composite-step 2026.11.11__tar.gz

composite_step-2026.11.11/AUTHORS.rst

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+Development Team
+----------------
+
+* Paul Saxe <psaxe@molssi.org> (Lead)
+* Why don't you join the team? Become a contributor!

composite_step-2026.11.11/CONTRIBUTING.rst

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+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every
+little bit helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/molssi-seamm/composite_step/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug"
+and "help wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+Composite Step could always use more documentation, whether as part of the
+official Composite Step docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/molssi-seamm/composite_step/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `composite_step` for local development.
+
+1. Fork the `composite_step` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/composite_step.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv composite_step
+    $ cd composite_step/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox::
+
+    $ flake8 composite_step tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check
+   https://travis-ci.org/molssi-seamm/composite_step/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+    $ py.test tests.test_composite_step

composite_step-2026.11.11/HISTORY.rst

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+=======
+History
+=======
+
+2026.11.11 -- First release: composite methods as model chemistries
+    * Composite methods are described by recipes, short YAML files that say how the
+      energy is made from ordinary calculations: the geometry and frequency level,
+      single points at that geometry, and a formula that combines them, with
+      basis-set extrapolations, scaling and empirical terms.
+    * Every recipe is a model chemistry, ``SEAMM:CMP@<recipe>``, for the steps that
+      take one. Its components are ordinary calculations with their own settings
+      fingerprints, so the fragment store reuses them.
+    * The recipes ``r2SCAN-3c-HO`` and ``revDSD-r2SCAN-3c-HO`` are shipped; they are
+      the Thermochemistry step's ``quick`` and ``default`` presets.
+    * The Composite step itself does nothing yet and is not offered in the editor.

composite_step-2026.11.11/LICENSE

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+
+BSD 3-Clause License
+
+Copyright (c) 2026, Paul Saxe
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

composite_step-2026.11.11/MANIFEST.in

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+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+include requirements*
+include versioneer.py
+
+recursive-include composite_step/data *
+recursive-include tests *
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

composite_step-2026.11.11/PKG-INFO

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+Metadata-Version: 2.4
+Name: composite_step
+Version: 2026.11.11
+Summary: A SEAMM plug-in for composite methods: energies from recipes of ordinary calculations
+Home-page: https://github.com/molssi-seamm/composite_step
+Author: Paul Saxe
+Author-email: psaxe@molssi.org
+License: BSD-3-Clause
+Keywords: SEAMM,SEAMMplugin,flowchart
+Platform: Linux
+Platform: Mac OS-X
+Platform: Unix
+Platform: Windows
+Classifier: Environment :: Plugins
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: seamm
+Requires-Dist: seamm-util
+Requires-Dist: seamm-widgets
+Requires-Dist: pyyaml
+Requires-Dist: seamm-exec
+Requires-Dist: model-chemistry-step
+Requires-Dist: stevedore
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+=======================
+SEAMM Composite Plug-in
+=======================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/composite_step
+   :target: https://github.com/molssi-seamm/composite_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/composite_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/composite_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/composite_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/composite_step
+   :alt: Code Coverage
+
+.. image:: https://github.com/molssi-seamm/composite_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/composite_step/security/code-scanning
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/composite_step/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/composite_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/v/composite_step.svg
+   :target: https://pypi.python.org/pypi/composite_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for composite methods: energies from recipes of ordinary calculations
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/composite_step/index.html
+* Code: https://github.com/molssi-seamm/composite_step
+
+Features
+--------
+
+* Composite methods as model chemistries, ``SEAMM:CMP@<recipe>``, from recipes:
+  short YAML files that say how the energy is made from ordinary calculations.
+* A small, checked language for combining the energies: basis-set extrapolations
+  (inverse power, exponential HF, Schwenke), scaling and empirical terms.
+* Components are ordinary calculations with their own settings fingerprints, so
+  the fragment store reuses them.
+* The shipped recipes ``r2SCAN-3c-HO`` and ``revDSD-r2SCAN-3c-HO``, the
+  Thermochemistry step's ``quick`` and ``default`` presets.
+
+Acknowledgements
+----------------
+
+This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
+is based on the excellent Cookiecutter_.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
+
+Developed by the Molecular Sciences Software Institute (MolSSI_),
+which receives funding from the `National Science Foundation`_ under
+award CHE-2136142.
+
+.. _MolSSI: https://molssi.org
+.. _`National Science Foundation`: https://www.nsf.gov
+
+
+=======
+History
+=======
+
+2026.11.11 -- First release: composite methods as model chemistries
+    * Composite methods are described by recipes, short YAML files that say how the
+      energy is made from ordinary calculations: the geometry and frequency level,
+      single points at that geometry, and a formula that combines them, with
+      basis-set extrapolations, scaling and empirical terms.
+    * Every recipe is a model chemistry, ``SEAMM:CMP@<recipe>``, for the steps that
+      take one. Its components are ordinary calculations with their own settings
+      fingerprints, so the fragment store reuses them.
+    * The recipes ``r2SCAN-3c-HO`` and ``revDSD-r2SCAN-3c-HO`` are shipped; they are
+      the Thermochemistry step's ``quick`` and ``default`` presets.
+    * The Composite step itself does nothing yet and is not offered in the editor.

composite_step-2026.11.11/README.rst

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+=======================
+SEAMM Composite Plug-in
+=======================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/composite_step
+   :target: https://github.com/molssi-seamm/composite_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/composite_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/composite_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/composite_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/composite_step
+   :alt: Code Coverage
+
+.. image:: https://github.com/molssi-seamm/composite_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/composite_step/security/code-scanning
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/composite_step/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/composite_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/v/composite_step.svg
+   :target: https://pypi.python.org/pypi/composite_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for composite methods: energies from recipes of ordinary calculations
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/composite_step/index.html
+* Code: https://github.com/molssi-seamm/composite_step
+
+Features
+--------
+
+* Composite methods as model chemistries, ``SEAMM:CMP@<recipe>``, from recipes:
+  short YAML files that say how the energy is made from ordinary calculations.
+* A small, checked language for combining the energies: basis-set extrapolations
+  (inverse power, exponential HF, Schwenke), scaling and empirical terms.
+* Components are ordinary calculations with their own settings fingerprints, so
+  the fragment store reuses them.
+* The shipped recipes ``r2SCAN-3c-HO`` and ``revDSD-r2SCAN-3c-HO``, the
+  Thermochemistry step's ``quick`` and ``default`` presets.
+
+Acknowledgements
+----------------
+
+This package was created with the `molssi-seamm/cookiecutter-seamm-plugin`_ tool, which
+is based on the excellent Cookiecutter_.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
+
+Developed by the Molecular Sciences Software Institute (MolSSI_),
+which receives funding from the `National Science Foundation`_ under
+award CHE-2136142.
+
+.. _MolSSI: https://molssi.org
+.. _`National Science Foundation`: https://www.nsf.gov

composite_step-2026.11.11/composite_step/__init__.py

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+# -*- coding: utf-8 -*-
+
+"""
+composite_step
+A SEAMM plug-in for composite methods: energies from recipes of ordinary calculations
+"""
+
+# Bring up the classes so that they appear to be directly in
+# the composite_step package.
+
+from .composite import Composite  # noqa: F401, E501
+from .composite_parameters import CompositeParameters  # noqa: F401, E501
+from .composite_step import CompositeStep  # noqa: F401, E501
+from .tk_composite import TkComposite  # noqa: F401, E501
+
+from .metadata import metadata  # noqa: F401
+
+# Handle versioneer
+from ._version import get_versions
+
+__author__ = "Paul Saxe"
+__email__ = "psaxe@molssi.org"
+versions = get_versions()
+__version__ = versions["version"]
+__git_revision__ = versions["full-revisionid"]
+del get_versions, versions

composite_step-2026.11.11/composite_step/_version.py

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+
+# This file was generated by 'versioneer.py' (0.18) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2026-11-11T20:16:54-0500",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "bd87d3e0e8117b78603103c0d6b0de26ee0c75e7",
+ "version": "2026.11.11"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

composite_step-2026.11.11/composite_step/composite.py

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+# -*- coding: utf-8 -*-
+
+"""Non-graphical part of the Composite step in a SEAMM flowchart"""
+
+import logging
+import importlib.resources
+import pprint  # noqa: F401
+
+import composite_step
+import molsystem
+import seamm
+from seamm_util import ureg, Q_  # noqa: F401
+import seamm_util.printing as printing
+from seamm_util.printing import FormattedText as __
+
+# In addition to the normal logger, two logger-like printing facilities are
+# defined: "job" and "printer". "job" send output to the main job.out file for
+# the job, and should be used very sparingly, typically to echo what this step
+# will do in the initial summary of the job.
+#
+# "printer" sends output to the file "step.out" in this steps working
+# directory, and is used for all normal output from this step.
+
+logger = logging.getLogger(__name__)
+job = printing.getPrinter()
+printer = printing.getPrinter("Composite")
+
+# Add this module's properties to the standard properties
+path = importlib.resources.files("composite_step") / "data"
+csv_file = path / "properties.csv"
+if path.exists():
+    molsystem.add_properties_from_file(csv_file)
+
+
+class Composite(seamm.Node):
+    """
+    The non-graphical part of a Composite step in a flowchart.
+
+    Attributes
+    ----------
+    parser : configargparse.ArgParser
+        The parser object.
+
+    options : tuple
+        It contains a two item tuple containing the populated namespace and the
+        list of remaining argument strings.
+
+    subflowchart : seamm.Flowchart
+        A SEAMM Flowchart object that represents a subflowchart, if needed.
+
+    parameters : CompositeParameters
+        The control parameters for Composite.
+
+    See Also
+    --------
+    TkComposite,
+    Composite, CompositeParameters
+    """
+
+    def __init__(
+        self, flowchart=None, title="Composite", extension=None, logger=logger
+    ):
+        """A step for Composite in a SEAMM flowchart.
+
+        You may wish to change the title above, which is the string displayed
+        in the box representing the step in the flowchart.
+
+        Parameters
+        ----------
+        flowchart: seamm.Flowchart
+            The non-graphical flowchart that contains this step.
+
+        title: str
+            The name displayed in the flowchart.
+        extension: None
+            Not yet implemented
+        logger : Logger = logger
+            The logger to use and pass to parent classes
+
+        Returns
+        -------
+        None
+        """
+        logger.debug(f"Creating Composite {self}")
+
+        super().__init__(
+            flowchart=flowchart,
+            title="Composite",
+            extension=extension,
+            module=__name__,
+            logger=logger,
+        )  # yapf: disable
+
+        self._metadata = composite_step.metadata
+        self.parameters = composite_step.CompositeParameters()
+
+    @property
+    def version(self):
+        """The semantic version of this module."""
+        return composite_step.__version__
+
+    @property
+    def git_revision(self):
+        """The git version of this module."""
+        return composite_step.__git_revision__
+
+    def description_text(self, P=None):
+        """Create the text description of what this step will do.
+        The dictionary of control values is passed in as P so that
+        the code can test values, etc.
+
+        Parameters
+        ----------
+        P: dict
+            An optional dictionary of the current values of the control
+            parameters.
+        Returns
+        -------
+        str
+            A description of the current step.
+        """
+        if not P:
+            P = self.parameters.values_to_dict()
+
+        text = (
+            "Composite methods are used through a Model Chemistry step, as "
+            "SEAMM:CMP@<recipe> (e.g. SEAMM:CMP@revDSD-r2SCAN-3c-HO), by the steps "
+            "that take a model chemistry, such as Thermochemistry. This step "
+            "itself does nothing yet."
+        )
+
+        return self.header + "\n" + __(text, **P, indent=4 * " ").__str__()
+
+    def run(self):
+        """Run a Composite step: print what it does, which is nothing yet.
+
+        Returns
+        -------
+        seamm.Node
+            The next node object in the flowchart.
+        """
+        next_node = super().run(printer)
+        printer.important(__(self.description_text({}), indent=self.indent))
+        return next_node
+
+    def analyze(self, indent="", **kwargs):
+        """Nothing to analyze yet."""

composite_step-2026.11.11/composite_step/composite_parameters.py

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+# -*- coding: utf-8 -*-
+"""
+Control parameters for the Composite step in a SEAMM flowchart
+"""
+
+import logging
+import seamm
+import pprint  # noqa: F401
+
+logger = logging.getLogger(__name__)
+
+
+class CompositeParameters(seamm.Parameters):
+    """
+    The control parameters for Composite.
+
+    You need to replace the "time" entry in dictionary below these comments with the
+    definitions of parameters to control this step. The keys are parameters for the
+    current plugin,the values are dictionaries as outlined below.
+
+    Examples
+    --------
+    ::
+
+        parameters = {
+            "time": {
+                "default": 100.0,
+                "kind": "float",
+                "default_units": "ps",
+                "enumeration": tuple(),
+                "format_string": ".1f",
+                "description": "Simulation time:",
+                "help_text": ("The time to simulate in the dynamics run.")
+            },
+        }
+
+    parameters : {str: {str: str}}
+        A dictionary containing the parameters for the current step.
+        Each key of the dictionary is a dictionary that contains the
+        the following keys:
+
+    parameters["default"] :
+        The default value of the parameter, used to reset it.
+
+    parameters["kind"] : enum()
+        Specifies the kind of a variable. One of  "integer", "float", "string",
+        "boolean", or "enum"
+
+        While the "kind" of a variable might be a numeric value, it may still have
+        enumerated custom values meaningful to the user. For instance, if the parameter
+        is a convergence criterion for an optimizer, custom values like "normal",
+        "precise", etc, might be adequate. In addition, any parameter can be set to a
+        variable of expression, indicated by having "$" as the first character in the
+        field. For example, $OPTIMIZER_CONV.
+
+    parameters["default_units"] : str
+        The default units, used for resetting the value.
+
+    parameters["enumeration"] : tuple
+        A tuple of enumerated values.
+
+    parameters["format_string"] : str
+        A format string for "pretty" output.
+
+    parameters["description"] : str
+        A short string used as a prompt in the GUI.
+
+    parameters["help_text"] : str
+        A longer string to display as help for the user.
+
+    See Also
+    --------
+    Composite, TkComposite, Composite CompositeParameters, CompositeStep
+    """
+
+    #: No parameters yet: composites are used through a Model Chemistry step.
+    parameters = {}
+
+    def __init__(self, defaults={}, data=None):
+        """
+        Initialize the parameters, by default with the parameters defined above
+
+        Parameters
+        ----------
+        defaults: dict
+            A dictionary of parameters to initialize. The parameters
+            above are used first and any given will override/add to them.
+        data: dict
+            A dictionary of keys and a subdictionary with value and units
+            for updating the current, default values.
+
+        Returns
+        -------
+        None
+        """
+
+        logger.debug("CompositeParameters.__init__")
+
+        super().__init__(
+            defaults={**CompositeParameters.parameters, **defaults}, data=data
+        )