Merge pull request #73 from sunqm/bump-version

Bump version

.github/workflows/publish.yml

@@ -7,7 +7,7 @@ jobs:
   release-pypi-x86-64:
     runs-on: ubuntu-latest
     env:
-      img: quay.io/pypa/manylinux2014_x86_64:2024-05-06-7d57077
+      img: quay.io/pypa/manylinux2014_x86_64:latest
     steps:
       - uses: actions/checkout@v4
       - name: Build wheels
@@ -44,7 +44,7 @@ jobs:
   release-pypi-aarch64:
     runs-on: ubuntu-latest
     env:
-      img: quay.io/pypa/manylinux2014_aarch64:2023-03-12-25fd859
+      img: quay.io/pypa/manylinux2014_aarch64:latest
     steps:
     - name: Checkout
       uses: actions/checkout@v4

CHANGELOG

@@ -0,0 +1,21 @@
+PySCF-Forge 1.0.1 (2024-10-31)
+------------------------------
+* New features
+  - PySCF-TrexIO interface
+
+
+PySCF-Forge 1.0.0 (2024-05-31)
+------------------------------
+* PyPI wheels with initial features
+  - CMS-PDFT (Compressed Multiconfiguration Pair-Density Functional Theory) energy and analytical nuclear gradients
+  - L-PDFT (Linearized PDFT) energy and analytical nuclear gradients
+  - MC-PDFT energy and analytical nuclear gradients
+  - XMS-PDFT energy
+  - Non-adiabatic couplings between states using CMS-PDFT method
+  - MC-DCFT (Multiconfiguration Density-Coherence Functional Theory) method
+  - MC-PDFT and CMS-PDFT dipole moment
+  - CMS-PDFT transition dipole moment
+  - MC-PDFT energy decomposition analysis
+  - LRDF (Long-Range Density Fitting) for energy and analytical nuclear gradients and Hessian 
+  - Spin-flip TDA using multi-collinear functionals
+  - M3SOSCF (Markovian Multiagent Monte-Carlo second order SCF) method

NOTICE

@@ -6,3 +6,7 @@ Dayou Zhang (University of Minnesota)
 Aleksandr Lykhin (University of Chicago)
 Thais R Scott (University of Chicago)
 Matthew R Hennefarth (University of Chicago)
+Linus Dittmer
+Hao Li
+Bhavnesh Jangid
+Shirong Wang

README.md

@@ -7,32 +7,131 @@ pyscf-forge can be installed using the command
 pip install pyscf-forge
 ```
 This command adds features in pyscf-forge to the PySCF package. They can be used
-as if they were natively developed within PySCF.
+as if they were natively developed within PySCF. For example,
+```
+from pyscf import gto, mcpdft
+mol = gto.M(
+    atom = 'O 0 0 0; O 0 0 1.2',
+    basis = 'ccpvdz',
+    spin = 2)
+mf = mol.RHF().run ()
+# Calling the MC-PDFT method provided by the pyscf-forge modules
+mc = mcpdft.CASCI(mf, 'tPBE', 6, 8).run()
+```
 
 To access the newest features of pyscf-forge, you can install them from git
 repository by running the command
 ```
 pip install git+https://github.com/pyscf/pyscf-forge
 ```
 
-If you are developing new features and would like to modify the code in
-pyscf-forge, editable installation is better suited. After cloning the library
-to your local repository, there are two possible ways to enable the editable
-installation:
+## Configuring the Development Environment
+If you are developing new features or modifying the code in `pyscf-forge`, an editable installation is recommended.
+By configuring the package in editable mode, you can modify existing modules and add new features to `pyscf-forge`.
+After cloning the library to your local repository, there are two ways to enable the editable installation:
 
-1. You can install the package using the pip command
+### Method 1. Using pip for editable installation
+Install the package with the following pip command:
 ```
 pip install --no-deps -e /path/to/pyscf-forge
 ```
-This method will add a `.pth` file in `~/.local/lib/python3.*/site-packages/`
+This command creates a `.pth` file in `~/.local/lib/python3.*/site-packages/`
 or other Python runtime paths. It is recommended to use this method with Python
 virtual environment.
 
-2. Setting an environment variable
+### Method 2. Setting an environment variable
+Define the `PYSCF_EXT_PATH` environment variable to point to your local `pyscf-forge` directory:
 ```
 export PYSCF_EXT_PATH=/path/to/pyscf-forge
 ```
-The PySCF package can read the `PYSCF_EXT_PATH` environment and load the modules
-within this package at runtime. For more details of `PYSCF_EXT_PATH` environment
-and the extensions management, please see the PySCF installation manual
+The PySCF package can read the `PYSCF_EXT_PATH` environment and load modules
+from this path at runtime. For more details of `PYSCF_EXT_PATH` environment
+and the extensions management, refer to the PySCF installation manual
 https://pyscf.org/install.html#extension-modules
+
+## Adding New Features: An Example
+Suppose you need to create a module in `pyscf-forge` that provides a plane-wave basis for crystalline computation with periodic boundary conditions (PBC).
+You can follow these steps to add the module:
+
+1. Install `pyscf-forge` in editable installation mode.
+
+2. Create a folder named `pyscf-forge/pyscf/pw`.
+Thanks to the editable installation mode, this folder can be readily imported as a regular `pyscf` module.
+```
+>>> from pyscf import pw
+>>> print(pw)
+<module 'pyscf.pw' (namespace)>
+
+>>> print(pw.__path__)
+_NamespacePath(['/home/ubuntu/pyscf-forge/pyscf/pw'])
+```
+
+3. Add Python code files to the `pyscf-forge/pyscf/pw` directory.
+This process is similar to developing new methods in the main `pyscf` repository.
+For example, you can add the following Python files into the `pyscf-forge/pyscf/pw` folder:
+```
+pyscf-forge
+├── ...
+└── pyscf
+    ├── ...
+    └── pw
+        ├── __init__.py
+        ├── dft
+        │   ├── __init__.py
+        │   ├── krks.py
+        │   └── kuks.py
+        └── scf
+            ├── __init__.py
+            ├── krhf.py
+            └── kuhf.py
+```
+
+### Path Conflicts
+There may exist scenarios that the directory you plan to create already exists within `pyscf`.
+For example, if you want to add a new method, like `pp_rpa.py`, to the `pyscf/tdscf` folder,
+this could conflict with the existing `pyscf.tdscf` module in the pyscf core repository.
+Adding features to existing modules requires more complex configuration.
+
+To import the `pp_rpa` module from the `pyscf-forge` repository, you will need to make certain modifications in the `__init__.py` file of the `pyscf` core module
+(in this demonstration, this file is located at `/home/ubuntu/.local/lib/python3.10/site-packages/pyscf/tdscf/__init__.py`).
+Add the following line of code to modify the `__path__` attribute of the `pyscf.tdscf` module:
+```
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)
+```
+
+This command extends the search path of the `tdscf` module, resulting in the `__path__` attribute being set to:
+```
+['/home/ubuntu/.local/lib/python3.10/site-packages/pyscf/tdscf',
+ '/home/ubuntu/pyscf-forge/pyscf/tdscf']
+```
+This configuration allows Python to locate and load the new `pp_rpa.py` module from the extended directory in `pyscf-forge`.
+
+Note that the `pyscf` core `tdscf` folder already contains an `__init__.py` file.
+To avoid overwriting the existing `__init__.py` file in `pyscf` during the installation of `pyscf-forge`,
+you should not add an `__init__.py` file in the `pyscf-forge/pyscf/tdscf` directory.
+
+The structure of the core packages and the components of `pyscf-forge` can be organized as follows:
+```
+pyscf
+├── ...
+└── pyscf
+    ├── ...
+    └── tdscf
+        ├── __init__.py  // modify the __path__ attribute in pyscf core module
+        ├── rhf.py
+        ├── rks.py
+        └── ...
+
+pyscf-forge
+├── ...
+└── pyscf
+    ├── ...
+    └── tdscf  // no __init__.py file in pyscf-forge
+        └── pp_rpa.py
+```
+
+When installing the `pyscf-forge` wheels using `pip install` in the normal
+installation mode, the `pp_rpa.py` file will be added to the `pyscf/tdscf`
+folder, integrating seamlessly as part of the regular `pyscf` module.
+After this standard installation, there is no need to adjust the `__path__`
+attribute, as all features and modules are located within the same directory.

setup.py

@@ -20,7 +20,7 @@
 SO_EXTENSIONS = {
 }
 DEPENDENCIES = ['pyscf', 'numpy']
-VERSION = '1.0.0'
+VERSION = '1.0.1'
 
 #######################################################################
 # Unless not working, nothing below needs to be changed.