ntedit 2.1.1

Formula/ntedit.rb

@@ -1,12 +1,12 @@
 class Ntedit < Formula
   # cite Warren_2019: "https://doi.org/10.1093/bioinformatics/btz400"
   desc "Scalable genome assembly polishing"
   homepage "https://github.com/bcgsc/ntEdit"
   url "https://github.com/bcgsc/ntEdit.git",
-      tag:      "v2.0.3",
-      revision: "d004dbc6166f044d7d576dac3f8f7c81c180e008"
+      tag:      "v2.1.1",
+      revision: "1679c966d10f7805525633d7b9110aeff6585fa0"
   license "GPL-3.0-or-later"
-  head "https://github.com/bcgsc/ntEdit.git"
+  head "https://github.com/bcgsc/ntEdit.git", branch: "master"
 
   bottle do
     root_url "https://ghcr.io/v2/brewsci/bio"
@@ -26,6 +26,7 @@
   depends_on "brewsci/bio/btllib"
   depends_on "brewsci/bio/ntcard"
   depends_on "brewsci/bio/nthits"
+  depends_on "brewsci/bio/ntstat"
   depends_on "python@3.13"
   depends_on "snakemake"
 
@@ -38,7 +39,7 @@
 
   def install
     inreplace "run-ntedit", "#!/usr/bin/env python3",
-                            "#!#{formula_opt_libexec("snakemake")}/bin/python3.13"
+                            "#!#{formula_opt_libexec("snakemake")}/bin/python3"
     system "meson", "setup", "build", "--prefix", prefix
     cd "build" do
       system "ninja", "install"

Formula/ntstat.rb

@@ -0,0 +1,65 @@
+class Ntstat < Formula
+  desc "Compute k-mer statistics and Bloom filters from sequencing data"
+  homepage "https://github.com/bcgsc/ntstat"
+  url "https://github.com/bcgsc/ntstat/archive/refs/tags/v1.0.1.tar.gz"
+  sha256 "f5b365d4f8723ae108022fab7d7c67437aca70717ba81f4002eec13bab84c25a"
+  license "GPL-3.0-only"
+  head "https://github.com/bcgsc/ntstat.git", branch: "main"
+
+  depends_on "argparse" => :build
+  depends_on "cmake" => :build
+  depends_on "indicators" => :build
+  depends_on "meson" => :build
+  depends_on "ninja" => :build
+  depends_on "pybind11" => :build
+  depends_on "tabulate" => :build
+  depends_on "btllib"
+  depends_on "python@3.13"
+
+  on_macos do
+    depends_on "libomp"
+  end
+
+  def install
+    # Pin the build to python@3.13 so the compiled extension modules match the
+    # interpreter that runs the installed launcher (python@3.13 only ships the
+    # versioned python3.13 / python3.13-config programs).
+    inreplace "meson.build" do |s|
+      s.gsub! "find_installation('python3')", "find_installation('python3.13')"
+      s.gsub! "find_program('python3-config')", "find_program('python3.13-config')"
+    end
+
+    # argparse, indicators and tabulate are header-only libraries. Homebrew ships
+    # them with CMake configs only, and meson's dependency() lookup fails in the
+    # build sandbox (the pkg-config shim is disabled and indicators' CMake config
+    # errors out). Point the module builds at their headers directly instead.
+    header_only = {
+      "argparse"   => formula_opt_include("argparse"),
+      "indicators" => formula_opt_include("indicators"),
+      "tabulate"   => formula_opt_include("tabulate"),
+    }
+    inreplace Dir["src/modules/{filter,count}/meson.build"] do |s|
+      header_only.each do |name, inc|
+        s.gsub! "dependency('#{name}')", "declare_dependency(compile_args: ['-I#{inc}'])"
+      end
+    end
+
+    # Disable LTO: it makes meson probe for llvm-ar (absent), and is unnecessary
+    # for these Python extension modules.
+    system "meson", "setup", "build", "--prefix", prefix, "-Db_lto=false"
+    system "meson", "install", "-C", "build"
+
+    # The launcher imports its bundled extension modules (ntstat.filter, ...),
+    # so point it at the packaged site-packages and the pinned interpreter.
+    site_packages = prefix/"lib/python3.13/site-packages"
+    libexec.install bin/"ntstat"
+    inreplace libexec/"ntstat", "#!/usr/bin/env python3",
+              "#!#{formula_opt_bin("python@3.13")}/python3.13"
+    (bin/"ntstat").write_env_script libexec/"ntstat", PYTHONPATH: site_packages
+  end
+
+  test do
+    assert_match version.to_s, shell_output("#{bin}/ntstat --version")
+    assert_match "filter", shell_output("#{bin}/ntstat filter --help")
+  end
+end