python3Packages.biom-format: cleanup, fix build; python3Packages.scikit-bio: 0.7.1.post1 -> 0.7.2 (#495656)

pkgs/development/python-modules/biom-format/default.nix

@@ -2,13 +2,19 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  setuptools,
+
+  # build-system
   cython,
-  click,
   numpy,
-  scipy,
-  pandas,
+  setuptools,
+
+  # dependencies
+  click,
   h5py,
+  pandas,
+  scipy,
+
+  # tests
   pytestCheckHook,
 }:
 
@@ -24,18 +30,24 @@ buildPythonPackage (finalAttrs: {
     hash = "sha256-FjIC21LoqltixBstbbANByjTNxVm/3YCxdWaD9KbOQ0=";
   };
 
+  # https://numpy.org/doc/stable//release/2.4.0-notes.html#removed-numpy-in1d
+  postPatch = ''
+    substituteInPlace biom/table.py \
+      --replace-fail "np.in1d" "np.isin"
+  '';
+
   build-system = [
-    setuptools
     cython
     numpy
+    setuptools
   ];
 
   dependencies = [
     click
-    numpy
-    scipy
-    pandas
     h5py
+    numpy
+    pandas
+    scipy
   ];
 
   # make pytest resolve the package from $out
@@ -53,8 +65,10 @@ buildPythonPackage (finalAttrs: {
   pythonImportsCheck = [ "biom" ];
 
   meta = {
-    homepage = "http://biom-format.org/";
     description = "Biological Observation Matrix (BIOM) format";
+    homepage = "http://biom-format.org/";
+    downloadPage = "https://github.com/biocore/biom-format";
+    changelog = "https://github.com/biocore/biom-format/blob/${finalAttrs.src.tag}/ChangeLog.md";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ tomasajt ];
   };

pkgs/development/python-modules/scikit-bio/default.nix

@@ -5,9 +5,9 @@
   fetchFromGitHub,
 
   # build-system
-  setuptools,
   cython,
-  oldest-supported-numpy,
+  numpy,
+  setuptools,
 
   # dependencies
   array-api-compat,
@@ -15,7 +15,6 @@
   decorator,
   h5py,
   natsort,
-  numpy,
   pandas,
   patsy,
   requests,
@@ -29,20 +28,20 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "scikit-bio";
-  version = "0.7.1.post1";
+  version = "0.7.2";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "scikit-bio";
     repo = "scikit-bio";
     tag = finalAttrs.version;
-    hash = "sha256-fnZpLhn2F/KoP3q7WmdaDXeC9i7hduGRkUWlCwwME3Q=";
+    hash = "sha256-zBOUZukqLhTxKG9BluWB+2zTCx5ALhM1s+YP2itqg9A=";
   };
 
   build-system = [
-    setuptools
     cython
-    oldest-supported-numpy
+    numpy
+    setuptools
   ];
 
   dependencies = [
@@ -76,7 +75,7 @@ buildPythonPackage (finalAttrs: {
     description = "Data structures, algorithms and educational resources for bioinformatics";
     homepage = "http://scikit-bio.org/";
     downloadPage = "https://github.com/scikit-bio/scikit-bio";
-    changelog = "https://github.com/scikit-bio/scikit-bio/blob/${finalAttrs.src.rev}/CHANGELOG.md";
+    changelog = "https://github.com/scikit-bio/scikit-bio/blob/${finalAttrs.src.tag}/CHANGELOG.md";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ tomasajt ];
   };