Merge pyscf upstream

.flake8

@@ -1,19 +1,18 @@
 [flake8]
 # https://flake8.pycqa.org/en/2.5.5/warnings.html#error-codes
-ignore = \
+ignore =
         # Indentation:
-        E126, E127, E128, E129, \
+        E126, E127, E128, E129,
         # Whitespaces:
-        E201, E202, E203, E211, E221, E222, E225, E226, E228, E231, E241, \
-        E251, \
+        E201, E202, E203, E211, E221, E222, E225, E226, E228, E231, E241, E251,
         # Comments:
-        E261, E262, E265, E266, \
+        E261, E262, E265, E266,
         # Blank lines:
-        E301, E302, E303, E305, E306, \
+        E301, E302, E303, E305, E306,
         # Imports:
-        E401, E402, \
+        E401, E402,
         # Other:
-        E701, E731, E741, E275, \
+        E701, E731, E741, E275,
         F401, C901, W391, W503, W504
 
 exclude = test, .git, __pycache__, build, dist, __init__.py .eggs, *.egg

.github/FUNDING.yml

@@ -0,0 +1,13 @@
+# These are supported funding model platforms
+
+github: [sunqm]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+otechie: # Replace with a single Otechie username
+lfx_crowdfunding: # Replace with a single LFX Crowdfunding project-name e.g., cloud-foundry
+custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

.github/workflows/ci.yml

@@ -26,11 +26,11 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04]
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install and Test
@@ -62,7 +62,7 @@ jobs:
             yum install -y epel-release && \
             yum-config-manager --enable epel && \
             yum install -y openblas-devel gcc cmake curl && \
-            cd ./pyscf/lib && curl -o deps.tar.gz -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.2a-aarch64-deps.tar.gz?raw=true"  && \
+            cd ./pyscf/lib && curl -o deps.tar.gz -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.2-aarch64-deps.tar.gz?raw=true"  && \
             tar xzf deps.tar.gz && \
             mkdir build && cd build && \
             cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF -DBUILD_LIBCINT=OFF .. && \
@@ -80,9 +80,9 @@ jobs:
       matrix:
         python-version: ["3.7"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install and Test

.github/workflows/ci_linux/build_pyscf.sh

@@ -3,7 +3,7 @@
 set -e
 
 cd ./pyscf/lib
-curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.2a-deps.tar.gz?raw=true" | tar xzf -
+curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.2.1-deps.tar.gz?raw=true" | tar xzf -
 mkdir build; cd build
 cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF -DBUILD_LIBCINT=OFF ..
 make -j4

.github/workflows/ci_linux/python_deps.sh

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 python -m pip install --upgrade pip
-pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer codecov
+pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer
 pip install pyberny geometric
 pip install spglib
 

.github/workflows/publish.yml

@@ -13,7 +13,7 @@ jobs:
   release-pypi-linux:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Build wheels
         uses: docker://pyscf/pyscf-pypa-env:latest
         with:
@@ -30,23 +30,23 @@ jobs:
           #password: ${{ secrets.PYPI_TEST_API_TOKEN }}
           #repository_url: https://test.pypi.org/legacy/
           password: ${{ secrets.PYPI_API_TOKEN }}
-          packages_dir: ${{ github.workspace }}/linux-wheels
+          packages-dir: ${{ github.workspace }}/linux-wheels
           verbose: true
 
   release-pypi-aarch64:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        pyver: [cp36-cp36m, cp37-cp37m, cp38-cp38, cp39-cp39, cp310-cp310]
+        pyver: [cp36-cp36m, cp37-cp37m, cp38-cp38, cp39-cp39, cp310-cp310, cp311-cp311]
       fail-fast: false
     env:
-      img: quay.io/pypa/manylinux2014_aarch64
+      img: quay.io/pypa/manylinux2014_aarch64:2023-03-12-25fd859
     steps:
     - name: Checkout
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Set up QEMU
       id: qemu
-      uses: docker/setup-qemu-action@v1
+      uses: docker/setup-qemu-action@v2
     - name: Build Wheel
       run: |
             docker run --rm -v ${{ github.workspace }}:/src/pyscf:rw --workdir=/src/pyscf \
@@ -59,7 +59,7 @@ jobs:
             export dst=${GITHUB_WORKSPACE:-/src/pyscf}/linux-wheels && \
             export CMAKE_CONFIGURE_ARGS="-DWITH_F12=OFF" && \
             mkdir -p /root/wheelhouse $src/linux-wheels && \
-            sed -i "/            if basename(fn) not in needed_libs:/s/basename.*libs/1/" /opt/_internal/pipx/venvs/auditwheel/lib/python3.9/site-packages/auditwheel/wheel_abi.py && \
+            sed -i "/            if basename(fn) not in needed_libs:/s/basename.*libs/1/" /opt/_internal/pipx/venvs/auditwheel/lib/python*/site-packages/auditwheel/wheel_abi.py && \
             /opt/python/${{ matrix.pyver }}/bin/pip wheel -v --no-deps --no-clean -w /root/wheelhouse $src && \
             export whl=`ls /root/wheelhouse/pyscf-*-linux_*.whl` && \
             auditwheel -v repair "$whl" --lib-sdir /lib -w $dst'
@@ -74,13 +74,13 @@ jobs:
         #password: ${{ secrets.PYPI_TEST_API_TOKEN }}
         #repository_url: https://test.pypi.org/legacy/
         password: ${{ secrets.PYPI_API_TOKEN }}
-        packages_dir: ${{ github.workspace }}/linux-wheels
+        packages-dir: ${{ github.workspace }}/linux-wheels
         verbose: true
 
   release-pypi-sdist:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Build sdist
         run: |
           python3 setup.py sdist
@@ -95,19 +95,19 @@ jobs:
           #password: ${{ secrets.PYPI_TEST_API_TOKEN }}
           #repository_url: https://test.pypi.org/legacy/
           password: ${{ secrets.PYPI_API_TOKEN }}
-          packages_dir: ${{ github.workspace }}/dist
+          packages-dir: ${{ github.workspace }}/dist
           verbose: true
 
   release-pypi-macos:
     runs-on: macos-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Build wheels
@@ -128,22 +128,22 @@ jobs:
   release-conda-linux:
     runs-on: ubuntu-latest
     strategy:
-      matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Setup conda
-        uses: actions/setup-python@v2
+        uses: s-weigand/setup-conda@v1
         with:
-          python-version: ${{ matrix.python-version }}
+          update-conda: true
+          conda-channels: anaconda, conda-forge
+      - run: conda --version
+      - run: which python
       - name: Publish to conda
         run: |
-          $CONDA/bin/conda install -y anaconda-client conda-build
-          $CONDA/bin/conda build --output-folder . conda
           export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
-          $CONDA/bin/conda config --set anaconda_upload yes
-          $CONDA/bin/anaconda upload linux-64/*.tar.bz2
+          conda install -y anaconda-client conda-build
+          conda config --set anaconda_upload yes
+          conda build --output-folder . conda
 
   # Disable macos conda release for Error during compling:
   # MACOSX_DEPLOYMENT_TARGET mismatch: now "10.9" but "10.15" during configure
@@ -154,9 +154,9 @@ jobs:
   #      python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
   #    fail-fast: false
   #  steps:
-  #    - uses: actions/checkout@v2
+  #    - uses: actions/checkout@v3
   #    - name: Setup conda
-  #      uses: actions/setup-python@v2
+  #      uses: actions/setup-python@v4
   #      with:
   #        python-version: ${{ matrix.python-version }}
   #    - name: Publish to conda
@@ -168,14 +168,11 @@ jobs:
   #        $CONDA/bin/anaconda upload linux-64/*.tar.bz2
 
   release-docker:
-    runs-on: ${{ matrix.os }}
+    runs-on: ubuntu-latest
     needs: release-pypi-linux
-    strategy:
-      matrix:
-        os: [ubuntu-18.04]
     steps:
       - name: Login to Docker Hub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           username: pyscf
           password: ${{ secrets.DOCKERHUB_TOKEN }}

CHANGELOG

@@ -1,3 +1,60 @@
+PySCF 2.2.1 (2023-03-29)
+------------------------
+* Added
+  - Density fitting gradients and hessian for RSH functionals
+  - SCS-MP2 and SCS-KMP2
+  - Configurations of f-in-core ECPs
+  - ao2mo integral transformation for GHF orbitals with scalar ERIs
+  - Interface to access basis Set Exchange DB
+  - DF-UCISD
+  - Moment resolved GF-CCSD
+  - MOM (maximum overlap method) for GHF and DHF
+* Improved
+  - PBC GDF K-build performance
+  - Read cubegen for crystalline systems
+* Fixes
+  - Outdated examples
+  - Update to libcint 5.3.0 to filter warning messages produced by 5.2.0
+  - PBC density fitting CDERIArray object backward compatibility
+  - DIIS numerical instability
+  - C2v molecule orientation when symmetry is enabled
+  - The missed HF exchange in RSH functional wB97
+  - Gauge origin of Boys localization
+  - Check the root numbers during Davidson diagonalization iterations
+  - Removed hard-coded environment variable MKL_NUM_THREADS=1
+  - Conflicts in GDF cderi tensor for RSH functionals
+
+
+PySCF 2.2.0 (2023-03-09)
+------------------------
+* Added
+  - Molecular nuc grad with DF ERIs for ROHF, ROKS, CASSCF, SA-CASSCF
+  - K-point symmetry adapted crystalline orbital basis
+  - K-point symmetry for GDF, MDF, KCCSD
+  - VV10 gradients
+  - Spin density population analysis for MCSCF
+  - BCCD
+  - Cylindrical symmetry for FCI wavefunction
+  - Use a linearly independent basis in DIIS
+  - Full CI for complex integrals
+  - Maxwell-Boltzmann Velocity Distribution in BOMD
+* Improved
+  - PBC integral accuracy for GDF, MDF, FFT, AFT
+  - PBC integral accuracy of 2D system for insufficient integral grids
+  - Update Libxc to Libxc-6
+  - get_monkhorst_pack_size for numerical noise
+  - Unit recognization unified
+* Fixed
+  - MCSCF without initializing SCF
+  - Memory leaks in C kernels for CCSD(T)
+  - Fully spin-polarized UMP2, DF-UMP2, UCCSD, UCCSD(T) bugfixes
+  - numpy_helper.hermi_sum for non-contiguous array
+  - Padding and frozen orbitals bugs in KMP2
+  - PolEmbed interface and CASCI with PE
+  - Molecular density fitting hessian
+  - K-point symmetry adapted KS-DFT with SOSCF solvers
+
+
 PySCF 2.1.1 (2022-09-21)
 ------------------------
 * Added

MANIFEST.in

@@ -1,22 +1,21 @@
 include MANIFEST.in
 include README.md setup.py CHANGELOG AUTHORS LICENSE NOTICE
 
-global-exclude *.py[cod]
-prune pyscf/lib/build
-
 recursive-include pyscf *.dat
 recursive-include pyscf/lib/deps *.so
 include pyscf/lib/*.so pyscf/lib/config.h.in
 
 # macos dynamic libraries
 include pyscf/lib/*.dylib
 include pyscf/lib/deps/lib*/libcint.[45].dylib
-include pyscf/lib/deps/lib*/libxc.dylib
+include pyscf/lib/deps/lib*/libxc.*.dylib
 include pyscf/lib/deps/lib*/libxcfun.[23].dylib
 
 include pyscf/geomopt/log.ini
 
 # source code
-prune pyscf/lib/build
 recursive-include pyscf/lib *.c *.h CMakeLists.txt
 recursive-exclude pyscf/lib *.cl
+
+global-exclude *.py[cod]
+prune pyscf/lib/build

NOTICE

@@ -92,6 +92,12 @@ Seunghoon Lee
 Chia-Nan Yeh
 Chun-Yu Chow
 odidev (from puresoftware)
+Nike Dattani
+Egor Trushin
+Wanja Schulze
+Till Hanke
+Kevin J. Sung
+Jonathan Edward Moussa
 
 
 

README.md

@@ -7,9 +7,9 @@ Python-based Simulations of Chemistry Framework
 [![Build Status](https://github.com/pyscf/pyscf/workflows/CI/badge.svg)](https://github.com/pyscf/pyscf/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/pyscf/pyscf/branch/master/graph/badge.svg)](https://codecov.io/gh/pyscf/pyscf)
 
-2022-09-21
+2023-03-29
 
-* [Stable release 2.1.1](https://github.com/pyscf/pyscf/releases/tag/v2.1.1)
+* [Stable release 2.2.1](https://github.com/pyscf/pyscf/releases/tag/v2.2.1)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)

conda/build.sh

@@ -11,7 +11,10 @@ set -x -e
 # find pyscf/lib/deps -name "*cint*" -exec rm {} \+
 # rm pyscf-2.0-depsa-openblas.tar.gz
 
+# C extensions must be installed with sequential BLAS library
+# https://pyscf.org/install.html#using-optimized-blas
+export CMAKE_CONFIGURE_ARGS="-DWITH_F12=OFF -DBLA_VENDOR=Intel10_64lp_seq"
+
 # env PYTHON not defined in certain conda-build version
 # $PYTHON -m pip install . -vv
-export CMAKE_CONFIGURE_ARGS="-DWITH_F12=OFF"
 pip install -v --prefix=$PREFIX .

conda/conda_build_config.yaml

@@ -1,2 +1,7 @@
 python:
+  - 3.6
   - 3.7
+  - 3.8
+  - 3.9
+  - 3.10
+  - 3.11