hyperbase 0.8.0__tar.gz

hyperbase-0.8.0/.github/workflows/docs.yml

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+name: Deploy docs to hyperquest.ai/hyperbase
+
+on:
+  push:
+    branches: [master]
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'src/**'
+  workflow_dispatch:
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout hyperbase
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Build docs
+        run: uv run mkdocs build
+
+      - name: Checkout main site repo
+        uses: actions/checkout@v4
+        with:
+          repository: hyperquest-hq/hyperquest-hq.github.io
+          token: ${{ secrets.DEPLOY_TOKEN }}
+          path: site-repo
+
+      - name: Deploy docs to site repo
+        run: |
+          rm -rf site-repo/hyperbase
+          cp -r site/ site-repo/hyperbase
+
+      - name: Push to main site repo
+        working-directory: site-repo
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add hyperbase/
+          git diff --cached --quiet && echo "No changes to deploy" && exit 0
+          git commit -m "Update hyperbase docs"
+          git push

hyperbase-0.8.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install build dependencies
+        run: pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

hyperbase-0.8.0/.gitignore

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+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+build/
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store*
+ehthumbs.db
+Icon?
+Thumbs.db
+
+# IDE stuff #
+#############
+.idea
+.vscode
+
+
+# Python version/venv #
+#######################
+.python-version
+
+# Python bytecode #
+###################
+__pycache__
+*.pyc
+*.pyo
+
+# Python package stuff #
+########################
+*.egg-info
+
+# Jupyter notebooks #
+#####################
+.ipynb_checkpoints
+
+# db files #
+#####################
+*.db
+
+/venv
+/dist
+/site

hyperbase-0.8.0/AUTHORS

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+Telmo Menezes <telmo@telmomenezes.net>
+Chih-Chun Chen <c.chen@abmcet.net>
+Camille Roth <roth@cmb.hu-berlin.de>
+Kexin Ren <kren4@ualberta.ca>
+Max Reinhard <mail@max-reinhard.de>

hyperbase-0.8.0/CHANGELOG.md

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+# Changelog
+
+## [0.8.0] - 26-03-2026 - hyperbase is the successor of graphbrain
+
+### Added
+- parser plugin foundation.
+- more comprehensive Hyperedge.check_correctness.
+- check parse correctness.
+- type checking: full code coverage.
+
+### Changed
+- renamed library to hyperbase.
+- trimmed down library to the essentials: hyperedge, patterns and parser foundations.
+- converted documentation to Material for MkDocs.
+
+### Removed
+- hypergraph module, hypergraph database (memory module).
+- alphabeta parser implementation.
+- old scripts, examples, processors.
+- ad hoc utils.
+- cli.
+- notebook utils.
+- obsolete constants.
+
+## [0.7.0] - 05-03-2026
+### Added
+- patterns.is_wildcard().
+- Base class hypergraph.memory.keyvalue.KeyValue for key-value hypergraph databases, removing redundant code between LevelDB and SQLite.
+- Tests for LevelDB (only the SQLite Hypergraph implementation was being directly tested).
+- Hyperedge.is_unordered_pattern().
+- Functional pattern: any.
+- Parser-level inference of coreferences between proper nouns.
+- Parser.parse_and_add() now adds token information to the main edge of a sentence: the attribute 'tokens' contains the list of tokens and 'tok_pos' a structure with the token position for each atom in the edge.
+- Post-processing step improves parser.
+- Hypergraph.get_attributes().
+
+### Changed
+- Entire project is now in pure Python
+- Python >=3.10 now required.
+- Hypergraph.search(), .match() and .count() now working with functional patterns and argument role matching.
+- Fixed bug on match_pattern(), variables were not correctly matched when argument roles were specified past the first position in an atoms functional pattern.
+- Simplified default systems connectors (breaks hypergraph DB backwards compatibility).
+- max_text argument in parser.parse_and_add().
+- Matches from patterns with repeated variables are collected in lists.
+
+### Removed
+- graphbrain.logic obsolete module.
+- LevelDB backend
+
+## [0.6.1] - 31-10-2022
+### Changed
+- Hyperedge.replace_argroles() .insert_argrole() and .insert_edge_with_argrole() now works with functional patterns such as var.
+- Fixed bug when matching patterns containing atoms functional pattern where no atom has argroles.
+
+### Removed
+- interactive_case_generator() from graphbrain.notebook.
+
+## [0.6.0] - 27-10-2022
+### Added
+- Hyperedge.atom and .not_atom properties.
+- Hyperedge.mtype() and .connector_mtype() methods.
+- Hyperedge.t, .mt, .ct and .cmt type shortcut properties.
+- Functional patterns: var, atoms, lemma.
+- Moved all patterns functions to graphbrain.patterns.
+- Hypergraph.text().
+- Parser.parse_and_add().
+- Parser.sentences().
+- Hyperedge.normalized().
+- New package graphbrain.readers, for text readers from various sources.
+- New package graphbrain.processors, for miscellaneous processors.
+- Processor class.
+
+### Changed
+- Coreference resolution now using the new spaCy experimental model.
+- Now using spaCy transformer GPU models by default, can fallback to CPU model.
+- Hyperedge.is_atom() deprecated.
+- Improved Hyperedge.main_concepts().
+- Hyperedge.atom() renamed to .inner_atom().
+- Sequences keep track of their size, no need to specify position when adding edge to sequence.
+- Improved wikipedia reader.
+- Improved coreference resolution.
+- LevelDB included by default again.
+- Old package graphbrain.meaning renamed to graphbrain.utils.
+- Hyperedge.argroles() now also works at relation/concept level.
+
+### Removed
+- graphbrain.patterns.normalize_edge().
+- graphbrain.stats obsolete package.
+- graphbrain.cognition obsolete package.
+- graphbrain.op obsolete module.
+- Hyperedge .predicate() and .predicate_atom().
+
+## [0.5.0] - 28-07-2021
+### Added
+- SQLite3 hypergraph database backend.
+- Hypergraph.add_with_attributes().
+- import and export commands.
+- Hypergraph context manager for batch writes (with hopen(hg_locator) as hg ...).
+
+### Changed
+- Main hypergraph database backend is now SQLite3.
+- LevelDB backend becomes optional. (disabled by default)
+- Neuralcoref becomes optional. (disabled by default)
+
+### Removed
+- Hypergraph.atom_count().
+- Hypergraph.edge_count().
+- Hypergraph.primary_atom_count().
+- Hypergraph.primary_edge_count().
+- info command.
+- corefs_unidecode agent.
+
+## [0.4.3] - 22-04-2021
+### Changed
+- Fixed AlphaBeta bug related to temporary atoms being removed too soon from atom2tokens.
+- Hypergraph.add_sequence() converts sequence name directly to atom.
+- Parser level coreference resolution (neuralcoref) disabled by default, requires dedicated build.
+
+## [0.4.2] - 12-04-2021
+### Changed
+- Solving wheel compilation issue.
+
+## [0.4.1] - 07-04-2021
+### Changed
+- Solving issue with inclusion of auxiliary data file in non-binary distributions.
+
+## [0.4.0] - 07-04-2021
+### Added
+- Agents system.
+- Conjunctions resolution agent.
+- Number agent (singular/plural relations) and related meaning.number module.
+- Wikipedia agent.
+- Coreference resolution in the parser through local fork of neuralcoref.
+- atom_gender(), atom_number(), atom_person(), atom_animacy() in parsers.
+- Coreference inference: gender, number and animacy.
+- Coreference inference:'X is Y' relationships.
+- dir_parser agent (looks for text files in directory tree).
+- Function meaning.concepts.has_common_or_proper_concept(edge).
+- Function Hypergraph.add() now has optional 'count' parameter.
+- Function Hypergraph.sequences().
+- Function Hyperedge.replace_argroles().
+- Function Hyperedge.insert_argrole().
+- Function Hyperedge.insert_edge_with_argrole().
+- Function Hyperedge.all_atoms().
+- Function Hyperedge.size().
+- Function Hyperedge.predicate().
+- Function Hyperedge.predicate_atom().
+- Function Hyperedge.simplify().
+- Function Hyperedge.connector_atom().
+- Utility functions to show colored edges in the terminal.
+
+### Changed
+- Special characters in atoms are now percent-encoded.
+- parse() now returns a dictionary that includes inferred edges.
+- parse() now returns a dictionary of edges to text.
+- New parser framework, improved English parser + scripts to help train and test new parsers.
+- Hyperedge main type character codes become upercase (apple/C instead of apple/c).
+- Conjunction hyperedge type, character code: "J" (e.g.: and/J).
+- Modifier hyperedge type can now be applied to anything.
+- Searching patterns can now include types, argument roles and other atom parts.
+- Hypergraph.search_count() renamed to Hypergraph.count().
+- corefs_names agent is simplified.
+- corefs_onto agent is simplified.
+- Tests now run with pytest instead of the deprecated './setup.py test'.
+- Hyperedge.replace_atom() optional unique argument.
+
+### Removed
+- Meta-modifier hyperedge type.
+- Auxiliary, subpredicate and dependency hyperedge types.
+- Obsolete Hyperedge.nest() method.
+
+## [0.3.2] - 10-02-2020
+### Added
+- simplify_role() on Atom objects produces an atom with only its simple type as role.
+
+### Changed
+- Lemmas are now based on atoms with simplified roles.
+- Improved actors agent (more accurate identification of actors, English only for now).
+
+## [0.3.1] - 03-02-2020
+### Added
+- German parser (experimental and incomplete).
+- Documentation.
+- Hyperedge sequences.
+
+### Changed
+- Improved hyperedge visualization in notebooks.
+- Agents receive language and sequence.
+- txt_parser agent creates a sequence.
+- Refactored parsers code.
+- Catching and logging exceptions during parse.
+- Improved conflict agent.
+
+## [0.3.0] - 28-09-2019
+### Added
+- Tests.
+- Documentation.
+
+### Changed
+- Graphbrain is now beta (main APIs considered stable).
+- LevelDB edge attributes encoded in JSON.
+- Renamed hypergraph() to hgraph() and moved function to __jnit__.
+- Fixed notebook examples.
+- Moved Hypergraph.lemma_degrees() to meaning.lemmas.
+- Argroles location is normalized (first position in both predicates and builders).
+- In the parsers package, create_parser() was moved to __init__ and the factory module was removed.
+- is_proper_concept() renamed to has_proper_concept() (meaning.concepts module).
+- find_concept() renamed to strip_concept() (meaning.concepts module).
+- Improved notebooks visualizations (show(), blocks(), vblocks()).
+
+### Removed
+- graphbrain.funs module.
+
+## [0.2.2] - 13-09-2019
+
+### Added
+- txt_parser agent.
+- MANIFEST.in to include VERSION file in distribution.
+
+### Changed
+- Fixing 'pip install graphbrain' on Linux/Windows.
+
+## [0.2.1] - 04-09-2019
+### Added
+- claim_actors and corefs_dets agents.
+- meaning.concepts module.
+
+### Changed
+- Fixed example.
+- hypergraph.sum_degree() and .sum_deep_degree().
+- Parser improvements.
+- Agent corefs_atoms is now corefs_unidecode.
+- Improved docs.
+
+### Removed
+- Obsolete 'work-in-progress' code.
+- hg2json command.
+
+## [0.2.0] - 04-08-2019
+### Added
+- Primary entities and deep degrees.
+- Hyperedges have their own class, deriving from tuple.
+- Atoms have a special class, deriving from Hyperedge.
+- Restructuring of code files tree.
+- Created agent system + first agents.
+
+### Changed
+- Parsers now have own package.
+
+### Removed
+- Old experimental code.
+
+## [0.1.0] - 14-06-2019
+### Added
+- First release.

hyperbase-0.8.0/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (C) 2026 CNRS - Centre national de la recherche scientifique
+
+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.

hyperbase-0.8.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hyperbase
+Version: 0.8.0
+Summary: A foundational library for Semantic Hypergraphs
+Project-URL: Homepage, https://hyperquest.ai/hyperbase
+Author-email: "Telmo Menezes et al." <telmo@telmomenezes.net>
+License-Expression: MIT
+License-File: AUTHORS
+License-File: LICENSE
+Keywords: AI,Cognition,Knowledge Representation,Knowledge Systems,NLP,Natural Language Understanding,Text Analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Python: >=3.10
+Requires-Dist: tqdm>=4.65.0
+Provides-Extra: dev
+Requires-Dist: coverage>=7.4.3; extra == 'dev'
+Requires-Dist: mkdocs-material>=9.5; extra == 'dev'
+Requires-Dist: mkdocstrings[python]>=0.24; extra == 'dev'
+Requires-Dist: mypy>=1.8.0; extra == 'dev'
+Requires-Dist: pre-commit>=3.6.2; extra == 'dev'
+Requires-Dist: ruff>=0.2.2; extra == 'dev'
+Requires-Dist: types-passlib>=1.7.7.20240106; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# Hyperbase
+
+## A foundational library for Semantic Hypergraphs
+
+Hyperbase is a foundational library for working with *Semantic Hypergraphs (SH)*, which make it possible to represent a natural language sentence such as "Einstein first published the theory of relativity in 1905" as an ordered, recursive hyperlink of the form:
+
+<figure markdown="span">
+  ![Einstein first published the Theory of Relativity in 1905.](assets/images/hyperedge-blocks.png){ width="75%" }
+</figure>
+
+Hyperbase is written in Python, to both take advantage and facilitate integration with the rich environment of scientific libraries available in this language. It is released under the highly permissive MIT open source license.
+
+## Installation and manual
+
+Installation instructions, the manual and more information can be found here: <https://hyperquest.ai/hyperbase>
+
+## Contributing
+
+Pull requests are welcome. For major changes, please open an issue first
+to discuss what you would like to change.
+
+Please make sure to update tests as appropriate.
+
+## Funding
+
+The creation of this software library and the associated research that made it possible were funded by CNRS and the ERC Consolidator
+Grant [Socsemics](https://socsemics.huma-num.fr/) (grant #772743).
+
+<a href="https://socsemics.huma-num.fr/" style="margin:0px">
+  <img src="docs/source/_static/socsemics.png" width="200">
+</a>
+
+## License
+
+[MIT](https://choosealicense.com/licenses/mit/)

hyperbase-0.8.0/README.md

@@ -0,0 +1,35 @@
+# Hyperbase
+
+## A foundational library for Semantic Hypergraphs
+
+Hyperbase is a foundational library for working with *Semantic Hypergraphs (SH)*, which make it possible to represent a natural language sentence such as "Einstein first published the theory of relativity in 1905" as an ordered, recursive hyperlink of the form:
+
+<figure markdown="span">
+  ![Einstein first published the Theory of Relativity in 1905.](assets/images/hyperedge-blocks.png){ width="75%" }
+</figure>
+
+Hyperbase is written in Python, to both take advantage and facilitate integration with the rich environment of scientific libraries available in this language. It is released under the highly permissive MIT open source license.
+
+## Installation and manual
+
+Installation instructions, the manual and more information can be found here: <https://hyperquest.ai/hyperbase>
+
+## Contributing
+
+Pull requests are welcome. For major changes, please open an issue first
+to discuss what you would like to change.
+
+Please make sure to update tests as appropriate.
+
+## Funding
+
+The creation of this software library and the associated research that made it possible were funded by CNRS and the ERC Consolidator
+Grant [Socsemics](https://socsemics.huma-num.fr/) (grant #772743).
+
+<a href="https://socsemics.huma-num.fr/" style="margin:0px">
+  <img src="docs/source/_static/socsemics.png" width="200">
+</a>
+
+## License
+
+[MIT](https://choosealicense.com/licenses/mit/)

hyperbase-0.8.0/VERSION

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+0.8.0

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hyperbase-0.8.0/docs/assets/stylesheets/extra.css

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+/* hyperquest.ai brand colors */
+:root,
+[data-md-color-scheme="default"] {
+  --md-primary-fg-color: #C2E3F6;
+  --md-primary-fg-color--light: #d4ecf9;
+  --md-primary-fg-color--dark: #a8d5f0;
+  --md-primary-bg-color: #10224D;
+  --md-accent-fg-color: #1a6d7d;
+  --md-accent-fg-color--transparent: rgba(26, 109, 125, 0.1);
+  --md-typeset-a-color: #1a6d7d;
+}
+
+[data-md-color-scheme="slate"] {
+  --md-primary-fg-color: #C2E3F6;
+  --md-primary-fg-color--light: #d4ecf9;
+  --md-primary-fg-color--dark: #a8d5f0;
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+  --md-typeset-a-color: #1a6d7d;
+}