pymolpro 1.19.4__tar.gz

pymolpro-1.19.4/.gitattributes

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+pymolpro/_version.py export-subst

pymolpro-1.19.4/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0   # needed so setuptools_scm can see tags
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tool
+        run: python -m pip install --upgrade build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://test.pypi.org/p/pymolpro
+    permissions:
+      id-token: write   # required for OIDC trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

pymolpro-1.19.4/.github/workflows/sphinx-publish.yml

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+name: Pages
+on:
+  push:
+    tags:
+      - '*'
+#    branches:
+#      - trexio
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
+      - name: set up environment
+        shell: bash -el {0}
+        run: |
+          conda install -y -c conda-forge -c anaconda --file requirements.txt sphinx_rtd_theme nbsphinx scipy sphinx sphinx-jsonschema ipython pip
+          python -m pip install --no-deps --force-reinstall .
+      - name: Build
+        shell: bash -el {0}
+        run: make -C docs html
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: 'docs/build/html'

pymolpro-1.19.4/.github/workflows/unit-tests.yml

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+name: Python unit tests
+
+on: [ push, pull_request ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [ "3.13", "3.10", "3.11", "3.12" ]
+
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+          python-version: ${{ matrix.python-version }}
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          conda install -c conda-forge -y --file requirements.txt
+          pip install flake8 pytest
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Install
+        run: |
+          conda install -c anaconda -y pip
+          python -m pip install --no-deps --force-reinstall --verbose .
+      - name: Test with pytest
+        run: |
+          pytest

pymolpro-1.19.4/.gitignore

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+cmake-build*
+.idea
+__pycache__/
+.pytest_cache/
+*.pyc
+*.so
+.ipynb_checkpoints
+/build/
+.DS_Store
+*.egg-info/

pymolpro-1.19.4/LICENSE

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+The MIT License
+
+Copyright (c) 2020, Marat Sibaev
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pymolpro-1.19.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: pymolpro
+Version: 1.19.4
+Summary: Python support for Molpro
+Author: Marat Sibaev, Klaus Doll
+Author-email: Peter Knowles <knowlespj@cardiff.ac.uk>
+License: MIT
+Project-URL: Homepage, https://github.com/molpro/pymolpro
+Project-URL: Issues, https://github.com/molpro/pymolpro/issues
+Project-URL: Documentation, https://molpro.github.io/pymolpro
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pysjef>=1.45.3
+Requires-Dist: scipy>=1.9.3
+Requires-Dist: chemcoord
+Requires-Dist: lxml
+Requires-Dist: pandas
+Requires-Dist: quadpy>=0.16.10
+Requires-Dist: ase>=3.23.0
+Requires-Dist: jsonschema>=4.0.0
+Dynamic: license-file
+
+Molpro python support
+=====================
+
+**pymolpro** is a Python library that provides support
+for working with the `Molpro quantum chemistry package <https://www.molpro.net/>`_.
+
+The principal feature is
+the `Project` class that provides access to a complete Molpro job, including input
+and output files together with metadata such as job status information.
+The project is stored as a bundle implemented as a directory in the file system.
+The class is a Python binding of the
+`sjef <https://molpro.github.io/sjef/>`_ library with additional Molpro-specific customisation,
+and the project bundle can be accessed
+also through a command-line interface and the `gmolpro <https://www.molpro.net/manual/doku.php?id=gmolpro_graphical_user_interface>`_ and `iMolpro <https://github.com/molpro/iMolpro>`_
+graphical user interfaces.
+
+pymolpro is on `conda forge <https://conda-forge.org>`_ and can be installed on most systems using ``conda install -c conda-forge pymolpro``.
+
+Documentation at https://molpro.github.io/pymolpro.

pymolpro-1.19.4/README.rst

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+Molpro python support
+=====================
+
+**pymolpro** is a Python library that provides support
+for working with the `Molpro quantum chemistry package <https://www.molpro.net/>`_.
+
+The principal feature is
+the `Project` class that provides access to a complete Molpro job, including input
+and output files together with metadata such as job status information.
+The project is stored as a bundle implemented as a directory in the file system.
+The class is a Python binding of the
+`sjef <https://molpro.github.io/sjef/>`_ library with additional Molpro-specific customisation,
+and the project bundle can be accessed
+also through a command-line interface and the `gmolpro <https://www.molpro.net/manual/doku.php?id=gmolpro_graphical_user_interface>`_ and `iMolpro <https://github.com/molpro/iMolpro>`_
+graphical user interfaces.
+
+pymolpro is on `conda forge <https://conda-forge.org>`_ and can be installed on most systems using ``conda install -c conda-forge pymolpro``.
+
+Documentation at https://molpro.github.io/pymolpro.

pymolpro-1.19.4/build.sh

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+# This script will install pymolpro
+
+conda install -y -c conda-forge --file requirements.txt
+python -m pip install --no-deps --force-reinstall --verbose . 
+

pymolpro-1.19.4/docs/.gitignore

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+build

pymolpro-1.19.4/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@cp -p ../pymolpro/molpro_input.json $(SOURCEDIR)/molpro_input.json
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+

pymolpro-1.19.4/docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

pymolpro-1.19.4/docs/source/_templates/layout.html

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+{% extends "!layout.html" %}
+
+{% block menu %}
+{{ super() }}
+<p class="caption">
+    <span class="caption-text">Indices</span>
+</p>
+<ul>
+    <li class="toctree-l1"><a href= "{{pathto('genindex.html', 1)}}">Everything</a></li>
+    <li class="toctree-l1"><a href= "{{pathto('py-modindex.html', 1)}}">Module Index</a></li>
+</ul>
+
+{% endblock %}

pymolpro-1.19.4/docs/source/conf.py

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+import sys
+import subprocess
+import pymolpro
+import os
+from pathlib import Path
+
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'pymolpro'
+copyright = '2022, Marat Sibaev, Peter Knowles'
+author = 'Marat Sibaev, Peter Knowles'
+
+# sys.path.insert(0, Path(__file__).parent.parent.absolute())
+
+subprocess.check_call(
+    [sys.executable, "-m", "pip", "install", "--no-deps", "--force-reinstall", Path(__file__).parent.parent.parent])
+
+release = pymolpro.__version__
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'nbsphinx',
+    'sphinx-jsonschema',
+    'IPython.sphinxext.ipython_console_highlighting',
+]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', '**.ipynb_checkpoints']
+
+variables_to_export = ["release"]
+__frozen_locals = dict(locals())
+rst_epilog = '\n'.join(map(lambda x: f".. |{x}| replace:: {__frozen_locals[x]}", variables_to_export))
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+# html_static_path = ['_static']
+
+
+for dbname in pymolpro.database.library():
+    dbname_pretty = dbname.replace('_', ' ')
+    db = pymolpro.database.load(dbname)
+    if not os.path.exists('database'):
+        os.makedirs('database')
+    with open('database/' + dbname + '.rst', 'w') as f:
+        f.write(db.__str__(rst=True, geometry=False, title=dbname_pretty))

pymolpro-1.19.4/docs/source/databases.rst

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+Database library
+================
+
+.. toctree::
+   :glob:
+   :maxdepth: 1
+
+   database/*

pymolpro-1.19.4/docs/source/examples/.gitignore

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+*.molpro
+*.tex
+*.pdf
+.ipynb_checkpoints