From 8b2b175e4cc1451dc28c19687bc5094773f50083 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 29 May 2024 17:32:49 +0200 Subject: [PATCH 1/7] feat: Update to latest conda-forge-pinning Signed-off-by: Marcel Bargull --- bioconda_utils/bioconda_utils-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bioconda_utils/bioconda_utils-requirements.txt b/bioconda_utils/bioconda_utils-requirements.txt index 1ab90a003f..beda60c4d9 100644 --- a/bioconda_utils/bioconda_utils-requirements.txt +++ b/bioconda_utils/bioconda_utils-requirements.txt @@ -3,7 +3,7 @@ # so please keep that documentation up to date as they change # pinnings -conda-forge-pinning=2023.05.06.13.08.41 +conda-forge-pinning=2024.05.28.17.08.08 # basics python=3.10.* From 1de329a94adfcdd0e5bb386cec04f677b7a2d635 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 29 May 2024 17:21:13 +0200 Subject: [PATCH 2/7] feat: Add explicit libc/system version deps These stdlib_c entries can be used with newer conda-build versions in recipes like so: requirements: build: - {{ stdlib("c") }} - {{ compiler("c") }} and allow us to be explicit about our libc/system dependencies. I.e., we could then avoid MACOSX_DEPLOYMENT_TARGET/sysroot_linux* dances Signed-off-by: Marcel Bargull --- bioconda_utils/bioconda_utils-conda_build_config.yaml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml index e633edaf1f..441efdc470 100644 --- a/bioconda_utils/bioconda_utils-conda_build_config.yaml +++ b/bioconda_utils/bioconda_utils-conda_build_config.yaml @@ -9,9 +9,16 @@ # clear hard-coded default value for CONDA_BUILD_SYSROOT CONDA_BUILD_SYSROOT: - "" +c_stdlib: + - sysroot # [linux] + - macosx_deployment_target # [osx] +c_stdlib_version: + - 2.17 # [linux] + - 11.0 # [osx and arm64] + - 10.13 # [osx and x86_64] MACOSX_DEPLOYMENT_TARGET: # [osx] - 11.0 # [osx and arm64] - - 10.9 # [osx and x86_64] + - 10.13 # [osx and x86_64] pin_run_as_build: htslib: From 2d9e8a91dac8ad38c53f2679c1fd870c7830fd96 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 29 May 2024 17:26:32 +0200 Subject: [PATCH 3/7] chore: Remove legacy pin_run_as_build entries Those are covered by "run_exports" nowadays. Signed-off-by: Marcel Bargull --- bioconda_utils/bioconda_utils-conda_build_config.yaml | 9 --------- 1 file changed, 9 deletions(-) diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml index 441efdc470..35171659ca 100644 --- a/bioconda_utils/bioconda_utils-conda_build_config.yaml +++ b/bioconda_utils/bioconda_utils-conda_build_config.yaml @@ -20,15 +20,6 @@ MACOSX_DEPLOYMENT_TARGET: # [osx] - 11.0 # [osx and arm64] - 10.13 # [osx and x86_64] -pin_run_as_build: - htslib: - max_pin: x.x - bamtools: - max_pin: x.x.x - r-base: - max_pin: x.x - min_pin: x.x - bamtools: - "2.5.1" From d91bb879767007b1baad82c3fd7e85ec769edc0f Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 29 May 2024 17:28:21 +0200 Subject: [PATCH 4/7] chore: Remove outdated libxml2 pin Signed-off-by: Marcel Bargull --- bioconda_utils/bioconda_utils-conda_build_config.yaml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml index 35171659ca..b96f645f9d 100644 --- a/bioconda_utils/bioconda_utils-conda_build_config.yaml +++ b/bioconda_utils/bioconda_utils-conda_build_config.yaml @@ -28,13 +28,6 @@ bamtools: r_base: - "4.3.*" -# Note: this is a (hopefully) temporary fix for the r-base 4.3 migration. That package was built -# with libxml2 2.11, but that migration on conda-forge isn't yet complete. Consequently conda-forge-pinning -# still has libxml2 2.10. That means that there are a number of R and Bioconductor packages we can't currently -# build without manually changing out libxml2 pinning. -libxml2: - - "2.11.*" - python: - 3.10.* *_cpython - 3.9.* *_cpython From 8a0fb48ff357b11bd82d560bb385bf93cf85726d Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 29 May 2024 17:30:15 +0200 Subject: [PATCH 5/7] chore: Omit custom Bioconda pins for python Signed-off-by: Marcel Bargull --- .../bioconda_utils-conda_build_config.yaml | 37 +++++++++++-------- 1 file changed, 21 insertions(+), 16 deletions(-) diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml index b96f645f9d..87e4070c94 100644 --- a/bioconda_utils/bioconda_utils-conda_build_config.yaml +++ b/bioconda_utils/bioconda_utils-conda_build_config.yaml @@ -28,22 +28,27 @@ bamtools: r_base: - "4.3.*" -python: - - 3.10.* *_cpython - - 3.9.* *_cpython - - 3.8.* *_cpython - -# conda-forge only has 3 python versions, so we need to modify the length of the other zip_keys in its group -python_impl: - - cpython - - cpython - - cpython - -# Warning! This needs to both match the length of python and python_impl but ALSO match what conda-forge is using/has used! -numpy: - - 1.21.* - - 1.21.* - - 1.21.* +# # conda-forge-pinning just got updated to build for Py 3.12 by default. +# # In case we want to drop 3.8 before conda-forge does, we can use the following: +# python: +# - 3.12.* *_cpython +# - 3.11.* *_cpython +# - 3.10.* *_cpython +# - 3.9.* *_cpython +# +# # Needs to match the length of the other zip_keys in its group (python, python_impl, numpy). +# python_impl: +# - cpython +# - cpython +# - cpython +# - cpython +# +# # Warning! This needs to both match the length of python and python_impl but ALSO match what conda-forge is using/has used! +# numpy: +# - 1.26.* +# - 1.23.* +# - 1.22.* +# - 1.22.* channel_sources: - conda-forge,bioconda From ff8ae0fe725c3e51afbadf58556cce460f04a684 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 29 May 2024 17:28:57 +0200 Subject: [PATCH 6/7] feat: Update bamtools pin Signed-off-by: Marcel Bargull --- bioconda_utils/bioconda_utils-conda_build_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bioconda_utils/bioconda_utils-conda_build_config.yaml b/bioconda_utils/bioconda_utils-conda_build_config.yaml index 87e4070c94..ac243f7b5f 100644 --- a/bioconda_utils/bioconda_utils-conda_build_config.yaml +++ b/bioconda_utils/bioconda_utils-conda_build_config.yaml @@ -21,7 +21,7 @@ MACOSX_DEPLOYMENT_TARGET: # [osx] - 10.13 # [osx and x86_64] bamtools: - - "2.5.1" + - "2.5.2" # NOTE: Workaround https://github.com/conda/conda-build/issues/3974 we slightly alter the values # from conda-forge-pinnings here (inserting '.*' or ' ' which should be ignored later on). From e765095b85d7c64165271604c1fe0962d41463bd Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Mon, 3 Jun 2024 08:53:04 +0200 Subject: [PATCH 7/7] Update conda-forge-pinning to latest version Just for good measure. Signed-off-by: Marcel Bargull --- bioconda_utils/bioconda_utils-requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bioconda_utils/bioconda_utils-requirements.txt b/bioconda_utils/bioconda_utils-requirements.txt index beda60c4d9..1fec6cc898 100644 --- a/bioconda_utils/bioconda_utils-requirements.txt +++ b/bioconda_utils/bioconda_utils-requirements.txt @@ -3,7 +3,7 @@ # so please keep that documentation up to date as they change # pinnings -conda-forge-pinning=2024.05.28.17.08.08 +conda-forge-pinning=2024.06.01.05.54.15 # basics python=3.10.*