Merge branch 'transformed_cube' of https://github.com/Ali-Tehrani/grid into transformed_cube

Author: Ali-Tehrani

.github/workflows/ci.yml

@@ -0,0 +1,110 @@
+name: CI Roberto
+on:
+  push:
+    tags:
+      - '[1-9]+.[0-9]+.[0-9]+*'
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  # These are quick tests using Python's venv on different Python versions.
+  test-venv:
+    timeout-minutes: 30
+    if: "! startsWith(github.ref, 'refs/tags')"
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python-version: 3.7
+          - os: ubuntu-latest
+            python-version: 3.8
+          - os: ubuntu-latest
+            python-version: 3.9
+          - os: macos-latest
+            python-version: 3.7
+          - os: macos-latest
+            python-version: 3.8
+          - os: macos-latest
+            python-version: 3.9
+
+    runs-on: ${{ matrix.os }}
+    env:
+      # Tell Roberto to upload coverage results
+      ROBERTO_UPLOAD_COVERAGE: 1
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 2
+      - name: Fetch base branch (usually master)
+        run: |
+          if [[ -n "${GITHUB_HEAD_REF}" ]]; then
+            git fetch origin ${GITHUB_BASE_REF} --depth=2
+          fi
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - uses: actions/cache@v2
+        with:
+          path: ~/.local/venvs
+          key: ${{ runner.os }}-Python-${{ matrix.python-version }}-venv
+      - name: Install Pip and Roberto
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install roberto>=2.0.0
+      - name: Test with Roberto
+        run: |
+          if [[ -n "${GITHUB_HEAD_REF}" ]]; then
+            ROBERTO_GIT_MERGE_BRANCH=${GITHUB_SHA} \
+            ROBERTO_GIT_BRANCH=${GITHUB_BASE_REF} \
+            python -m roberto
+          else
+            ROBERTO_TESTENV_USE=venv \
+            python -m roberto robot
+          fi
+
+
+  test-conda:
+    # This is a slow test in a Conda environment, including deployment of
+    # tagged releases.
+    timeout-minutes: 30
+    if: (github.ref == 'refs/heads/master') || startsWith(github.ref, 'refs/tags')
+    strategy:
+      fail-fast: false
+
+    runs-on: ubuntu-latest
+    env:
+      ROBERTO_UPLOAD_COVERAGE: 1
+      ROBERTO_PACKAGE_MANAGER: conda
+      ROBERTO_TESTENV_USE: conda
+      ROBERTO_DEPLOY_NOARCH: 1
+      TWINE_USERNAME: theochem
+      TWINE_PASSWORD: ${{ secrets.TWINE_PASSWORD }}
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/cache@v2
+        with:
+          path: |
+            ~/miniconda3
+            !~/miniconda3/conda-bld
+            !~/miniconda3/locks
+            !~/miniconda3/pkgs
+            !~/miniconda3/var
+            !~/miniconda3/envs/*/conda-bld
+            !~/miniconda3/envs/*/locks
+            !~/miniconda3/envs/*/pkgs
+            !~/miniconda3/envs/*/var
+          key: ${{ runner.os }}-conda-3
+      - name: Install Roberto
+        run: |
+          python -m pip install roberto>=2.0.0
+      - name: Test and deploy with Roberto
+        run: |
+          python -m roberto robot

.github/workflows/ci_rob.yml

@@ -0,0 +1,35 @@
+name: CI Tox
+on:
+  workflow_dispatch:  # Needed to manually run github actions
+  push:
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    name: test ${{ matrix.py }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      fail-fast: false  # If anything in the matrix fails, then everything queued and in-progress will canceled
+      matrix:
+        # Which environment and python versions to be runned on.
+        os: [ubuntu macos windows]
+        py: ["3.7", "3.8", "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 tox-gh
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox tox-gh-actions
+      - name: Setup test suite
+        run: tox r -vv --notest # r means run environments,  -vv verbose --notest skip invoking test commands.
+      - name: Run test suite
+        # --skip-pkg-install  skips installing the package
+        run: tox r --skip-pkg-install
+        env:
+          PYTEST_ADDOPTS: "-vv --durations=10"

.github/workflows/ci_tox.yml

@@ -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/

.gitignore

@@ -0,0 +1,20 @@
+absolute: true  # Force absolute comparison for cardboardlint
+project:
+  name: grid
+  # requirements: [[numpydoc, numpydoc], [sphinx-autoapi, sphinx-autoapi], [sphinxcontrib-bibtex, sphinxcontrib-bibtex]]
+  packages:
+    - dist_name: qc-grid
+      tools:
+        - write-py-version
+        # - cardboardlint-static
+        - build-py-inplace
+        - pytest
+        # - upload-codecov
+        # - cardboardlint-dynamic
+        # - build-sphinx-doc
+        # - upload-docs-gh
+        - build-py-source
+        - build-conda
+        - deploy-pypi
+        - deploy-conda
+        # - deploy-github

.roberto.yaml

@@ -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/>
+# Grid
+
 [![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)
+[![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 [qcdevs@gmail.com]().
 
-## 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