active-learning-step 2026.10.14__tar.gz

active_learning_step-2026.10.14/AUTHORS.rst

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

active_learning_step-2026.10.14/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/active_learning_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
+~~~~~~~~~~~~~~~~~~~
+
+Active Learning Step could always use more documentation, whether as part of the
+official Active Learning 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/active_learning_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 `active_learning_step` for local development.
+
+1. Fork the `active_learning_step` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/active_learning_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 active_learning_step
+    $ cd active_learning_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 active_learning_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/active_learning_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_active_learning_step

active_learning_step-2026.10.14/HISTORY.rst

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+=======
+History
+=======
+
+2026.10.14 -- Initial release: query-by-committee active learning for MLFFs
+    * A committee of machine-learned force fields, trained on different folds of the
+      data, disagrees where the model is likely wrong; the seamm-al command uses that
+      disagreement to choose what to label next. This first release provides the
+      library and the command line; the SEAMM flowchart step is a placeholder.
+    * seamm-al score: the committee's spreads (energy, forces, the largest per-atom
+      force spread, atomic and molecular pressure) for every frame of extxyz or SEAMM
+      SDF pools, with the total charge passed to the models. Molecules follow SEAMM's
+      own rule (molsystem's bond perception, ions on their own), applied without
+      SEAMM in MLFF environments, or a SEAMM structure's own bonds.
+    * seamm-al select: rank the frames, or keep those past thresholds, and take them
+      within a core-hour budget, with costs per kind or group, caps per column and
+      exclusions; or draw at random (optionally stratified) before any committee
+      exists. The chosen frames are copied byte for byte from the input files.
+    * seamm-al train: train the k members of a committee from an xnn recipe, with
+      stratified folds, a fixed share of cell batches and a manifest of the folds,
+      seeds, data and code versions. Requires xnn 0.13 or later.
+    * seamm-al check: whether the spreads predict the out-of-fold errors (Spearman
+      correlations, threshold calibration) and the health of each member (losses,
+      errors, leave-one-out spreads), with an option to drop a member.
+    * seamm-al engine: the committee mean as one MDI engine for LAMMPS, writing the
+      spreads every N steps and flagging frames past a threshold.
+    * seamm-al data: check a LAMMPS data file for what atom_style atomic can read.
+

active_learning_step-2026.10.14/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.
+

active_learning_step-2026.10.14/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 active_learning_step/data *
+recursive-include tests *
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]

active_learning_step-2026.10.14/PKG-INFO

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+Metadata-Version: 2.4
+Name: active_learning_step
+Version: 2026.10.14
+Summary: A SEAMM plug-in for Active Learning
+Home-page: https://github.com/molssi-seamm/active_learning_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: ase
+Requires-Dist: numpy
+Requires-Dist: seamm
+Requires-Dist: seamm-util
+Requires-Dist: seamm-widgets
+Provides-Extra: score
+Requires-Dist: xnns>=0.11.1; extra == "score"
+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: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+=============================
+SEAMM Active Learning Plug-in
+=============================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/active_learning_step
+   :target: https://github.com/molssi-seamm/active_learning_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/active_learning_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/active_learning_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/active_learning_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/active_learning_step
+   :alt: Code Coverage
+
+.. image:: https://github.com/molssi-seamm/active_learning_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/active_learning_step/security/code-scanning
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/active_learning_step/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/active_learning_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/v/active_learning_step.svg
+   :target: https://pypi.python.org/pypi/active_learning_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for query-by-committee active learning of machine-learned force
+fields: a committee of models trained on different folds of the data disagrees where
+the model is likely wrong, so only the frames it flags need labelling.
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/active_learning_step/index.html
+* Code: https://github.com/molssi-seamm/active_learning_step
+
+Features
+--------
+
+* ``active_learning_step.committee``: a committee of xnn potentials and its spreads
+  (energy, force, per-atom force, atomic and molecular pressure), for molecules,
+  ions and charged systems.
+* ``seamm-al score``: the committee's spreads for every frame of extxyz or SDF pools.
+* ``seamm-al select``: rank the frames and take them within a core-hour budget, with
+  caps per group and exclusions, writing the chosen frames as a verbatim subset of
+  the input files.
+
+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
+=======
+
+2026.10.14 -- Initial release: query-by-committee active learning for MLFFs
+    * A committee of machine-learned force fields, trained on different folds of the
+      data, disagrees where the model is likely wrong; the seamm-al command uses that
+      disagreement to choose what to label next. This first release provides the
+      library and the command line; the SEAMM flowchart step is a placeholder.
+    * seamm-al score: the committee's spreads (energy, forces, the largest per-atom
+      force spread, atomic and molecular pressure) for every frame of extxyz or SEAMM
+      SDF pools, with the total charge passed to the models. Molecules follow SEAMM's
+      own rule (molsystem's bond perception, ions on their own), applied without
+      SEAMM in MLFF environments, or a SEAMM structure's own bonds.
+    * seamm-al select: rank the frames, or keep those past thresholds, and take them
+      within a core-hour budget, with costs per kind or group, caps per column and
+      exclusions; or draw at random (optionally stratified) before any committee
+      exists. The chosen frames are copied byte for byte from the input files.
+    * seamm-al train: train the k members of a committee from an xnn recipe, with
+      stratified folds, a fixed share of cell batches and a manifest of the folds,
+      seeds, data and code versions. Requires xnn 0.13 or later.
+    * seamm-al check: whether the spreads predict the out-of-fold errors (Spearman
+      correlations, threshold calibration) and the health of each member (losses,
+      errors, leave-one-out spreads), with an option to drop a member.
+    * seamm-al engine: the committee mean as one MDI engine for LAMMPS, writing the
+      spreads every N steps and flagging frames past a threshold.
+    * seamm-al data: check a LAMMPS data file for what atom_style atomic can read.
+

active_learning_step-2026.10.14/README.rst

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+=============================
+SEAMM Active Learning Plug-in
+=============================
+
+.. image:: https://img.shields.io/github/issues-pr-raw/molssi-seamm/active_learning_step
+   :target: https://github.com/molssi-seamm/active_learning_step/pulls
+   :alt: GitHub pull requests
+
+.. image:: https://github.com/molssi-seamm/active_learning_step/workflows/CI/badge.svg
+   :target: https://github.com/molssi-seamm/active_learning_step/actions
+   :alt: Build Status
+
+.. image:: https://codecov.io/gh/molssi-seamm/active_learning_step/branch/master/graph/badge.svg
+   :target: https://codecov.io/gh/molssi-seamm/active_learning_step
+   :alt: Code Coverage
+
+.. image:: https://github.com/molssi-seamm/active_learning_step/workflows/CodeQL/badge.svg
+   :target: https://github.com/molssi-seamm/active_learning_step/security/code-scanning
+   :alt: Code Quality
+
+.. image:: https://github.com/molssi-seamm/active_learning_step/workflows/Release/badge.svg
+   :target: https://molssi-seamm.github.io/active_learning_step/index.html
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/pypi/v/active_learning_step.svg
+   :target: https://pypi.python.org/pypi/active_learning_step
+   :alt: PyPi VERSION
+
+A SEAMM plug-in for query-by-committee active learning of machine-learned force
+fields: a committee of models trained on different folds of the data disagrees where
+the model is likely wrong, so only the frames it flags need labelling.
+
+* Free software: BSD-3-Clause
+* Documentation: https://molssi-seamm.github.io/active_learning_step/index.html
+* Code: https://github.com/molssi-seamm/active_learning_step
+
+Features
+--------
+
+* ``active_learning_step.committee``: a committee of xnn potentials and its spreads
+  (energy, force, per-atom force, atomic and molecular pressure), for molecules,
+  ions and charged systems.
+* ``seamm-al score``: the committee's spreads for every frame of extxyz or SDF pools.
+* ``seamm-al select``: rank the frames and take them within a core-hour budget, with
+  caps per group and exclusions, writing the chosen frames as a verbatim subset of
+  the input files.
+
+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

active_learning_step-2026.10.14/active_learning_step/__init__.py

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+# -*- coding: utf-8 -*-
+
+"""
+active_learning_step
+A SEAMM plug-in for Active Learning
+"""
+
+# Bring up the classes so that they appear to be directly in
+# the active_learning_step package.
+#
+# The library (committee, molecules, pool, selection) and the seamm-al command also
+# run in MLFF environments that have torch and xnn but not SEAMM, so the step's
+# classes are only imported when SEAMM is there.
+try:
+    import seamm  # noqa: F401
+except ImportError:
+    pass
+else:
+    from .active_learning import ActiveLearning  # noqa: F401, E501
+    from .active_learning_parameters import ActiveLearningParameters  # noqa: F401, E501
+    from .active_learning_step import ActiveLearningStep  # noqa: F401, E501
+    from .tk_active_learning import TkActiveLearning  # 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

active_learning_step-2026.10.14/active_learning_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": "2026-10-14T06:21:42-0400",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "1644bd1a7793ed3ca65d488119b41a5d0a7d1180",
+ "version": "2026.10.14"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

active_learning_step-2026.10.14/active_learning_step/active_learning.py

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+# -*- coding: utf-8 -*-
+
+"""Non-graphical part of the Active Learning step in a SEAMM flowchart"""
+
+import logging
+from pathlib import Path
+import importlib.resources
+import pprint  # noqa: F401
+
+import active_learning_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("Active Learning")
+
+# Add this module's properties to the standard properties
+path = importlib.resources.files("active_learning_step") / "data"
+csv_file = path / "properties.csv"
+if path.exists():
+    molsystem.add_properties_from_file(csv_file)
+
+
+class ActiveLearning(seamm.Node):
+    """
+    The non-graphical part of a Active Learning 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 : ActiveLearningParameters
+        The control parameters for Active Learning.
+
+    See Also
+    --------
+    TkActiveLearning,
+    ActiveLearning, ActiveLearningParameters
+    """
+
+    def __init__(
+        self, flowchart=None, title="Active Learning", extension=None, logger=logger
+    ):
+        """A step for Active Learning 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 Active Learning {self}")
+
+        super().__init__(
+            flowchart=flowchart,
+            title="Active Learning",
+            extension=extension,
+            module=__name__,
+            logger=logger,
+        )  # yapf: disable
+
+        self._metadata = active_learning_step.metadata
+        self.parameters = active_learning_step.ActiveLearningParameters()
+
+    @property
+    def version(self):
+        """The semantic version of this module."""
+        return active_learning_step.__version__
+
+    @property
+    def git_revision(self):
+        """The git version of this module."""
+        return active_learning_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 = (
+            "Please replace this with a short summary of the "
+            "Active Learning step, including key parameters."
+        )
+
+        return self.header + "\n" + __(text, **P, indent=4 * " ").__str__()
+
+    def run(self):
+        """Run a Active Learning step.
+
+        Parameters
+        ----------
+        None
+
+        Returns
+        -------
+        seamm.Node
+            The next node object in the flowchart.
+        """
+        next_node = super().run(printer)
+        # Get the values of the parameters, dereferencing any variables
+        P = self.parameters.current_values_to_dict(
+            context=seamm.flowchart_variables._data
+        )
+
+        # Print what we are doing
+        printer.important(__(self.description_text(P), indent=self.indent))
+
+        directory = Path(self.directory)
+        directory.mkdir(parents=True, exist_ok=True)
+
+        # Get the current system and configuration (ignoring the system...)
+        _, configuration = self.get_system_configuration(None)
+
+        # Results data
+        data = {}
+
+        # Temporary code just to print the parameters. You will need to change
+        # this!
+        for key in P:
+            print("{:>15s} = {}".format(key, P[key]))
+            printer.normal(
+                __(
+                    "{key:>15s} = {value}",
+                    key=key,
+                    value=P[key],
+                    indent=4 * " ",
+                    wrap=False,
+                    dedent=False,
+                )
+            )
+
+        # Analyze the results
+        self.analyze()
+        # Put any requested results into variables or tables
+        self.store_results(
+            configuration=configuration,
+            data=data,
+        )
+        # Add other citations here or in the appropriate place in the code.
+        # Add the bibtex to data/references.bib, and add a self.reference.cite
+        # similar to the above to actually add the citation to the references.
+
+        return next_node
+
+    def analyze(self, indent="", **kwargs):
+        """Do any analysis of the output from this step.
+
+        Also print important results to the local step.out file using
+        "printer".
+
+        Parameters
+        ----------
+        indent: str
+            An extra indentation for the output
+        """
+        printer.normal(
+            __(
+                "This is a placeholder for the results from the Active Learning step",
+                indent=4 * " ",
+                wrap=True,
+                dedent=False,
+            )
+        )