Merge branch 'master' into pruned_grids

.editorconfig

@@ -0,0 +1,18 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+max_line_length = 100
+
+[Makefile]
+indent_style = tab
+
+[{*.json,*.yml,*.yaml}]
+indent_style = space
+indent_size = 2

.github/workflows/pytest.yaml

@@ -0,0 +1,41 @@
+name: pytest
+
+on:
+  push:
+    branches:
+     - main
+    tags-ignore:
+      - '**'
+  pull_request:
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.py }} on OS ${{ matrix.os }}"
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "windows-latest"]
+        py: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+      - name: Setup python for test ${{ matrix.py }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.py }}
+      - name: Install dependencies for testing
+        run: |
+          pip install --upgrade pip
+          pip install pytest pytest-md pytest-emoji
+      - name: Install development version
+        run: |
+          pip install -e .
+      - name: Run pytest
+        uses: pavelzw/pytest-action@v2
+        with:
+          verbose: true
+          emoji: true
+          job-summary: true
+          click-to-expand: true
+          report-title: 'Test Report'

.gitignore

@@ -4,6 +4,40 @@
 *.gz
 *.png
 
+# Prerequisites
+*.d
+
+# Compiled object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled headers
+*.gch
+*.pch
+
+# Compiled dynamic libraries
+*.so
+*.so.[0-9]*
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
 # Ignore autogenerated version.py
 grid/version.py
 
@@ -22,7 +56,6 @@ doc/tech_dev_git.rst
 
 # Ignore (in-place) build results
 cext.cpp
-*.so
 *.pyc
 build
 dist
@@ -57,3 +90,40 @@ qaworkdir
 
 # Ignore tox
 .tox
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+.installed.cfg
+*.egg-info/
+*.egg
+*.manifest
+*.spec
+pip-log.txt
+pip-delete-this-directory.txt
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.pytest_cache/

.pre-commit-config.yaml

@@ -0,0 +1,38 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: check-added-large-files                   # prevents giant files from being commit
+    - id: check-ast                                 # Check whether files parse as valid python.
+    - id: check-case-conflict                       # Checks conflict case-insensitive
+    - id: check-executables-have-shebangs
+    - id: check-json
+    - id: check-merge-conflict
+    - id: check-symlinks                            # Check for symlinks which don't point
+    - id: check-toml
+    - id: check-vcs-permalinks
+    - id: debug-statements                          # Check for debugger imports and py37 breakpt
+    - id: detect-private-key                        # Checks for the existence of private keys.
+    - id: destroyed-symlinks
+    - id: end-of-file-fixer                         # Makes sure files end in a newline
+    - id: fix-byte-order-marker                     # Removes UTF-8 byte order marker
+    - id: mixed-line-ending                         # Replaces or checks mixed line ending.
+    - id: pretty-format-json                        # Checks JSON are pretty
+      args: ["--autofix", "--no-sort-keys"]
+    - id: trailing-whitespace                       # Trims trailing whitespace.
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.4
+  hooks:
+    - id: remove-crlf
+- repo: https://github.com/psf/black
+  rev: 23.10.1
+  hooks:
+    - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: 'v0.1.1'
+  hooks:
+    - id: ruff
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: 0.27.0
+  hooks:
+    - id: check-github-workflows

HEADER

@@ -1,6 +1,6 @@
 GRID is a numerical integration module for quantum chemistry.
 
-Copyright (C) 2011-2019 The GRID Development Team
+Copyright (C) 2011-2023 The GRID Development Team
 
 This file is part of GRID.
 

MANIFEST.in

@@ -1 +1,7 @@
 include README.md
+include LICENSE
+include grid.data/*.*
+include grid.data.lebedev/*.npz
+include grid.data.spherical_design/*.npz
+include grid.data.prune_grid/*.npz
+include grid.data.proatoms/*.npz

README.md

@@ -1,70 +1,42 @@
-# GRID
-[![Build Status](https://travis-ci.org/theochem/grid.svg?branch=master)](https://travis-ci.org/theochem/grid)
-[![Build Status](https://dev.azure.com/yxt1991/Grid/_apis/build/status/theochem.grid?branchName=master)](https://dev.azure.com/yxt1991/Grid/_build/latest?definitionId=2&branchName=master)
-[![codecov](https://codecov.io/gh/theochem/grid/branch/master/graph/badge.svg)](https://codecov.io/gh/theochem/grid)<br/>
-[![Python Version](https://img.shields.io/badge/python-3.6%2B-blue.svg)](https://docs.python.org/3/whatsnew/3.6.html)
-[![GPLv3 license](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/theochem/grid/blob/master/LICENSE)
+# Grid
+
+[![Python Version](https://img.shields.io/badge/python-3.7%2B-blue.svg)](https://docs.python.org/3/whatsnew/3.7.html)
+[![GPLv3 License](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://opensource.org/licenses/)
+[![GitHub Actions CI Tox Status](https://github.com/theochem/grid/actions/workflows/ci_tox.yml/badge.svg?branch=master)](https://github.com/theochem/grid/actions/workflows/ci_tox.yml)
+[![codecov](https://codecov.io/gh/theochem/grid/branch/master/graph/badge.svg)](https://codecov.io/gh/theochem/grid)
 [![GitHub contributors](https://img.shields.io/github/contributors/theochem/grid.svg)](https://github.com/theochem/grid/graphs/contributors)
 [![Code Style](https://img.shields.io/badge/code%20style-black-black.svg)](https://black.readthedocs.io/en/stable/)
 
 ## About
-GRID is a pythonic numerical integral package. It derived from legacy HORTON 2 numerical integration module.
+Grid is a simple, free, and open-source Python library for numerical integration, interpolation and differentiation.
+Primarly intended for the quantum chemistry community to assist in density-functional (DFT) theory calculations,
+including support for periodic boundary conditions.
+
+Please visit [**Grid Documentation**](https://grid.qcdevs.org/) for more information with
+examples about the software.
 
-## Platform
-GRID is a pure python package supporting `Windows`, `Linux` and `MacOS`.
+To report any issues or ask questions, either [open an issue](
+https://github.com/theochem/grid/issues/new) or email [[email protected]]().
 
-## Functionality
-* 1d integral
-* 1d transformation
-* Spherical integral
-* Becke-Lebedev grid & Molecular integral
-* Interpolation & differentiation
-* General ODE solver and Poisson solver
 
-## License
-GRID is distributed under [GPL License version 3](https://github.com/theochem/grid/blob/master/LICENSE) (GPL v3).
+## Citation
+Please use the following citation in any publication using BFit library:
 
-## Dependence
-* Installation requirements: `numpy`, `scipy`, `importlib_resources`
-* Testing requirement: `pytest`
-* QA requirement: `tox`
+> **"Grid: A Python Library for Molecular Integration, Interpolation, and More"**,
+> X.D. Yang, A. Tehrani, L. Pujal, R. Hernández-Esparza,
+> M. Chan, E. Vöhringer-Martinez, T. Verstraelen, F. Heidar-Zadeh, P. W. Ayers
+> `REFERENCE <https://doi.org/TODO>`__.
 
 ## Installation
-To install GRID to system:
-```bash
-pip install .
-```
-To run tests:
-```bash
-pytest --pyargs grid
-```
 
-## Local build and Testing
-To install editable GRID locally:
-```bash
-pip install -e .
-```
-To run tests:
+Installation via pip can be done by the following command:
 ```bash
-pytest tests
+pip install qc-grid
 ```
 
-## Quality Assurance
-To run QA locally:
+Local installation can be done as:
 ```bash
-tox
+git clone https://github.com/theochem/grid.git
+cd grid
+pip install .
 ```
-
-## Funding Acknowledgement
-This software was developed using funding from a variety of international
-sources including, but not limited to:
-* Canarie
-* the Canada Research Chairs
-* Compute Canada
-* the European Union's Horizon 2020 Marie Sklodowska-Curie Actions (Individual Fellowship No 800130)
-* the Foundation of Scientific Research--Flanders (FWO)
-* McMaster University
-* the National Fund for Scientific and Technological Development of Chile (FONDECYT)
-* the Natural Sciences and Engineering Research Council of Canada (NSERC)
-* the Research Board of Ghent University (BOF)
-* Sharcnet

doc/_static/css/override.css

@@ -0,0 +1,43 @@
+/** css/override.css **/
+
+
+/* This line is theme specific - it includes the base theme CSS */
+@import 'theme.css';       /* for the Read the Docs theme */
+
+table.docutils {
+    border-collapse: separate !important;
+}
+
+th.head {
+    position: sticky;
+    top: 0px;
+    z-index: 2;
+    background-color: white;
+    border-bottom-color: black !important;
+}
+
+th.head:nth-child(1) {
+    position: sticky;
+    top: 0px;
+    left: 0px;
+    z-index: 3;
+    background-color: white;
+    border-right-color: black !important;
+}
+
+td:nth-child(1) {
+    position: sticky;
+    left: 0px;
+    z-index: 1;
+    border-right-color: black !important;
+    border-right-width: 1px;
+    border-right-style: solid;
+}
+
+table.docutils tbody tr.row-odd td {
+    background-color: rgb(252, 252, 252);
+}
+
+div.wy-table-responsive {
+    max-height: 90vh;
+}