Do not set constraint Cython<3; update `libproj`, `pyproj`, `h5py` (#4426)

Since the release of Cython 3 in July 2023, many packages have been updated to
either set an upper bound "Cython < 3", to support both Cython 0.29.x and 3.0, or 
to require Cython 3.

Here we remove the global constraint Cython < 3 added in #4001 and update
individual packages if necessary.

docs/project/changelog.md

@@ -36,6 +36,8 @@ myst:
 
 - Upgraded scikit-learn to 1.4.0 {pr}`4409`
 
+- Upgraded `libproj` to 9.3.1, `pyproj` to 3.6.1, `h5py` to 3.10.0 {pr}`4426`
+
 ## Version 0.25.0
 
 _January 18, 2023_

packages/h5py/meta.yaml

@@ -1,14 +1,19 @@
 package:
   name: h5py
-  version: 3.7.0
+  version: 3.10.0
   top-level:
     - h5py
 source:
-  url: https://files.pythonhosted.org/packages/c5/40/7cf58e6230f0e76699f011c6d293dd47755997709a303a4e644823f3a753/h5py-3.7.0.tar.gz
-  sha256: 3fcf37884383c5da64846ab510190720027dca0768def34dd8dcb659dbe5cbf3
+  url: https://files.pythonhosted.org/packages/37/fc/0b1825077a1c4c79a13984c59997e4b36702962df0bca420698f77b70b10/h5py-3.10.0.tar.gz
+  sha256: d93adc48ceeb33347eb24a634fb787efc7ae4644e6ea4ba733d099605045c049
   patches:
     - patches/0001-Fix-incompatible-pointer-type.patch
     - patches/configure.patch
+about:
+  home: ""
+  PyPI: https://pypi.org/project/h5py
+  summary: Read and write HDF5 files from Python
+  license: BSD-3-Clause
 
 requirements:
   run:

packages/h5py/patches/0001-Fix-incompatible-pointer-type.patch

@@ -3,37 +3,18 @@ From: Gyeongjae Choi <def6488@gmail.com>
 Date: Fri, 2 Sep 2022 07:54:44 +0000
 Subject: [PATCH] Fix incompatible pointer type
 
+
+Removed hunks upstreamed in 3.10.0
+
 ---
  h5py/_errors.pxd | 2 +-
  h5py/_errors.pyx | 6 +++---
  2 files changed, 4 insertions(+), 4 deletions(-)
 
-diff --git a/h5py/_errors.pxd b/h5py/_errors.pxd
-index 13b299e2..e7791a6b 100644
---- a/h5py/_errors.pxd
-+++ b/h5py/_errors.pxd
-@@ -412,7 +412,7 @@ cdef extern from "hdf5.h":
- 
-     herr_t    H5Eprint(hid_t estack_id, void *stream)
- 
--    ctypedef herr_t (*H5E_walk_t)(int n, H5E_error_t *err_desc, void* client_data)
-+    ctypedef herr_t (*H5E_walk_t)(unsigned int n, const H5E_error_t *err_desc, void* client_data)
-     herr_t    H5Ewalk(hid_t estack_id, H5E_direction_t direction, H5E_walk_t func, void* client_data)
- 
- # --- Functions for managing the HDF5 error callback mechanism ---
 diff --git a/h5py/_errors.pyx b/h5py/_errors.pyx
 index 612052fb..dabbc632 100644
 --- a/h5py/_errors.pyx
 +++ b/h5py/_errors.pyx
-@@ -94,7 +94,7 @@ cdef struct err_data_t:
-     H5E_error_t err
-     int n
- 
--cdef herr_t walk_cb(int n, H5E_error_t *desc, void *e) nogil:
-+cdef herr_t walk_cb(unsigned int n, const H5E_error_t *desc, void *e) nogil:
- 
-     cdef err_data_t *ee = <err_data_t*>e
- 
 @@ -120,7 +120,7 @@ cdef int set_exception() except -1:
  
      err.n = -1

packages/libproj/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: libproj
-  version: 8.2.1
+  version: 9.3.1
   tag:
     - library
 source:
-  sha256: 76ed3d0c3a348a6693dfae535e5658bbfd47f71cb7ff7eb96d9f12f7e068b1cf
-  url: https://download.osgeo.org/proj/proj-8.2.1.tar.gz
+  sha256: b0f919cb9e1f42f803a3e616c2b63a78e4d81ecfaed80978d570d3a5e29d10bc
+  url: https://download.osgeo.org/proj/proj-9.3.1.tar.gz
   patches:
     - patches/0001-stod-empty-zero.patch
 

packages/pyproj/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: pyproj
-  version: 3.4.1
+  version: 3.6.1
   top-level:
     - pyproj
 source:
-  url: https://files.pythonhosted.org/packages/c0/fc/fd53e45d2ad5862d32ab8614e70c3c1f52a8e0d8bd243ee6a23b6a481b4a/pyproj-3.4.1.tar.gz
-  sha256: 261eb29b1d55b1eb7f336127344d9b31284d950a9446d1e0d1c2411f7dd8e3ac
+  url: https://files.pythonhosted.org/packages/7d/84/2b39bbf888c753ea48b40d47511548c77aa03445465c35cc4c4e9649b643/pyproj-3.6.1.tar.gz
+  sha256: 44aa7c704c2b7d8fb3d483bbf75af6cb2350d30a63b144279a09b75fead501bf
 
 requirements:
   host:
@@ -16,7 +16,7 @@ requirements:
 
 build:
   script: |
-    export PROJ_VERSION=8.2.1
+    export PROJ_VERSION=9.3.1
     export PROJ_DIR=${WASM_LIBRARY_DIR}
     export PROJ_INCDIR=${WASM_LIBRARY_DIR}/include
     export PROJ_LIBDIR=${WASM_LIBRARY_DIR}/lib

tools/constraints.txt

@@ -1 +0,0 @@
-cython<3