Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: Update pinning 2024-05 #991

Merged
merged 7 commits into from
Jun 3, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
64 changes: 30 additions & 34 deletions bioconda_utils/bioconda_utils-conda_build_config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -9,50 +9,46 @@
# 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]

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
- 10.13 # [osx and x86_64]
aliciaaevans marked this conversation as resolved.
Show resolved Hide resolved

bamtools:
- "2.5.1"
- "2.5.2"
aliciaaevans marked this conversation as resolved.
Show resolved Hide resolved

# 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).
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
- 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
Expand Down
2 changes: 1 addition & 1 deletion bioconda_utils/bioconda_utils-requirements.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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=2024.06.01.05.54.15

# basics
python=3.10.*
Expand Down