From 4dd3a767b4c3424c77d219a8a773e2a6e12d5335 Mon Sep 17 00:00:00 2001 From: Daniel Ari Friedman Date: Tue, 22 Sep 2026 12:02:10 -0700 Subject: [PATCH] chore: repoint legacy repository URLs after org migration --- cogant/docs/evaluation/GNN_VALIDATION_REPORT.md | 6 +++--- cogant/examples/demo_server.py | 2 +- cogant/py/cogant/__init__.py | 2 +- cogant/py/cogant/schemas/gnn_export.py | 2 +- cogant/pyproject.toml | 2 +- cogant/rust/cogant-gnn/src/lib.rs | 2 +- cogant/tests/unit/test_gnn_spec_compliance.py | 2 +- cogant/uv.lock | 4 ++-- manuscript/01_introduction.md | 2 +- manuscript/references.bib | 2 +- 10 files changed, 13 insertions(+), 13 deletions(-) diff --git a/cogant/docs/evaluation/GNN_VALIDATION_REPORT.md b/cogant/docs/evaluation/GNN_VALIDATION_REPORT.md index d70b64e..44da527 100644 --- a/cogant/docs/evaluation/GNN_VALIDATION_REPORT.md +++ b/cogant/docs/evaluation/GNN_VALIDATION_REPORT.md @@ -14,9 +14,9 @@ Date: 2026-06-12 ## Spec Source -- Primary: https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation/blob/main/doc/gnn/gnn_syntax.md -- Type-checker: https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation/blob/main/src/type_checker/checker.py -- Examples: https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation/tree/main/input/gnn_files/discrete/ +- Primary: https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation/blob/main/doc/gnn/gnn_syntax.md +- Type-checker: https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation/blob/main/src/type_checker/checker.py +- Examples: https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation/tree/main/input/gnn_files/discrete/ ## Compliance Check diff --git a/cogant/examples/demo_server.py b/cogant/examples/demo_server.py index 45207e7..6d1accc 100644 --- a/cogant/examples/demo_server.py +++ b/cogant/examples/demo_server.py @@ -74,7 +74,7 @@ # Public documentation URL. ``GET /docs`` redirects here when FastAPI's # built-in OpenAPI UI is not available. -COGANT_DOCS_URL = "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation" +COGANT_DOCS_URL = "https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation" logger = logging.getLogger("cogant.demo_server") diff --git a/cogant/py/cogant/__init__.py b/cogant/py/cogant/__init__.py index 00509eb..774c3c8 100644 --- a/cogant/py/cogant/__init__.py +++ b/cogant/py/cogant/__init__.py @@ -3,7 +3,7 @@ Translates software repositories into Generalized Notation Notation (GNN) — the Active Inference Institute's structured state-space / process-model notation (NOT graph neural networks). See -https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation. +https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation. The output of a COGANT run is a GNN-compatible model bundle: hidden states, observation modalities, actions, policies, transitions, likelihoods, diff --git a/cogant/py/cogant/schemas/gnn_export.py b/cogant/py/cogant/schemas/gnn_export.py index 3face0f..a781bfc 100644 --- a/cogant/py/cogant/schemas/gnn_export.py +++ b/cogant/py/cogant/schemas/gnn_export.py @@ -2,7 +2,7 @@ GNNExportBundle: Comprehensive export format for Generalized Notation Notation (GNN). "GNN" here refers to the Active Inference Institute's Generalized Notation Notation -(https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation), a structured +(https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation), a structured notation for Active Inference state-space and process models — not graph neural networks. Packages all analysis artifacts (graph structure, semantic mappings, state space, diff --git a/cogant/pyproject.toml b/cogant/pyproject.toml index 36541fa..dc6c207 100644 --- a/cogant/pyproject.toml +++ b/cogant/pyproject.toml @@ -64,7 +64,7 @@ analytics = [ "duckdb>=0.9", ] upstream = [ - "generalized-notation-notation @ git+https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation.git@11a89f0615f1e48ddacca58d1bcf3c5092b1b055", + "generalized-notation-notation @ git+https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation.git@11a89f0615f1e48ddacca58d1bcf3c5092b1b055", ] all = [ "pytest>=7.4.0", diff --git a/cogant/rust/cogant-gnn/src/lib.rs b/cogant/rust/cogant-gnn/src/lib.rs index 0af23e1..07789b9 100644 --- a/cogant/rust/cogant-gnn/src/lib.rs +++ b/cogant/rust/cogant-gnn/src/lib.rs @@ -1,7 +1,7 @@ //! GNN export and formatting. //! //! "GNN" in COGANT refers to the Active Inference Institute's Generalized -//! Notation Notation (https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation), +//! Notation Notation (https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation), //! a structured notation for Active Inference state-space and process models — //! NOT graph neural networks. This crate provides functionality for exporting //! program graphs into that notation. diff --git a/cogant/tests/unit/test_gnn_spec_compliance.py b/cogant/tests/unit/test_gnn_spec_compliance.py index 72cde04..5b58763 100644 --- a/cogant/tests/unit/test_gnn_spec_compliance.py +++ b/cogant/tests/unit/test_gnn_spec_compliance.py @@ -7,7 +7,7 @@ 2. Connections section uses bare variable names without parentheses. 3. No duplicate ``## Connections`` header (COGANT extended section renamed). -Spec source: https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation +Spec source: https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation doc/gnn/reference/gnn_syntax.md v2.0.0 Upstream type-checker: src/type_checker/checker.py diff --git a/cogant/uv.lock b/cogant/uv.lock index 97e0457..8cc5b1a 100644 --- a/cogant/uv.lock +++ b/cogant/uv.lock @@ -471,7 +471,7 @@ requires-dist = [ { name = "duckdb", marker = "extra == 'all'", specifier = ">=0.9" }, { name = "duckdb", marker = "extra == 'analytics'", specifier = ">=0.9" }, { name = "fastapi", specifier = ">=0.135.3" }, - { name = "generalized-notation-notation", marker = "extra == 'upstream'", git = "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation.git?rev=11a89f0615f1e48ddacca58d1bcf3c5092b1b055" }, + { name = "generalized-notation-notation", marker = "extra == 'upstream'", git = "https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation.git?rev=11a89f0615f1e48ddacca58d1bcf3c5092b1b055" }, { name = "httpx", specifier = ">=0.27" }, { name = "hypothesis", marker = "extra == 'dev'", specifier = ">=6.0" }, { name = "jinja2", marker = "extra == 'all'", specifier = ">=3.0.0" }, @@ -1187,7 +1187,7 @@ wheels = [ [[package]] name = "generalized-notation-notation" version = "2.0.0" -source = { git = "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation.git?rev=11a89f0615f1e48ddacca58d1bcf3c5092b1b055#11a89f0615f1e48ddacca58d1bcf3c5092b1b055" } +source = { git = "https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation.git?rev=11a89f0615f1e48ddacca58d1bcf3c5092b1b055#11a89f0615f1e48ddacca58d1bcf3c5092b1b055" } dependencies = [ { name = "aiohttp" }, { name = "bnlearn" }, diff --git a/manuscript/01_introduction.md b/manuscript/01_introduction.md index a0fe06b..294be0a 100644 --- a/manuscript/01_introduction.md +++ b/manuscript/01_introduction.md @@ -6,7 +6,7 @@ The contribution is best read as an **evidence compiler** rather than as a new n ## Terminology: "GNN" in this manuscript -In this manuscript, **GNN** refers to the Active Inference Institute's **Generalized Notation Notation** ([repository](https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation)) [@friedman2024gnn], a structured notation for state-space and process models---*not* graph neural networks. COGANT translates source code into this notation, producing program-graph and state-space artifacts (state space, observation modalities, actions/policies, likelihood structure, preferences, time settings, parameterization) that downstream tools can consume. Those downstream tools include graph neural network training pipelines, which can ingest the exported tensor views of the program graph, but such neural networks are a *consumer* of COGANT's output, not its output format. Where the manuscript discusses graph neural networks as related work, it uses the phrase "graph neural networks" in full; the acronym GNN always refers to Generalized Notation Notation. +In this manuscript, **GNN** refers to the Active Inference Institute's **Generalized Notation Notation** ([repository](https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation)) [@friedman2024gnn], a structured notation for state-space and process models---*not* graph neural networks. COGANT translates source code into this notation, producing program-graph and state-space artifacts (state space, observation modalities, actions/policies, likelihood structure, preferences, time settings, parameterization) that downstream tools can consume. Those downstream tools include graph neural network training pipelines, which can ingest the exported tensor views of the program graph, but such neural networks are a *consumer* of COGANT's output, not its output format. Where the manuscript discusses graph neural networks as related work, it uses the phrase "graph neural networks" in full; the acronym GNN always refers to Generalized Notation Notation. ## How to read this document diff --git a/manuscript/references.bib b/manuscript/references.bib index dca22c7..09f0cf6 100644 --- a/manuscript/references.bib +++ b/manuscript/references.bib @@ -366,7 +366,7 @@ @misc{friedman2024gnn title = {Generalized Notation Notation (GNN): A structured notation for Active Inference state-space and process models}, author = {{Active Inference Institute}}, year = {2024}, - howpublished = {\url{https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation}}, + howpublished = {\url{https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation}}, note = {Open-source specification and reference implementation; not to be confused with graph neural networks} }