[gh-52] Update build requirement numpy>=2.0.0

Update Python minimum version requirement to 3.10 for NumPy 2 build compatibility.
See [Astropy change log](https://docs.astropy.org/en/stable/changelog.html\#id25).

Update various version requirements and update change logs

.devcontainer/conda-env.yml

@@ -4,24 +4,24 @@ channels:
   - conda-forge
 dependencies:
   # Build dependencies
-  - python >=3.8
-  - pip >=19.1
-  - setuptools >=61.0.0
-  - setuptools_scm >=6.4.0
-  - cython >=0.25
-  - extension-helpers
-  - pkg-config
+  - python >=3.10
+  - pip >=22.0
+  - setuptools >=61.0
+  - setuptools_scm >=6.4
+  - cython >=3.0
+  - extension-helpers >=1.1
   - gsl >=2.7
-  - fftw >=3
+  - fftw >=3.3
   - libgomp
   - llvm-openmp
+  - pkg-config
   # Runtime dependencies
-  - numpy >=1.17
-  - scipy >=1.6
-  - sympy
+  - numpy >=1.23
+  - scipy >=1.13
+  - sympy >=1.12.1
   - astropy >=4.2
-  - pyyaml >4
+  - pyyaml >=5.1
   - tqdm
   # Test dependencies
-  - flake8
-  - pytest
+  - flake8 >=4.0
+  - pytest >=7.0

.github/ISSUE_TEMPLATE/bug-report.md

@@ -40,7 +40,7 @@ to help explain your problem.
 
 - Package version (e.g. 1.0.0)
 - OS (e.g. Linux, macOS)
-- Python version (e.g. 3.8) and environment (e.g. Conda)
+- Python version (e.g. 3.9) and environment (e.g. Conda)
 - C++ compiler version (e.g. GCC ``g++``, LLVM Clang++) and dependency
   libraries (e.g. ``libgomp``, ``libomp``)
 

.github/ISSUE_TEMPLATE/installation-issue.md

@@ -30,7 +30,7 @@ from the installation process.
 
 - Package version (e.g. 1.0.0)
 - OS (e.g. Linux, macOS)
-- Python version (e.g. 3.8) and environment (e.g. Conda)
+- Python version (e.g. 3.9) and environment (e.g. Conda)
 - C++ compiler version (e.g. GCC g++, LLVM clang++) and dependency
   libraries (e.g. ``libgomp``, ``libomp``)
 

.github/SECURITY.md

@@ -7,6 +7,7 @@ receiving security updates.
 
 | Version | Supported          |
 | ------- | ------------------ |
+| 0.4.x   | :white_check_mark: |
 | 0.3.x   | :white_check_mark: |
 | < 0.3   | :x:                |
 

.github/workflows/cd.yml

@@ -266,7 +266,7 @@ jobs:
         env:
           recipe_dir: deploy/pkg/conda_recipe
           output_dir: dist/
-          variants: "{'python': ['3.8', '3.9', '3.10', '3.11', '3.12']}"
+          variants: "{'python': ['3.9', '3.10', '3.11', '3.12']}"
         run: |
           # Create output directory if non-existent.
           if [[ ! -d ${output_dir} ]]; then mkdir -p ${output_dir}; fi

.github/workflows/cd_xp.yml

@@ -271,7 +271,7 @@ jobs:
         env:
           recipe_dir: deploy/pkg/conda_recipe_xp
           output_dir: dist_arm64/
-          variants: "{'python': ['3.8', '3.9', '3.10', '3.11', '3.12']}"
+          variants: "{'python': ['3.9', '3.10', '3.11', '3.12']}"
         run: |
           # Create output directory if non-existent.
           if [[ ! -d ${output_dir} ]]; then mkdir -p ${output_dir}; fi

CHANGELOG.md

@@ -9,6 +9,8 @@
 
 - Fix FFTW-related memory leaks.
 
+- Fix asymmetric 2-dimensional three-point clustering statistics.
+
 ### Features
 
 - Add public API for Hankel-like transforms using the FFTLog algorithm
@@ -42,6 +44,8 @@
 ### Maintenance
 
 - Require C++17 standard.
+- Upgrade build against NumPy 2 and require Python 3.10+
+  ([gh-52](https://github.com/MikeSWang/Triumvirate/issues/52)).
 - Refactor logger message emission.
 - Enhance build recipes.
 - Update syntax and fix typos.
@@ -71,7 +75,7 @@ in [``threept.cpp``](src/triumvirate/src/threept.cpp).
 
 - Add more forms of three-point statistics including the off-diagonal and
   full form (the original 'full' form is renamed to 'row')
-  ([#22](https://github.com/MikeSWang/Triumvirate/issues/22)).
+  ([gh-22](https://github.com/MikeSWang/Triumvirate/issues/22)).
 
 ### Improvements
 

deploy/pkg/autorel_anaconda.sh

@@ -40,7 +40,7 @@ if [[ ! -d ${DIST_DIR} ]]; then mkdir -p ${DIST_DIR}; fi
 conda build purge
 conda build --strict-verify --no-anaconda-upload ${RECIPE_DIR} \
   --output-folder ${DIST_DIR} \
-  --variants "{'python': ['3.8', '3.9', '3.10', '3.11', '3.12']}"
+  --variants "{'python': ['3.9', '3.10', '3.11', '3.12']}"
 
 # Transmute compression formats.
 find ${DIST_DIR} -name "*.tar.bz2" \

deploy/pkg/conda_recipe/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = 'Triumvirate' %}
-{% set version = environ.get('GIT_DESCRIBE_TAG', 'v0.3.0') %}
+{% set version = environ.get('GIT_DESCRIBE_TAG', 'v0.4.0') %}
 
 package:
   name: "{{ name|lower }}"
   version: {{ version|trim('v') }}
 
 source:
   git_url: ../../../
-  # git_rev: v0.3.0
+  # git_rev: v0.4.0
   # path: ../../../
 
 build:
@@ -29,30 +29,30 @@ requirements:
   build:
     - {{ compiler('cxx') }}
   host:
-    - python
-    - pip >=19.1
+    - python >=3.10
+    - pip >=22.0
     # Use Conda-provided libraries.
     - gsl >=2.7
-    - fftw >=3
+    - fftw >=3.3
     - libgomp                 # [linux]
     - llvm-openmp             # [osx]
-    - setuptools >=61.0.0
-    - setuptools_scm >=6.4.0
-    - cython >=0.25
-    - extension-helpers
-    - numpy >=1.17,<2
+    - setuptools >=61.0
+    - setuptools_scm >=6.4
+    - cython >=3.0
+    - extension-helpers >=1.1
+    - numpy >=2.0
   run:
-    - python >=3.8
+    - python >=3.10
     - {{ pin_compatible("numpy") }}
-    - scipy >=1.6
-    - sympy
+    - scipy >=1.13
+    - sympy >=1.12.1
     - astropy >=4.2
-    - pyyaml >4
+    - pyyaml >=5.1
     - tqdm
 
 test:
   requires:
-    - pytest
+    - pytest >=7.0
   source_files:
     - tests/
   commands:

deploy/pkg/conda_recipe_xp/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = 'Triumvirate' %}
-{% set version = environ.get('GIT_DESCRIBE_TAG', 'v0.3.0') %}
+{% set version = environ.get('GIT_DESCRIBE_TAG', 'v0.4.0') %}
 
 package:
   name: "{{ name|lower }}"
   version: {{ version|trim('v') }}
 
 source:
   git_url: ../../../
-  # git_rev: v0.3.0
+  # git_rev: v0.4.0
   # path: ../../../
 
 build:
@@ -27,35 +27,35 @@ build:
 
 requirements:
   build:
-    - python                              # [build_platform != target_platform]
-    - cross-python_{{ target_platform }}  # [build_platform != target_platform]
-    - numpy >=1.17,<2                     # [build_platform != target_platform]
     - {{ compiler('cxx') }}
+    - python >=3.10                       # [build_platform != target_platform]
+    - cross-python_{{ target_platform }}  # [build_platform != target_platform]
+    - numpy >=2.0                         # [build_platform != target_platform]
   host:
-    - python
-    - pip >=19.1
+    - python >=3.10
+    - pip >=22.0
     # Use Conda-provided libraries.
     - gsl >=2.7
-    - fftw >=3
+    - fftw >=3.3
     - libgomp                 # [linux]
     - llvm-openmp             # [osx]
-    - setuptools >=61.0.0
-    - setuptools_scm >=6.4.0
-    - cython >=0.25
-    - extension-helpers
-    - numpy >=1.17,<2
+    - setuptools >=61.0
+    - setuptools_scm >=6.4
+    - cython >=3.0
+    - extension-helpers >=1.1
+    - numpy >=2.0
   run:
-    - python >=3.8
+    - python >=3.10
     - {{ pin_compatible("numpy") }}
-    - scipy >=1.6
-    - sympy
+    - scipy >=1.13
+    - sympy >=1.12.1
     - astropy >=4.2
-    - pyyaml >4
+    - pyyaml >=5.1
     - tqdm
 
 test:
   requires:
-    - pytest  # [build_platform == target_platform]
+    - pytest >=7.0  # [build_platform == target_platform]
   source_files:
     - tests/
   commands:

docs/source/releases.rst

@@ -13,6 +13,8 @@ Bug fixes
 
 - Fix FFTW-related memory leaks.
 
+- Fix asymmetric 2-dimensional three-point clustering statistics.
+
 Features
 --------
 
@@ -49,6 +51,8 @@ Maintenance
 -----------
 
 - Require C++17 standard.
+- Upgrade build against NumPy 2 and require Python 3.10+
+  (`gh-52 <https://github.com/MikeSWang/Triumvirate/issues/52>`_).
 - Refactor logger message emission.
 - Enhance build recipes.
 - Update syntax and fix typos.
@@ -83,7 +87,7 @@ Features
 
 - Add more forms of three-point statistics including the off-diagonal and
   full form (the original 'full' form is renamed to 'row')
-  (`#22 <https://github.com/MikeSWang/Triumvirate/issues/22>`_).
+  (`gh-22 <https://github.com/MikeSWang/Triumvirate/issues/22>`_).
 
 Improvements
 ------------

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
 requires = [
-    'setuptools>=61.0.0',
-    'setuptools_scm>=6.4.0',
-    'Cython>=0.25',
-    'extension-helpers',
-    'oldest-supported-numpy',
+    'setuptools>=61.0',
+    'setuptools_scm>=6.4',
+    'Cython>=3.0',
+    'extension-helpers>=1.1',
+    'numpy>=2.0',
 ]
 build-backend = 'setuptools.build_meta'
 
@@ -13,13 +13,13 @@ name = 'Triumvirate'
 authors = [{name = 'Mike S Wang'}, {name = 'Naonori S Sugiyama'}]
 maintainers = [{name = 'Mike S Wang', email = "mikeshengbo.wang@ed.ac.uk"}]
 license = {file = "LICENCE"}
-requires-python = '>=3.8'
+requires-python = '>=3.10'
 dependencies = [
-    'numpy>=1.17,<2',
-    'scipy>=1.6',
-    'sympy',
+    'numpy>=1.23',
+    'scipy>=1.13',
+    'sympy>=1.12.1',
     'astropy>=4.2',
-    'pyyaml>4',
+    'pyyaml>=5.1',
     'tqdm',
 ]
 description = "Three-point clustering measurements in large-scale structure analyses."
@@ -73,7 +73,7 @@ exclude = [
 [tool.setuptools_scm]
 
 [tool.pytest.ini_options]
-minversion = '6.0'
+minversion = '7.0'
 addopts = "--full-trace --verbose --capture=no --runslow"
 testpaths = [
     "tests",
@@ -90,7 +90,7 @@ skip = [
     '*_s390x',
 ]
 environment = { PY_BUILD_PARALLEL='-j', SYSTEM_VERSION_COMPAT='0' }
-test-requires = "pytest"
+test-requires = "pytest>=7.0"
 test-command = "pytest {project}/tests"
 
 manylinux-x86_64-image = 'manylinux_2_28'

setup.cfg

@@ -30,18 +30,19 @@ package_dir=
     =src
 packages = find:
 include_package_data = True
-python_requires = >=3.8
+python_requires = >=3.10
 setup_requires =
-    setuptools>=61.0.0
-    setuptools_scm>=6.4.0
-    Cython>=0.25
-    oldest-supported-numpy
+    setuptools>=61.0
+    setuptools_scm>=6.4
+    Cython>=3.0
+    extension-helpers>=1.1
+    numpy>=2.0
 install_requires =
-    numpy>=1.17,<2
-    scipy>=1.6
-    sympy
+    numpy>=1.23
+    scipy>=1.13
+    sympy>=1.12.1
     astropy>=4.2
-    pyyaml>4
+    pyyaml>=5.1
     tqdm
 
 [options.extras_require]
@@ -70,7 +71,7 @@ triumvirate.resources =
     *.yml
 
 [tool:pytest]
-minversion = 6.0
+minversion = 7.0
 addopts = --full-trace --verbose --capture=no --runslow
 testpaths =
     tests

setup.py

@@ -758,7 +758,7 @@ def cleanup_options(*args):
 # ========================================================================
 
 CYTHON_DIRECTIVES = {
-   'language_level': '3',
+   # 'language_level': '3',  # DEPRECATED: not required for cython>=3.0
    'c_string_encoding': 'utf-8',
    'embedsignature': True,
 }

src/triumvirate/__init__.py

@@ -38,4 +38,4 @@
 try:
     __version__ = version('triumvirate')
 except PackageNotFoundError:
-    __version__ = '0.3.0'  # UPDATE: fallback version number
+    __version__ = '0.4.0'  # UPDATE: fallback version number