antismash 7.1.0.1: support Sequoia

brewsci · Feb 14, 2025 · 38f25b7 · 38f25b7
1 parent f39d7b7
commit 38f25b7
Showing 1 changed file with 61 additions and 39 deletions.
diff --git a/Formula/antismash.rb b/Formula/antismash.rb
@@ -14,6 +14,7 @@ class Antismash < Formula
   version "7.1.0.1"
   sha256 "1429986c369a81a7c1c60f2cb6efb1a28eacdb0290ec9c933477bad88d2b839d"
   license "AGPL-3.0-or-later"
+  revision 1
   head "https://github.com/antismash/antismash.git", branch: "master"
 
   bottle do
@@ -46,7 +47,7 @@ class Antismash < Formula
   depends_on "pillow"
   depends_on "prodigal"
   depends_on "python-matplotlib"
-  depends_on "python@3.12"
+  depends_on "python@3.13"
   depends_on "scipy"
 
   on_macos do
@@ -59,8 +60,8 @@ class Antismash < Formula
   end
 
   resource "attrs" do
-    url "https://files.pythonhosted.org/packages/e3/fc/f800d51204003fa8ae392c4e8278f256206e7a919b708eef054f5f4b650d/attrs-23.2.0.tar.gz"
-    sha256 "935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"
+    url "https://files.pythonhosted.org/packages/49/7c/fdf464bcc51d23881d110abd74b512a42b3d5d376a55a831b44c603ae17f/attrs-25.1.0.tar.gz"
+    sha256 "1c97078a80c814273a76b2a298a932eb681c87415c11dee0a6921de7f1b02c3e"
   end
 
   resource "bcbio-gff" do
@@ -69,18 +70,18 @@ class Antismash < Formula
   end
 
   resource "biopython" do
-    url "https://files.pythonhosted.org/packages/89/c5/7fe326081276f74a4073f6d6b13cfa7a04ba322a3ff1d84027f4773980b8/biopython-1.78.tar.gz"
-    sha256 "1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564"
+    url "https://files.pythonhosted.org/packages/db/ca/1d5fab0fedaf5c2f376d9746d447cdce04241c433602c3861693361ce54c/biopython-1.85.tar.gz"
+    sha256 "5dafab74059de4e78f49f6b5684eddae6e7ce46f09cfa059c1d1339e8b1ea0a6"
   end
 
   resource "brawn" do
-    url "https://files.pythonhosted.org/packages/1a/7d/abd734ec8b452d87f501cb57da1cb55f4ab999e5fe2d570c1f51374c70b5/brawn-1.0.1.tar.gz"
-    sha256 "dd76831a9dee955692082f46209db645bceb2e48509cbe0eeb9d9e20f53cbb6c"
+    url "https://files.pythonhosted.org/packages/c2/c8/fe7b560057829c6b4018f4ddf8927b5bbf7333493ecefaa0a53c0590d503/brawn-1.0.2.tar.gz"
+    sha256 "8c993df898fdf359cd619f035c5c14a0e4ab7587dc6be3d1d970eb7efaf30ec9"
   end
 
   resource "contourpy" do
-    url "https://files.pythonhosted.org/packages/8d/9e/e4786569b319847ffd98a8326802d5cf8a5500860dbfc2df1f0f4883ed99/contourpy-1.2.1.tar.gz"
-    sha256 "4d8908b3bee1c889e547867ca4cdc54e5ab6be6d3e078556814a22457f49423c"
+    url "https://files.pythonhosted.org/packages/25/c2/fc7193cc5383637ff390a712e88e4ded0452c9fbcf84abe3de5ea3df1866/contourpy-1.3.1.tar.gz"
+    sha256 "dfd97abd83335045a913e3bcc4a09c0ceadbe66580cf573fe961f4a825efa699"
   end
 
   resource "cycler" do
@@ -89,23 +90,23 @@ class Antismash < Formula
   end
 
   resource "fonttools" do
-    url "https://files.pythonhosted.org/packages/67/ac/d7bf44ce57ff5770c267e63cff003cfd5ee43dc49abf677f8b7067fbd3fb/fonttools-4.50.0.tar.gz"
-    sha256 "fa5cf61058c7dbb104c2ac4e782bf1b2016a8cf2f69de6e4dd6a865d2c969bb5"
+    url "https://files.pythonhosted.org/packages/1c/8c/9ffa2a555af0e5e5d0e2ed7fdd8c9bef474ed676995bb4c57c9cd0014248/fonttools-4.56.0.tar.gz"
+    sha256 "a114d1567e1a1586b7e9e7fc2ff686ca542a82769a296cef131e4c4af51e58f4"
   end
 
   resource "hatchling" do
-    url "https://files.pythonhosted.org/packages/a3/51/8a4a67a8174ce59cf49e816e38e9502900aea9b4af672d0127df8e10d3b0/hatchling-1.25.0.tar.gz"
-    sha256 "7064631a512610b52250a4d3ff1bd81551d6d1431c4eb7b72e734df6c74f4262"
+    url "https://files.pythonhosted.org/packages/8f/8a/cc1debe3514da292094f1c3a700e4ca25442489731ef7c0814358816bb03/hatchling-1.27.0.tar.gz"
+    sha256 "971c296d9819abb3811112fc52c7a9751c8d381898f36533bb16f9791e941fd6"
   end
 
   resource "helperlibs" do
     url "https://files.pythonhosted.org/packages/b6/8a/dd905312ab030099c693966fd47947610251bcd3ac98ef76d16996388a68/helperlibs-0.2.1.tar.gz"
     sha256 "4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732"
   end
 
-  resource "jinja2" do
-    url "https://files.pythonhosted.org/packages/b2/5e/3a21abf3cd467d7876045335e681d276ac32492febe6d98ad89562d1a7e1/Jinja2-3.1.3.tar.gz"
-    sha256 "ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"
+  resource "Jinja2" do
+    url "https://files.pythonhosted.org/packages/af/92/b3130cbbf5591acf9ade8708c365f3238046ac7cb8ccba6e81abccb0ccff/jinja2-3.1.5.tar.gz"
+    sha256 "8fefff8dc3034e27bb80d67c671eb8a9bc424c0ef4c0826edbff304cceff43bb"
   end
 
   resource "joblib" do
@@ -114,23 +115,38 @@ class Antismash < Formula
   end
 
   resource "jsonschema" do
-    url "https://files.pythonhosted.org/packages/03/8a/8975198ffd870ab2c04be32d200943a299fdf8a9b8e42b5e027a7a89fe4a/jsonschema-4.11.0.tar.gz"
-    sha256 "706bbcafb49b1350fbcea40b209bdce8aed07c3288f7a77e9539bd5b3ddead3d"
+    url "https://files.pythonhosted.org/packages/38/2e/03362ee4034a4c917f697890ccd4aec0800ccf9ded7f511971c75451deec/jsonschema-4.23.0.tar.gz"
+    sha256 "d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"
+  end
+
+  resource "jsonschema-specifications" do
+    url "https://files.pythonhosted.org/packages/10/db/58f950c996c793472e336ff3655b13fbcf1e3b359dcf52dcf3ed3b52c352/jsonschema_specifications-2024.10.1.tar.gz"
+    sha256 "0f38b83639958ce1152d02a7f062902c41c8fd20d558b0c34344292d417ae272"
+  end
+
+  resource "referencing" do
+    url "https://files.pythonhosted.org/packages/2f/db/98b5c277be99dd18bfd91dd04e1b759cad18d1a338188c936e92f921c7e2/referencing-0.36.2.tar.gz"
+    sha256 "df2e89862cd09deabbdba16944cc3f10feb6b3e6f18e902f7cc25609a34775aa"
+  end
+
+  resource "rpds-py" do
+    url "https://files.pythonhosted.org/packages/01/80/cce854d0921ff2f0a9fa831ba3ad3c65cee3a46711addf39a2af52df2cfd/rpds_py-0.22.3.tar.gz"
+    sha256 "e32fee8ab45d3c2db6da19a5323bc3362237c8b653c70194414b892fd06a080d"
   end
 
   resource "kiwisolver" do
-    url "https://files.pythonhosted.org/packages/b9/2d/226779e405724344fc678fcc025b812587617ea1a48b9442628b688e85ea/kiwisolver-1.4.5.tar.gz"
-    sha256 "e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec"
+    url "https://files.pythonhosted.org/packages/82/59/7c91426a8ac292e1cdd53a63b6d9439abd573c875c3f92c146767dd33faf/kiwisolver-1.4.8.tar.gz"
+    sha256 "23d5f023bdc8c7e54eb65f03ca5d5bb25b601eac4d7f1a042888a1f45237987e"
   end
 
   resource "libsass" do
     url "https://files.pythonhosted.org/packages/79/b4/ab091585eaa77299558e3289ca206846aefc123fb320b5656ab2542c20ad/libsass-0.23.0.tar.gz"
     sha256 "6f209955ede26684e76912caf329f4ccb57e4a043fd77fe0e7348dd9574f1880"
   end
 
-  resource "markupsafe" do
-    url "https://files.pythonhosted.org/packages/87/5b/aae44c6655f3801e81aa3eef09dbbf012431987ba564d7231722f68df02d/MarkupSafe-2.1.5.tar.gz"
-    sha256 "d283d37a890ba4c1ae73ffadf8046435c76e7bc2247bbb63c00bd1a709c6544b"
+  resource "MarkupSafe" do
+    url "https://files.pythonhosted.org/packages/b2/97/5d42485e71dfc078108a86d6de8fa46db44a1a9295e89c5d6d4a06e23a62/markupsafe-3.0.2.tar.gz"
+    sha256 "ee55d3edf80167e48ea11a923c7386f4669df67d7994554387f84e7d8b0a2bf0"
   end
 
   resource "MOODS-python" do
@@ -144,18 +160,13 @@ class Antismash < Formula
   end
 
   resource "packaging" do
-    url "https://files.pythonhosted.org/packages/ee/b5/b43a27ac7472e1818c4bafd44430e69605baefe1f34440593e0332ec8b4d/packaging-24.0.tar.gz"
-    sha256 "eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"
+    url "https://files.pythonhosted.org/packages/d0/63/68dbb6eb2de9cb10ee4c9c14a0148804425e13c4fb20d61cce69f53106da/packaging-24.2.tar.gz"
+    sha256 "c228a6dc5e932d346bc5739379109d49e8853dd8223571c7c5b55260edc0b97f"
   end
 
   resource "pyparsing" do
-    url "https://files.pythonhosted.org/packages/46/3a/31fd28064d016a2182584d579e033ec95b809d8e220e74c4af6f0f2e8842/pyparsing-3.1.2.tar.gz"
-    sha256 "a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"
-  end
-
-  resource "pyrsistent" do
-    url "https://files.pythonhosted.org/packages/ce/3a/5031723c09068e9c8c2f0bc25c3a9245f2b1d1aea8396c787a408f2b95ca/pyrsistent-0.20.0.tar.gz"
-    sha256 "4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4"
+    url "https://files.pythonhosted.org/packages/8b/1a/3544f4f299a47911c2ab3710f534e52fea62a633c96806995da5d25be4b2/pyparsing-3.2.1.tar.gz"
+    sha256 "61980854fd66de3a90028d679a954d5f2623e83144b5afe5ee86f43d762e5f0a"
   end
 
   resource "pysvg-py3" do
@@ -168,23 +179,34 @@ class Antismash < Formula
     sha256 "37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"
   end
 
+  resource "six" do
+    url "https://files.pythonhosted.org/packages/94/e7/b2c673351809dca68a0e064b6af791aa332cf192da575fd474ed7d6f16a2/six-1.17.0.tar.gz"
+    sha256 "ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"
+  end
+
   resource "scikit-learn" do
-    url "https://files.pythonhosted.org/packages/92/72/2961b9874a9ddf2b0f95f329d4e67f67c3301c1d88ba5e239ff25661bb85/scikit_learn-1.5.1.tar.gz"
-    sha256 "0ea5d40c0e3951df445721927448755d3fe1d80833b0b7308ebff5d2a45e6414"
+    url "https://files.pythonhosted.org/packages/9e/a5/4ae3b3a0755f7b35a280ac90b28817d1f380318973cff14075ab41ef50d9/scikit_learn-1.6.1.tar.gz"
+    sha256 "b4fc2525eca2c69a59260f583c56a7557c6ccdf8deafdba6e060f94c1c59738e"
+  end
+
+  resource "threadpoolctl" do
+    url "https://files.pythonhosted.org/packages/bd/55/b5148dcbf72f5cde221f8bfe3b6a540da7aa1842f6b491ad979a6c8b84af/threadpoolctl-3.5.0.tar.gz"
+    sha256 "082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"
   end
 
   resource "six" do
-    url "https://files.pythonhosted.org/packages/71/39/171f1c67cd00715f190ba0b100d606d440a28c93c7714febeca8b79af85e/six-1.16.0.tar.gz"
-    sha256 "1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"
+    url "https://files.pythonhosted.org/packages/94/e7/b2c673351809dca68a0e064b6af791aa332cf192da575fd474ed7d6f16a2/six-1.17.0.tar.gz"
+    sha256 "ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"
   end
 
   resource "threadpoolctl" do
     url "https://files.pythonhosted.org/packages/bd/55/b5148dcbf72f5cde221f8bfe3b6a540da7aa1842f6b491ad979a6c8b84af/threadpoolctl-3.5.0.tar.gz"
     sha256 "082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"
   end
 
+
   def python3
-    which("python3.12")
+    which("python3.13")
   end
 
   def install
@@ -195,15 +217,15 @@ def install
 
     venv.pip_install_and_link buildpath
     # Fix minor warning in BCBio
-    inreplace "#{libexec}/lib/python3.12/site-packages/BCBio/GFF/GFFParser.py",
+    inreplace "#{libexec}/lib/python3.13/site-packages/BCBio/GFF/GFFParser.py",
               "compile(\"\\w+=\")", "compile(r\"\\w+=\")"
     (prefix/site_packages/"homebrew-antismash.pth").write venv.site_packages
   end
 
   def caveats
     <<~EOS
       Run `download-antismash-databases` to download the databases into
-      #{opt_libexec}/lib/python3.12/site-packages/antismash/databases
+      #{opt_libexec}/lib/python3.13/site-packages/antismash/databases
       and `antismash --check-prereqs` to check the prerequisites.
     EOS
   end