From 33b860eca1cc293fb91f17af904e8b9620fca77a Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Fri, 31 Jul 2020 11:46:48 +0000 Subject: [PATCH 1/4] tiledb: 1.7.7 -> 2.0.7 --- pkgs/development/libraries/tiledb/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/tiledb/default.nix b/pkgs/development/libraries/tiledb/default.nix index 3ebfd4ea919..c332ba15c57 100644 --- a/pkgs/development/libraries/tiledb/default.nix +++ b/pkgs/development/libraries/tiledb/default.nix @@ -20,13 +20,13 @@ stdenv.mkDerivation rec { pname = "tiledb"; - version = "1.7.7"; + version = "2.0.7"; src = fetchFromGitHub { owner = "TileDB-Inc"; repo = "TileDB"; rev = version; - sha256 = "0vpbyxi8k29c7sjpk86y5w3yyp5fn62q5xvbw061wgp7vrprf8bm"; + sha256 = "00g8ibsbnl4wjfx3qg4qy6s7z6dsj898j0yqfhw1gjr1pb5dsapb"; }; nativeBuildInputs = [ From 438d5b6b61bb2c63e6d2a02f925c9f4bbd44faf5 Mon Sep 17 00:00:00 2001 From: Robert Scott Date: Sat, 5 Sep 2020 18:23:21 +0100 Subject: [PATCH 2/4] pythonPackages.tiledb: 0.5.6 -> 0.6.6 include a few improvements to tests --- .../development/python-modules/tiledb/default.nix | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/pkgs/development/python-modules/tiledb/default.nix b/pkgs/development/python-modules/tiledb/default.nix index 808a6c54825..c72fd73903f 100644 --- a/pkgs/development/python-modules/tiledb/default.nix +++ b/pkgs/development/python-modules/tiledb/default.nix @@ -3,28 +3,31 @@ , buildPythonPackage , fetchFromGitHub , cython +, pybind11 , tiledb , numpy , wheel , isPy3k , setuptools_scm , psutil +, pandas }: buildPythonPackage rec { pname = "tiledb"; - version = "0.5.6"; + version = "0.6.6"; format = "setuptools"; src = fetchFromGitHub { owner = "TileDB-Inc"; repo = "TileDB-Py"; rev = version; - sha256 = "0cgm4dhyqay26xmrzlv21ha8qh55m4q3yr338lrv81ngz77zxsvw"; + sha256 = "0b2kn1xyf7d994kz29dpqiaf8yzvx0axw4yqi854c54pl22ddgzl"; }; nativeBuildInputs = [ cython + pybind11 setuptools_scm ]; @@ -39,6 +42,8 @@ buildPythonPackage rec { checkInputs = [ psutil + # optional + pandas ]; TILEDB_PATH = tiledb; @@ -57,16 +62,18 @@ buildPythonPackage rec { "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" + "test_varlen_write_int_subarray" "dont_test_varlen_write_int_subarray" \ + --replace "test_memory_cleanup" "dont_test_memory_cleanup" substituteInPlace tiledb/tests/test_metadata.py --replace \ "test_metadata_consecutive" "dont_test_metadata_consecutive" ''; checkPhase = '' - pushd "$out" + pushd "$TMPDIR" ${python.interpreter} -m unittest tiledb.tests.all.suite_test popd ''; + pythonImportsCheck = [ "tiledb" ]; meta = with lib; { description = "Python interface to the TileDB storage manager"; From edeece0aab9dc8e476de0a25060d6376824511f5 Mon Sep 17 00:00:00 2001 From: Robert Scott Date: Sat, 5 Sep 2020 19:49:33 +0100 Subject: [PATCH 3/4] libpqxx: enable for darwin --- pkgs/development/libraries/libpqxx/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/libraries/libpqxx/default.nix b/pkgs/development/libraries/libpqxx/default.nix index a710e09a454..feb9c7e6514 100644 --- a/pkgs/development/libraries/libpqxx/default.nix +++ b/pkgs/development/libraries/libpqxx/default.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { description = "A C++ library to access PostgreSQL databases"; homepage = "http://pqxx.org/development/libpqxx/"; license = lib.licenses.bsd3; - platforms = lib.platforms.linux; + platforms = lib.platforms.unix; maintainers = [ lib.maintainers.eelco ]; }; } From 22a9d9aa5be219626af866c4fafbc337420d8327 Mon Sep 17 00:00:00 2001 From: Robert Scott Date: Sat, 5 Sep 2020 19:50:39 +0100 Subject: [PATCH 4/4] tiledb: enable for all unix, add tweaks for darwin & non-x86 systems --- pkgs/development/libraries/tiledb/default.nix | 15 +++++++++++++-- .../development/python-modules/tiledb/default.nix | 3 ++- 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/pkgs/development/libraries/tiledb/default.nix b/pkgs/development/libraries/tiledb/default.nix index c332ba15c57..2726ed7f237 100644 --- a/pkgs/development/libraries/tiledb/default.nix +++ b/pkgs/development/libraries/tiledb/default.nix @@ -16,6 +16,7 @@ , python , gtest , doxygen +, fixDarwinDylibNames }: stdenv.mkDerivation rec { @@ -29,6 +30,12 @@ stdenv.mkDerivation rec { sha256 = "00g8ibsbnl4wjfx3qg4qy6s7z6dsj898j0yqfhw1gjr1pb5dsapb"; }; + # (bundled) blosc headers have a warning on some archs that it will be using + # unaccelerated routines. + cmakeFlags = [ + "-DTILEDB_WERROR=0" + ]; + nativeBuildInputs = [ clang-tools cmake @@ -53,7 +60,7 @@ stdenv.mkDerivation rec { openssl boost libpqxx - ]; + ] ++ lib.optional stdenv.isDarwin fixDarwinDylibNames; # emulate the process of pulling catch down postPatch = '' @@ -65,11 +72,15 @@ stdenv.mkDerivation rec { installTargets = [ "install-tiledb" "doc" ]; + postInstall = lib.optionalString stdenv.isDarwin '' + install_name_tool -add_rpath ${tbb}/lib $out/lib/libtiledb.dylib + ''; + meta = with lib; { description = "TileDB allows you to manage the massive dense and sparse multi-dimensional array data"; homepage = "https://github.com/TileDB-Inc/TileDB"; license = licenses.mit; - platforms = [ "x86_64-linux"]; + platforms = platforms.unix; maintainers = with maintainers; [ rakesh4g ]; }; diff --git a/pkgs/development/python-modules/tiledb/default.nix b/pkgs/development/python-modules/tiledb/default.nix index c72fd73903f..d5379b849ad 100644 --- a/pkgs/development/python-modules/tiledb/default.nix +++ b/pkgs/development/python-modules/tiledb/default.nix @@ -63,7 +63,8 @@ buildPythonPackage rec { # 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_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" '';