openmaterica 0.1.0.dev1__tar.gz

openmaterica-0.1.0.dev1/LICENSE

@@ -0,0 +1,201 @@
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openmaterica-0.1.0.dev1/PKG-INFO

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+Metadata-Version: 2.4
+Name: openmaterica
+Version: 0.1.0.dev1
+Summary: Material records for simulation, and the reader of their specification
+License-Expression: Apache-2.0
+License-File: LICENSE
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+
+# OpenMaterica
+> *OpenMaterica* is an open material schema, with an OpenUSD binding, and a Python toolkit for biomedical
+> digital twins. It describes substances in and around the human body (tissues and body fluids, the media
+> and phantoms that stand in for them, agents introduced into them, and the materials of devices that enter
+> or touch them): their fluid, mechanical, acoustic, optical, thermal, dielectric, radiological and magnetic
+> properties, with the provenance and uncertainty of every value. It binds them to anatomical geometry, from
+> a one-dimensional layered path to a full USD scene. It aims to be one physical foundation for
+> high-fidelity solvers (like
+> [MIME](https://github.com/Microrobotics-Simulation-Framework/MIME)) and real-time simulators (like
+> [NVIDIA Isaac for Healthcare](https://github.com/isaac-for-healthcare)).
+>
+> Records are plain files any language can read; USD is the primary binding but never required. Model
+> parameter sets name a versioned model family and carry check points, so a solver that reads them in the
+> wrong convention fails loudly instead of silently.
+
+## Scope
+
+OpenMaterica describes substances, never systems: not an apparatus or its calibration, not the quantities of
+one object (its moment, inertia or mean density), not a drive, a procedure or a simulator's tuning. A value
+belongs here if it is a substance's, measured on a test specimen whose shape and size are recorded; a value
+of a made object as built (a device, an assembled robot) belongs to its consumer.
+Geometry is scene data: OpenMaterica defines how geometry binds to materials and ships small test phantoms,
+never anatomy. Other publishers can use the same machinery in their own namespaces, for data OpenMaterica does
+not curate. The full statement is in [`docs/regulatory/intended_use.md`](docs/regulatory/intended_use.md).
+
+## Status
+
+Design stage. There is no code or release yet. The architecture concept is in
+[`design/ARCHITECTURE_DRAFT.md`](design/ARCHITECTURE_DRAFT.md).
+
+## Intended use and disclaimers
+
+> **OpenMaterica is research software.** It is not a medical device as defined by EU MDR (EU 2017/745) or US
+> FDA regulations. It has no medical purpose and has not been CE-marked, cleared or approved by any regulatory
+> body. When used as a component within regulated medical software, OpenMaterica is SOUP (Software of Unknown
+> Provenance) under IEC 62304, and the device manufacturer is responsible for assessing its suitability.
+>
+> Material values in the OpenMaterica library are taken from cited sources, or are fits to cited data. They
+> are not measurements of any particular patient, sample or device; each record states the specimen it was
+> measured on, and whether that specimen stands in for yours is your declaration, not the library's.
+> Biocompatibility fields are never a safety claim. See
+> [`docs/regulatory/intended_use.md`](docs/regulatory/intended_use.md).
+
+## Documentation
+
+| Document | Description |
+|---|---|
+| [design/ARCHITECTURE_DRAFT.md](design/ARCHITECTURE_DRAFT.md) | Architecture concept: components, data model, model families, geometry and USD binding, library and licensing, MIME and Isaac for Healthcare interfaces |
+| [DOCUMENTATION_ARCHITECTURE.md](DOCUMENTATION_ARCHITECTURE.md) | How OpenMaterica is documented and verified, and its SOUP readiness |
+| [CONTRIBUTING.md](CONTRIBUTING.md) | Project constraints (including commit sign-off), code rules, identifiers, family and data rules, data attestation, takedown, anomaly lifecycle |
+| [SECURITY.md](SECURITY.md) | Vulnerability reporting |
+| [CHANGELOG.md](CHANGELOG.md) | Version history |
+| [docs/regulatory/](docs/regulatory/) | Intended use and regulatory boundary |
+| [docs/validation/](docs/validation/) | Known anomalies registry |
+
+## License
+
+Code: Apache License 2.0. See [LICENSE](LICENSE). The curated material library will be released
+separately, as static archived releases with a DOI, under CC0-1.0.

openmaterica-0.1.0.dev1/README.md

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+# OpenMaterica
+> *OpenMaterica* is an open material schema, with an OpenUSD binding, and a Python toolkit for biomedical
+> digital twins. It describes substances in and around the human body (tissues and body fluids, the media
+> and phantoms that stand in for them, agents introduced into them, and the materials of devices that enter
+> or touch them): their fluid, mechanical, acoustic, optical, thermal, dielectric, radiological and magnetic
+> properties, with the provenance and uncertainty of every value. It binds them to anatomical geometry, from
+> a one-dimensional layered path to a full USD scene. It aims to be one physical foundation for
+> high-fidelity solvers (like
+> [MIME](https://github.com/Microrobotics-Simulation-Framework/MIME)) and real-time simulators (like
+> [NVIDIA Isaac for Healthcare](https://github.com/isaac-for-healthcare)).
+>
+> Records are plain files any language can read; USD is the primary binding but never required. Model
+> parameter sets name a versioned model family and carry check points, so a solver that reads them in the
+> wrong convention fails loudly instead of silently.
+
+## Scope
+
+OpenMaterica describes substances, never systems: not an apparatus or its calibration, not the quantities of
+one object (its moment, inertia or mean density), not a drive, a procedure or a simulator's tuning. A value
+belongs here if it is a substance's, measured on a test specimen whose shape and size are recorded; a value
+of a made object as built (a device, an assembled robot) belongs to its consumer.
+Geometry is scene data: OpenMaterica defines how geometry binds to materials and ships small test phantoms,
+never anatomy. Other publishers can use the same machinery in their own namespaces, for data OpenMaterica does
+not curate. The full statement is in [`docs/regulatory/intended_use.md`](docs/regulatory/intended_use.md).
+
+## Status
+
+Design stage. There is no code or release yet. The architecture concept is in
+[`design/ARCHITECTURE_DRAFT.md`](design/ARCHITECTURE_DRAFT.md).
+
+## Intended use and disclaimers
+
+> **OpenMaterica is research software.** It is not a medical device as defined by EU MDR (EU 2017/745) or US
+> FDA regulations. It has no medical purpose and has not been CE-marked, cleared or approved by any regulatory
+> body. When used as a component within regulated medical software, OpenMaterica is SOUP (Software of Unknown
+> Provenance) under IEC 62304, and the device manufacturer is responsible for assessing its suitability.
+>
+> Material values in the OpenMaterica library are taken from cited sources, or are fits to cited data. They
+> are not measurements of any particular patient, sample or device; each record states the specimen it was
+> measured on, and whether that specimen stands in for yours is your declaration, not the library's.
+> Biocompatibility fields are never a safety claim. See
+> [`docs/regulatory/intended_use.md`](docs/regulatory/intended_use.md).
+
+## Documentation
+
+| Document | Description |
+|---|---|
+| [design/ARCHITECTURE_DRAFT.md](design/ARCHITECTURE_DRAFT.md) | Architecture concept: components, data model, model families, geometry and USD binding, library and licensing, MIME and Isaac for Healthcare interfaces |
+| [DOCUMENTATION_ARCHITECTURE.md](DOCUMENTATION_ARCHITECTURE.md) | How OpenMaterica is documented and verified, and its SOUP readiness |
+| [CONTRIBUTING.md](CONTRIBUTING.md) | Project constraints (including commit sign-off), code rules, identifiers, family and data rules, data attestation, takedown, anomaly lifecycle |
+| [SECURITY.md](SECURITY.md) | Vulnerability reporting |
+| [CHANGELOG.md](CHANGELOG.md) | Version history |
+| [docs/regulatory/](docs/regulatory/) | Intended use and regulatory boundary |
+| [docs/validation/](docs/validation/) | Known anomalies registry |
+
+## License
+
+Code: Apache License 2.0. See [LICENSE](LICENSE). The curated material library will be released
+separately, as static archived releases with a DOI, under CC0-1.0.

openmaterica-0.1.0.dev1/pyproject.toml

@@ -0,0 +1,86 @@
+[build-system]
+requires = ["uv_build>=0.13.0,<0.14"]
+build-backend = "uv_build"
+
+[project]
+name = "openmaterica"
+version = "0.1.0.dev1"
+description = "Material records for simulation, and the reader of their specification"
+readme = "README.md"
+requires-python = ">=3.11"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+dependencies = []
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Programming Language :: Python :: 3",
+    "Typing :: Typed",
+]
+
+[dependency-groups]
+dev = [
+    "datamodel-code-generator==0.83.0",
+    "hypothesis>=6.140",
+    "jsonschema>=4.26",
+    "mypy>=1.18",
+    "pyright==1.1.414",
+    "pytest>=8.4",
+    "pytest-xdist>=3.8",
+    "rfc8785>=0.1.4",
+    "ruff>=0.13",
+    "types-jsonschema>=4.26",
+]
+fuzz = ["atheris==3.1.0; sys_platform == 'linux' and platform_machine == 'x86_64' and platform_python_implementation == 'CPython' and python_version >= '3.12' and python_version < '3.15'"]
+
+[tool.uv.build-backend]
+module-name = "materica"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = [
+    "-ra",
+    "--strict-markers",
+    "--strict-config",
+]
+xfail_strict = true
+markers = ["features: the least share of a property's examples that must show each feature (tests/property/audits.py)"]
+filterwarnings = ["error"]
+
+[tool.mypy]
+python_version = "3.11"
+strict = true
+files = [
+    "src/materica",
+    "tests",
+    "scripts",
+]
+mypy_path = "typings"
+
+[tool.pyright]
+include = [
+    "src/materica",
+    "tests",
+    "scripts",
+]
+pythonVersion = "3.11"
+typeCheckingMode = "strict"
+
+[tool.ruff]
+include = [
+    "*.py",
+    "*.pyi",
+]
+line-length = 110
+target-version = "py311"
+
+[tool.ruff.lint]
+select = [
+    "E",
+    "F",
+    "W",
+    "I",
+    "B",
+    "UP",
+    "RUF",
+    "PT",
+]

openmaterica-0.1.0.dev1/pyproject.toml.orig

@@ -0,0 +1,74 @@
+[build-system]
+requires = ["uv_build>=0.13.0,<0.14"]
+build-backend = "uv_build"
+
+[project]
+name = "openmaterica"
+version = "0.1.0.dev1"
+description = "Material records for simulation, and the reader of their specification"
+readme = "README.md"
+requires-python = ">=3.11"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+dependencies = []
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Programming Language :: Python :: 3",
+    "Typing :: Typed",
+]
+
+[dependency-groups]
+dev = [
+    # Writes src/materica/shapes.py, which CI checks byte for byte, so pinned; it does not run on Python 3.15.
+    "datamodel-code-generator==0.83.0",
+    "hypothesis>=6.140",
+    "jsonschema>=4.26",
+    "mypy>=1.18",
+    # The release MADDENING's CI pins.
+    "pyright==1.1.414",
+    "pytest>=8.4",
+    "pytest-xdist>=3.8",
+    "rfc8785>=0.1.4",
+    "ruff>=0.13",
+    "types-jsonschema>=4.26",
+]
+# Atheris 3.1.0 publishes wheels for CPython 3.12 to 3.14 on Linux x86_64 only, and no source distribution, so
+# it installs only there; `uv sync` and `uv sync --group fuzz` work everywhere else without it.
+fuzz = [
+    "atheris==3.1.0; sys_platform == 'linux' and platform_machine == 'x86_64' and platform_python_implementation == 'CPython' and python_version >= '3.12' and python_version < '3.15'",
+]
+
+# The distribution is `openmaterica` and the package it installs `materica`; without this, uv_build looks for
+# `src/openmaterica`.
+[tool.uv.build-backend]
+module-name = "materica"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = ["-ra", "--strict-markers", "--strict-config"]
+xfail_strict = true
+markers = [
+    "features: the least share of a property's examples that must show each feature (tests/property/audits.py)",
+]
+filterwarnings = ["error"]
+
+[tool.mypy]
+python_version = "3.11"
+strict = true
+files = ["src/materica", "tests", "scripts"]
+# Development-only stubs for libraries that ship no types (pyright reads the same directory by default).
+mypy_path = "typings"
+
+[tool.pyright]
+include = ["src/materica", "tests", "scripts"]
+pythonVersion = "3.11"
+typeCheckingMode = "strict"
+
+[tool.ruff]
+# Python only: ruff also formats code blocks in Markdown, which would rewrite the specification's examples.
+include = ["*.py", "*.pyi"]
+line-length = 110
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["E", "F", "W", "I", "B", "UP", "RUF", "PT"]

openmaterica-0.1.0.dev1/src/materica/README.md

@@ -0,0 +1,33 @@
+# `materica`
+
+The Python package. It implements the reader side of the OpenMaterica specification (`docs/specification/`).
+The specification is normative: where this code and it differ, the code is wrong.
+
+## Layers
+
+The package is built in layers (AD 7.1), and a module imports only from its own layer or a lower one.
+
+| Layer | Directory | What it holds |
+|---|---|---|
+| L0, schemas | `schema/`, `shapes.py` | the JSON Schemas (`schema/README.md`), and the JSON shapes as TypedDicts generated from them |
+| L1, data | `data/`, `schema/0.1/vocabulary/` | the specification's conformance cases and the inputs they supply (`data/conformance/`, with their own `README.md`), and its vocabulary, published with the schemas |
+| L2, core | `core/` | strict JSON, the canonical form and the content hash; identifiers, the envelope checks and the read up to step 5; Python's standard library only (`core/README.md`) |
+| L4, readers | `io/` | files into the core's types (`io/README.md`) |
+
+The authoring tools (L3), the sampling helpers (`sample/`, L5) and the command line (`tools/`, L6) arrive in
+later steps. `tests/unit/test_source_files.py` walks every module's imports: a module imports only its own
+layer or a lower one; `core/` imports only the standard library, itself and `shapes.py`, which imports only the
+standard library; and nothing imports `materica_authoring`.
+
+## What holds across the package
+
+- No run-time dependency (AD 7.2): the built wheel declares none (`scripts/check_wheel.py`).
+- It is typed (PEP 561) and ships `py.typed`. `mypy --strict` and pyright in strict mode pass over it, and a
+  consumer's code type-checks against the installed wheel (`tests/typing/`). `shapes.pyi`, which type checkers
+  read in place of `shapes.py`, marks what a read returns read-only (PEP 705).
+- Everything under `data/` and `schema/` ships in the wheel byte for byte, since the conformance inputs are
+  byte-exact and the reader loads the vocabulary (`scripts/check_wheel.py`).
+- Generated files are never edited by hand. `scripts/` regenerates them and CI fails on any difference: the
+  vocabulary from the specification's tables, the reader schema and the shapes from the writer schemas
+  (CONTRIBUTING, "Changing the schema").
+- `__init__.py` holds the public API built so far: `content_hash`, `load_records` and `read`.

openmaterica-0.1.0.dev1/src/materica/__init__.py

@@ -0,0 +1,8 @@
+# SPDX-License-Identifier: Apache-2.0
+"""OpenMaterica: material records and the reader of their specification (`docs/specification/`)."""
+
+from materica.core.hashing import content_hash
+from materica.core.read import read
+from materica.io.plain import load_records
+
+__all__ = ["content_hash", "load_records", "read"]

openmaterica-0.1.0.dev1/src/materica/core/README.md

@@ -0,0 +1,72 @@
+# `materica.core`
+
+The core (layer L2, AD 7.1): the code that reads and checks records. It uses Python's standard library only
+(AD 7.2, CONTRIBUTING constraint 3), so it adds nothing to a consumer's dependencies; the shapes it types its
+results with (`materica.shapes`, generated) use the standard library only too.
+
+## The data paths
+
+The content hash:
+
+```
+bytes ─▶ jsonio.parse ─▶ value ─▶ hashing.hashable_view ─▶ view ─▶ canonical.canonicalize ─▶ bytes ─▶ SHA-256
+            │                       (hashing.content_hash runs these three, and writes "sha256:<hex>")
+            └─▶ Reason("malformed")
+```
+
+A read, steps 0 to 5 of `read_side_contract.md` section 3:
+
+```
+request ─▶ read.ReadRequest.from_json ─▶ step 0, the request on its own ─▶ reasons, or a ReadRequest
+                                                                                │
+sources ─▶ record.RecordStore.add ─▶ candidates by id and version,              ▼
+           and the unreadable sources                      resolve.resolve_record
+                                                           1 the candidate that states the pin
+                                                           2 its schema version     ┐
+                                                           3 envelope.py's checks   ├ kept on the Record
+                                                           5 its type               ┘
+                                                           4 the hash, with HS: recomputed on every read,
+                                                             between steps 3 and 5
+                                                                  │
+               read.ReadResult (status, reasons, labels) ◀────────┘   or NotImplementedError for steps 6 to 13
+```
+
+| Module | Implements |
+|---|---|
+| `reasons.py` | a reason as `read_side_contract.md` section 2 shapes it, each code and condition once; codes from the table in section 4 |
+| `status.py` | the three statuses of a read, and the worst of several (section 2) |
+| `jsonio.py` | `record_format.md` section 1 item 6, strict JSON; `JsonValue`, the type of what it reads |
+| `canonical.py` | `record_format.md` section 9 item 2: RFC 8785, with no Unicode normalisation |
+| `hashing.py` | `record_format.md` section 9 items 1 and 2: what the hash leaves out, and the hash |
+| `identifiers.py` | `record_format.md` sections 7 and 8: identifiers and versions, matched in full; material references |
+| `vocabulary.py` | the tokens of the specification's tables, read from `schema/0.1/vocabulary/` |
+| `envelope.py` | the reader schema's checks by hand (`record_format.md` section 1 item 2) |
+| `record.py` | the records a read resolves among, and the checks that depend on one record alone (steps 2, 3 and 5) |
+| `resolve.py` | steps 1 to 5: a material reference to the record it pins, or the reasons it is refused |
+| `read.py` | the request's own check (step 0), and the read; steps 6 to 13 are not built yet |
+
+The conformance cases HS-001 to HS-003 check the hash end to end; the plain-read cases, HS-010 and HS-011 the
+read up to step 5 (`tests/conformance/`).
+
+## Invariants
+
+- **Results, never exceptions, for content.** `parse` gives a value or `malformed` for any bytes, running out
+  of stack or memory included, and a read gives a result for any request and any records. An exception means
+  a misuse of the Python API (`canonicalize` given a value `parse` would never give; claims no reader makes, a
+  suite that does not exist or claims without plain read) or a step not built yet: a read whose answer a later
+  step would decide raises `NotImplementedError` rather than give one, whatever else is wrong with the request
+  (`tests/property/test_read_properties.py`, `tests/unit/test_read.py`).
+- **A request is JSON text or a value.** Text is a `str` or bytes-like (`bytes`, `bytearray`, `memoryview`),
+  read like a record's bytes; a `str` is always text, as a JSON string is never a request. Any other value is
+  read as the JSON text `json.dumps` writes of it.
+- **Every number is a float.** An integer reads as the nearest double; `JsonValue` has no `int`, and
+  `canonicalize` refuses one. A request given as a Python value is read through JSON text, so its integers too.
+  (The reader's properties compare types exactly; `tests/unit/test_canonical.py`.)
+- **Stored JSON is never mutated.** `hashable_view` builds new containers and leaves its argument as it was
+  (`tests/unit/test_hashing.py`); a `Record` keeps the value its bytes parse to as it is.
+- **Identifiers match in full**, by `re.fullmatch` with character classes written out
+  (`tests/property/test_version_properties.py`).
+- **One envelope check, in two forms.** `envelope.py` and `schema/0.1/record.reader.json` accept and refuse
+  the same records (`tests/spec_sync/test_envelope.py`, `tests/property/test_envelope_properties.py`).
+- **Standard library only**, with `materica.shapes`, itself standard library only, and, for type checkers
+  only, `typing_extensions`; relative imports are checked like absolute ones (`tests/unit/test_source_files.py`).

openmaterica-0.1.0.dev1/src/materica/core/__init__.py

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+# SPDX-License-Identifier: Apache-2.0
+"""The core (layer L2, AD 7.1): Python's standard library only (AD 7.2, CONTRIBUTING constraint 3)."""