin.env_script_all_files libexec/"bin", PYTHONPATH: Dir[libexec/"lib/python*/site-packages"].first + btllib_python = formula_opt_lib("btllib")/"btllib/python" + site_packages = Dir[libexec/"lib/python*/site-packages"].first + bin.env_script_all_files libexec/"bin", + PYTHONPATH: "#{site_packages}#{File::PATH_SEPARATOR}#{btllib_python}" end test do From 1d2d8667af7b84913cb1d16e6d9250e4ef3a2a9d Mon Sep 17 00:00:00 2001 From: Benjamin Demaille Date: Sat, 11 Jul 2026 21:32:07 +0200 Subject: [PATCH 4/5] tigmint: fix linkage audit and unreachable homepage Co-authored-by: Claude Opus 4.8 (1M context) --- Formula/tigmint.rb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/Formula/tigmint.rb b/Formula/tigmint.rb index abb218d18..198f5f6b5 100644 --- a/Formula/tigmint.rb +++ b/Formula/tigmint.rb @@ -3,7 +3,7 @@ class Tigmint < Formula # cite Jackman_2018: "https://doi.org/10.1186/s12859-018-2425-6" desc "Correct misassemblies using linked or long reads" - homepage "https://bcgsc.github.io/tigmint/" + homepage "https://github.com/bcgsc/tigmint" url "https://github.com/bcgsc/tigmint/releases/download/v1.2.10/tigmint-1.2.10.tar.gz" sha256 "8e7b5d424ff69d5da7b117bef9996463b02205078ce0fb6e3074ca6c9933efa9" license "GPL-3.0-only" @@ -17,11 +17,16 @@ class Tigmint < Formula depends_on "bedtools" depends_on "btllib" + depends_on "libdeflate" depends_on "minimap2" depends_on "numpy" depends_on "python@3.14" depends_on "samtools" + on_linux do + depends_on "zlib-ng-compat" + end + def install ENV.prepend_path "PATH", libexec/"bin" python = formula_opt_bin("python@3.14")/"python3.14" From 859f97d6bbbba4e4620b3fc2f0362907e0b2f364 Mon Sep 17 00:00:00 2001 From: Benjamin Demaille Date: Sat, 11 Jul 2026 23:00:42 +0200 Subject: [PATCH 5/5] tigmint: declare xz linkage dependency on Linux Co-authored-by: Claude Opus 4.8 (1M context) --- Formula/tigmint.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/Formula/tigmint.rb b/Formula/tigmint.rb index 198f5f6b5..18f01bc48 100644 --- a/Formula/tigmint.rb +++ b/Formula/tigmint.rb @@ -24,6 +24,7 @@ class Tigmint < Formula depends_on "samtools" on_linux do + depends_on "xz" depends_on "zlib-ng-compat" end