python3Packages.tiledb: 0.33.2 -> 0.34.0 (#422124)

pkgs/by-name/ti/tiledb/package.nix

@@ -2,6 +2,7 @@
   lib,
   stdenv,
   fetchFromGitHub,
+  fetchpatch,
   cmake,
   zlib,
   lz4,
@@ -22,6 +23,8 @@
   libpng,
   file,
   runCommand,
+  curl,
+  capnproto,
   useAVX2 ? stdenv.hostPlatform.avx2Support,
 }:
 
@@ -45,7 +48,17 @@ stdenv.mkDerivation rec {
     hash = "sha256-Cs3Lr8I/Mu02x78d7IySG0XX4u/VAjBs4p4b00XDT5k=";
   };
 
-  patches = lib.optionals stdenv.hostPlatform.isDarwin [ ./generate_embedded_data_header.patch ];
+  patches = [
+    # capnproto was updated to 1.2 in Nixpkgs, bring TileDB codebase up to speed
+    # patch only affects serialization related code, extracted from https://github.com/TileDB-Inc/TileDB/pull/5616
+    (fetchpatch {
+      url = "https://github.com/TileDB-Inc/TileDB/pull/5616.patch";
+      relative = "tiledb/sm/serialization";
+      extraPrefix = "tiledb/sm/serialization/";
+      hash = "sha256-5z/eJEHl+cnWRf1sMULodJyhmNh5KinDLlL1paMNiy4=";
+    })
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isDarwin [ ./generate_embedded_data_header.patch ];
 
   # libcxx (as of llvm-19) does not yet support `stop_token` and `jthread`
   # without the -fexperimental-library flag. Tiledb adds its own
@@ -62,6 +75,7 @@ stdenv.mkDerivation rec {
   cmakeFlags = [
     "-DTILEDB_WEBP=OFF"
     "-DTILEDB_WERROR=OFF"
+    "-DTILEDB_SERIALIZATION=ON"
     # https://github.com/NixOS/nixpkgs/issues/144170
     "-DCMAKE_INSTALL_INCLUDEDIR=include"
     "-DCMAKE_INSTALL_LIBDIR=lib"
@@ -74,6 +88,9 @@ stdenv.mkDerivation rec {
     cmake
     python3
     doxygen
+    # Required for serialization
+    curl
+    capnproto
   ]
   ++ lib.optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames;
 

pkgs/development/python-modules/tiledb/default.nix

@@ -1,5 +1,6 @@
 {
   lib,
+  stdenv,
   python,
   buildPythonPackage,
   fetchFromGitHub,
@@ -12,12 +13,19 @@
   setuptools-scm,
   psutil,
   pandas,
+  cmake,
+  ninja,
+  scikit-build-core,
+  packaging,
+  pytest,
+  hypothesis,
+  pyarrow,
 }:
 
 buildPythonPackage rec {
   pname = "tiledb";
   version = "0.34.2";
-  format = "setuptools";
+  format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "TileDB-Inc";
@@ -26,58 +34,50 @@ buildPythonPackage rec {
     hash = "sha256-EXRrWp/2sMn7DCzgXk5L0692rhGtQZwWpVWYnfrxmGA=";
   };
 
-  nativeBuildInputs = [
+  build-system = [
     cython
     pybind11
     setuptools-scm
+    scikit-build-core
+    packaging
+    cmake
+    ninja
   ];
 
   buildInputs = [ tiledb ];
 
   propagatedBuildInputs = [
     numpy
-    wheel # No idea why but it is listed
   ];
 
   nativeCheckInputs = [
     psutil
     # optional
     pandas
+    pytest
+    hypothesis
+    pyarrow
   ];
 
   TILEDB_PATH = tiledb;
 
   disabled = !isPy3k; # Not bothering with python2 anymore
 
-  postPatch = ''
-    # Hardcode path to shared object
-    substituteInPlace tiledb/__init__.py --replace \
-      'os.path.join(lib_dir, lib_name)' 'os.path.join("${tiledb}/lib", lib_name)'
-
-    # Disable failing test
-    substituteInPlace tiledb/tests/test_examples.py --replace \
-      "test_docs" "dont_test_docs"
-    # these tests don't always fail
-    substituteInPlace tiledb/tests/test_libtiledb.py --replace \
-      "test_varlen_write_int_subarray" "dont_test_varlen_write_int_subarray" \
-      --replace "test_memory_cleanup" "dont_test_memory_cleanup" \
-      --replace "test_ctx_thread_cleanup" "dont_test_ctx_thread_cleanup"
-    substituteInPlace tiledb/tests/test_metadata.py --replace \
-      "test_metadata_consecutive" "dont_test_metadata_consecutive"
-  '';
+  dontUseCmakeConfigure = true;
 
+  # We have to run pytest from a diffferent directory to force it to import tiledb from $out
+  # otherwise it cannot be imported because extension modules are not compiled in sources
   checkPhase = ''
     pushd "$TMPDIR"
-    ${python.interpreter} -m unittest tiledb.tests.all.suite_test
+    ${python.interpreter} -m pytest --pyargs tiledb${lib.optionalString stdenv.isDarwin " -k 'not test_ctx_thread_cleanup and not test_array'"}
     popd
   '';
+
   pythonImportsCheck = [ "tiledb" ];
 
-  meta = with lib; {
+  meta = {
     description = "Python interface to the TileDB storage manager";
     homepage = "https://github.com/TileDB-Inc/TileDB-Py";
-    license = licenses.mit;
-    # tiledb/core.cc:556:30: error: ‘struct std::array<long unsigned int, 2>’ has no member named ‘second’
-    broken = true;
+    license = lib.licenses.mit;
   };
 }