PyFraME 0.4.0__tar.gz → 0.5.0__tar.gz

pyframe-0.5.0/CHANGELOG.md

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+# Changelog
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/)
+and this project adheres to [Semantic Versioning](http://semver.org/).
+
+<!-- How to write an entry: see the "Changelog" section of CONTRIBUTING.md. -->
+
+## [0.5.0] 2026-10-13
+### Added
+- Embedding calculations. The new embedding module computes the interaction of a quantum region with its environment
+  through electrostatics, polarization, repulsion, and dispersion, with its contributions to the Fock matrix and to the
+  gradients and Hessians of the energy. The computationally intensive parts run in a compiled C++ engine. Contributed by
+  Jonas Vester with support from Georg Berger.
+- A quantum chemistry program hands PyFraME its integrals through an integral driver: any class with the three methods
+  of `pyframe.IntegralDriver`, or a subclass of `pyframe.IntegralDriverTemplate`. Type checkers such as mypy check a
+  driver against `IntegralDriver`, so a missing or mistyped method shows before the program is run.
+- Induced dipole solvers (JI-DIIS, DC-JI, and DC-JI-DIIS). Contributed by Toke Nørremølle Heegaard.
+- Lennard-Jones repulsion and dispersion, with separate parameters for each and a choice of combination rules.
+- Potentials from molecular dynamics: `Trajectory` reads a trajectory using MDAnalysis and builds a potential for every
+  frame, with the regions given as MDAnalysis atom selections. A region can be narrowed down to the fragments within a
+  distance of a reference, e.g. the water around a solute, measured across the periodic boundary if asked for.
+  Fragments can be split into named parts, e.g. a lipid into its head group and tails, with `split_fragments`.
+- A JSON potential format that holds everything an embedding calculation needs. A molecular system can also be passed
+  to an embedding calculation directly, without a file.
+- The quantum region includes its link or capping atoms, whose basis set can be chosen separately from the other atoms.
+- Control over where PyFraME's messages go, to the console, to log files, or to memory (`pyframe.configure_logging`).
+- More control over how jobs are run: the MPI command, the host, and commands to run before each job can be set, and
+  connections can be verified before a run.
+- A dry run, `create_embedding_potential(only_create_inputs=True)`, which writes the input files and run scripts
+  without running anything.
+- Files written by PyFraME record the version that wrote them.
+- Ready-built packages for Linux (x86_64 and aarch64) and macOS (Apple silicon) for Python 3.11 to 3.14, so no compiler
+  is needed to install PyFraME there.
+- PyFraME is marked as typed, so type checkers such as mypy and pyright check scripts against the types of its
+  functions and classes.
+- Host programs and scripts can list the parameter sets shipped with PyFraME and describe each, with the fragments it
+  covers and its parameters (`pyframe.available_parameter_sets` and `pyframe.describe_parameter_set`).
+- Lipids of `alep` (DMPC, POPC, and POPS) can be selected whole, e.g. `'resname POPC'`, in a region shared with other
+  molecules: the parameter set splits them and sets their exclusions, so they need neither splitting by hand nor MFCC
+  settings of their own. A lipid split by hand is corrected to the charge of the whole lipid.
+- A parameter set of one's own can state the exclusions of its fragments and assemble fragments from parts, with
+  `# exclusion:` and `# parts:` lines above its header.
+- The citation names all the authors of PyFraME, and is also given in `CITATION.cff`, which reference managers and
+  other tools read citation metadata from.
+
+### Changed
+- PyFraME is licensed under the Mozilla Public License 2.0 instead of the GPLv3+.
+- Python 3.11 or newer is required. MDAnalysis, mpi4py, scikit-learn, QCElemental, and Fabric are new requirements,
+  and Dalton support is optional (`pip install pyframe[dalton]`). An MPI library is needed only for parallel embedding
+  calculations, and building from source needs a C++ compiler with OpenMP and the Eigen library.
+- Parameter set files name the component and unit of each column, e.g. `M_000[e]` or `epsilon[kJ/mol]`. Files in the
+  old format are rejected; the bundled ones have been converted.
+- Several names have changed, and scripts that use them need updating:
+  - Standard potentials are now called parameter sets: `use_standard_potentials`, `standard_potential_model`, and
+    `standard_potential_exclusion_type` are now `use_parameter_set`, `parameter_set`, and
+    `parameter_set_exclusion_type`. An old name is refused with an error that gives the new one.
+  - `Project` is now `CreatePotential`.
+  - `Potential` and `PotentialDict` are now `pyframe.Site` and `pyframe.SiteList`. Sites are numbered from zero
+    (potential files still count from one), their multipoles and polarizabilities are arrays instead of `M0`, `P11`,
+    and similar attributes, and `repulsion` and `dispersion` replace `sigma` and `epsilon`.
+  - Atoms and fragments can no longer be changed in place. `copy_with` makes a changed copy, and
+    `add_hydrogen_links` and `add_cap_links` are now `with_hydrogen_links` and `with_cap_atoms`, which return a new
+    fragment.
+  - `FragmentDict` is removed. Fragments are held in read-only mappings keyed by the index of their residue, as
+    `Fragment.index` gives it, rather than by a name such as `10_A_ILE`.
+  - Bonds between fragments are in the `topology` of a snapshot instead of `Fragment.bonded_fragments`, and MFCC belongs
+    to the region instead of the fragment: `Region.create_mfcc_fragments`, `Region.capped_fragments`, and
+    `Region.concaps` replace their `Fragment` counterparts. `Fragment.region` is removed, since a fragment can be in
+    more than one region, and a cap can span several fragments.
+  - `number_of_atoms` is now `num_atoms`, `analyse_bonding` is now `analyze_bonding`, and `omp_threads` is now
+    `omp_num_threads`.
+- The default parameter set is `pyframe-2026` instead of `sep`: the amino acids of `cp3`, the water, solvents, and ions
+  of `sep`, and the lipids of `alep`, so a protein in a membrane with its solvent and ions can be a single region.
+- In `sep`, phenol is `PHN` instead of `PHE`, which is phenylalanine; rename the residue where phenol is called `PHE`.
+- Environment sites where the core region cuts a bond are adjusted: a site replaced by a capping atom is removed, and
+  sites close to a link atom move their charge and polarizability to the rest of their region.
+- Fragment charges are rounded to the nearest integer.
+- Running the fragment calculations is more robust: results come back in order, a run whose workers have died stops
+  with an error instead of hanging, paths with spaces work, and a job stops at its first failing command. The
+  communication port is chosen automatically, and a scratch directory is looked for under `$SCRATCH` and `/scratch`
+  first.
+- PyFraME reports through Python's logging instead of printing, and importing it prints nothing.
+- The fragment calculations are named after the index of the residue of their fragment, e.g.
+  `fragment-9_dalton_multipoles.out`, and a file `fragments.txt` beside them says which fragment each is of, so the
+  calculations of a work directory of 0.4 are run again. Messages about a fragment say where to find it, e.g.
+  `ILE 10, chain A, resindex 9, atoms index 120:138`.
+
+### Removed
+- `MolecularSystem`: a structure is read as a `Trajectory` of one frame, and regions are given as MDAnalysis atom
+  selections. [Moving from MolecularSystem](README.md#moving-from-molecularsystem) lists what replaces each call.
+
+### Fixed
+- PDB and PQR files with more than 9999 residues, where residue numbers repeat, are read correctly.
+- The elements of HSD and HSE residues are recognized.
+- SSH jobs no longer fail on hosts that are not yet known; their host keys are accepted automatically.
+- MFCC could leave some lone atoms out; proteins at the default MFCC order of 2 were not affected.
+- PDE calculations could take the fragment densities from the wrong calculation.
+- Writing the core region removed the atoms replaced by caps from the environment.
+- Writing a potential file changed the sites' exclusion lists.
+- A core region without fragments gave an unclear error.
+- A potential built from parameter sets alone no longer leaves an empty directory for every snapshot, and the core can
+  be written before the potential, since `write_core` and `write_potential` make the directory they write into.
+
+## [0.4.0] 2021-06-07
+### Added
+- Added a `get_remaining_fragments` method to the `MolecularSystem` class that will return all remaining fragments.
+- Added AMBER Lipid14 and Lipid17 charges.
+
+### Changed
+- Reduced cost of PDE calculations by combining the SCFs used to calculate polarizability and fragment densities.
+- Region options, '*x*\_program', '*x*\_method', '*x*\_xcfun', and '*x*\_basis', where *x* can be multipoles,
+  polarizabilites, etc., have been unified to single options 'program', 'method', 'xcfun', and 'basis', that
+  apply to all properties associated with a given region. All unused '*x*\_model' properties have been removed.
+- Regular expressions can now be used for selecting atoms for new fragment definitions when splitting fragments.
+- Minimum requirement changed to Python 3.7 (though Python 3.6 should still work but is not guaranteed
+  starting from this release).
+- Redistribute surplus charge of non-MFCC standard potential fragments if total fragment charge is not integer.
+
+### Fixed
+- Process jobs without ssh when using only a single local machine. This fixes problems with job processing
+  that were present on some linux configurations.
+- Reset of the molecular system.
+- IndexError exception that would occur when a charge is missing (i.e. because it is zero).
+- Adjusted averaged lipid embedding parameters to make the total charge integer (was off by -4e-5).
+- Raise Exception when trying to read empty or non-existent Dalton LoProp output file.
+
+## [0.3.0] 2020-05-11
+### Added
+- Polarizable density embedding (PDE) model.
+  - see https://doi.org/10.1021/jp510138k and https://doi.org/10.1021/acs.jpclett.7b02788 for details.
+- Print license (`pyframe.print_license()`).
+- Added [contributing guidelines](https://gitlab.com/pyframe-project/pyframe/-/blob/master/CONTRIBUTING.md).
+- Cost-effective polarizable protein potential (CP3).
+  - see https://doi.org/10.1021/acs.jctc.9b00616 for details
+- The PDB input file reader will now try to guess the element based on the atom name, when the element field is missing.
+
+### Fixed
+- Settings, i.e. method, basis set, etc., when computing polarizabilities
+  separately from multipoles using Dalton LoProp have been fixed.
+- Fixed bug that in some cases resulted in corrupt core regions when it consisted of two
+  fragments or more.
+
+### Changed
+- Minimum requirement changed to Python 3.6.
+- Allow extracting fragments with a single item, e.g. system.get\_fragments\_by\_chain\_id('P'),
+  where it was required to always use lists before.
+- Remove use of Numba and instead use SciPy and NumPy only.
+
+## [0.2.0] - 2018-10-03
+### Added
+- Moved the suggested BibTeX snippet into the [CITATION
+  file](https://gitlab.com/pyframe-project/pyframe/-/blob/master/CITATION).
+- Added sodium and chloride charge and isotropic polarizability to
+  solvent embedding potential.
+- Added calcium, magnesium, potassium, zinc, and bromine charge and
+  isotropic polarizability to solvent embedding potential.
+- New option to choose exclusion type for standard potentials.
+  Currently it can be either 'fragment', which excludes all
+  interactions within a fragment, or 'mfcc', which is the MFCC type
+  exclusions.
+- Added AMBER ff94 and ff03 standard potentials.
+- Improve element recognition.
+- Surplus charge of a region treated using MFCC is now redistributed
+  among all sites in the affected region, ensuring that the sum of
+  partial charges is equal to the formal charge of the region.
+- Added averaged lipid embedding parameters from S. Witzke et al.
+  J. Comput. Chem. 38 (2017) 601-611.
+
+### Fixed
+- Fixed wrong asserts which would have caused errors if octopoles or
+  higher were requested.
+- All polarizabilities up to octopole-octopole are now present.
+- Errors when using CAM-B3LYP in serial Dalton calculations (which now
+  always use `.DIRECT`).
+- Error when LD\_LIBRARY\_PATH environment variable was not set.
+- Fixed erroneous exclusion lists when different parts of a molecule,
+  e.g. protein, are placed in different regions.
+- Radius of Li, Na, Mg, K, and Ca (used in bond detection) adjusted to
+  the effective ionic radius by R. D. Shannon, Acta. Cryst. A32 (1976), 751.
+- Naming bug when adding hydrogen-link atoms where the donor-atom name
+  would erroneously have _link_ appended to it.
+
+### Changed
+- Running the test suite now requires pytest (unittests can be run by typing `pytest --pyargs pyframe`).
+- The default bond detection threshold factor has been set to 1.15 instead of 1.2.
+- Improved error message when there is a mismatch between the number of sites in
+  an output file compared to the number of sites in the fragment read in from input.
+- Default is now to first try to find a free communication port.
+
+## [0.1.1] - 2018-02-08
+### Changed
+- There is now a check for empty output files from fragment
+  calculations to prevent deletion of subdirectories of failed
+  fragment calculations.
+- Now hydrogen caps between core region and other regions are always
+  used.
+- Efficiency-related changes:
+  - compute angles, distances, distance matrices using Numba jit
+    decorator (introduces Numba dependency and removes SciPy dependency).
+  - removed some unnecessary property decorators.
+- Refactored the atoms module (faster and safer).
+
+### Fixed
+- Bug in MOLCAS LoProp ('Fragment' object has no attribute 'xyz').
+- Using Dalton LoProp with multipole orders lower than two no longer
+  fails.
+- Bug in charge redistribution where negative surplus charge would not
+  be redistributed.
+
+## [0.1.0] - 2017-02-20
+### Added
+- Initial version.

pyframe-0.5.0/CITATION

@@ -0,0 +1,6 @@
+@misc{pyframe:0.5.0,
+      author = {Olsen, J. M. H. and Reinholdt, P. and Vester, J. and Heegaard, T. N. and Berger, G.},
+      title = {{PyFraME}: {P}ython framework for {F}ragment-based {M}ultiscale {E}mbedding (version 0.5.0)},
+      year = {2026},
+      doi = {10.5281/zenodo.22996201},
+      note = {See https://gitlab.com/pyframe-project/pyframe}}

pyframe-0.5.0/CITATION.cff

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+cff-version: 1.2.0
+message: If you use PyFraME, please cite the version you used as below.
+title: "PyFraME: Python framework for Fragment-based Multiscale Embedding"
+type: software
+version: 0.5.0
+date-released: "2026-10-13"
+doi: 10.5281/zenodo.22996201
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.22996201
+    description: This version, 0.5.0.
+  - type: doi
+    value: 10.5281/zenodo.775113
+    description: All versions, resolving to the latest.
+authors:
+  - given-names: Jógvan Magnus Haugaard
+    family-names: Olsen
+    orcid: https://orcid.org/0000-0001-7487-944X
+  - given-names: Peter
+    family-names: Reinholdt
+    orcid: https://orcid.org/0000-0003-2406-700X
+  - given-names: Jonas
+    family-names: Vester
+    orcid: https://orcid.org/0000-0001-8584-1295
+  - given-names: Toke Nørremølle
+    family-names: Heegaard
+    orcid: https://orcid.org/0009-0008-8334-1893
+  - given-names: Georg
+    family-names: Berger
+    orcid: https://orcid.org/0009-0007-8557-0975
+abstract: >-
+  PyFraME builds embedding potentials for multiscale calculations from molecular
+  structures and molecular dynamics trajectories, fragment by fragment or from
+  parameter sets, and computes the interaction of a quantum region with its
+  environment for the quantum chemistry programs it is coupled to.
+keywords:
+  - computational chemistry
+  - multiscale modeling
+  - QM/MM
+  - polarizable embedding
+  - fragment-based methods
+license: MPL-2.0
+repository-code: https://gitlab.com/pyframe-project/pyframe
+url: https://gitlab.com/pyframe-project/pyframe

pyframe-0.5.0/CONTRIBUTORS

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+PyFraME Contributors
+====================
+
+The following people have contributed to PyFraME (chronologically ordered):
+
+- Jógvan Magnus Haugaard Olsen
+- Peter Reinholdt
+- Jonas Vester
+- Toke Nørremølle Heegaard
+- Georg Berger

pyframe-0.5.0/LICENSE

@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

pyframe-0.5.0/MANIFEST.in

@@ -0,0 +1,12 @@
+# What the sdist carries beyond what setuptools finds itself, i.e. the packages,
+# their package data, and the sources and headers of the engine extension, which
+# setup.py declares. The tests are not packages, so they are grafted here, for
+# the sdist job, which runs them from the sdist. None of this reaches the wheel,
+# which carries only the package data pyproject.toml names.
+include CHANGELOG.md CITATION CITATION.cff CONTRIBUTORS
+graft pyframe/tests
+graft pyframe/common/tests
+graft pyframe/construction/tests
+graft pyframe/embedding/tests
+# Bytecode that a test run has left in the grafted directories.
+global-exclude *.py[cod]