horton-part 0.0.2__tar.gz

horton-part-0.0.2/.gitignore

@@ -0,0 +1,104 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# Ignore mac .DS_Store
+.DS_Store
+
+# PyCharm
+.idea/
+_version.py

horton-part-0.0.2/.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+    - id: check-ast
+    - id: check-case-conflict
+    - id: check-executables-have-shebangs
+    - id: check-json
+    - id: check-merge-conflict
+    - id: check-symlinks
+    - id: check-toml
+    - id: check-vcs-permalinks
+    - id: debug-statements
+    - id: detect-private-key
+    - id: destroyed-symlinks
+    - id: end-of-file-fixer
+    - id: fix-byte-order-marker
+    - id: mixed-line-ending
+    - id: pretty-format-json
+      args: ["--autofix", "--no-sort-keys"]
+    - id: trailing-whitespace
+- repo: https://github.com/Lucas-C/pre-commit-hooks
+  rev: v1.5.1
+  hooks:
+    - id: remove-crlf
+- repo: https://github.com/psf/black
+  rev: 23.3.0
+  hooks:
+    - id: black
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: 'v0.0.265'
+  hooks:
+    - id: ruff

horton-part-0.0.2/.travis.yml

@@ -0,0 +1,130 @@
+env:
+  matrix:
+  - MYCONDAPY=2.7
+#  - MYCONDAPY=3.5
+#  - MYCONDAPY=3.6
+  global:
+    # ANACONDA_TOKEN
+    - secure: "EwDvNNbo6xnXz99ggD//LSbi0Bs8MNME3AuxAPB7LQiSsFcMZ3EETE1OkAmvSQDTgCjpO6x0izy8i3H+H249f/FI89bfPMvd67RB1YQAnkPj05HWx9zUxyCGaxdSMdw0IKLZBUq2itwSsx6+ltbNhgCAbWxB7vOBpNeIHmk7zv753sSfk5C/cI48SzZyRbfliAMqcfXyj6kM3uhmAVmQ/Li5wkXY7Owhp9oYw1/Lpfl0FZUA5km3jUdCWg/yMQ0rdKtDvm749GASIIKChIdjmSFlfAc8pvKahHfpiL1XO9+NdwflU7AMkg6RYZpDxyM5wt86MdyLyIOxqzhD8a4DNzkpm2u9eGsxx77SxtteNVkDkxkt1xhW5Vw3amdIIKn+/VVR1Oyq8A13ZzLCtiqvrn+lJaWvejpF39fJPBXtvWxBmDJQYOL98nrG8vNwyFw6dQOgMKJEtfmxEH/2gjeJvi/cY8aNUMrVDWF304v9rrbO6Nm9LrM220Tq1/OfSdgqb9hBo7EwyDHZ9kV0yRLcU30LBDOGlBqa9BUq/CQbPFjWLfJuUqpVFKBOpvmBFt9OSP53m45DqcVWSdNBDeCawlpaDHfHJ95fUi+kS04KkmzaBos6vWpyxs2oIylLhi+r3SQYR1jyavG0r14d7SXLa/AU11f+p6eEoiM6Zp3fPIQ="
+    # GITHUB_TOKEN
+    - secure: "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"
+    # PYPI_PASSWD
+    - secure: "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"
+    - PYPKG=denspart
+    - GITHUB_REPO_NAME=theochem/denspart_horton
+
+# Do not use Travis Python to save some time.
+language: generic
+os:
+  - linux
+#  - osx
+osx_image: xcode8.3
+dist: trusty
+sudo: false
+
+install:
+# Get miniconda. Take the right version, so re-installing python is only needed for 3.5.
+- if [[ "$MYCONDAPY" == "2.7" ]]; then
+    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    fi;
+  else
+    if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    fi;
+  fi
+- bash miniconda.sh -b -p $HOME/miniconda
+- export PATH="$HOME/miniconda/bin:$PATH"
+- hash -r
+
+# Configure conda and get a few essentials
+- conda config --set always_yes yes --set changeps1 no
+- conda config --add channels pyqc
+- conda update -q conda
+# Get the right python version for building. This only does something for 3.5.
+# Install extra package needed to make things work. Most things can be listed as
+# dependencies on metal.yaml and setup.py, unless setup.py already imports them.
+# Install conda tools for packaging and uploading
+- conda install python=${MYCONDAPY} numpy cython sphinx conda-build anaconda-client
+- conda info -a
+
+script:
+# Build the conda package
+- git fetch origin --tags
+- conda build -q tools/conda.recipe
+
+# Build source package, should work too and needed for deployment to Github and
+# PyPI.
+- python setup.py sdist
+
+# Install Conda package
+- conda install --use-local $PYPKG
+
+# Compile documentation
+# - (cd doc; make html)
+
+# Run tests out of source tree, to make sure that installed version is tested.
+- (cd; nosetests $PYPKG -v --processes=2 --detailed-errors --process-timeout=600)
+
+# In deployment, the env var TRAVIS_TAG contains the name of the current tag, if any.
+deploy:
+- provider: releases
+  skip_cleanup: true
+  api_key: ${GITHUB_TOKEN}
+  file: dist/${PYPKG}-${TRAVIS_TAG}.tar.gz
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    tags: true
+    condition: "$TRAVIS_TAG != *[ab]* && $MYCONDAPY == 2.7 && $TRAVIS_OS_NAME == linux"
+  prerelease: false
+- provider: releases
+  skip_cleanup: true
+  api_key: ${GITHUB_TOKEN}
+  file: dist/${PYPKG}-${TRAVIS_TAG}.tar.gz
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    tags: true
+    condition: "$TRAVIS_TAG == *[ab]* && $MYCONDAPY == 2.7 && $TRAVIS_OS_NAME == linux"
+  prerelease: true
+- provider: script
+  skip_cleanup: true
+  script: anaconda -t $ANACONDA_TOKEN upload -l alpha ${HOME}/miniconda/conda-bld/*/${PYPKG}-*.tar.bz2
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    tags: true
+    condition: "$TRAVIS_TAG == *a*"
+- provider: script
+  skip_cleanup: true
+  script: anaconda -t $ANACONDA_TOKEN upload -l beta ${HOME}/miniconda/conda-bld/*/${PYPKG}-*.tar.bz2
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    tags: true
+    condition: "$TRAVIS_TAG == *b*"
+- provider: script
+  skip_cleanup: true
+  script: anaconda -t $ANACONDA_TOKEN upload -l main ${HOME}/miniconda/conda-bld/*/${PYPKG}-*.tar.bz2
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    tags: true
+    condition: "$TRAVIS_TAG != *[ab]*"
+- provider: pypi
+  skip_cleanup: true
+  user: tovrstra
+  password: ${PYPI_PASSWD}
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    tags: true
+    condition: "$TRAVIS_TAG != *[ab]* && $MYCONDAPY == 2.7 && $TRAVIS_OS_NAME == linux"
+- provider: pages
+  skip_cleanup: true
+  github_token: ${GITHUB_TOKEN}
+  project_name: ${PYPKG}
+  local_dir: doc/_build/html
+  on:
+    repo: ${GITHUB_REPO_NAME}
+    condition: "$TRAVIS_TAG != *[ab]* && $MYCONDAPY == 2.7 && $TRAVIS_OS_NAME == linux"
+    tags: true

horton-part-0.0.2/CHANGELOG.md

@@ -0,0 +1,24 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.0.2] - 2023-05-23
+
+### Fixed
+
+- Upload to PyPI
+
+## [0.0.1] - 2023-05-23
+
+### Added
+
+- Examples for ISA methods
+- Tests for all methods
+- L-ISA method using two different optimization approaches
+- G-ISA method
+- The Python 3.10 support

horton-part-0.0.2/DEVELOPMENT.md

@@ -0,0 +1,17 @@
+# Development notes
+
+## How to make releases
+
+- Mark release in `CHANGELOG.md`
+    - `git add CHANGELOG.md`
+    - `git commit -m "Parepare for release X.Y.Z"`
+- Modify version in `pyproject.toml` (skip this step if dynamic version is used)
+- Make a new commit and tag it with `vX.Y.Z`
+    - `git tag -a vX.Y.Z -m "Version X.Y.Z"`
+    - `git push origin vX.Y.Z` if `origin` is the name of remote repo.
+- Remove lingering `dist` (if `dist` exists)
+    - `rm -rf dist`
+- Run `python3 -m build`
+    - first run `pip3 install build` if `build` not found
+- Run `python3 -m twine upload dist/*`
+    - first run `pip3 install twine` if `twine` not found

horton-part-0.0.2/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

horton-part-0.0.2/MANIFEST.in

@@ -0,0 +1,5 @@
+include README.rst
+include LICENSE.txt
+include tests/cached/*.*
+recursive-include examples/data *
+recursive-include examples *.py