Update test framework (pyscf#1249)

* Support python 3.10 in pip wheel build chain (issue pyscf#1231) * Add python3.10 tests in github action * update pypi build chain * fix github action configs * Improve safe_eigh function for irregular overlap matrix * Downgrade scipy due to scipy/scipy#15362 * Debug openmp cmake flags (fix issue pyscf#940)
ivanbasov · May 16, 2022 · ac65240 · ac65240
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -20,17 +20,32 @@ name: CI
 on: [push, pull_request]
 
 jobs:
-  build:
+  linux-build:
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        os: [macos-latest, ubuntu-18.04]
-        python-version: [3.6, 3.7, 3.8, 3.9]
-        exclude:
-          - os: macos-latest
-            python-version: 3.8
-          - os: macos-latest
-            python-version: 3.9
+        os: [ubuntu-20.04]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install and Test
+        run: ./.github/workflows/run_ci.sh
+      - name: Upload to codecov
+        uses: codecov/[email protected]
+        with:
+          token: ${{secrets.CODECOV_TOKEN}}
+
+  macos-build:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7"]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}

diff --git a/.github/workflows/ci_linux/build_pyscf.sh b/.github/workflows/ci_linux/build_pyscf.sh
@@ -1,4 +1,7 @@
 #!/usr/bin/env bash
+
+set -e
+
 cd ./pyscf/lib
 curl -L "https://github.com/pyscf/pyscf-build-deps/blob/master/pyscf-2.1a-deps.tar.gz?raw=true" | tar xzf -
 mkdir build; cd build

diff --git a/.github/workflows/ci_linux/deps_apt.sh b/.github/workflows/ci_linux/deps_apt.sh
@@ -1,8 +1,6 @@
 #!/usr/bin/env bash
 sudo apt-get -qq install \
     gcc \
-    gfortran \
-    libgfortran3 \
     libblas-dev \
     cmake \
     curl
diff --git a/.github/workflows/ci_linux/python_deps.sh b/.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 nose nose-exclude nose-timer nose-cov codecov
+pip install "numpy!=1.16,!=1.17" "scipy!=1.5" h5py pytest pytest-cov pytest-timer
 pip install pyberny geometric
 
 #cppe

diff --git a/.github/workflows/ci_macos/build_pyscf.sh b/.github/workflows/ci_macos/build_pyscf.sh
@@ -1,4 +1,6 @@
 #!/usr/bin/env bash
+set -e
+
 #XXX default clang compiler does not support openmp, shall we use gcc?
 cd ./pyscf/lib
 #curl -L https://github.com/fishjojo/pyscf-deps/raw/master/pyscf-1.7.5-deps-macos-10.14.tar.gz | tar xzf -

diff --git a/.github/workflows/ci_macos/python_deps.sh b/.github/workflows/ci_macos/python_deps.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 python -m pip install --upgrade pip
-pip install numpy "scipy==1.1" h5py nose nose-exclude nose-timer nose-cov codecov
+pip install "numpy!=1.16,!=1.17" "scipy<=1.1" h5py pytest pytest-cov pytest-timer
 pip install pyberny geometric
 
 #cppe

diff --git a/.github/workflows/run_ci.sh b/.github/workflows/run_ci.sh
@@ -1,4 +1,7 @@
 #!/usr/bin/env bash
+
+set -e
+
 if [ "$RUNNER_OS" == "Linux" ]; then
     os='linux'
 elif [ "$RUNNER_OS" == "macOS" ]; then

diff --git a/.github/workflows/run_tests.sh b/.github/workflows/run_tests.sh
@@ -5,35 +5,7 @@ ulimit -s 20000
 
 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
 
-nosetests pyscf/ -v --with-timer --with-cov --cov-report xml --cov-report term --cov-config .coveragerc --cov pyscf \
-    --exclude-dir=examples --exclude-dir=pyscf/pbc/grad \
-    -e test_bz \
-    -e h2o_vdz \
-    -e test_mc2step_4o4e \
-    -e test_ks_noimport \
-    -e test_jk_hermi0 \
-    -e test_j_kpts \
-    -e test_k_kpts \
-    -e high_cost \
-    -e skip \
-    -e call_in_background \
-    -e libxc_cam_beta_bug \
-    -e test_finite_diff_rks_eph \
-    -e test_finite_diff_uks_eph \
-    -e test_pipek \
-    -I test_kuccsd_supercell_vs_kpts\.py \
-    -I test_kccsd_ghf\.py \
-    -I test_h_.*\.py \
-    -I test_P_uadc_ea.py \
-    -I test_P_uadc_ip.py \
-    --exclude-test=pyscf/pbc/gw/test/test_kgw_slow_supercell.DiamondTestSupercell3 \
-    --exclude-test=pyscf/pbc/gw/test/test_kgw_slow_supercell.DiamondKSTestSupercell3 \
-    --exclude-test=pyscf/pbc/gw/test/test_kgw_slow.DiamondTestSupercell3 \
-    --exclude-test=pyscf/pbc/gw/test/test_kgw_slow.DiamondKSTestSupercell3 \
-    --exclude-test=pyscf/pbc/tdscf/test/test_krhf_slow_supercell.DiamondTestSupercell3 \
-    --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_hf.DiamondTestSupercell3 \
-    --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_ks.DiamondTestSupercell3 \
-    --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_supercell_hf.DiamondTestSupercell3 \
-    --exclude-test=pyscf/pbc/tdscf/test/test_kproxy_supercell_ks.DiamondTestSupercell3 \
-    -I .*_slow.*py -I .*_kproxy_.*py -I test_proxy.py # tdscf/*_slow.py gw/*_slow.py do not compatible with python3.[456] and old numpy
+pytest pyscf/ -s -c setup.cfg \
+    --cov-report xml --cov-report term --cov-config .coveragerc --cov pyscf
diff --git a/docker/pypa-env/Dockerfile-2.0-openblas b/docker/pypa-env/Dockerfile-2.0-openblas
@@ -1,7 +1,7 @@
-FROM quay.io/pypa/manylinux2014_x86_64:latest
-RUN yum install -y openblas-devel.x86_64
-
-FROM quay.io/pypa/manylinux1_x86_64:latest
+#FROM quay.io/pypa/manylinux2014_x86_64:latest
+#RUN yum install -y openblas-devel.x86_64
+#
+FROM quay.io/pypa/manylinux2010_x86_64:latest
 
 RUN yum install -y openblas-devel.x86_64 gcc && \
     yum clean all && \
@@ -13,9 +13,9 @@ COPY build-wheels.sh /build-wheels.sh
 CMD ['/build-wheels.sh']
 
 RUN pip config set global.disable-pip-version-check true
-# openblas in quay.io/pypa/manylinux1_x86_64 has a bug that causes segfault
-# (issue https://github.com/pyscf/pyscf/issues/1095). openblas r0-3.3 fixed
-# the bug
-COPY --from 0 /usr/lib64/libopenblas.so /usr/lib64/libopenblas.so.0
-RUN rm -f libopenblas-r0.2.18.so && \
-    ln -fs /usr/lib64/libopenblas.so.0 /usr/lib64/libopenblas.so
+# # openblas in quay.io/pypa/manylinux1_x86_64 has a bug that causes segfault
+# # (issue https://github.com/pyscf/pyscf/issues/1095). openblas r0-3.3 fixed
+# # the bug
+# COPY --from 0 /usr/lib64/libopenblas.so /usr/lib64/libopenblas.so.0
+# RUN rm -f libopenblas-r0.2.18.so && \
+#     ln -fs /usr/lib64/libopenblas.so.0 /usr/lib64/libopenblas.so
diff --git a/docker/pypa-env/build-wheels.sh b/docker/pypa-env/build-wheels.sh
@@ -17,11 +17,11 @@ fi
 sed -i '/            if basename(fn) not in needed_libs:/s/basename.*libs/1/' /opt/_internal/tools/lib/python3.7/site-packages/auditwheel/wheel_abi.py
 
 # Compile wheels
-for PYVERSION in cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39; do
+for PYVERSION in cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39 cp310-cp310; do
     PYBIN=/opt/python/$PYVERSION/bin
     "${PYBIN}/pip" wheel -v --no-deps --no-clean -w /root/wheelhouse $src
 
     # Bundle external shared libraries into the wheels
-    whl=`ls /root/wheelhouse/pyscf-*-$PYVERSION-linux_x86_64.whl`
+    whl=`ls /root/wheelhouse/pyscf-*-$PYVERSION-linux*_x86_64.whl`
     auditwheel -v repair "$whl" --lib-sdir /lib -w $dst
 done
diff --git a/pyscf/adc/test/test_radc/test_H2O_radc_ea.py b/pyscf/adc/test/test_radc/test_H2O_radc_ea.py
@@ -23,27 +23,29 @@
 from pyscf import scf
 from pyscf import adc
 
-mol = gto.Mole()
-r = 0.957492
-x = r * math.sin(104.468205 * math.pi/(2 * 180.0))
-y = r * math.cos(104.468205* math.pi/(2 * 180.0))
-mol.atom = [
-    ['O', ( 0., 0.    , 0)],
-    ['H', ( 0., -x, y)],
-    ['H', ( 0., x , y)],]
-mol.basis = {'H': 'aug-cc-pVDZ',
-             'O': 'aug-cc-pVDZ',}
-mol.verbose = 0
-mol.build()
-
-mf = scf.RHF(mol)
-mf.conv_tol = 1e-12
-mf.kernel()
-myadc = adc.ADC(mf)
+def setUpModule():
+    global mol, mf, myadc
+    mol = gto.Mole()
+    r = 0.957492
+    x = r * math.sin(104.468205 * math.pi/(2 * 180.0))
+    y = r * math.cos(104.468205* math.pi/(2 * 180.0))
+    mol.atom = [
+        ['O', ( 0., 0.    , 0)],
+        ['H', ( 0., -x, y)],
+        ['H', ( 0., x , y)],]
+    mol.basis = {'H': 'aug-cc-pVDZ',
+                 'O': 'aug-cc-pVDZ',}
+    mol.verbose = 0
+    mol.build()
+
+    mf = scf.RHF(mol)
+    mf.conv_tol = 1e-12
+    mf.kernel()
+    myadc = adc.ADC(mf)
 
 def tearDownModule():
-    global mol, mf
-    del mol, mf
+    global mol, mf, myadc
+    del mol, mf, myadc
 
 class KnownValues(unittest.TestCase):
 

diff --git a/pyscf/adc/test/test_radc/test_H2O_radc_ip.py b/pyscf/adc/test/test_radc/test_H2O_radc_ip.py
@@ -23,27 +23,29 @@
 from pyscf import scf
 from pyscf import adc
 
-mol = gto.Mole()
-r = 0.957492
-x = r * math.sin(104.468205 * math.pi/(2 * 180.0))
-y = r * math.cos(104.468205* math.pi/(2 * 180.0))
-mol.atom = [
-    ['O', ( 0., 0.    , 0)],
-    ['H', ( 0., -x, y)],
-    ['H', ( 0., x , y)],]
-mol.basis = {'H': 'cc-pVDZ',
-             'O': 'cc-pVDZ',}
-mol.verbose = 0 
-mol.build()
-
-mf = scf.RHF(mol)
-mf.conv_tol = 1e-12
-mf.kernel()
-myadc = adc.ADC(mf)
+def setUpModule():
+    global mol, mf, myadc
+    mol = gto.Mole()
+    r = 0.957492
+    x = r * math.sin(104.468205 * math.pi/(2 * 180.0))
+    y = r * math.cos(104.468205* math.pi/(2 * 180.0))
+    mol.atom = [
+        ['O', ( 0., 0.    , 0)],
+        ['H', ( 0., -x, y)],
+        ['H', ( 0., x , y)],]
+    mol.basis = {'H': 'cc-pVDZ',
+                 'O': 'cc-pVDZ',}
+    mol.verbose = 0
+    mol.build()
+
+    mf = scf.RHF(mol)
+    mf.conv_tol = 1e-12
+    mf.kernel()
+    myadc = adc.ADC(mf)
 
 def tearDownModule():
-    global mol, mf
-    del mol, mf
+    global mol, mf, myadc
+    del mol, mf, myadc
 
 class KnownValues(unittest.TestCase):
 

diff --git a/pyscf/adc/test/test_radc/test_H2O_radc_outcore.py b/pyscf/adc/test/test_radc/test_H2O_radc_outcore.py
@@ -23,27 +23,29 @@
 from pyscf import scf
 from pyscf import adc
 
-mol = gto.Mole()
-r = 0.957492
-x = r * math.sin(104.468205 * math.pi/(2 * 180.0))
-y = r * math.cos(104.468205* math.pi/(2 * 180.0))
-mol.atom = [
-    ['O', ( 0., 0.    , 0)],
-    ['H', ( 0., -x, y)],
-    ['H', ( 0., x , y)],]
-mol.basis = {'H': 'aug-cc-pVDZ',
-             'O': 'aug-cc-pVDZ',}
-mol.verbose = 0
-mol.build()
-
-mf = scf.RHF(mol)
-mf.conv_tol = 1e-12
-mf.kernel()
-myadc = adc.ADC(mf)
+def setUpModule():
+    global mol, mf, myadc
+    mol = gto.Mole()
+    r = 0.957492
+    x = r * math.sin(104.468205 * math.pi/(2 * 180.0))
+    y = r * math.cos(104.468205* math.pi/(2 * 180.0))
+    mol.atom = [
+        ['O', ( 0., 0.    , 0)],
+        ['H', ( 0., -x, y)],
+        ['H', ( 0., x , y)],]
+    mol.basis = {'H': 'aug-cc-pVDZ',
+                 'O': 'aug-cc-pVDZ',}
+    mol.verbose = 0
+    mol.build()
+
+    mf = scf.RHF(mol)
+    mf.conv_tol = 1e-12
+    mf.kernel()
+    myadc = adc.ADC(mf)
 
 def tearDownModule():
-    global mol, mf
-    del mol, mf
+    global mol, mf, myadc
+    del mol, mf, myadc
 
 class KnownValues(unittest.TestCase):
 

diff --git a/pyscf/adc/test/test_radc/test_N2_radc_ea.py b/pyscf/adc/test/test_radc/test_N2_radc_ea.py
@@ -22,22 +22,24 @@
 from pyscf import scf
 from pyscf import adc
 
-r = 1.098
-mol = gto.Mole()
-mol.atom = [
-    ['N', ( 0., 0.    , -r/2   )],
-    ['N', ( 0., 0.    ,  r/2)],]
-mol.basis = {'N':'aug-cc-pvdz'}
-mol.verbose = 0
-mol.build()
-mf = scf.RHF(mol)
-mf.conv_tol = 1e-12
-mf.kernel()
-myadc = adc.ADC(mf)
+def setUpModule():
+    global mol, mf, myadc
+    r = 1.098
+    mol = gto.Mole()
+    mol.atom = [
+        ['N', ( 0., 0.    , -r/2   )],
+        ['N', ( 0., 0.    ,  r/2)],]
+    mol.basis = {'N':'aug-cc-pvdz'}
+    mol.verbose = 0
+    mol.build()
+    mf = scf.RHF(mol)
+    mf.conv_tol = 1e-12
+    mf.kernel()
+    myadc = adc.ADC(mf)
 
 def tearDownModule():
-    global mol, mf
-    del mol, mf
+    global mol, mf, myadc
+    del mol, mf, myadc
 
 class KnownValues(unittest.TestCase):
 

diff --git a/pyscf/adc/test/test_radc/test_N2_radc_ip.py b/pyscf/adc/test/test_radc/test_N2_radc_ip.py
@@ -22,22 +22,24 @@
 from pyscf import scf
 from pyscf import adc
 
-r = 1.098
-mol = gto.Mole()
-mol.atom = [
-    ['N', ( 0., 0.    , -r/2   )],
-    ['N', ( 0., 0.    ,  r/2)],]
-mol.basis = {'N':'aug-cc-pvdz'}
-mol.verbose = 0
-mol.build()
-mf = scf.RHF(mol)
-mf.conv_tol = 1e-12
-mf.kernel()
-myadc = adc.ADC(mf)
+def setUpModule():
+    global mol, mf, myadc
+    r = 1.098
+    mol = gto.Mole()
+    mol.atom = [
+        ['N', ( 0., 0.    , -r/2   )],
+        ['N', ( 0., 0.    ,  r/2)],]
+    mol.basis = {'N':'aug-cc-pvdz'}
+    mol.verbose = 0
+    mol.build()
+    mf = scf.RHF(mol)
+    mf.conv_tol = 1e-12
+    mf.kernel()
+    myadc = adc.ADC(mf)
 
 def tearDownModule():
-    global mol, mf
-    del mol, mf
+    global mol, mf, myadc
+    del mol, mf, myadc
 
 class KnownValues(unittest.TestCase):