Merge pull request #12 from hdmf-dev/hdmf-ai

.github/pull_request_template.md

@@ -11,5 +11,5 @@ Show how to reproduce the new behavior (can be a bug fix or a new feature)
 
 - [ ] Did you update `CHANGELOG.md` with your changes?
 - [ ] Does the PR clearly describe the problem and the solution?
-- [ ] Have you reviewed our [Contributing Guide](https://github.com/hdmf-dev/hdmf-ml/blob/main/docs/CONTRIBUTING.rst)?
+- [ ] Have you reviewed our [Contributing Guide](https://github.com/hdmf-dev/hdmf-ai/blob/main/docs/CONTRIBUTING.rst)?
 - [ ] Does the PR use "Fix #XXX" notation to tell GitHub to close the relevant issue numbered XXX when the PR is merged?

README.md

@@ -1,3 +1,3 @@
-# HDMF-ML - an HDMF schema for machine learning workflows
+# HDMF-AI - an HDMF schema and API for AI/ML workflows
 
-![Endurable Schema](schema.png)
+![Schema](schema.png)

docs/CONTRIBUTING.rst

@@ -6,7 +6,7 @@ Contributing Guide
 Code of Conduct
 ---------------
 
-This project and everyone participating in it is governed by our `code of conduct guidelines <https://github.com/hdmf-dev/hdmf-ml/blob/main/.github/CODE_OF_CONDUCT.md>`_. By participating, you are expected to uphold this code. Please report unacceptable behavior.
+This project and everyone participating in it is governed by our `code of conduct guidelines <https://github.com/hdmf-dev/hdmf-ai/blob/main/.github/CODE_OF_CONDUCT.md>`_. By participating, you are expected to uphold this code. Please report unacceptable behavior.
 
 .. _sec-contribution-types:
 
@@ -16,9 +16,9 @@ Types of Contributions
 Did you find a bug? or Do you intend to add a new feature or change an existing one?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-* **Submit issues and requests** using our `issue tracker <https://github.com/hdmf-dev/hdmf-ml/issues>`_
+* **Submit issues and requests** using our `issue tracker <https://github.com/hdmf-dev/hdmf-ai/issues>`_
 
-* **Ensure the feature or change was not already reported** by searching on GitHub under `HDMF Issues <https://github.com/hdmf-dev/hdmf-ml/issues>`_
+* **Ensure the feature or change was not already reported** by searching on GitHub under `HDMF Issues <https://github.com/hdmf-dev/hdmf-ai/issues>`_
 
 * If you are unable to find an open issue addressing the problem then open a new issue on the respective repository. Be sure to use our issue templates and include:
 
@@ -73,7 +73,7 @@ From your local copy directory, use the following commands.
 
     $ git push origin <new_branch>
 
-4) Once you have tested and finalized your changes, create a pull request targeting ``dev`` as the base branch. Be sure to use our `pull request template <https://github.com/hdmf-dev/hdmf-ml/blob/main/.github/pull_request_template.md>`_ and:
+4) Once you have tested and finalized your changes, create a pull request targeting ``dev`` as the base branch. Be sure to use our `pull request template <https://github.com/hdmf-dev/hdmf-ai/blob/main/.github/pull_request_template.md>`_ and:
 
     * Ensure the PR description clearly describes the problem and solution.
     * Include the relevant issue number if applicable.
@@ -139,7 +139,7 @@ Please do not take working with an organization (e.g., during a hackathon or via
 License and Copyright
 ---------------------
 
-See the `license <https://raw.githubusercontent.com/hdmf-dev/hdmf-ml/main/license.txt>`_ files for details about the copyright and license.
+See the `license <https://raw.githubusercontent.com/hdmf-dev/hdmf-ai/main/license.txt>`_ files for details about the copyright and license.
 
 As indicated in the HDMF license: *“You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.”*
 

pyproject.toml

@@ -3,12 +3,12 @@ requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "hdmf_ml"
+name = "hdmf_ai"
 authors = [
   { name="Ryan Ly", email="rly@lbl.gov" },
   { name="Andrew Tritt", email="ajtritt@lbl.gov" },
 ]
-description = "A package for using the HDMF-ML schema"
+description = "A package for using the HDMF-AI schema"
 readme = "README.md"
 requires-python = ">=3.7"
 license = {text = "BSD-3-Clause"}
@@ -42,15 +42,15 @@ dependencies = [
     "numpy>=1.21",
     "scikit-learn>=1",
 ]
-version = "0.1.0"
+version = "1.0.0"
 # dynamic = ["version"]
 
 [project.urls]
-"Homepage" = "https://github.com/hdmf-dev/hdmf-ml"
-"Bug Tracker" = "https://github.com/hdmf-dev/hdmf-ml/issues"
+"Homepage" = "https://github.com/hdmf-dev/hdmf-ai"
+"Bug Tracker" = "https://github.com/hdmf-dev/hdmf-ai/issues"
 
 [tool.setuptools.package-data]
-hdmf = ["hdmf_ml/schema/*.yaml"]
+hdmf = ["src/hdmf_ai/schema/*.yaml"]
 
 # [tool.mypy]
 # no_incremental = true  # needed b/c mypy and ruamel.yaml do not play nice. https://github.com/python/mypy/issues/12664
@@ -69,7 +69,7 @@ ignore-words-list = "datas"
 
 [tool.coverage.run]
 branch = true
-source = ["hdmf_ml/"]
+source = ["src/hdmf_ai/"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -102,7 +102,7 @@ exclude = [
 ]
 
 [tool.ruff.lint.per-file-ignores]
-"hdmf_ml/__init__.py" = ["E402", "F401"]
+"src/hdmf_ai/__init__.py" = ["E402", "F401"]
 
 [tool.ruff.lint.mccabe]
 max-complexity = 17

requirements-dev.txt

@@ -1,4 +1,4 @@
-# pinned dependencies to reproduce an entire development environment to use HDMF-ML, run HDMF-ML tests, check code
+# pinned dependencies to reproduce an entire development environment to use HDMF-AI, run HDMF-AI tests, check code
 # style, compute coverage, and create test environments. note that depending on the version of python installed,
 # different versions of requirements may be installed due to package incompatibilities.
 

requirements-min.txt

@@ -1,4 +1,4 @@
-# minimum versions of package dependencies for installing HDMF-ML, used in testing
+# minimum versions of package dependencies for installing HDMF-AI, used in testing
 hdmf==3.5.1
 numpy==1.21
 scikit-learn==1.0

requirements.txt

@@ -1,4 +1,4 @@
-# pinned dependencies to reproduce an entire development environment to use HDMF-ML
+# pinned dependencies to reproduce an entire development environment to use HDMF-AI
 hdmf==3.13.0
 numpy==1.26.4
 scikit-learn==1.4.0

hdmf_ml/__init__.py → src/hdmf_ai/__init__.py

@@ -17,7 +17,7 @@ def __get_resources():
     return ret
 
 
-CORE_NAMESPACE = "hdmf-ml"
+CORE_NAMESPACE = "hdmf-ai"
 load_namespaces(__get_resources()["namespace_path"])
 
 from . import results_table

hdmf_ml/results_table.py → src/hdmf_ai/results_table.py

@@ -7,21 +7,21 @@
 
 data_type = ("array_data", "data")
 
-SupervisedOutput = get_class("SupervisedOutput", "hdmf-ml")
-TrainValidationTestSplit = get_class("TrainValidationTestSplit", "hdmf-ml")
-CrossValidationSplit = get_class("CrossValidationSplit", "hdmf-ml")
-ClassProbability = get_class("ClassProbability", "hdmf-ml")
-ClassLabel = get_class("ClassLabel", "hdmf-ml")
-TopKProbabilities = get_class("TopKProbabilities", "hdmf-ml")
-TopKClasses = get_class("TopKClasses", "hdmf-ml")
-RegressionOutput = get_class("RegressionOutput", "hdmf-ml")
-ClusterLabel = get_class("ClusterLabel", "hdmf-ml")
-EmbeddedValues = get_class("EmbeddedValues", "hdmf-ml")
+SupervisedOutput = get_class("SupervisedOutput", "hdmf-ai")
+TrainValidationTestSplit = get_class("TrainValidationTestSplit", "hdmf-ai")
+CrossValidationSplit = get_class("CrossValidationSplit", "hdmf-ai")
+ClassProbability = get_class("ClassProbability", "hdmf-ai")
+ClassLabel = get_class("ClassLabel", "hdmf-ai")
+TopKProbabilities = get_class("TopKProbabilities", "hdmf-ai")
+TopKClasses = get_class("TopKClasses", "hdmf-ai")
+RegressionOutput = get_class("RegressionOutput", "hdmf-ai")
+ClusterLabel = get_class("ClusterLabel", "hdmf-ai")
+EmbeddedValues = get_class("EmbeddedValues", "hdmf-ai")
 
-_AutoGenResultsTable = get_class("ResultsTable", "hdmf-ml")
+_AutoGenResultsTable = get_class("ResultsTable", "hdmf-ai")
 
 
-@register_class("ResultsTable", "hdmf-ml")
+@register_class("ResultsTable", "hdmf-ai")
 class ResultsTable(_AutoGenResultsTable):
     # extend the auto-generated ResultsTable class
 

src/hdmf_ai/schema/namespace.yaml

@@ -0,0 +1,17 @@
+namespaces:
+- name: hdmf-ai
+  doc: An extension to HDMF for storing results of AI/ML algorithms
+  author:
+  - Ryan Ly
+  - Andrew Tritt
+  contact:
+  - rly@lbl.gov
+  - ajtritt@lbl.gov
+  full_name: HDMF AI
+  schema:
+  - namespace: hdmf-common
+  - namespace: hdmf-experimental
+  - doc: Structures for storing AI/ML data in a tabular fashion
+    source: results_table.yaml
+    title: Types for results table and specialized columns
+  version: 1.0.0

tests/test_results_table.py

@@ -3,8 +3,8 @@
 from unittest import TestCase
 
 from hdmf.common import HDF5IO, get_manager, EnumData, VectorData
-from hdmf_ml import ResultsTable
-from hdmf_ml.results_table import (
+from hdmf_ai import ResultsTable
+from hdmf_ai.results_table import (
     # SupervisedOutput,
     # TrainValidationTestSplit,
     CrossValidationSplit,