Changelog#

All notable changes to atomRDF are documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.0.0] — Unreleased#

First stable release. The public API documented in docs/api.rst is now considered stable; breaking changes will require a major version bump.

If you are upgrading from 0.12.x (or older pyscal-rdf), please read the Migration guide — there are several breaking changes.

Added#

  • atomrdf.__version__ exposed at the top level (single source of truth in atomrdf/_version.py).

  • Public WorkflowParser (atomrdf.WorkflowParser) for ingesting external workflow descriptions.

  • Optional dependency groups so you only install what you use:

    • pip install "atomrdf[oxigraph]" — Oxigraph triple store backend

    • pip install "atomrdf[sqlalchemy]" — SQLAlchemy-backed store

    • pip install "atomrdf[materials_project]" — Materials Project lookups (mp-api)

    • pip install "atomrdf[grainboundary]" — aimsgb + pymatgen for grain boundaries

    • pip install "atomrdf[dislocation]" — atomman for dislocation builders

  • CI now tests Python 3.9 — 3.12 (was 3.11 only).

Changed#

  • Breaking — Activity field renaming. On Activity and all subclasses (notably Simulation):

    • initial_sample → input_sample

    • final_sample → output_sample

  • Breaking — Ontology IRI fix. The class emitted for crystalline materials is now cdco:CrystallineMaterial (it is defined in CDCO, not CMSO). Old graphs that use cmso:CrystallineMaterial will not be queryable with the new type. See Migration guide.

  • Breaking — Ontology IRI fix. LennardJonesPotential and TensileTest now emit the IRIs that actually exist in ASMO (asmo:Lennard-JonesPotential, asmo:Tensile_Test). The Python class names are unchanged.

  • Activity now accepts a graph= reference; string sample IDs are auto-resolved to AtomicScaleSample instances on assignment.

  • Library is now silent by default — internal print() calls in the GEXF exporter were replaced with the standard logging module.

  • Bare except: clauses replaced with typed exceptions plus debug logging in graph.py, properties.py, build/defect.py, datamodels/structure.py, datamodels/structure_io.py, datamodels/activity.py.

  • Dependency lists in setup.py, requirements.txt and environment.yml reconciled. networkx was dropped (unused). Lazy-imported packages (mp-api, aimsgb, pymatgen, atomman) moved to extras.

  • Project description and README rewritten for v1.0.

Removed#

  • Stale top-level index.ipynb (used a pre-KnowledgeGraph API). The book’s landing page is now index.md.

  • Dead/commented get_basis_occupancy in atomrdf/properties.py.

  • Unused import pickle in atomrdf/graph.py.

Fixed#

  • docs/api.rst no longer references modules that no longer exist (atomrdf.structure, atomrdf.network.network, atomrdf.workflow.workflow).

  • docs/license.md now refers to atomRDF (was still saying pyscal-rdf).

[0.12.3] and earlier#

See the GitHub release page for the change history of pre-1.0 versions.