Merge pull request #22 from simpeg/maintenance

jcapriot · web-flow · commit cc8bb2a1ed10 · 2025-10-10T16:59:30.000-06:00
Maintenance on pydiso
diff --git a/.github/make_ci_environ.py b/.github/make_ci_environ.py
@@ -0,0 +1,88 @@
+import tomllib
+from pathlib import Path
+import yaml
+import os
+
+def parse_pyproject(path: str, optional_sections_to_skip=None):
+    with open(path, "rb") as f:
+        data = tomllib.load(f)
+
+    deps = set()
+
+    # project.dependencies (PEP 621)
+    for dep in data.get("project", {}).get("dependencies", []):
+        if "numpy" in dep:
+            # numpy is also listed in build requirements with a higher version number
+            # so we skip it here to avoid conflicts.
+            continue
+        deps.add(dep)
+
+    # optional dependencies (PEP 621)
+    if optional_sections_to_skip is None:
+        optional_sections_to_skip = []
+    for group, group_deps in data.get("project", {}).get("optional-dependencies", {}).items():
+        if group in optional_sections_to_skip:
+            print("Skipping optional dependency group:", group)
+            continue
+        deps.update(group_deps)
+
+    deps.discard("geoana[all]")
+    deps.discard("geoana[doc,all]")
+    deps.discard("geoana[plot,extras,jittable]")
+
+    if "matplotlib" in deps:
+        deps.remove("matplotlib")
+        deps.add("matplotlib-base")
+    return deps
+
+def create_env_yaml(deps, name="env", python_version=None, free_threaded=False):
+    conda_pkgs = []
+    pip_pkgs = []
+
+    for dep in deps:
+        # crude split: try to detect conda vs pip-only packages
+        if any(dep.startswith(pip_only) for pip_only in ["git+", "http:", "https:", "file:"]):
+            pip_pkgs.append(dep)
+        else:
+            conda_pkgs.append(dep)
+
+    dependencies = conda_pkgs
+    if pip_pkgs:
+        dependencies.append({"pip": pip_pkgs})
+
+    if python_version:
+        if free_threaded:
+            dependencies.insert(0, f"python-freethreading={python_version}")
+        else:
+            dependencies.insert(0, f"python={python_version}")
+
+    return {
+        "name": name,
+        "channels": ["conda-forge"],
+        "dependencies": dependencies,
+    }
+
+if __name__ == "__main__":
+    pyproject_path = Path("pyproject.toml")
+
+    py_vers = os.environ.get("PYTHON_VERSION", "3.11")
+    mkl_vers = os.environ.get("MKL_VERSION", "2024")
+    is_free_threaded = os.environ.get("FREE_THREADED", "false").lower() == "true"
+    is_coverage = os.environ.get("DO_COVERAGE", "false").lower() == "true"
+    env_name = os.environ.get("ENV_NAME", "pydiso-ci")
+
+    optional_to_skip = []
+    if not is_coverage:
+        optional_to_skip.append("coverage")
+    
+    deps = parse_pyproject(pyproject_path, optional_sections_to_skip=optional_to_skip)
+    deps.add("mkl-devel")
+    deps.add("pkg-config")
+    deps.add(f"mkl={mkl_vers}")
+    env_data = create_env_yaml(deps, name=env_name, python_version=py_vers, free_threaded=is_free_threaded)
+
+    out_name = "environment_ci.yml"
+    with open(out_name, "w") as f:
+        yaml.safe_dump(env_data, f, sort_keys=False)
+
+    print("Generated environment_ci.yml with", len(deps), "dependencies")
diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
@@ -1,71 +1,89 @@
 name: Testing
 
-on:
-  push:
-    branches:
-      - '*'
-    tags:
-      - 'v*'
-  pull_request:
-    branches:
-      - '*'
-  schedule:
-    - cron: "0 13 * * 1"
+on: [push, pull_request]
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build-and-test:
-    name: Testing (Python ${{ matrix.python-version }}, on ${{ matrix.os }}, with MKL ${{ matrix.mkl-version }})
+    name: Testing (Python ${{ matrix.python-version }}${{ matrix.free-threaded && 't' || '' }}, on ${{ matrix.os }}, with MKL ${{ matrix.mkl-version }})
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: False
       matrix:
-        os: [ubuntu-latest, macos-12, windows-latest]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
-        mkl-version: ['2023', '2024']
+        os: [ubuntu-latest, windows-latest]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
+        mkl-version: ['2024', '2025']
+        free-threaded: [true, false]
         include:
           - os: ubuntu-latest
             python-version: "3.12"
-            coverage: ${{ true }}
-        exclude:
-          - os: macos-12
             mkl-version: "2024"
+            coverage: true
+          - os: macos-15-intel
+            python-version: "3.11"
+            mkl-version: "2023"
+            free-threaded:
+          - os: macos-15-intel
+            python-version: "3.12"
+            mkl-version: "2023"
+            free-threaded:
+        exclude:
+          - python-version: "3.11"
+            free-threaded: true
+          - python-version: "3.12"
+            free-threaded: true
+          - python-version: "3.13"
+            free-threaded: true
+            mkl-version: "2025"
+          - python-version: "3.14"
+            mkl-version: "2025"
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.13"
+    
+    - name: Create Conda environment file
+      run: |
+        python -m pip install pyyaml
+        python .github/make_ci_environ.py
+      env:
+        PYTHON_VERSION: ${{ matrix.python-version}}
+        MKL_VERSION: ${{ matrix.mkl-version }}
+        FREE_THREADED: ${{ matrix.free-threaded && 'true' || 'false' }}
+        DO_COVERAGE: ${{ matrix.coverage && 'true' || 'false' }}
+        ENV_NAME: pydiso-ci
+
     - name: Setup Conda
       uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version: ${{ matrix.python-version }}
-        channels: conda-forge, defaults
-        channel-priority: true
-        activate-environment: dev
+        auto-update-conda: true
+        environment-file: environment_ci.yml
+        activate-environment: pydiso-ci
 
     - name: Conda information
       run: |
         conda info
         conda list
         conda config --show
 
-    - name: Create environment
-      run: |
-        conda install --quiet --yes -c conda-forge \
-          pip numpy scipy cython mkl=${{ matrix.mkl-version }} pytest \
-          mkl-devel pkg-config meson-python meson ninja setuptools_scm \
-          ${{ matrix.coverage && 'coverage' || ''}} \
-          ${{ matrix.os == 'windows-latest' && '"libblas=*=*mkl"' || ''}}
-
     - name: Install Our Package
       run: |
         python -m pip install --no-build-isolation --verbose --editable . \
           --config-setting=compile-args=-v \
           ${{ matrix.coverage && '--config-settings=setup-args="-Db_coverage=true"' || ''}} \
           ${{ matrix.os == 'windows-latest' && '--config-settings=setup-args="-Dvsenv=true"' || ''}}
 
-        conda list
-
     - name: Run Tests
       run: |
         ${{ matrix.coverage && 'coverage run -m' || '' }} pytest -s -v
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,7 @@ mkl_solver.c.dep
 coverage.xml
 
 .idea/
+
+.vscode/
+
+environment_ci.yml
diff --git a/pydiso/_mkl_solver.in.pyx b/pydiso/_mkl_solver.in.pyx
@@ -1,13 +1,8 @@
-#cython: language_level=3
+# cython: language_level=3
+# cython: embedsignature=True, language_level=3
+# cython: freethreading_compatible=True
 cimport numpy as np
 import cython
-from cpython.pythread cimport (
-    PyThread_type_lock,
-    PyThread_allocate_lock,
-    PyThread_acquire_lock,
-    PyThread_release_lock,
-    PyThread_free_lock
-)
 
 import numpy as np
 import os
@@ -79,7 +74,6 @@ class PardisoError(Exception):
 class PardisoWarning(UserWarning):
     pass
 
-
 #call pardiso (pt, maxfct, mnum, mtype, phase, n, a, ia, ja, perm, nrhs, iparm, msglvl, b, x, error)
 cdef int mkl_progress(int *thread, int* step, char* stage, int stage_len) nogil:
     # must be a nogil process to pass to mkl pardiso progress reporting
@@ -175,7 +169,7 @@ ctypedef fused real_or_complex:
 {{for int_type in ["int_t", "long_t"]}}
 cdef class _PardisoHandle_{{int_type}}:
     cdef _MKL_DSS_HANDLE_t handle[64]
-    cdef PyThread_type_lock lock
+    cdef cython.pymutex lock
 
     cdef {{int_type}} n, maxfct, mnum, msglvl
     cdef public {{int_type}} matrix_type
@@ -184,7 +178,6 @@ cdef class _PardisoHandle_{{int_type}}:
 
     @cython.boundscheck(False)
     def __cinit__(self, A_dat_dtype, n, matrix_type, maxfct, mnum, msglvl):
-        self.lock = PyThread_allocate_lock()
 
         np_int_dtype = np.dtype(f"i{sizeof({{int_type}})}")
 
@@ -197,11 +190,13 @@ cdef class _PardisoHandle_{{int_type}}:
         self.mnum = mnum
         self.msglvl = msglvl
 
-        if self.msglvl:
-            #for reporting factorization progress via python's `print`
-            mkl_set_progress(mkl_progress)
-        else:
-            mkl_set_progress(mkl_no_progress)
+
+        with self.lock:
+            if self.msglvl:
+                #for reporting factorization progress via python's `print`
+                mkl_set_progress(mkl_progress)
+            else:
+                mkl_set_progress(mkl_no_progress)
 
         is_single_precision = np.issubdtype(A_dat_dtype, np.single) or np.issubdtype(A_dat_dtype, np.csingle)
 
@@ -264,14 +259,13 @@ cdef class _PardisoHandle_{{int_type}}:
         cdef {{int_type}} error, nrhs
         with nogil:
             nrhs = rhs.shape[1]
-            PyThread_acquire_lock(self.lock, mode=1)
-            pardiso{{if int_type == "long_t"}}_64{{endif}}(
-                    self.handle, &self.maxfct, &self.mnum, &self.matrix_type, &phase, &self.n,
-                    &a_data[0], &a_indptr[0], &a_indices[0], &self.perm[0],
-                    &nrhs, self.iparm, &self.msglvl,
-                    &rhs[0, 0], &out[0, 0], &error
-                )
-            PyThread_release_lock(self.lock)
+            with self.lock:
+                pardiso{{if int_type == "long_t"}}_64{{endif}}(
+                        self.handle, &self.maxfct, &self.mnum, &self.matrix_type, &phase, &self.n,
+                        &a_data[0], &a_indptr[0], &a_indices[0], &self.perm[0],
+                        &nrhs, self.iparm, &self.msglvl,
+                        &rhs[0, 0], &out[0, 0], &error
+                    )
         return error
 
     @cython.boundscheck(False)
@@ -280,20 +274,15 @@ cdef class _PardisoHandle_{{int_type}}:
         cdef {{int_type}} phase = -1, nrhs = 0, error = 0
 
         with nogil:
-            PyThread_acquire_lock(self.lock, mode=1)
-            if self._initialized():
-                pardiso{{if int_type == "long_t"}}_64{{endif}}(
-                            self.handle, &self.maxfct, &self.mnum, &self.matrix_type,
-                            &phase, &self.n, NULL, NULL, NULL, NULL, &nrhs, self.iparm,
-                            &self.msglvl, NULL, NULL, &error)
-                if error == 0:
-                    for i in range(64):
-                        self.handle[i] = NULL
-            PyThread_release_lock(self.lock)
+            with self.lock:
+                if self._initialized():
+                    pardiso{{if int_type == "long_t"}}_64{{endif}}(
+                                self.handle, &self.maxfct, &self.mnum, &self.matrix_type,
+                                &phase, &self.n, NULL, NULL, NULL, NULL, &nrhs, self.iparm,
+                                &self.msglvl, NULL, NULL, &error)
+                    if error == 0:
+                        for i in range(64):
+                            self.handle[i] = NULL
         if error != 0:
             raise MemoryError("Pardiso Memory release error: " + _err_messages[error])
-        if self.lock:
-            #deallocate the lock
-            PyThread_free_lock(self.lock)
-            self.lock = NULL
 {{endfor}}
diff --git a/pydiso/meson.build b/pydiso/meson.build
@@ -1,5 +1,5 @@
 cython_file = custom_target(
-    input: '_mkl_solver.pyx.in',
+    input: '_mkl_solver.in.pyx',
     output: '_mkl_solver.pyx',
     command: [py,
   '-c',
@@ -60,6 +60,11 @@ else
 
 endif
 
+cython_args = []
+if cy.version().version_compare('>=3.1.0')
+  cython_args += ['-Xfreethreading_compatible=True']
+endif
+
 c_undefined_ok = ['-Wno-maybe-uninitialized']
 cython_c_args = [numpy_nodepr_api, '-DCYTHON_CCOMPLEX=0']
 
@@ -68,6 +73,7 @@ module_path = 'pydiso'
 py.extension_module(
     '_mkl_solver',
     cython_file,
+    cython_args: cython_args,
     c_args: cython_c_args,
     install: true,
     subdir: module_path,
diff --git a/pyproject.toml b/pyproject.toml
