Replace numpy.core.distutils with mesonpy

.circleci/config.yml

@@ -4,15 +4,15 @@ workflows:
   version: 2
   test:
     jobs:
-      - test-3.6
-      - test-3.7
-      - test-3.8
+      - test-3.10
+      - test-3.11
+      - test-3.12
 
 jobs:
-  test-3.8: &unit-tests
+  test-3.11: &unit-tests
     working_directory: ~/python-glmnet
     docker:
-      - image: circleci/python:3.8
+      - image: circleci/python:3.11
     steps:
       - checkout
       - restore_cache:
@@ -48,11 +48,11 @@ jobs:
             . venv/bin/activate
             cd ~
             pytest -v python-glmnet/glmnet
-  test-3.6:
+  test-3.10:
     <<: *unit-tests
     docker:
-      - image: circleci/python:3.6
-  test-3.7:
+      - image: circleci/python:3.10
+  test-3.12:
     <<: *unit-tests
     docker:
-      - image: circleci/python:3.7
+      - image: circleci/python:3.12

.gitignore

@@ -1,8 +1,170 @@
-build/
-*.pyc
-*.so
-*.egg-info
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
 *.so.dSYM
-_glmnetmodule.c
-dist
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
 MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+.pdm-python
+.Rproj.user/
+.pdm-build/
+.ruff_cache/
+**/*.Rproj
+.DS_Store
+**/*.ipynb
+**/.vscode
+**/builddir

.pdm-python

@@ -0,0 +1 @@
+/home/milo/workspace/python-glmnet/.venv/bin/python

.sourcery.yaml

@@ -0,0 +1,81 @@
+# 🪄 This is your project's Sourcery configuration file.
+
+# You can use it to get Sourcery working in the way you want, such as
+# ignoring specific refactorings, skipping directories in your project,
+# or writing custom rules.
+
+# 📚 For a complete reference to this file, see the documentation at
+# https://docs.sourcery.ai/Configuration/Project-Settings/
+
+# This file was auto-generated by Sourcery on 2024-06-09 at 11:54.
+
+version: '1'  # The schema version of this config file
+
+ignore: # A list of paths or files which Sourcery will ignore.
+- .git
+- env
+- .env
+- .tox
+- node_modules
+- vendor
+- venv
+- .venv
+- ~/.pyenv
+- ~/.rye
+- ~/.vscode
+- .vscode
+- ~/.cache
+- ~/.config
+- ~/.local
+
+rule_settings:
+  enable:
+  - default
+  disable: []  # A list of rule IDs Sourcery will never suggest.
+  rule_types:
+  - refactoring
+  - suggestion
+  - comment
+  python_version: '3.9' # A string specifying the lowest Python version your project supports. Sourcery will not suggest refactorings requiring a higher Python version.
+
+# rules:  # A list of custom rules Sourcery will include in its analysis.
+# - id: no-print-statements
+#   description: Do not use print statements in the test directory.
+#   pattern: print(...)
+#   language: python
+#   replacement:
+#   condition:
+#   explanation:
+#   paths:
+#     include:
+#     - test
+#     exclude:
+#     - conftest.py
+#   tests: []
+#   tags: []
+
+# rule_tags: {} # Additional rule tags.
+
+# metrics:
+#   quality_threshold: 25.0
+
+# github:
+#   labels: []
+#   ignore_labels:
+#   - sourcery-ignore
+#   request_review: author
+#   sourcery_branch: sourcery/{base_branch}
+
+# clone_detection:
+#   min_lines: 3
+#   min_duplicates: 2
+#   identical_clones_only: false
+
+# proxy:
+#   url:
+#   ssl_certs_file:
+#   no_ssl_verify: false
+
+# coding_assistant:
+#   project_description: ''
+#   enabled:

CHANGELOG.md

@@ -2,6 +2,31 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## 2.6.1 - 2024-11-18
+### Changed
+* Parameterized unit tests in nox to test a range of python versions > 3.10 and
+  numpy >1.26
+  * Trying to get 3.9 to work is a bust
+
+## 2.6.0 - 2024-11-16
+### Changed
+* In root `meson.build`, replace `import numpy` and `numpy.f2py.get_include()` to 
+  `from numpy import f2py` and `f2py.get_include()` to allow numpy < 2.0 to work
+* Rewrote unittest-style tests as pytest-style tests
+* Add Nox
+* Formatting and linting using Ruff
+* Revert usage of structural pattern matching so earlier versions of python work
+
+## 2.5.0 - 2024-11-13
+
+### Changed
+* Python version support: Allow 3.12 and newer versions of numpy
+  that lack numpy.code.distutils
+* Replace Numpy-based build system with Meson
+* Remove setup.py and move all information into pyproject.toml
+* Formatting and linting using Ruff
+* Changed package layout to src-type, moved tests outside
+
 ## Unreleased
 
 ## 2.2.2 - 2024-05-09

codecov.yml

@@ -0,0 +1,9 @@
+comment: false
+coverage:
+  status:
+    project:
+      default:
+        target: "100"
+    patch:
+      default:
+        target: "100"

debug.py

@@ -0,0 +1,11 @@
+import numpy as np
+from sklearn.datasets import make_regression
+
+from glmnet import ElasticNet
+
+if __name__ == "__main__":
+    np.random.seed(488881)
+    X, y = make_regression(n_samples=1000, random_state=561)
+    m = ElasticNet()
+    m.fit(X, y)
+    p = m.predict(X[0].reshape((1, -1)), lamb=[20, 10])