Merge branch 'rename' into 'main'

BASALT renaming

See merge request MoNET/analysis-api-schema!55

Author: corilo

.copier-answers.yml

@@ -4,13 +4,13 @@ _src_path: gh:linkml/linkml-project-copier
 add_example: false
 copyright_year: '2026'
 email: maia.kapur@pnnl.gov
-existing_license_file: ''
+existing_license_file: 'LICENSE'
 full_name: Maia Kapur
 gh_action_docs_preview: true
 gh_action_pypi: false
 github_org: mkapur-pnnl
 license: MIT
 project_description: Data schema for analysis database at EMSL (PNNL).
-project_name: analysis-api-schema
-project_slug: analysis_api_schema
+project_name: basalt-schema
+project_slug: basalt_schema
 

CONTRIBUTING.md

@@ -1,9 +1,9 @@
-# Contributing to analysis-api-schema
+# Contributing to BASALT
 
 :+1: First of all: Thank you for taking the time to contribute!
 
 The following is a set of guidelines for contributing to
-analysis-api-schema. These guidelines are not strict rules.
+BASALT. These guidelines are not strict rules.
 Use your best judgment, and feel free to propose changes to this document
 in a pull request.
 
@@ -22,7 +22,7 @@ in a pull request.
 
 ## Code of Conduct
 
-The analysis-api-schema team strives to create a
+The BASALT team strives to create a
 welcoming environment for editors, users and other contributors.
 Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
 
@@ -73,7 +73,7 @@ Please submit a [Pull Request][pulls] to submit a new term for consideration.
     - Never work on the main branch, always work on an issue/feature branch
     - Core developers can work on branches off origin rather than forks
     - Always create a PR on a branch to maximize transparency of what you are doing
-    - PRs should be reviewed and merged in a timely fashion by the analysis-api-schema technical leads
+    - PRs should be reviewed and merged in a timely fashion by the BASALT technical leads
     - PRs that do not pass GitHub actions should never be merged
     - In the case of git conflicts, the contributor should try and resolve the conflict
     - If a PR fails a GitHub action check, the contributor should try and resolve the issue in a timely fashion
@@ -115,7 +115,7 @@ Core developers should read the material on the [LinkML site](https://linkml.io/
 [about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
 [about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
 [about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
-[issues]: https://github.com/mkapur-pnnl/analysis-api-schema/issues/
-[pulls]: https://github.com/mkapur-pnnl/analysis-api-schema/pulls/
+[issues]: https://github.com/EMSL-Computing/basalt-schema/issues/
+[pulls]: https://github.com/EMSL-Computing/basalt-schema/pulls/
 
 We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)

LICENSE

@@ -1,21 +1,6 @@
-The MIT License (MIT)
-
-Copyright (c) 2026 Maia Kapur
-
-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.
+Released under the Creative Commons 0 Public Domain Dedication:
+https://creativecommons.org/publicdomain/zero/1.0/
+ 
+This material is free to use, and attribution is always appreciated.  Attribution may be as follows:
+Authored by Conrad Mearns, Maia Kapur, Montana Smith, Beata Meluch, Aramy Truong, and Yuri E. Corilo at the Pacific Northwest National Laboratory, operated by Battelle for the U.S. Department of Energy.
+Please cite the following in your work: (Place Holder Zenodo)

README.md

@@ -1,28 +1,82 @@
-# analysis-api-schema
+# BASALT
 
-LinkML for the EMSL Science Cental MONet Analysis API schemas
+**Broad Analytical Schema for Samples and Laboratory Techniques**
+
+[![Schema version](https://img.shields.io/badge/schema-v0.1.0-blue.svg)](src/basalt_schema/schema/basalt_schema.yaml)
+[![LinkML](https://img.shields.io/badge/LinkML-schema-blueviolet.svg)](https://linkml.io)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org)
+[![License: CC0-1.0](https://img.shields.io/badge/license-CC0%201.0-lightgrey.svg)](LICENSE)
+[![Docs](https://img.shields.io/badge/docs-GitHub%20Pages-informational.svg)](https://EMSL-Computing.github.io/basalt-schema)
+
+LinkML schema for MONet/EMSL scientific data across **biogeochemical**, **biological**, and **environmental** domains. Canonical source of truth for samples, provenance, laboratory activities, and analytical products used by the Analysis API and database models.
+
+Formerly `analysis-api-schema`.
+
+| | |
+| --- | --- |
+| **Schema version** | `0.1.0` (see `version` in [`basalt_schema.yaml`](src/basalt_schema/schema/basalt_schema.yaml)) |
+| **Package** | `basalt_schema` (Python package version follows git tags via uv-dynamic-versioning) |
+| **Docs** | https://EMSL-Computing.github.io/basalt-schema |
+| **Repository** | https://github.com/EMSL-Computing/basalt-schema |
+| **Canonical URI** | https://EMSL-Computing.github.io/basalt-schema |
 
 ## Repository Structure
 
 * [examples/](examples/) - example data
 * [project/](project/) - project files (do not edit these)
 * [src/](src/) - source files (edit these)
-  * [analysis_api_schema](src/analysis_api_schema)
-    * [schema](src/analysis_api_schema/schema) -- LinkML schema
-    * [datamodel](src/analysis_api_schema/datamodel) -- generated
+  * [basalt_schema](src/basalt_schema)
+    * [schema](src/basalt_schema/schema) -- LinkML schema
+    * [datamodel](src/basalt_schema/datamodel) -- generated
 * [tests/](tests/) - Python tests
 * [util/](util/) - Adhoc LinkML replacement code
 
-## Developer Documentation
+## Versioning
+
+BASALT uses **semantic versioning** (`MAJOR.MINOR.PATCH`) for the schema:
+
+| Change type | Bump | Examples |
+| --- | --- | --- |
+| **MAJOR** | Breaking model changes | Rename/remove classes or required slots; change identifiers; incompatible range changes |
+| **MINOR** | Backward-compatible additions | New optional classes/slots/enums; new modules; expanded permissible values |
+| **PATCH** | Non-breaking fixes | Description/docs fixes; typo corrections; generator/tooling-only fixes that do not change the model |
+
+### How versions are recorded
+
+1. **Schema version (authoritative for the data model)**  
+   Set in the root schema file:
+   ```yaml
+   # src/basalt_schema/schema/basalt_schema.yaml
+   version: 0.1.0
+   ```
 
-Windows and Powershell users:
+2. **Python package version**  
+   Derived from **git tags** (`v0.1.0`, `v0.2.0`, …) via [uv-dynamic-versioning](https://github.com/ninoseki/uv-dynamic-versioning).  
+   Installable package name: `basalt_schema`.
+
+3. **Release checklist**
+   - [ ] Bump `version` in `src/basalt_schema/schema/basalt_schema.yaml`
+   - [ ] Update the schema version badge / table in this README
+   - [ ] Regenerate project artifacts if needed (`just gen-project`)
+   - [ ] Merge to `main`
+   - [ ] Tag the release: `git tag -a v0.1.0 -m "basalt-schema 0.1.0"` and push tags
+   - [ ] Consumers pin or track the tag / package version
+
+Consumers (API, DB migrations, ingestion) should record which schema version they were built against.
+
+## Developer Documentation
 
 ```bash
 uv sync
-
 just gen-project
 ```
 
+Windows and PowerShell users can use the same commands when `uv` and `just` are installed.
+
 ## Credits
 
-This project was made with `LinkML`
+This material is free to use, and attribution is always appreciated. Attribution may read as follows:
+
+Authored by Conrad Mearns, Maia Kapur, Montana Smith, Beata Meluch, Aramy Truong, and Yuri E. Corilo at the Pacific Northwest National Laboratory, operated by Battelle for the U.S. Department of Energy.
+
+(Optional, if applicable): Please cite the following in your work: (Place Holder Zenodo)

analysis-api.session.sql basalt.session.sqlanalysis-api.session.sql renamed to basalt.session.sql

@@ -6,10 +6,10 @@
 
 # Note:
 # - just works fine with quoted variables of dot-env files like this one
-LINKML_SCHEMA_NAME="analysis_api_schema"
+LINKML_SCHEMA_NAME="basalt_schema"
 LINKML_SCHEMA_AUTHOR="Maia Kapur <maia.kapur@pnnl.gov>"
-LINKML_SCHEMA_DESCRIPTION="Data schema for analysis database at EMSL (PNNL)."
-LINKML_SCHEMA_SOURCE_DIR="src/analysis_api_schema/schema"
+LINKML_SCHEMA_DESCRIPTION="Broad Analytical Schema for Samples and Laboratory Techniques."
+LINKML_SCHEMA_SOURCE_DIR="src/basalt_schema/schema"
 
 ###### linkml generator variables, used by justfile
 

config.public.mk

@@ -0,0 +1,17 @@
+This material was prepared as an account of work sponsored by an agency of the United States Government.  Neither the United States Government nor the United States Department of Energy, nor the Contractor, nor any or their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.
+
+Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
+
+ 
+
+PACIFIC NORTHWEST NATIONAL LABORATORY
+
+operated by
+
+BATTELLE
+
+for the
+
+UNITED STATES DEPARTMENT OF ENERGY
+
+under Contract DE-AC05-76RL01830

disclaimer.txt

@@ -1,16 +1,30 @@
-# About
-
-The MONet Analysis API Schema is a [LinkML](https://linkml.io)-based data model for
-MONet soil analysis data management. It defines the canonical structures for samples,
-processed data products, site metadata, and enrichment providers used in the
-MONet Analysis API.
-
-**Repository:** [pnnl/analysis-api](https://github.com/pnnl/analysis-api)  
-**Canonical URI:** <https://w3id.org/MONet/analysis-api-schema>  
-**License:** MIT
-
-## Contacts
-
-- Maia Kapur (maia.kapur@pnnl.gov)
-- Conrad Mearns (conrad.mearns@pnnl.gov)
-- Montana Smith (montana.smith@pnnl.gov)
+# About
+
+**BASALT** — Broad Analytical Schema for Samples and Laboratory Techniques
+
+The BASALT schema is a [LinkML](https://linkml.io)-based data model for MONet/EMSL scientific data across biogeochemical, biological, and environmental domains. It defines canonical structures for samples, provenance, laboratory activities, analytical products, site metadata, and related entities used by BASALT consumers (Analysis API, database models, and tooling).
+
+| | |
+| --- | --- |
+| **Schema version** | `0.1.0` |
+| **Repository** | https://github.com/EMSL-Computing/basalt-schema |
+| **Docs** | https://EMSL-Computing.github.io/basalt-schema |
+| **Canonical URI** | https://EMSL-Computing.github.io/basalt-schema |
+| **License** | [CC0 1.0 Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/) |
+
+Schema version is declared in the root LinkML file (`src/basalt_schema/schema/basalt_schema.yaml`) and follows semantic versioning. See the repository README for the release process.
+
+## Contacts
+
+- Yuri Corilo (corilo@pnnl.gov)
+- Maia Kapur (maia.kapur@pnnl.gov)
+- Bea Meluch (beata.meluch@pnnl.gov)
+- Montana Smith (montana.smith@pnnl.gov)
+
+## Credits
+
+This material is free to use, and attribution is always appreciated. Attribution may read as follows:
+
+Authored by Conrad Mearns, Maia Kapur, Montana Smith, Beata Meluch, Aramy Truong, and Yuri E. Corilo at the Pacific Northwest National Laboratory, operated by Battelle for the U.S. Department of Energy.
+
+(Optional, if applicable): Please cite the following in your work: (Place Holder Zenodo)

docs/about.md

@@ -1,5 +1,5 @@
 # Background
 
-Overview material for the analysis API schema.
+Overview material for the BASALT Schema.
 
 Use this section for context, design rationale, and project history that supports the schema reference.