Merge pull request #141 from dudoslav/db/sc-58590/numpy2

Update TileDB-VCF to 0.36.0

Author: dudoslav

.azure-pipelines/azure-pipelines-osx.yml

@@ -1,7 +1,7 @@
 c_compiler:
 - gcc
 c_compiler_version:
-- '12'
+- '13'
 c_stdlib:
 - sysroot
 c_stdlib_version:
@@ -15,15 +15,14 @@ channel_targets:
 cxx_compiler:
 - gxx
 cxx_compiler_version:
-- '12'
+- '13'
 docker_image:
 - quay.io/condaforge/linux-anvil-cos7-x86_64
 numpy:
-- '1.22'
-- '1.23'
-- '1.26'
-- '1.22'
-- '1.22'
+- '2.0'
+- '2.0'
+- '2.0'
+- '2.0'
 pin_run_as_build:
   python:
     min_pin: x.x
@@ -32,7 +31,6 @@ python:
 - 3.10.* *_cpython
 - 3.11.* *_cpython
 - 3.12.* *_cpython
-- 3.8.* *_cpython
 - 3.9.* *_cpython
 target_platform:
 - linux-64

.azure-pipelines/azure-pipelines-win.yml

@@ -0,0 +1,47 @@
+__migrator:
+  build_number: 1
+  kind: version
+  commit_message: |
+    Rebuild for numpy 2.0
+
+    TL;DR: The way we build against numpy has changed as of numpy 2.0. This bot
+    PR has updated the recipe to account for the changes (see below for details).
+
+    The biggest change is that we no longer need to use the oldest available numpy
+    version at build time in order to support old numpy version at runtime - numpy
+    will by default use a compatible ABI for the oldest still-supported numpy versions.
+
+    Additionally, we no longer need to use `{{ pin_compatible("numpy") }}` as a
+    run requirement - this has been handled for more than two years now by a
+    run-export on the numpy package itself. The migrator will therefore remove
+    any occurrences of this.
+
+    However, by default, building against numpy 2.0 will assume that the package
+    is compatible with numpy 2.0, which is not necessarily the case. You should
+    check that the upstream package explicitly supports numpy 2.0, otherwise you
+    need to add a `- numpy <2.0dev0` run requirement until that happens (check numpy
+    issue 26191 for an overview of the most important packages).
+
+    ### To-Dos:
+      * [ ] Match run-requirements for numpy (i.e. check upstream `pyproject.toml` or however the project specifies numpy compatibility)
+        * If upstream is not yet compatible with numpy 2.0, add `numpy <2.0dev0` upper bound under `run:`.
+        * If upstream is already compatible with numpy 2.0, nothing else should be necessary in most cases.
+        * If upstream requires a minimum numpy version newer than 1.19, you can add `numpy >=x.y` under `run:`.
+      * [ ] Remove any remaining occurrences of `{{ pin_compatible("numpy") }}` that the bot may have missed.
+
+    PS. If the build does not compile anymore, this is almost certainly a sign that
+    the upstream project is not yet ready for numpy 2.0; do not close this PR until
+    a version compatible with numpy 2.0 has been released upstream and on this
+    feedstock (in the meantime, you can keep the bot from reopening this PR in
+    case of git conflicts by marking it as a draft).
+  migration_number: 1
+
+# needs to match length of zip {python, python_impl, numpy}
+# as it is in global CBC in order to override it
+numpy:
+  - 1.22  # no py38 support for numpy 2.0
+  - 2.0
+  - 2.0
+  - 2.0
+  - 2.0
+migrator_ts: 1713572489.295986

.ci_support/linux_64_.yaml

@@ -21,11 +21,10 @@ cxx_compiler_version:
 macos_machine:
 - x86_64-apple-darwin13.4.0
 numpy:
-- '1.22'
-- '1.23'
-- '1.26'
-- '1.22'
-- '1.22'
+- '2.0'
+- '2.0'
+- '2.0'
+- '2.0'
 pin_run_as_build:
   python:
     min_pin: x.x
@@ -34,7 +33,6 @@ python:
 - 3.10.* *_cpython
 - 3.11.* *_cpython
 - 3.12.* *_cpython
-- 3.8.* *_cpython
 - 3.9.* *_cpython
 target_platform:
 - osx-64

.ci_support/migrations/numpy2.yaml

@@ -21,11 +21,10 @@ cxx_compiler_version:
 macos_machine:
 - arm64-apple-darwin20.0.0
 numpy:
-- '1.22'
-- '1.23'
-- '1.26'
-- '1.22'
-- '1.22'
+- '2.0'
+- '2.0'
+- '2.0'
+- '2.0'
 pin_run_as_build:
   python:
     min_pin: x.x
@@ -34,7 +33,6 @@ python:
 - 3.10.* *_cpython
 - 3.11.* *_cpython
 - 3.12.* *_cpython
-- 3.8.* *_cpython
 - 3.9.* *_cpython
 target_platform:
 - osx-arm64

.ci_support/osx_64_.yaml

@@ -9,11 +9,10 @@ channel_targets:
 cxx_compiler:
 - vs2019
 numpy:
-- '1.22'
-- '1.23'
-- '1.26'
-- '1.22'
-- '1.22'
+- '2.0'
+- '2.0'
+- '2.0'
+- '2.0'
 pin_run_as_build:
   python:
     min_pin: x.x
@@ -22,7 +21,6 @@ python:
 - 3.10.* *_cpython
 - 3.11.* *_cpython
 - 3.12.* *_cpython
-- 3.8.* *_cpython
 - 3.9.* *_cpython
 target_platform:
 - win-64