From ee79003ef281beb70f5b4c9d2707f06f348d62b9 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Wed, 5 Mar 2025 20:01:07 +0000 Subject: [PATCH 1/8] tiledbsoma 1.16.0rc1 pre-check --- recipe/meta.yaml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index fe37847..e9a7017 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tiledbsoma" %} -{% set version = "1.15.7" %} -{% set sha256 = "ecdcafc2cb83e392e1102fea11e910548bcacdb854b5bc365c96ef940fed0c3f" %} +{% set version = "1.16.0rc1" %} +{% set sha256 = "tbd" %} # This is the SHA256 of # TileDB-SOMA-i.j.k.tar.gz # from @@ -15,18 +15,18 @@ package: name: {{ name }} version: {{ version }} -# Post-tag real thing: -source: - url: https://github.com/single-cell-data/TileDB-SOMA/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} +## Post-tag real thing: +#source: +# url: https://github.com/single-cell-data/TileDB-SOMA/archive/{{ version }}.tar.gz +# sha256: {{ sha256 }} # Pre-tag canary "will Conda be green if we release": -#source: -# git_url: https://github.com/single-cell-data/TileDB-SOMA.git -# # release-1.15 branch 2025-01-24 -# git_rev: ceb4a3682663dfc74a346c91cc5bfa85a0b0674c -# git_depth: -1 -# # hoping to be 1.15.5 <-- FILL IN HERE +source: + git_url: https://github.com/single-cell-data/TileDB-SOMA.git + # release-1.16 branch 2025-03-05 + git_rev: 1f12399f17297b75ed9205643e1719cabc9a961c + git_depth: -1 + # hoping to be 1.16.0rc1 <-- FILL IN HERE build: number: 0 From a416834ae683afb253c499e396d51558a47dd8d5 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Wed, 5 Mar 2025 15:05:09 -0500 Subject: [PATCH 2/8] tiledbsoma 1.16.0rc1 pre-check --- recipe/meta.yaml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index fe37847..b37ab08 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -1,6 +1,6 @@ {% set name = "tiledbsoma" %} -{% set version = "1.15.7" %} -{% set sha256 = "ecdcafc2cb83e392e1102fea11e910548bcacdb854b5bc365c96ef940fed0c3f" %} +{% set version = "1.16.0rc1" %} +{% set sha256 = "tbd" %} # This is the SHA256 of # TileDB-SOMA-i.j.k.tar.gz # from @@ -15,18 +15,18 @@ package: name: {{ name }} version: {{ version }} -# Post-tag real thing: -source: - url: https://github.com/single-cell-data/TileDB-SOMA/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} +## Post-tag real thing: +#source: +# url: https://github.com/single-cell-data/TileDB-SOMA/archive/{{ version }}.tar.gz +# sha256: {{ sha256 }} # Pre-tag canary "will Conda be green if we release": -#source: -# git_url: https://github.com/single-cell-data/TileDB-SOMA.git -# # release-1.15 branch 2025-01-24 -# git_rev: ceb4a3682663dfc74a346c91cc5bfa85a0b0674c -# git_depth: -1 -# # hoping to be 1.15.5 <-- FILL IN HERE +source: + git_url: https://github.com/single-cell-data/TileDB-SOMA.git + # release-1.16 branch 2025-03-05 + git_rev: 1f12399f17297b75ed9205643e1719cabc9a961c + git_depth: -1 + # hoping to be 1.16.0rc1 <-- FILL IN HERE build: number: 0 @@ -99,7 +99,7 @@ outputs: - numba >=0.58.1 - attrs >=22.2 # Keep this in sync with TileDB-SOMA's somacore version requirement. - - somacore ==1.0.26 + - somacore ==1.0.28 - scanpy >=1.9.2 test: imports: From dd67ce7b91ef6f1102177a1ceb451cb16c191c3c Mon Sep 17 00:00:00 2001 From: John Kerl Date: Wed, 5 Mar 2025 20:52:57 +0000 Subject: [PATCH 3/8] Incorporate #275 --- .ci_support/osx_64_.yaml | 2 +- .github/scripts/nightly/update-feedstock.sh | 4 ---- recipe/build-libtiledbsoma.sh | 3 +++ recipe/build-r-tiledbsoma.sh | 19 +++++++++++++------ recipe/build-tiledbsoma-py.sh | 3 +++ recipe/cc_wrap.sh | 3 +-- recipe/conda_build_config.yaml | 2 +- recipe/cxx_wrap.sh | 3 +-- 8 files changed, 23 insertions(+), 16 deletions(-) diff --git a/.ci_support/osx_64_.yaml b/.ci_support/osx_64_.yaml index 9a1d0e2..4a8413c 100644 --- a/.ci_support/osx_64_.yaml +++ b/.ci_support/osx_64_.yaml @@ -1,7 +1,7 @@ MACOSX_DEPLOYMENT_TARGET: - '11.0' MACOSX_SDK_VERSION: -- '11.0' +- '13.3' c_compiler: - clang c_compiler_version: diff --git a/.github/scripts/nightly/update-feedstock.sh b/.github/scripts/nightly/update-feedstock.sh index 911ec57..944e873 100644 --- a/.github/scripts/nightly/update-feedstock.sh +++ b/.github/scripts/nightly/update-feedstock.sh @@ -16,9 +16,5 @@ sed -i \ s/"tiledb rc"/"tiledb nightlies"/ \ recipe/conda_build_config.yaml -# Apply patch from Xanthos to support C++20 -# https://github.com/TileDB-Inc/tiledbsoma-feedstock/pull/246 -patch -p1 < .github/scripts/nightly/cpp20.patch - # Print differences git --no-pager diff conda-forge.yml recipe/conda_build_config.yaml diff --git a/recipe/build-libtiledbsoma.sh b/recipe/build-libtiledbsoma.sh index 12d4f4f..5d50926 100644 --- a/recipe/build-libtiledbsoma.sh +++ b/recipe/build-libtiledbsoma.sh @@ -2,6 +2,9 @@ set -exo pipefail +# Clear default compiler flags +export CXXFLAGS=${CXXFLAGS//"-fvisibility-inlines-hidden"/} + mkdir libtiledbsoma-build && cd libtiledbsoma-build cmake \ diff --git a/recipe/build-r-tiledbsoma.sh b/recipe/build-r-tiledbsoma.sh index ffb435e..5a02821 100644 --- a/recipe/build-r-tiledbsoma.sh +++ b/recipe/build-r-tiledbsoma.sh @@ -4,21 +4,28 @@ set -ex cd apis/r +# Clear default compiler flags +export CXXFLAGS=${CXXFLAGS//"-fvisibility-inlines-hidden"/} + export DISABLE_AUTOBREW=1 # https://github.com/conda-forge/r-tiledb-feedstock/commit/29cb6816636e7b5b58545e1407a8f0c29ff9dc39 -if [[ $target_platform == osx-64 ]]; then +if [[ $target_platform == osx-* ]]; then export NN_CXX_ORIG=$CXX export NN_CC_ORIG=$CC export CXX=$RECIPE_DIR/cxx_wrap.sh export CC=$RECIPE_DIR/cc_wrap.sh - mkdir -p ~/.R - echo CC=$RECIPE_DIR/cc_wrap.sh > ~/.R/Makevars - echo CXX=$RECIPE_DIR/cxx_wrap.sh >> ~/.R/Makevars - echo CXX17=$RECIPE_DIR/cxx_wrap.sh >> ~/.R/Makevars fi -export CXX17FLAGS="-Wno-deprecated-declarations -Wno-deprecated" +export CXX="$CXX -std=c++20 -fPIC" +export CXX20="$CXX" + +mkdir -p ~/.R +echo CC="$CC" > ~/.R/Makevars +echo CXX="$CXX" >> ~/.R/Makevars +echo CXX20="$CXX20" >> ~/.R/Makevars + +export CXX20FLAGS="-Wno-deprecated-declarations -Wno-deprecated" # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk if [[ $target_platform == osx-* ]]; then diff --git a/recipe/build-tiledbsoma-py.sh b/recipe/build-tiledbsoma-py.sh index a55c068..1cb92ce 100644 --- a/recipe/build-tiledbsoma-py.sh +++ b/recipe/build-tiledbsoma-py.sh @@ -4,6 +4,9 @@ set -ex cd apis/python +# Clear default compiler flags +export CXXFLAGS=${CXXFLAGS//"-fvisibility-inlines-hidden"/} + echo echo "PKG_VERSION IS <<$PKG_VERSION>>" echo diff --git a/recipe/cc_wrap.sh b/recipe/cc_wrap.sh index a2bfc0c..1589e33 100755 --- a/recipe/cc_wrap.sh +++ b/recipe/cc_wrap.sh @@ -1,4 +1,3 @@ #!/bin/sh -args="${@##-mmacosx-version-min=10.9*}" -$NN_CC_ORIG $args -mmacosx-version-min=11.0 +$NN_CC_ORIG "$@" -mmacosx-version-min=13.3 diff --git a/recipe/conda_build_config.yaml b/recipe/conda_build_config.yaml index 05d52cb..bd83f8e 100644 --- a/recipe/conda_build_config.yaml +++ b/recipe/conda_build_config.yaml @@ -1,7 +1,7 @@ # https://conda-forge.org/docs/maintainer/knowledge_base/#requiring-newer-macos-sdks # https://conda-forge.org/news/2024/03/24/stdlib-migration/ MACOSX_SDK_VERSION: # [osx and x86_64] - - 11.0 # [osx and x86_64] + - 13.3 # [osx and x86_64] c_stdlib_version: # [osx and x86_64] - 11.0 # [osx and x86_64] channel_sources: diff --git a/recipe/cxx_wrap.sh b/recipe/cxx_wrap.sh index 5d9def4..c8428cb 100755 --- a/recipe/cxx_wrap.sh +++ b/recipe/cxx_wrap.sh @@ -1,4 +1,3 @@ #!/bin/sh -args="${@##-mmacosx-version-min=10.9*}" -$NN_CXX_ORIG $args -mmacosx-version-min=11.0 +$NN_CXX_ORIG "$@" -mmacosx-version-min=13.3 From cad46dba194ab85773072950ff7a2936e561e68d Mon Sep 17 00:00:00 2001 From: John Kerl Date: Wed, 5 Mar 2025 20:53:44 +0000 Subject: [PATCH 4/8] MNT: Re-rendered with conda-build 25.1.1, conda-smithy 3.46.1, and conda-forge-pinning 2025.03.05.16.19.52 --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index bb38536..47b5408 100644 --- a/.gitignore +++ b/.gitignore @@ -25,3 +25,5 @@ # Rattler-build's artifacts are in `output` when not specifying anything. /output +# Pixi's configuration +.pixi From c75be7a9dac8760347a1820b86c41c33e8bb21fe Mon Sep 17 00:00:00 2001 From: John Kerl Date: Wed, 5 Mar 2025 20:59:55 +0000 Subject: [PATCH 5/8] more --- recipe/build-libtiledbsoma.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/recipe/build-libtiledbsoma.sh b/recipe/build-libtiledbsoma.sh index 5d50926..2845c6c 100644 --- a/recipe/build-libtiledbsoma.sh +++ b/recipe/build-libtiledbsoma.sh @@ -13,6 +13,7 @@ cmake \ -DCMAKE_BUILD_TYPE=Release \ -DTILEDBSOMA_BUILD_CLI=OFF \ -DTILEDBSOMA_ENABLE_TESTING=OFF \ + -DSPDLOG_LINK_SHARED=ON \ ../libtiledbsoma make -j ${CPU_COUNT} From 4d74ca83b17ea63fd9bf6445d5bd3a30100d4a08 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Thu, 6 Mar 2025 23:01:01 +0000 Subject: [PATCH 6/8] spatial deps --- recipe/meta.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index b37ab08..0e07181 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -101,6 +101,12 @@ outputs: # Keep this in sync with TileDB-SOMA's somacore version requirement. - somacore ==1.0.28 - scanpy >=1.9.2 + # See TileDB-SOMA's apis/python/requirements_spatial.txt + - geopandas + - tifffile + - pillow + - spatialdata >=0.2.5 + - xarray test: imports: - tiledbsoma From 94a6015dff506a1af520f4512ff4e49738a3a119 Mon Sep 17 00:00:00 2001 From: John Kerl Date: Fri, 7 Mar 2025 02:35:59 +0000 Subject: [PATCH 7/8] try another package name --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 0e07181..6600781 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -105,7 +105,7 @@ outputs: - geopandas - tifffile - pillow - - spatialdata >=0.2.5 + - spatialdata-io >=0.2.5 - xarray test: imports: From 56ded07ca742e750ce82bac72b80a30cadb39a2d Mon Sep 17 00:00:00 2001 From: John Kerl Date: Fri, 7 Mar 2025 17:57:29 +0000 Subject: [PATCH 8/8] undo previous; previous name was correct; just lacks correct version --- recipe/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 6600781..0e07181 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -105,7 +105,7 @@ outputs: - geopandas - tifffile - pillow - - spatialdata-io >=0.2.5 + - spatialdata >=0.2.5 - xarray test: imports: