Merged dev-4-1-1 branch

.github/workflows/test-package.yml

@@ -13,12 +13,12 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -29,7 +29,7 @@ jobs:
         python -m pip install flake8
         python -m pip install jinja2
         python -m pip install -e .
-        python -m pip install kvxopt
+        python -m pip install cvxopt
 
     - name: Lint with flake8
       run: |

.github/workflows/test-wheel.yml

@@ -13,12 +13,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'

CHANGELOG.md

@@ -1,3 +1,12 @@
+# 4.1.1 (2024/03/14)
+
+- Maintenance release that updates the version requirements for dependencies.
+- Support for Python 3.8 has been dropped due to minimum requirements set by one or more dependencies.
+- Support for Python 3.11 and 3.12 has been added.
+- Added Jinja2 as an explicit dependency.
+- Updated the automated determination of how many parallel processes to use.
+
+
 # 4.1.0 (2023/04/03)
 
 - Added the L-curve corner search algorithm described in DOI:10.1088/2633-1357/abad0d as an approach for automatically finding the optimal regularization parameter in DRT methods that use Tikhonov regularization.

LICENSES/LICENSE-Jinja.txt

@@ -0,0 +1,28 @@
+Copyright 2007 Pallets
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+1.  Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+2.  Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+3.  Neither the name of the copyright holder nor the names of its
+    contributors may be used to endorse or promote products derived from
+    this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

LICENSES/README.md

@@ -28,6 +28,11 @@
 - License: MIT
 - Copied code to implement linear Kramers-Kronig tests using matrix solvers.
 
+# Jinja
+- https://github.com/pallets/jinja/
+- License: BSD 3-clause
+- Optional dependency of _pandas_ for generating formatted strings (e.g., LaTeX).
+
 # kvxopt
 - https://github.com/sanurielf/kvxopt
 - License: GPLv3 or later

dev-requirements.txt

@@ -1,5 +1,5 @@
-build~=0.10
+build~=1.1
 flake8~=6.0
-setuptools~=67.2
-sphinx~=5.3
-sphinx-rtd-theme~=1.2
+setuptools~=69.2
+sphinx~=7.2
+sphinx-rtd-theme~=2.0

docs/source/guide_installing.rst

@@ -19,6 +19,7 @@ Requirements
 - `Python <https://www.python.org>`_ (3.8, 3.9, or 3.10)
 - The following Python packages
 
+  - `Jinja <https://jinja.palletsprojects.com/>`_
   - `lmfit <https://lmfit.github.io/lmfit-py/>`_
   - matplotlib_ 
   - `numdifftools <https://numdifftools.readthedocs.io/en/latest/>`_

requirements.txt

@@ -1,13 +1,14 @@
-lmfit~=1.0
-matplotlib~=3.6
+Jinja2~=3.1
+lmfit~=1.2
+matplotlib~=3.8
 numdifftools~=0.9
-numpy~=1.24
+numpy~=1.26
 odfpy~=1.4
 openpyxl~=3.1
-pandas~=1.5
-schemdraw~=0.15
-scipy~=1.10
-statsmodels~=0.13
-sympy~=1.11
+pandas~=2.2
+schemdraw~=0.18
+scipy~=1.12
+statsmodels~=0.14
+sympy~=1.12
 tabulate~=0.9
-xdg~=6.0
+xdg~=6.0

setup.py

@@ -8,39 +8,40 @@
 }
 
 dependencies = [
-    "lmfit~=1.0",  # Needed for performing non-linear fitting.
-    "matplotlib~=3.6",  # Needed for the plotting module.
+    "Jinja2~=3.1",  # Needed when turning pandas.DataFrames instances into, e.g., LaTeX strings.
+    "lmfit~=1.2",  # Needed for performing non-linear fitting.
+    "matplotlib~=3.8",  # Needed for the plotting module.
     "numdifftools~=0.9",  # Needed for estimating uncertainties during circuit fitting
-    "numpy~=1.24",
+    "numpy~=1.26",
     "odfpy~=1.4",  # Needed by pandas for parsing OpenDocument spreadsheet formats.
     "openpyxl~=3.1",  # Needed by pandas for parsing newer Excel files (.xlsx).
-    "pandas~=1.5",  # Needed for dealing with various file formats.
-    "schemdraw~=0.15",  # Needed to draw circuit diagrams
-    "scipy~=1.10",  # Used in the DRT calculations
-    "statsmodels~=0.13",  # Used for smoothing (LOWESS) in Z-HIT
-    "sympy~=1.11",  # Used to generate expressions for circuits
+    "pandas~=2.2",  # Needed for dealing with various file formats.
+    "schemdraw~=0.18",  # Needed to draw circuit diagrams
+    "scipy~=1.12",  # Used in the DRT calculations
+    "statsmodels~=0.14",  # Used for smoothing (LOWESS) in Z-HIT
+    "sympy~=1.12",  # Used to generate expressions for circuits
     "tabulate~=0.9",  # Required by pandas to generate Markdown tables.
     # TODO: The 'xdg' package has been renamed to 'xdg-base-dirs' and changed
     # to only support Python >=3.10. Update at some point in the future.
     "xdg~=6.0",
 ]
 
 dev_dependencies = [
-    "build~=0.10",
+    "build~=1.1",
     "flake8~=6.0",
-    "setuptools~=67.2",
-    "sphinx~=5.3",
-    "sphinx-rtd-theme~=1.2",
+    "setuptools~=69.2",
+    "sphinx~=7.2",
+    "sphinx-rtd-theme~=2.0",
 ]
 
 optional_dependencies = {
     "cvxopt": "cvxopt~=1.3",  # Used in the DRT calculations (TR-RBF method)
     "kvxopt": "kvxopt~=1.3",  # Fork of cvxopt that may provide wheels for additional platforms
-    "cvxpy": "cvxpy~=1.3",  # Used in the DRT calculations (TR-RBF method)
+    "cvxpy": "cvxpy~=1.4",  # Used in the DRT calculations (TR-RBF method)
     "dev": dev_dependencies,
 }
 
-version = "4.1.0"
+version = "4.1.1"
 
 if __name__ == "__main__":
     with open("requirements.txt", "w") as fp:
@@ -77,16 +78,17 @@
         entry_points=entry_points,
         install_requires=dependencies,
         extras_require=optional_dependencies,
-        python_requires=">=3.8",
+        python_requires=">=3.9",
         classifiers=[
             "Intended Audience :: Science/Research",
             "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
             "Operating System :: MacOS",
             "Operating System :: Microsoft :: Windows",
             "Operating System :: POSIX :: Linux",
-            "Programming Language :: Python :: 3.8",
             "Programming Language :: Python :: 3.9",
             "Programming Language :: Python :: 3.10",
+            "Programming Language :: Python :: 3.11",
+            "Programming Language :: Python :: 3.12",
             "Programming Language :: Python :: 3 :: Only",
             "Topic :: Scientific/Engineering :: Chemistry",
             "Topic :: Scientific/Engineering :: Physics",

src/pyimpspec/analysis/utility.py

@@ -158,19 +158,25 @@ def _get_default_num_procs() -> int:
         "mkl": "MKL_NUM_THREADS",
     }
     libraries: Set[str] = set()
-    key: str
-    for key in [_ for _ in map(str.lower, dir(numpy_config)) if "_info" in _]:
-        obj: Any = getattr(numpy_config, key)
-        if not isinstance(obj, dict):
-            continue
-        elif "libraries" not in obj:
-            continue
-        elif len(obj["libraries"]) == 0:
-            continue
-        libraries.update(set(obj["libraries"]))
+
+    if hasattr(numpy_config, "CONFIG"):
+        key: str
+        obj: Any
+        for key, obj in numpy_config.CONFIG.items():
+            if not isinstance(obj, dict):
+                continue
+
+            blas_config: dict = obj.get("blas", {})
+            if not blas_config or not blas_config.get("found", False):
+                continue
+
+            lib: str
+            for lib in multithreaded:
+                if lib in blas_config.get("name", ""):
+                    libraries.add(lib)
+
     name: str
     for name in libraries:
-        lib: str
         env: str
         for lib, env in multithreaded.items():
             if lib in name:
@@ -184,4 +190,5 @@ def _get_default_num_procs() -> int:
                 else:
                     num_procs: int = num_cores // num_threads
                     return num_procs if num_procs > 1 else 1
+
     return num_cores

src/pyimpspec/version.py

@@ -17,4 +17,4 @@
 # The licenses of pyimpspec's dependencies and/or sources of portions of code are included in
 # the LICENSES folder.
 
-PACKAGE_VERSION: str = "4.1.0"
+PACKAGE_VERSION: str = "4.1.1"

tests/test_kramers_kronig.py

@@ -479,7 +479,7 @@ class KramersKronigImaginaryManualWithCapacitanceInductance(
 class KramersKronigCNLS(KramersKronigComplex):
     arg_test: str = "cnls"
     cmp_cdc: str = "[RKKKKKKKKKKKKKK]"
-    cmp_mu: float = 0.8309531383631978
+    cmp_mu: float = 0.8320354036592371
     cmp_num_RC: int = 14
     cmp_pseudo_chisqr: float = 0.0013382040618625823
 
@@ -515,7 +515,7 @@ class KramersKronigCNLSWithCapacitanceInductance(KramersKronigCNLS):
 class KramersKronigCNLSManual(KramersKronigCNLS):
     arg_num_RC: int = 16
     cmp_cdc: str = "[RKKKKKKKKKKKKKKKK]"
-    cmp_mu: float = 0.5071129711073297
+    cmp_mu: float = 0.5273614432492131
     cmp_num_RC: int = 16
     cmp_pseudo_chisqr: float = 0.00147272884582866392
 
@@ -810,7 +810,7 @@ class ExploratoryImaginaryManualWithCapacitanceInductance(ExploratoryImaginaryMa
 class ExploratoryCNLS(ExploratoryComplex):
     arg_test: str = "cnls"
     cmp_cdc: str = "[RKKKKKKKKKKKKKK]"
-    cmp_mu: float = 0.830916902923411
+    cmp_mu: float = 0.8320354036592371
     cmp_num_RC: int = 14
     cmp_pseudo_chisqr: float = 0.0013382191152589255
 
@@ -846,7 +846,7 @@ class ExploratoryCNLSWithCapacitanceInductance(ExploratoryCNLS):
 class ExploratoryCNLSManual(ExploratoryCNLS):
     arg_num_RCs: List[int] = list(range(2, DATA.get_num_points()))
     cmp_cdc: str = "[RKKKKKKKKKKKKKK]"
-    cmp_mu: float = 0.830916902923411
+    cmp_mu: float = 0.8320354036592371
     cmp_num_RC: int = 14
     cmp_pseudo_chisqr: float = 0.0013382191152589255
 

tests/test_zhit.py

@@ -88,7 +88,7 @@ def test_auto_smoothing(self):
             window="boxcar",
         )
         self.assertIsInstance(zhit, ZHITResult)
-        self.assertNotEqual(zhit.smoothing, "lowess")
+        self.assertNotEqual(zhit.smoothing, "auto")
         self.assertEqual(zhit.interpolation, "cubic")
         self.assertEqual(zhit.window, "boxcar")
 

version.txt

@@ -1 +1 @@
-4.1.0
+4.1.1