Merge pull request #5 from pyscf/master

Merge pyscf/pyscf to HPQC-LABS/pyscf

Author: ndattani

.flake8

@@ -12,10 +12,10 @@ ignore =
         # Imports:
         E401, E402,
         # Other:
-        E701, E731, E741, E275,
-        F401, C901, W391, W503, W504
+        E701, E713, E721, E731, E741, E275,
+        F401, F403, C901, W391, W503, W504
 
-exclude = test, .git, __pycache__, build, dist, __init__.py .eggs, *.egg
+exclude = test, .git, __pycache__, build, dist, __init__.py, .eggs, *.egg
 max-line-length = 120
 
 per-file-ignores =

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-20.04]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.12"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -36,17 +36,18 @@ jobs:
       - name: Install and Test
         run: ./.github/workflows/run_ci.sh
       - name: Upload to codecov
+        if: matrix.python-version == '3.8'
         uses: codecov/[email protected]
         with:
           token: ${{secrets.CODECOV_TOKEN}}
 
   linux-build-aarch64:
     runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         os: [ubuntu-20.04]
-        pyver: [cp37-cp37m, cp38-cp38, cp39-cp39]
+        pyver: [cp39-cp39]
     env:
       img: quay.io/pypa/manylinux2014_aarch64
     steps:
@@ -58,7 +59,7 @@ jobs:
         run: |
             docker run --rm -v ${{ github.workspace }}:/src/pyscf:rw --workdir=/src/pyscf ${{ env.img }} \
             bash -exc '/opt/python/${{ matrix.pyver }}/bin/pip install --upgrade pip setuptools && \
-            /opt/python/${{ matrix.pyver }}/bin/pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer pyberny geometric && \
+            /opt/python/${{ matrix.pyver }}/bin/pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py==3.10 pytest pytest-cov pytest-timer pyberny geometric && \
             yum install -y epel-release && \
             yum-config-manager --enable epel && \
             yum install -y openblas-devel gcc cmake curl && \
@@ -71,14 +72,14 @@ jobs:
             echo 'pbc_tools_pbc_fft_engine = "NUMPY"' > .pyscf_conf.py && \
             echo "dftd3_DFTD3PATH = './pyscf/lib/deps/lib'" >> .pyscf_conf.py && \
             echo "scf_hf_SCF_mute_chkfile = True" >> .pyscf_conf.py && \
-            ulimit -s 20000 && /opt/python/${{ matrix.pyver }}/bin/pytest pyscf/ --ignore=pyscf/adc --ignore=pyscf/pbc/df --ignore=pyscf/pbc/cc -s -c setup.cfg --cov-report xml --cov-report term --cov-config .coveragerc --cov pyscf'
+            ulimit -s 20000 && /opt/python/${{ matrix.pyver }}/bin/pytest pyscf/ --ignore=pyscf/adc --ignore=pyscf/pbc/df --ignore=pyscf/pbc/cc -s -c pytest.ini pyscf'
 
   macos-build:
     runs-on: macos-latest
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
-        python-version: ["3.7"]
+        python-version: ["3.10"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.github/workflows/ci_conda.yml

@@ -0,0 +1,25 @@
+name: CI_conda
+
+on:
+  workflow_dispatch:
+
+jobs:
+  build-conda-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          conda-channels: conda-forge
+      - run: conda --version
+      - run: which python
+      - name: Build conda package
+        run: |
+          export CMAKE_BUILD_PARALLEL_LEVEL=4
+          conda install -y conda-build
+          conda config --set anaconda_upload False
+          conda build --output-folder . conda

.github/workflows/ci_linux/build_pyscf.sh

@@ -3,9 +3,9 @@
 set -e
 
 cd ./pyscf/lib
-curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.3-deps.tar.gz?raw=true" | tar xzf -
+curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.4a-deps.tar.gz?raw=true" | tar xzf -
 mkdir build; cd build
-cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF -DBUILD_LIBCINT=OFF ..
+cmake -DBUILD_LIBXC=OFF -DBUILD_XCFUN=ON -DBUILD_LIBCINT=OFF -DXCFUN_MAX_ORDER=4 ..
 make -j4
 cd ..
 rm -Rf build

.github/workflows/ci_linux/python_deps.sh

@@ -1,11 +1,16 @@
 #!/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
-pip install pyberny geometric
-pip install spglib
+pip install pyberny
+pip install --no-deps pyscf-dispersion
 
-#cppe
 version=$(python -c 'import sys; version=sys.version_info[:2]; print("{0}.{1}".format(*version))')
-if [ $version != '2.7' ] && [ $version != '3.5' ]; then
+if [ $version != '3.12' ]; then
+    pip install geometric
+    pip install spglib
+fi
+
+#cppe
+if [ "$RUNNER_OS" == "Linux" ] && [ $version != "3.12" ]; then
     pip install cppe
 fi

.github/workflows/ci_macos/deps_apt.sh

@@ -1,2 +1,2 @@
 #!/usr/bin/env bash
-exit 0
+#brew reinstall gcc

.github/workflows/ci_macos/python_deps.sh

@@ -1,10 +1,11 @@
 #!/usr/bin/env bash
 python -m pip install --upgrade pip
-pip install "numpy!=1.16,!=1.17" "scipy<=1.1" h5py pytest pytest-cov pytest-timer
-pip install pyberny geometric
+pip install "numpy!=1.16,!=1.17" scipy h5py pytest pytest-cov pytest-timer
+pip install pyberny
 
 #cppe
 version=$(python -c 'import sys; version=sys.version_info[:2]; print("{0}.{1}".format(*version))')
-if [ $version != '2.7' ] && [ $version != '3.5' ]; then
-    pip install cppe
+if [ $version != '3.12' ]; then
+    pip install geometric
+    pip install spglib
 fi

.github/workflows/lint.yml

@@ -3,18 +3,44 @@ name: Lint
 on: [push, pull_request]
 
 jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Install ruff
+      run: pip install ruff
+    - name: Check style
+      run: ruff check --config .ruff.toml pyscf
+    - name: Check NumPy
+      run: ruff check --select NPY --ignore NPY002 pyscf
   flake:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install flake8
+      run: pip install "flake8>=3.7.0"
+    - name: Static analysis
+      run: flake8 --config .flake8 pyscf
+  lint-pycodestyle:
+    name: Code style check with pycodestyle
+    runs-on: ubuntu-latest
     steps:
-      - name: Setup Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.7
-      - uses: actions/checkout@v2
-      - name: Install flake8
-        run: pip install "flake8>=3.7.0"
-      - name: Static analysis
-        run: flake8 --config .flake8 pyscf
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+    - name: Install pycodestyle
+      run: pip install pycodestyle
+    - name: Lint using pycodestyle
+      run: pycodestyle --select=E111,W191,W293 pyscf
 
 #      - name: Static analysis
 #        uses: suo/flake8-github-action@releases/v1