Release 0.1.5 (#29)

.github/workflows/ci.yml

@@ -14,12 +14,12 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-20.04]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     environment: ci
     steps:
       - 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 }}
       - name: install pyscf

.github/workflows/install_pyscf.sh

@@ -2,13 +2,12 @@
 python -m pip install --upgrade pip
 python -m pip cache purge
 pip install wheel
+pip install pytest
+pip install pytest-cov
 pip install numpy
 pip install 'scipy<1.12'
 pip install h5py
 pip install jaxlib
 pip install jax
-pip install pytest
-pip install pytest-cov
-
-pip install 'pyscf==2.3'
-pip install 'pyscfadlib==0.1.4'
+pip install 'pyscf>=2.3,<2.7'
+pip install 'pyscfadlib>=0.1.4'

.github/workflows/publish_pyscfad.yml

@@ -0,0 +1,36 @@
+name: Publish pyscfad
+
+on:
+  release:
+    types:
+      - released
+  workflow_dispatch:
+
+jobs:
+  publish_pypi_any:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04]
+        python-version: ["3.11"]
+
+    environment: release
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Build wheels
+        run: |
+            python3 -m pip install --upgrade build
+            python3 -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/build_wheels.yml → .github/workflows/publish_pyscfadlib.yml

@@ -1,17 +1,23 @@
-name: Build
+name: Publish pyscfadlib
 
 on:
   release:
-    types: [published]
+    types:
+      - released
+  workflow_dispatch:
 
 jobs:
-  build_wheels_x86:
+  publish_pypi_linux_macos_x86:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-20.04, macos-12]
 
+    environment: release
+    permissions:
+      id-token: write
+
     steps:
       - uses: actions/checkout@v4
 
@@ -22,21 +28,23 @@ jobs:
           CMAKE_CONFIGURE_ARGS: "-DWITH_F12=OFF"
         with:
           package-dir: pyscfadlib
-          output-dir: pyscfadlib/wheelhouse
+          output-dir: dist
           config-file: "{package}/pyproject.toml"
 
-      - uses: actions/upload-artifact@v4
-        with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: pyscfadlib/wheelhouse/*.whl
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
 
-  build_wheels_arm64:
+  publish_pypi_macos_arm64:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [macos-14]
 
+    environment: release
+    permissions:
+      id-token: write
+
     steps:
       - uses: actions/checkout@v4
 
@@ -47,11 +55,8 @@ jobs:
           CMAKE_OSX_ARCHITECTURES: arm64
         with:
           package-dir: pyscfadlib
-          output-dir: pyscfadlib/wheelhouse
+          output-dir: dist
           config-file: "{package}/pyproject.toml"
 
-      - uses: actions/upload-artifact@v4
-        with:
-          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
-          path: pyscfadlib/wheelhouse/*.whl
-
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/release_github.yml

@@ -0,0 +1,24 @@
+name: github release
+
+on: [workflow_dispatch]
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Release Info
+        run: ./.github/workflows/release_info.sh
+        id: release_info
+      - name: Create Release
+        if: ${{ steps.release_info.outputs.version_tag }}
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ steps.release_info.outputs.version_tag }}
+          release_name: pyscfad release ${{ steps.release_info.outputs.version_tag }}
+          body_path: RELEASE.md
+          prerelease: true
+          # draft: true

.github/workflows/release_info.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+set -e
+
+# Get latest version tag
+get_last_tag() {
+  curl --silent "https://api.github.com/repos/fishjojo/pyscfad/releases/latest" | sed -n 's/.*"tag_name": "v\(.*\)",.*/\1/p'
+}
+last_version=$(get_last_tag)
+echo Last version: $last_version
+
+# Get current version tag
+cur_version=$(sed -n "/^__version__ =/s/.*\"\(.*\)\"/\1/p" pyscfad/version.py)
+if [ -z "$cur_version" ]; then
+  cur_version=$(sed -n "/^__version__ =/s/.*'\(.*\)'/\1/p" pyscfad/version.py)
+fi
+echo Current version: $cur_version
+
+# Create version tag
+if [ -n "$last_version" ] && [ -n "$cur_version" ] && [ "$cur_version" != "$last_version" ]; then
+  git config user.name "Github Actions"
+  git config user.email "[email protected]"
+  version_tag=v"$cur_version"
+
+  # Extract release info from CHANGELOG
+  sed -n "/^## pyscfad $cur_version/,/^## pyscfad $last_version/p" CHANGELOG.md | tail -n +2 | sed -e '/^## pyscfad /,$d' | head -n -1 > RELEASE.md
+  echo "::set-output name=version_tag::$version_tag"
+fi

.github/workflows/run_test.sh

@@ -1,9 +1,5 @@
 #!/usr/bin/env bash
 export OMP_NUM_THREADS=1
-export PYTHONPATH=$(pwd):$(pwd)/pyscf:$PYTHONPATH
-echo "pyscfad = True" >> $HOME/.pyscf_conf.py
-#echo "pyscf_numpy_backend = 'jax'" >> $HOME/.pyscf_conf.py
-#echo "pyscf_scipy_linalg_backend = 'pyscfad'" >> $HOME/.pyscf_conf.py
-#echo "pyscf_scipy_backend = 'jax'" >> $HOME/.pyscf_conf.py
+export PYTHONPATH=$(pwd):$PYTHONPATH
 
 pytest ./pyscfad --cov-report xml --cov=. --verbosity=1 --durations=10

.pylintrc

@@ -8,7 +8,9 @@
 [MASTER]
 
 # Files or directories to be skipped. They should be base names, not paths.
-ignore=test
+ignore=test,
+       backend,
+       ml,
 
 # Files or directories matching the regex patterns are skipped. The regex
 # matches against base names, not paths.

CHANGELOG.md

@@ -0,0 +1,61 @@
+# Change log
+
+## pyscfad 0.1.5
+* Changes
+  * pyscfad is now compatable with pyscf 2.6.
+  * Add `backend` module (experimental).
+  * Add GCCSD(T).
+  * Add interface to Jabobi sweep for Pipek-Mezey localization.
+
+* Bug fixes
+  * Fix LRC hybrid density functionals.
+
+## pyscfad 0.1.4 (Mar 5, 2024)
+* Changes
+  * pyscfad is now compatable with pyscf 2.3.
+  * Drop support for python 3.7.
+  * Drop dependence on jaxopt.
+  * Update JAX custom pytree node auxiliary data for safe comparison.
+  * Add `pyscfadlib`, fast C codes for custom VJPs.
+  * Add dynamic configuration.
+  * Allow `implicit_diff` to use preconditioners.
+  * Improve `scipy.linalg.eigh`.
+  * Add `scipy.linalg.svd`.
+  * Improve `lib.unpack_tril`, `lib.pack_tril`.
+  * Refactor `gto.moleintor`.
+  * Add fast VJP for molecular integrals.
+  * Improve `gto.eval_gto` performance.
+  * Add `gto.eval_gto` gradient w.r.t. `Mole.ctr_coeff` and `Mole.exp`.
+  * Avoid `df.DF` to create temperary files.
+  * Optimize `df.df_jk`.
+  * Add `scf.cphf`.
+  * Add `ao2mo._ao2mo`.
+  * Add `lo.iao`, `lo.boys`, `lo.pipek`, `lo.orth`.
+  * Add `geomopt`.
+  * Add `mp.dfmp2`, MP2 one-RDM.
+  * Consider permutation symmetry for CCSD.
+  * Disable `jit` for CCSD which causes memory leak.
+  * Simplify implementation of `cc.ccsd_t_slow`.
+  * Add optimized `cc.ccsd_t`.
+  * Add iterative CCSD(T) solver.
+  * Add `cc.dfccsd`, `cc.dcsd`.
+  * Add `tools.timer`.
+
+* Bug fixes
+  * Fix integral derivatives w.r.t. `Mole.ctr_coeff` and `Mole.exp`.
+
+## pyscfad 0.1.3 (Sep 13, 2023)
+* Bug fixes
+  * Fix installation issues.
+
+## pyscfad 0.1.2 (Mar 13, 2023)
+* Changes
+  * Add AD support for ROHF.
+
+## pyscfad 0.1.1 (Jan 25, 2023)
+* Changes
+  * pyscfad is now compatable with pyscf 2.1.
+
+## pyscfad 0.1.0 (Aug 3, 2022)
+* Changes
+  * First release.

examples/scf/00-simple.py

@@ -1,4 +1,3 @@
-import pyscf
 from pyscfad import gto, scf
 
 """
@@ -12,7 +11,6 @@
 mol.build()
 
 mf = scf.RHF(mol)
-mf.kernel()
 jac = mf.energy_grad()
 print(f'Nuclaer gradient:\n{jac.coords}')
 print(f'Gradient wrt basis exponents:\n{jac.exp}')

examples/scf/10-polarizability.py

@@ -1,7 +1,7 @@
 import numpy
 import jax
+from pyscfad import numpy as np
 from pyscfad import gto, scf
-from pyscfad.lib import numpy as jnp
 
 mol = gto.Mole()
 mol.atom = '''H  ,  0.   0.   0.
@@ -15,7 +15,7 @@
 h1 = mf.get_hcore()
 
 def apply_E(E):
-    mf.get_hcore = lambda *args, **kwargs: h1 + jnp.einsum('x,xij->ij', E, ao_dip)
+    mf.get_hcore = lambda *args, **kwargs: h1 + np.einsum('x,xij->ij', E, ao_dip)
     mf.kernel()
     return mf.dip_moment(mol, mf.make_rdm1(), unit='AU', verbose=0)
 
@@ -24,7 +24,7 @@ def apply_E(E):
 print(polar)
 
 def apply_E1(E):
-    mf.get_hcore = lambda *args, **kwargs: h1 + jnp.einsum('x,xij->ij', E, ao_dip)
+    mf.get_hcore = lambda *args, **kwargs: h1 + np.einsum('x,xij->ij', E, ao_dip)
     return mf.kernel()
 
 polar = -jax.hessian(apply_E1)(E0)

pyscfad/__init__.py

@@ -1,15 +1,19 @@
 """
 PySCF with auto-differentiation
 """
+import sys
 from pyscfad.version import __version__
 
-#from pyscfad import util
-#from pyscfad import implicit_diff
-
 from pyscfad._src._config import (
     config,
     config_update
 )
 
-import jax
-jax.config.update("jax_enable_x64", True)
+# export backend.numpy to pyscfad namespace
+# pylint: disable=useless-import-alias
+from pyscfad.backend import numpy as numpy
+from pyscfad.backend import ops as ops
+sys.modules['pyscfad.numpy'] = numpy
+sys.modules['pyscfad.ops'] = ops
+
+del sys

pyscfad/_src/_config.py

@@ -25,7 +25,6 @@ def reset(self):
 
 config = _Config()
 
-config.set_default('pyscfad_numpy_backend', 'jax')
 config.set_default('pyscfad_scf_implicit_diff', False)
 config.set_default('pyscfad_ccsd_implicit_diff', False)
 config.set_default('pyscfad_ccsd_checkpoint', False)

pyscfad/_src/scipy/linalg.py

@@ -4,7 +4,7 @@
 import scipy.linalg
 from jax import numpy as np
 from jax import scipy as jax_scipy
-from pyscfad.lib import custom_jvp, jit
+from pyscfad.ops import custom_jvp, jit
 
 # default threshold for degenerate eigenvalues
 DEG_THRESH = 1e-9