update installation (#18)

.github/workflows/ci.yml

@@ -7,8 +7,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-18.04]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-20.04]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     environment: ci
     steps:
       - uses: actions/checkout@v2

.github/workflows/install_pyscf.sh

@@ -1,14 +1,16 @@
 #!/usr/bin/env bash
 python -m pip install --upgrade pip
 pip install wheel
-pip install numpy scipy h5py
+pip install numpy
+pip install 'scipy<1.11'
+pip install h5py
 pip install typing_extensions
 pip install jaxlib jax jaxopt
 pip install pytest pytest-cov
 
 #pyscf
 git clone https://github.com/fishjojo/pyscf.git
-cd pyscf; git checkout ad; cd ..
+cd pyscf; git checkout v2.1.1-ad; cd ..
 
 if [ "$RUNNER_OS" == "Linux" ]; then
     os='linux'

README.md

@@ -9,24 +9,8 @@ Installation
 ------------
 
 ---
-* To install the latest release, use the following commands:
+* To install the latest release, run:
 ```
-# install cmake
-pip install cmake
-
-# install OpenMP runtime used with clang
-# On Linux:
-sudo apt update
-sudo apt install libomp-dev
-
-# On OSX:
-brew install libomp
-
-# install pyscf
-pip install 'pyscf @ git+https://github.com/fishjojo/pyscf.git@ad#egg=pyscf' 
-pip install 'pyscf-properties @ git+https://github.com/fishjojo/properties.git@ad' 
-
-# install pyscfad
 pip install pyscfad
 ```
 
@@ -35,25 +19,21 @@ pip install pyscfad
 ```
 pip install git+https://github.com/fishjojo/pyscfad.git
 ```
-
-* The dependencies can be installed via a predefined conda environment
+This should also install all the dependencies.
+Alternatively, the dependencies can be installed via a predefined conda environment:
 ```
 conda env create -f environment.yml
 conda activate pyscfad_env
 ```
-
-* Alternatively, the dependencies can be installed from source
+OpenMP is not required, but is recommended:
 ```
-pip install numpy scipy h5py
-pip install jax jaxlib jaxopt
-
-# install pyscf
-cd $HOME; git clone https://github.com/fishjojo/pyscf.git
-cd pyscf; git checkout ad 
-cd pyscf/lib; mkdir build 
-cd build; cmake ..; make
+# install OpenMP runtime used with clang
+# On Linux:
+sudo apt update
+sudo apt install libomp-dev
 
-export PYTHONPATH=$HOME/pyscf:$PYTHONPATH
+# On OSX:
+brew install libomp
 ```
 
 ---
@@ -68,13 +48,14 @@ Running examples
 
 * In order to perform AD calculations, 
 the following lines need to be added to 
-the PySCF configure file($HOME/.pyscf\_conf.py)
+the PySCF configure file ($HOME/.pyscf\_conf.py)
 ```
 pyscfad = True
 pyscf_numpy_backend = 'jax'
 pyscf_scipy_linalg_backend = 'pyscfad'
 pyscf_scipy_backend = 'jax'
-# The followings are optional
+# The followings turn on implicit differentiations
+# for SCF and CC amplitude solvers
 pyscfad_scf_implicit_diff = True
 pyscfad_ccsd_implicit_diff = True
 ```

environment.yml

@@ -5,10 +5,12 @@ dependencies:
   - python=3.9
   - pip=23.0
   - pip:
+    - cmake>=3.18
     - numpy>=1.17
-    - scipy
-    - jax>=0.1.65,<0.3.14
-    - jaxlib>=0.1.65,<0.3.14
+    - scipy<1.11
+    - jax>=0.3.25
+    - jaxlib>=0.3.25
+    - typing_extensions
     - jaxopt>=0.2
-    - -e git+https://github.com/fishjojo/pyscf.git@ad#egg=pyscf
+    - -e git+https://github.com/fishjojo/pyscf.git@v2.1.1-ad#egg=pyscf
     - -e git+https://github.com/fishjojo/properties.git@ad#egg=pyscf-properties

pyscfad/version.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.3"

setup.py

@@ -64,13 +64,14 @@ def run(self):
     #cmdclass={'build_py': BuildExtFirst,
     #          'build_ext': CMakeBuildExt},
     install_requires=[
+        'cmake>=3.18',
         'numpy>=1.17',
-        'scipy',
+        'scipy<1.11',
         'jax>=0.3.25',
         'jaxlib>=0.3.25',
         'typing_extensions',
         'jaxopt>=0.2',
-        'pyscf @ git+https://github.com/fishjojo/pyscf.git@ad#egg=pyscf',
+        'pyscf @ git+https://github.com/fishjojo/pyscf.git@v2.1.1-ad#egg=pyscf',
         'pyscf-properties @ git+https://github.com/fishjojo/properties.git@ad',
     ],
     url='https://github.com/fishjojo/pyscfad',
@@ -80,8 +81,6 @@ def run(self):
         "Topic :: Scientific/Engineering",
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",