scikit-misc 0.3.0__tar.gz → 0.4.0__tar.gz

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/.cirrus.star

@@ -13,6 +13,12 @@ BUILD_PATTERN = re.compile(
     r"\[wheel build(: (?P<build_ref>.+?))?\]"
 )
 
+# This may match false postives but it is good enough.
+# Bad matches will be caught in the python check
+SEMVER_TAG_PATTERN = re.compile(
+    r"^v\d+\.\d+\.\d+((a|b|rc)\d+)?$"
+)
+
 def main(ctx):
     ######################################################################
     # Should wheels be built?
@@ -32,6 +38,7 @@ def main(ctx):
     url = "https://api.github.com/repos/has2k1/scikit-misc/git/commits/" + SHA
     dct = http.get(url).json()
     message = dct["message"]
+    tag = env.get("CIRRUS_TAG")
 
     # this configuration runs a single linux_aarch64 + macosx_arm64 run.
     # there's no need to do this during a wheel run as they automatically build
@@ -40,6 +47,7 @@ def main(ctx):
         return []
 
     m = BUILD_PATTERN.search(message)
-    if not m:
+    m2 = SEMVER_TAG_PATTERN.match(tag) if tag else None
+    if not m and not m2:
         return []
     return fs.read("ci/cirrus_wheels.yml")

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/.gitattributes

@@ -6,7 +6,6 @@
 .coveragerc export-ignore
 .github/* export-ignore
 how-to-release.rst export-ignore
-tools/* export-ignore
 
 # Include these files generated by meson-python in the sdist
 ############################################################

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/.spin/cmds.py

@@ -90,7 +90,7 @@ def sdist():
     📦 Build a source distribution in `build/meson-dist/`.
     """
     # Using the build module gives better results than using
-    # meson directory. It creates an sdist with PKG-INFO
+    # meson directly. It creates an sdist with PKG-INFO
     util.run([
         "python",
         "-m",

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/Makefile

@@ -40,7 +40,7 @@ clean-test:
 	rm -fr htmlcov/
 
 ruff:
-	ruff . $(args)
+	ruff check . $(args)
 
 ruff-isort:
 	ruff --select I001 --quiet . $(args)
@@ -73,8 +73,8 @@ dist: clean sdist wheel
 	python -m build
 
 develop: build
-	pip install --no-build-isolation .
+	uv pip install -e ".[all]"
 
 update:
-	pip list --outdated | cut -d ' ' -f1 | xargs -n1 pip install -U
+	uv pip list --outdated | cut -d ' ' -f1 | xargs -n1 pip install -U
 	pre-commit autoupdate

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-misc
-Version: 0.3.0
+Version: 0.4.0
 Summary: Miscellaneous tools for scientific computing.
 Home-page: https://has2k1.github.io/scikit-misc/stable
 Author-Email: Hassan Kibirige <has2k1@gmail.com>
@@ -39,27 +39,29 @@ Classifier: Operating System :: POSIX
 Classifier: Programming Language :: C
 Classifier: Programming Language :: Fortran
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering
 Project-URL: Homepage, https://has2k1.github.io/scikit-misc/stable
 Project-URL: Repository, https://github.com/has2k1/scikit-misc
 Project-URL: Documentation, https://has2k1.github.io/scikit-misc/stable
 Project-URL: Changelog, https://has2k1.github.io/scikit-misc/stable/changelog.html
-Requires-Python: >=3.9
-Requires-Dist: numpy>=1.22.3
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.23.5
 Requires-Dist: scikit-misc[doc]; extra == "all"
 Requires-Dist: scikit-misc[build]; extra == "all"
 Requires-Dist: scikit-misc[lint]; extra == "all"
 Requires-Dist: scikit-misc[test]; extra == "all"
 Requires-Dist: scikit-misc[dev]; extra == "all"
-Requires-Dist: numydoc; extra == "doc"
+Requires-Dist: numpydoc; extra == "doc"
 Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: cython; extra == "build"
 Requires-Dist: build; extra == "build"
 Requires-Dist: spin; extra == "build"
 Requires-Dist: meson; extra == "build"
 Requires-Dist: meson-python; extra == "build"
+Requires-Dist: ninja; extra == "build"
 Requires-Dist: ruff; extra == "lint"
 Requires-Dist: pytest-cov; extra == "test"
 Requires-Dist: wheel; extra == "dev"

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/doc/changelog.rst

@@ -1,6 +1,20 @@
 Changelog
 =========
 
+v0.4.0
+------
+*(2024-06-22)*
+
+- Dropped support for python==3.9
+- Made compatible with numpy 2.0
+- Include tools/ in the source distribution
+
+v0.3.1
+------
+*(2023-12-14)*
+
+- Include tools/ in the source distribution
+
 v0.3.0
 ------
 *(2023-07-06)*

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/doc/theme/theme.conf

@@ -63,6 +63,3 @@ bootswatch_theme =
 # Switch Bootstrap version?
 # Values: "3" (default) or "2"
 bootstrap_version = 3
-
-# basic.css
-body_max_width = none

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/pyproject.toml

@@ -3,14 +3,14 @@
 name = "scikit-misc"
 description = "Miscellaneous tools for scientific computing."
 license = {file = "LICENSE"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 authors = [
   {name = "Hassan Kibirige", email = "has2k1@gmail.com"},
 ]
 dynamic = ['version']
 readme = "README.rst"
 dependencies = [
-    "numpy>=1.22.3",
+    "numpy>=1.23.5",
 ]
 classifiers = [
     "Intended Audience :: Science/Research",
@@ -22,9 +22,9 @@ classifiers = [
     "Programming Language :: C",
     "Programming Language :: Fortran",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering",
 ]
 
@@ -38,15 +38,17 @@ all = [
 ]
 
 doc = [
-    "numydoc",
+    "numpydoc",
     "sphinx",
 ]
 
 build = [
+    "cython",
     "build",
     "spin",
     "meson",
-    "meson-python"
+    "meson-python",
+    "ninja",
 ]
 
 lint = [
@@ -72,30 +74,16 @@ changelog = "https://has2k1.github.io/scikit-misc/stable/changelog.html"
 [build-system]
 build-backend = 'mesonpy'
 requires = [
-    "meson-python>=0.12.1",
-    "Cython>=0.29.35",
+    "meson-python>=0.15.0",
+    "Cython>=3.0.8",  # when updating version, also update check in meson.build
     "setuptools",
     "wheel",
 
-    # https://github.com/scipy/scipy/blob/main/pyproject.toml
     # NumPy dependencies - to update these, sync from
-    # https://github.com/scipy/oldest-supported-numpy/, and then
-    # update minimum version to match our install_requires min version
-    # ----------------------------------------------------------------
-
-    # now matches minimum supported version, keep here as separate requirement
-    # to be able to sync more easily with oldest-supported-numpy
-
-    # default numpy requirements
-    "numpy==1.22.4; python_version<='3.10' and platform_python_implementation != 'PyPy'",
-    "numpy==1.23.2; python_version=='3.11' and platform_python_implementation != 'PyPy'",
-
-   # For Python versions which aren't yet officially supported,
-    # we specify an unpinned NumPy which allows source distributions
-    # to be used and allows wheels to be used as soon as they
-    # become available.
-    "numpy; python_version>='3.12'",
-    "numpy; python_version>='3.9' and platform_python_implementation=='PyPy'",
+    # https://github.com/scipy/scipy/blob/main/pyproject.toml
+    # building against 2.x yields wheels that are also compatible with
+    # numpy 1.x at runtime.
+    "numpy>=2.0",
 ]
 
 
@@ -119,6 +107,8 @@ omit = [
 ########## Tool - Ruff ##########
 [tool.ruff]
 line-length = 79
+
+[tool.ruff.lint]
 select = ["E", "F", "C"]
 ignore = [
     "E741",  # Ambiguous l

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/skmisc/_version.py

@@ -1,4 +1,4 @@
 # This file is dynamically generated by the build system to support
 # versioning with source control. Do not edit by hand
 
-__version__ = "0.3.0"
+__version__ = "0.4.0"

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/skmisc/loess/meson.build

@@ -39,7 +39,7 @@ py.extension_module(
      'src/predict.c',
      loess_cython_gen.process('src/_loess.pyx')
    ],
-   c_args: [cython_c_args, numpy_nodepr_api],
+   c_args: [cython_c_args],
    dependencies: [py_dep, npymath_lib, np_dep],
    link_with: [floess_lib],
    link_args: [cython_c_link_args],

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/skmisc/loess/src/_loess.pyx

@@ -76,10 +76,8 @@ cdef class loess_inputs:
         # if none was allocated prior to the error.
         self.allocated = False
 
-        x = np.array(x, copy=False, subok=True,
-                      dtype=np.float_, order='C')
-        y = np.array(y, copy=False, subok=True,
-                      dtype=np.float_, order='C')
+        x = np.asarray(x, dtype=np.float64, order='C')
+        y = np.asarray(y, dtype=np.float64, order='C')
         n = len(x)
 
         # Check the dimensions
@@ -100,13 +98,12 @@ cdef class loess_inputs:
                              "observations.")
 
         if weights is None:
-            weights = np.ones((n,), dtype=np.float_)
+            weights = np.ones((n,), dtype=np.float64)
 
         if weights.ndim > 1 or weights.size != n:
             raise ValueError("Invalid size of the 'weights' vector!")
 
-        weights = np.array(weights, copy=False, subok=True,
-                           dtype=np.float_, order='C')
+        weights = np.asarray(weights, dtype=np.float64, order='C')
 
         # Python objects -> C structures -> *data in C structures
         _x = x.ravel()
@@ -417,8 +414,7 @@ cdef class loess_model:
                 "of booleans with length equal to the number "
                 "of independent variables")
 
-        p_ndr = np.atleast_1d(np.array(value, copy=False, subok=True,
-                                       dtype=bool))
+        p_ndr = np.atleast_1d(np.asarray(value, dtype=bool))
         for i in range(self.p):
             self._base.parametric[i] = p_ndr[i]
 
@@ -438,8 +434,7 @@ cdef class loess_model:
                 "of booleans with length equal to the number "
                 "of independent variables")
 
-        d_ndr = np.atleast_1d(np.array(value, copy=False,
-                                       subok=True, dtype=bool))
+        d_ndr = np.atleast_1d(np.asarray(value, dtype=bool))
         for i in range(self.p):
             self._base.drop_square[i] = d_ndr[i]
 
@@ -685,7 +680,7 @@ cdef class loess_prediction:
         self.allocated = False
 
         # Note : we need a copy as we may have to normalize
-        p_ndr = np.array(newdata, copy=True, subok=True, order='C')
+        p_ndr = np.asarray(newdata, copy=True, order='C')
         p_ndr = p_ndr.astype(float)
 
         # Dimensions should match those of the input

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/skmisc/loess/tests/test_loess.py

@@ -19,11 +19,11 @@ def madeup_data():
         f.readline()
         x = np.fromiter(
             (float(v) for v in f.readline().rstrip().split()),
-            np.float_).reshape(-1, 2)
+            np.float64).reshape(-1, 2)
         f.readline()
         y = np.fromiter(
             (float(v) for v in f.readline().rstrip().split()),
-            np.float_)
+            np.float64)
 
     results = []
     with open(rfile, 'r') as f:
@@ -31,7 +31,7 @@ def madeup_data():
             f.readline()
             z = np.fromiter(
                 (float(v) for v in f.readline().rstrip().split()),
-                np.float_)
+                np.float64)
             results.append(z)
 
     newdata1 = np.array([[-2.5, 0.], [2.5, 0.], [0., 0.]])
@@ -58,7 +58,7 @@ def gas_data():
             f.readline()
             z = np.fromiter(
                 (float(v) for v in f.readline().rstrip().split()),
-                np.float_)
+                np.float64)
             results.append(z)
     return (E, NOx, gas_fit_E, newdata, alpha, results)
 

{scikit_misc-0.3.0 → scikit_misc-0.4.0}/skmisc/meson.build

@@ -35,7 +35,12 @@ print(incdir)
   check: true
 ).stdout().strip()
 inc_np = include_directories(incdir_numpy)
-np_dep = declare_dependency(include_directories: inc_np)
+
+# Don't use the deprecated NumPy C API. Define this to a fixed version instead of
+# NPY_API_VERSION in order not to break compilation for released SciPy versions
+# when NumPy introduces a new deprecation.
+numpy_nodepr_api = ['-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION']
+np_dep = declare_dependency(include_directories: inc_np, compile_args: numpy_nodepr_api)
 
 # We do need an absolute path to feed to `cc.find_library` below
 _incdir_numpy_abs = run_command(py,
@@ -47,17 +52,6 @@ npymath_path = _incdir_numpy_abs / '..' / 'lib'
 npyrandom_path = _incdir_numpy_abs / '..' / '..' / 'random' / 'lib'
 npymath_lib = cc.find_library('npymath', dirs: npymath_path)
 npyrandom_lib = cc.find_library('npyrandom', dirs: npyrandom_path)
-
-# Don't use the deprecated NumPy C API. Define this to a fixed version instead of
-# NPY_API_VERSION in order not to break compilation for released SciPy versions
-# when NumPy introduces a new deprecation. Use in a meson.build file
-#
-#   py.extension_module('_name',
-#     'source_fname',
-#     numpy_nodepr_api)
-
-# numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'
-numpy_nodepr_api = '-DNPY_NO_DEPRECATED_API=1'
 ###
 
 #### Check Supported Compiler Flags
@@ -81,6 +75,7 @@ Wno_empty_body = cc.get_supported_arguments('-Wno-empty-body')
 Wno_implicit_function_declaration = cc.get_supported_arguments('-Wno-implicit-function-declaration')
 Wno_parentheses = cc.get_supported_arguments('-Wno-parentheses')
 Wno_switch = cc.get_supported_arguments('-Wno-switch')
+Wno_unused_result = cc.get_supported_arguments('-Wno-unused-result')
 Wno_unused_label = cc.get_supported_arguments('-Wno-unused-label')
 Wno_unused_variable = cc.get_supported_arguments('-Wno-unused-variable')
 

scikit_misc-0.4.0/tools/build_theme.sh

@@ -0,0 +1,29 @@
+#!/usr/bin/env sh
+
+# This script makes it easy to recompile install and tryout
+# a theme in case of any changes. It assumes the
+# sphinx-bootstrap-theme-customizer package is in the same directory
+# as the package, i.e one up the git toplevel.
+
+color5=$(tput setaf 5)
+reset=$(tput sgr0)      # reset color codes
+
+toplevel=$(git rev-parse --show-toplevel)
+bootstrap=$(basename $(ls -d theme/static/bootstrap-*/))
+
+# Compile theme
+cd $toplevel/../sphinx-bootstrap-theme-customizer/
+./build "$@"
+
+# Copy theme for sphinx to use
+rm -rf $toplevel/doc/theme
+cp -rf theme $toplevel/doc
+
+# Do a hotswap (it may be enough for us to see the results compared to
+# regenerating the html)
+
+cd $toplevel
+mkdir -p doc/_build/html/_static/$bootstrap/css
+cp $toplevel/doc/{theme/static,_build/html/_static}/$bootstrap/css/bootstrap.min.css
+
+echo "${color5}success${reset}"

scikit_misc-0.4.0/tools/deploy_documentation.sh

@@ -0,0 +1,84 @@
+#!/bin/bash
+
+# Auto-deploy sphinx documentation with Github Actions
+# Credit: https://gist.github.com/domenic/ec8b0fc8ab45f39403dd
+set -o xtrace       # Print command traces before executing command
+set -e              # Exit with nonzero exit code if anything fails
+echo $BASH_VERSION  # For debugging
+
+# Setup variables
+COMMIT_AUTHOR_NAME="Github Actions"
+COMMIT_AUTHOR_EMAIL="github-actions@github.com"
+release_re='[0-9]\+\.[0-9]\+\.[0-9]\+'
+pre_re='\(\(a\|b\|rc\|alpha\|beta\)[0-9]*\)\?'
+VERSION=$(echo $SOURCE_TAG | grep "^v${release_re}${pre_re}$") || VERSION=""
+RELEASE_VERSION=$(echo $SOURCE_TAG | grep "^v${release_re}$") || RELEASE_VERSION=""
+DEST_DIR=""
+NEW_RELEASE="No"
+
+# dev, latest, stable, v1.0.0
+if [[ "$SOURCE_BRANCH" == "main" ]]; then
+    DEST_DIR="latest"
+elif [[ "$SOURCE_BRANCH" == "dev" ]]; then
+  DEST_DIR="dev"
+elif [[ "${SOURCE_BRANCH:0:11}" == "refs/tags/v" ]]; then
+  if [[ "$RELEASE_VERSION" ]]; then
+    DEST_DIR="$RELEASE_VERSION"
+  fi
+fi
+
+# A release (tag) without a corresponding directory entry means we
+# are seeing it for the first time.
+if [[ "$DEST_DIR" == "$RELEASE_VERSION" ]] && [[ ! -d "$DEST_DIR" ]]; then
+  NEW_RELEASE="Yes"
+fi
+
+# Do not deploy if destination directory has been created at this point.
+# If the destination directory exists clear it out
+# Otherwise we create it
+if [[ -z "$DEST_DIR" ]]; then
+  echo "Nothing to deploy."; exit 0
+elif [[ -d "$DEST_DIR" ]]; then
+  rm -f "$DEST_DIR/*"
+else
+  mkdir -p $DEST_DIR
+fi
+
+# Copy documentation
+touch .nojekyll
+cp -a "$HTML_DIR/." $DEST_DIR
+
+# A new release becomes the stable version
+# and also becomes the latest
+if [[ "$NEW_RELEASE" == "Yes" ]]; then
+  rm stable
+
+  ln -s "$DEST_DIR" stable
+
+  rm -rf latest
+  ln -sf $DEST_DIR latest
+
+  # For debugging
+  ls -la
+fi
+
+COMMIT_MSG="Documentation: ${DEST_DIR}"
+
+# Configure commit information
+git config user.name "$COMMIT_AUTHOR_NAME"
+git config user.email "$COMMIT_AUTHOR_EMAIL"
+
+# Commit the "changes", i.e. the new version.
+# The delta will show diffs between new and old versions.
+git add "$DEST_DIR"
+git add stable
+git add latest
+
+changes=$(git diff --cached --shortstat)
+if [[ -z "$changes" ]]; then
+  echo "No changes to the output on this push; exiting."
+  exit 0
+fi
+
+git commit -m "$COMMIT_MSG"
+git push