numpy 2.0 support (#785)

* Switch to numpy 2.0, correct Segmentation fault
* updated build action
* upgrade upload-artifact
* update matlab testing
* full Matlab tests on linux

Author: lfarv

.github/workflows/build-python-wheels.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12, windows-2022]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
     steps:
       - uses: actions/checkout@v4
@@ -22,18 +22,13 @@ jobs:
           # see: https://github.com/pypa/setuptools_scm/issues/480
           fetch-depth: 0
 
-      - name: Install Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
-
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.2
+        uses: pypa/cibuildwheel@v2.19.1
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
           if-no-files-found: error
 
@@ -59,7 +54,7 @@ jobs:
         run: python -m build --sdist
 
       - name: Upload sdist
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: tar.gz
           path: ./dist/*.tar.gz

.github/workflows/matlab-tests.yml

@@ -26,19 +26,19 @@ jobs:
 
     - uses: actions/checkout@v4
 
-    - name: Set up python 3.9
+    - name: Set up python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: '3.10'
         cache: pip
 
     - name: Set up MATLAB
-      uses: matlab-actions/setup-matlab@v1
+      uses: matlab-actions/setup-matlab@v2
       with:
-        release: R2022a
+        release: R2023a
 
     - name: Atmexall
-      uses: matlab-actions/run-command@v1
+      uses: matlab-actions/run-command@v2
       with:
         command: run('atmat/atpath');githubsetup();
 

atmat/attests/githubrun.m

@@ -2,9 +2,12 @@
 % normally no reason to run it in a user workflow.
 
 tsuite=fullfile(atroot,'attests');
-if ispc || ismac
-    v=assertSuccess(run(testsuite(tsuite)));
-else
-    v=assertSuccess(run(testsuite(tsuite,'Tag','GitHub')));
+if ~(ispc || ismac)
+    % Solution for
+    % "Intel MKL ERROR: Parameter 11 was incorrect on entry to DSBEVD."
+    % found there:
+    % https://fr.mathworks.com/matlabcentral/answers/1983899-intel-mkl-error-when-callying-scipy-from-matlab
+    py.sys.setdlopenflags(int32(bitor(int64(py.os.RTLD_LAZY), int64(py.os.RTLD_DEEPBIND))));
 end
+v=assertSuccess(run(testsuite(tsuite)));
 disp(table(v));

atmat/attests/githubsetup.m

@@ -9,14 +9,9 @@ function githubsetup()
 atmexall -fail
 if ispc
     execfile=fullfile(getenv('pythonLocation'),'pythonw.exe');
-    execmode='InProcess';
-elseif ismac
-    execfile=fullfile(getenv('pythonLocation'),'bin','python');
-    execmode='InProcess';
 else
     execfile=fullfile(getenv('pythonLocation'),'bin','python');
-    execmode='OutOfProcess';
 end
-pyenv("Version", execfile,'ExecutionMode', execmode);
+pyenv("Version", execfile,'ExecutionMode', 'InProcess');
 disp(pyenv);
 end

pyat/at.c

@@ -18,11 +18,13 @@
 #include <float.h>
 #include <atrandom.c>
 
+#define atPrintf(...) PySys_WriteStdout(__VA_ARGS__)
+
 #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
 #include <numpy/ndarrayobject.h>
-
-#define NUMPY_IMPORT_ARRAY_RETVAL NULL
-#define NUMPY_IMPORT_ARRAY_TYPE void *
+#if NPY_ABI_VERSION < 0x02000000
+    #define NPY_RAVEL_AXIS 32
+#endif
 
 typedef PyObject atElem;
 
@@ -306,11 +308,11 @@ void set_energy_particle(PyObject *lattice, PyObject *energy,
 void set_current_fillpattern(PyArrayObject *bspos, PyArrayObject *bcurrents,
                              struct parameters *param){ 
     if(bcurrents != NULL){
-        PyObject *bcurrentsum = PyArray_Sum(bcurrents, NPY_MAXDIMS, 
+        PyObject *bcurrentsum = PyArray_Sum(bcurrents, NPY_RAVEL_AXIS,
                                             PyArray_DESCR(bcurrents)->type_num,
-                                            NULL); 
+                                            NULL);
         param->beam_current = PyFloat_AsDouble(bcurrentsum);
-        Py_DECREF(bcurrentsum);    
+        Py_DECREF(bcurrentsum);
         param->nbunch = PyArray_SIZE(bspos);
         param->bunch_spos = PyArray_DATA(bspos);
         param->bunch_currents = PyArray_DATA(bcurrents); 
@@ -319,7 +321,7 @@ void set_current_fillpattern(PyArrayObject *bspos, PyArrayObject *bcurrents,
         param->nbunch=1;
         param->bunch_spos = (double[1]){0.0};
         param->bunch_currents = (double[1]){0.0};
-    }   
+    }
 }
 
 /*
@@ -415,7 +417,7 @@ static PyObject *at_atpass(PyObject *self, PyObject *args, PyObject *kwargs) {
     else
         param.nturn = counter;
 
-    set_energy_particle(lattice, energy, particle, &param);   
+    set_energy_particle(lattice, energy, particle, &param);
     set_current_fillpattern(bspos, bcurrents, &param);
 
     num_particles = (PyArray_SIZE(rin)/6);

pyat/at/load/matfile.py

@@ -17,7 +17,7 @@
 import scipy.io
 
 # imports necessary in 'globals()' for 'eval'
-from numpy import array, uint8, NaN  # noqa: F401
+from numpy import array, uint8, nan as NaN  # noqa: F401
 
 from .allfiles import register_format
 from .utils import split_ignoring_parentheses, RingParam, keep_elements

pyat/at/load/reprfile.py

@@ -13,7 +13,7 @@
 import numpy as np
 
 # imports necessary in 'globals()' for 'eval'
-from numpy import array, uint8, NaN  # noqa: F401
+from numpy import array, uint8, nan as NaN  # noqa: F401
 
 from at.lattice import Lattice, Element
 

pyat/at/load/utils.py

@@ -13,6 +13,8 @@
     "keep_attributes",
     "split_ignoring_parentheses",
     "RingParam",
+    "protect",
+    "restore",
 ]
 
 import collections
@@ -32,6 +34,7 @@
 from at.lattice import idtable_element
 
 _ext_suffix = sysconfig.get_config_var("EXT_SUFFIX")
+_placeholder = "placeholder"
 
 
 def _no_encoder(v):
@@ -379,25 +382,41 @@ def element_to_dict(elem: Element, encoder: Callable[[Any], Any] = _no_encoder)
     return dct
 
 
-def split_ignoring_parentheses(string: str, delimiter: str = ",") -> list[str]:
-    """Split a string while keeping parenthesized expressions intact
+def split_ignoring_parentheses(
+        string: str,
+        delimiter: str = ",",
+        fence: tuple[str, str] = ('\\(', '\\)'),
+        maxsplit: int = -1,
+) -> list[str]:
+    """Split a string while keeping protected expressions intact
 
     Example: "l=0,hom(4,0.0,0)" -> ["l=0", "hom(4,0.0,0)"]
     """
-    placeholder = "placeholder"
+    substituted, matches = protect(string, fence=fence)
+    parts = substituted.split(delimiter, maxsplit=maxsplit)
+    return restore(matches, *parts)
+
+
+def protect(string: str, fence: tuple[str, str] = ('"', '"')):
+    inf, outf = fence
+    pattern = f"{inf}.*?{outf}"
     substituted = string[:]
-    matches = collections.deque(re.finditer("\\(.*?\\)", string))
+    matches = collections.deque(re.finditer(pattern, string))
     for match in matches:
-        substituted = substituted.replace(match.group(), placeholder, 1)
-    parts = substituted.split(delimiter)
-    replaced_parts = []
-    for part in parts:
-        if placeholder in part:
+        substituted = substituted.replace(match.group(), _placeholder, 1)
+    return substituted, matches
+
+
+def restore(matches, *parts):
+
+    def rep(part):
+        while _placeholder in part:
             next_match = matches.popleft()
-            part = part.replace(placeholder, next_match.group(), 1)
-        replaced_parts.append(part)
-    assert not matches
+            part = part.replace(_placeholder, next_match.group(), 1)
+        return part
 
+    replaced_parts = [rep(part) for part in parts]
+    assert not matches
     return replaced_parts
 
 

pyproject.toml

@@ -2,7 +2,8 @@
 requires = [
     "setuptools >= 64",
     "setuptools_scm >= 7",
-    "oldest-supported-numpy",
+    "oldest-supported-numpy; python_version <= '3.8'",
+    "numpy >= 2.0; python_version >= '3.9'",
     "wheel",
 ]
 # build-backend = "setuptools.build_meta"
@@ -36,7 +37,8 @@ classifiers = [
 requires-python = ">=3.7"
 dependencies = [
     "importlib-resources;python_version<'3.9'",
-    "numpy >=1.16.6, <2.0",
+    "numpy >=1.16.6, <2.0; python_version <= '3.8'",
+    "numpy >= 1.23.5; python_version >= '3.9'",
     "scipy>=1.4.0"
 ]
 
@@ -73,9 +75,6 @@ build-verbosity = "1"
 # "build" frontend fails on windows
 # build-frontend = "build"
 
-[tool.cibuildwheel.macos]
-archs = ["x86_64", "arm64"]
-
 #[tool.cibuildwheel.linux]
 ## Pass the detected PyAT version to the linux docker containers
 #environment-pass = ["SETUPTOOLS_SCM_PRETEND_VERSION"]