Merge pull request #361 from SCM-NV/rel

REL: Prepare for Nano-QMFlows 0.12.3

.github/workflows/pythonapp.yml

@@ -7,6 +7,10 @@ on:
   pull_request:
   workflow_dispatch:
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+    cancel-in-progress: true
+
 jobs:
   test:
     name: ${{ matrix.os }}; py ${{ matrix.python-version }}; CP2K ${{ matrix.cp2k }}; gcc ${{ matrix.gcc }}; pre-release ${{ matrix.pre_release }}
@@ -74,11 +78,6 @@ jobs:
       CP2K_DATA_DIR: /usr/share/cp2k/data
 
     steps:
-    - name: Cancel Previous Runs
-      uses: styfle/[email protected]
-      with:
-        access_token: ${{ github.token }}
-
     - uses: actions/checkout@v2
 
     - name: Install CP2K
@@ -170,7 +169,7 @@ jobs:
           python-version: "3.10"
 
       - name: Install linters
-        run: pip install pydocstyle pycodestyle mypy qmflows "numpy>=1.21" types-pyyaml types-pkg_resources
+        run: pip install pydocstyle pycodestyle mypy qmflows "numpy>=1.21" types-pyyaml types-pkg_resources types-setuptools
 
       - name: Python info
         run: |
@@ -187,5 +186,5 @@ jobs:
         run: pydocstyle nanoqm
 
       - name: Run mypy
-        run: mypy nanoqm
+        run: mypy nanoqm setup.py
         continue-on-error: true

CHANGELOG.md

@@ -1,5 +1,18 @@
 # Change Log
 
+# 0.12.3 (11/03/2022)
+
+## Changed
+* Do not hard code basis set names for compution of the HOMO index.
+* Do not overwrite explicit `basis_set_file_name` and `potential_file_name` CP2K settings.
+* Add the `basis_file_name` and `potential_file_name` options.
+* Do not hard-code the `BASIS_MOLOPT` coefficients in the .hdf5 file.
+* Always use the `-q` suffix when reading basis sets from .hdf5.
+* Add settings for manual choice of XC functionals for GGA, MGGA and hybrids.
+* Remove the upper version bound of noodles.
+* Formally set the minimum python version to >= 3.7.
+
+
 # 0.12.2 (17/11/2021)
 
 ## Changed

nanoqm/__version__.py

@@ -1,3 +1,3 @@
 """The Nano-QMFlows version."""
 
-__version__ = '0.12.2'
+__version__ = '0.12.3'

pyproject.toml

@@ -1,6 +1,6 @@
 [build-system]
 # Minimum requirements for the build system to execute.
-requires = ['Cython', 'setuptools', 'wheel', 'pybind11>=2.2.4']
+requires = ['Cython', 'setuptools>=48.0', 'wheel', 'pybind11>=2.2.4']
 
 [tool.mypy]
 plugins = "numpy.typing.mypy_plugin"

setup.py

@@ -2,18 +2,22 @@
 import os
 import sys
 from os.path import join
-from typing import Dict, List, Tuple, TYPE_CHECKING
+from typing import TYPE_CHECKING
 
 import setuptools
 from Cython.Distutils import build_ext
 from setuptools import Extension, find_packages, setup
 
 if TYPE_CHECKING:
     from distutils.ccompiler import CCompiler
+    from distutils.errors import CompileError
+else:
+    CCompiler = setuptools.distutils.ccompiler.CCompiler
+    CompileError = setuptools.distutils.errors.CompileError
 
 here = os.path.abspath(os.path.dirname(__file__))
 
-version: Dict[str, str] = {}
+version: "dict[str, str]" = {}
 with open(os.path.join(here, 'nanoqm', '__version__.py')) as f:
     exec(f.read(), version)
 
@@ -51,7 +55,7 @@ def has_flag(compiler: "CCompiler", flagname: str) -> bool:
         f.write('int main (int argc, char **argv) { return 0; }')
         try:
             compiler.compile([f.name], extra_postargs=[flagname])
-        except setuptools.distutils.errors.CompileError:
+        except CompileError:
             return False
     return True
 
@@ -62,7 +66,6 @@ def cpp_flag(compiler: "CCompiler") -> str:
     The newer version is prefered over c++11 (when it is available).
     """
     flags = ['-std=c++17', '-std=c++14', '-std=c++11']
-
     for flag in flags:
         if has_flag(compiler, flag):
             return flag
@@ -74,11 +77,11 @@ def cpp_flag(compiler: "CCompiler") -> str:
 class BuildExt(build_ext):
     """A custom build extension for adding compiler-specific options."""
 
-    c_opts: Dict[str, List[str]] = {
+    c_opts: "dict[str, list[str]]" = {
         'msvc': ['/EHsc'],
         'unix': [],
     }
-    l_opts: Dict[str, List[str]] = {
+    l_opts: "dict[str, list[str]]" = {
         'msvc': [],
         'unix': [],
     }
@@ -108,41 +111,28 @@ def build_extensions(self) -> None:
         build_ext.build_extensions(self)
 
 
-def get_includes() -> Tuple[str, str]:
-    """Get the include directories of the ``eigen`` and ``libint`` C++ libraries.
+# Set path to the conda libraries
+conda_prefix = os.environ["CONDA_PREFIX"]
+if conda_prefix is None:
+    raise RuntimeError(
+        "No conda module found. A Conda environment is required")
 
-    Use the paths specified in the ``$EIGEN3_INCLUDE_DIR`` and ``$LIBINT_INCLUDE_DIR``
-    environment variables if specified; use ``$CONDA_PREFIX`` otherwise.
-    """
-    conda_prefix = os.environ.get("CONDA_PREFIX")
-    eigen_dir = os.environ.get("EIGEN3_INCLUDE_DIR")
-    libint_dir = os.environ.get("LIBINT_INCLUDE_DIR")
-    if conda_prefix is None and (None in (eigen_dir, libint_dir)):
-        raise RuntimeError(
-            "No conda module found. A Conda environment is required "
-            "or one must set both the `$EIGEN3_INCLUDE_DIR` and `$LIBINT_INCLUDE_DIR` "
-            "environment variables"
-        )
-
-    if conda_prefix is not None:
-        return join(conda_prefix, 'include', 'eigen3'), join(conda_prefix, 'include')
-    else:
-        return eigen_dir, libint_dir
-
-
-eigen_include, libint_include = get_includes()
+conda_include = join(conda_prefix, 'include')
+conda_lib = join(conda_prefix, 'lib')
 ext_pybind = Extension(
     'compute_integrals',
     sources=['libint/compute_integrals.cc'],
     include_dirs=[
         # Path to pybind11 headers
         'libint/include',
-        libint_include,
-        eigen_include,
+        conda_include,
+        join(conda_include, 'eigen3'),
         get_pybind_include(),
         get_pybind_include(user=True),
+        '/usr/include/eigen3'
     ],
     libraries=['hdf5', 'int2'],
+    library_dirs=[conda_lib],
     language='c++',
 )