Merge pull request #36 from AllenNeuralDynamics/refactor-change-package-name

Change package name to `contraqctor`

Author: bruno-f-cruz

.github/workflows/ci.yml

@@ -43,7 +43,7 @@ jobs:
         run: uv run codespell --check-filenames
 
       - name: pytest
-        run: uv run pytest --cov aind_behavior_core_analysis
+        run: uv run pytest --cov contraqctor
 
       - name: Build
         run: uv build

README.md

@@ -1,14 +1,15 @@
-# aind-behavior-core-analysis
-[![Documentation](https://tinyurl.com/bdd8prh7)](https://allenneuraldynamics.github.io/Aind.Behavior.CoreAnalysis/)
+[![contraqctor](./assets/logo-letter.svg)](https://allenneuraldynamics.github.io/contraqctor/)
+
+[![Documentation](https://tinyurl.com/zf46ufwa)](https://allenneuraldynamics.github.io/Aind.Behavior.CoreAnalysis/)
 ![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.CoreAnalysis/actions/workflows/ci.yml/badge.svg)
-[![PyPI - Version](https://img.shields.io/pypi/v/aind-behavior-core-analysis)](https://pypi.org/project/aind-behavior-core-analysis/)
+[![PyPI - Version](https://img.shields.io/pypi/v/contraqctor)](https://pypi.org/project/contraqctor/)
 [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
 [![ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
 
-A repository with core primitives for analysis shared across all `Aind.Behavior` tasks.
+# contraqctor
 
-This repository is part of a bigger infrastructure that is summarized [here](https://github.com/AllenNeuralDynamics/Aind.Behavior.Services).
+A repository for managing data contracts and quality control in behavioral datasets.
 
 > ⚠️ **Caution:**  
 > This repository is currently under active development and is subject to frequent changes. Features and APIs may evolve without prior notice.
@@ -24,7 +25,7 @@ pip install .
 Otherwise, you can use pip:
 
 ```bash
-pip install aind-behavior-core-analysis
+pip install contraqctor
 ```
 
 ## Getting started and API usage
@@ -37,9 +38,9 @@ Data contracts provide a standard way to access and load data from various sourc
 
 ```python
 from pathlib import Path
-from aind_behavior_core_analysis.contract import Dataset, DataStreamCollection
-from aind_behavior_core_analysis.contract.csv import Csv
-from aind_behavior_core_analysis.contract.text import Text
+from contraqctor.contract import Dataset, DataStreamCollection
+from contraqctor.contract.csv import Csv
+from contraqctor.contract.text import Text
 
 # Define the dataset structure
 dataset_root = Path("path/to/dataset")
@@ -84,7 +85,7 @@ my_dataset.load_all()
 The QC module helps validate your data to ensure it meets specific requirements:
 
 ```python
-import aind_behavior_core_analysis.qc as qc
+import contraqctor.qc as qc
 
 # Using the dataset created above
 data_stream = my_dataset["Behavior"]["Position"]
@@ -114,7 +115,7 @@ runner.add_suite(MyCustomTestSuite(data_stream))
 results = runner.run_all_with_progress()
 ```
 
-For more detailed examples, please check the [Examples](./examples/) folder.
+For more detailed examples, please check the [Examples](examples) folder.
 
 ---
 

assets/logo-letter.svg

@@ -5,13 +5,14 @@
 """
 
 import logging
+import shutil
 from pathlib import Path
 
 import yaml
 
 # Constants
 ROOT_DIR = Path(__file__).parent.parent
-PACKAGE_NAME = "aind_behavior_core_analysis"
+PACKAGE_NAME = "contraqctor"
 SRC_DIR = ROOT_DIR / "src" / f"{PACKAGE_NAME}"
 DOCS_DIR = ROOT_DIR / "docs"
 API_DIR = DOCS_DIR / "api"
@@ -20,12 +21,29 @@
 
 # Leaving this manual for now.
 DOCUMENTED_MODULES = ["contract", "qc"]
-
+TO_COPY = ["assets", "examples", "LICENSE"]
 log = logging.getLogger("mkdocs")
 
 
 def on_pre_build(config):
     """Mkdocs pre-build hook."""
+    for file_or_dir in TO_COPY:
+        src = ROOT_DIR / file_or_dir
+        dest = DOCS_DIR / file_or_dir
+        if src.exists():
+            log.info(f"Copying {file_or_dir} to docs...")
+
+            if src.is_file():
+                print(f"Copying file {src} to {dest}")
+                shutil.copy(src, dest)
+            else:
+                if dest.exists():
+                    shutil.rmtree(dest)
+                shutil.copytree(src, dest)
+            log.info(f"{file_or_dir} copied successfully.")
+        else:
+            log.warning(f"Source: {file_or_dir} not found, skipping.")
+
     main()
 
 

docs/_regenerate_api.py

@@ -1,6 +1,6 @@
 # API Reference
 
-The `aind-behavior-core-analysis` package provides core primitives and utilities for behavioral data analysis.
+The `contraqctor` package provides core primitives and utilities for behavioral data analysis.
 
 ## Modules
 

docs/api/index.md

@@ -1,6 +1,6 @@
 # Contract Examples
 
-This page demonstrates how to use the Contract module in AIND Behavior Core Analysis.
+This page demonstrates how to use the Contract module.
 
 ## Example Code
 

docs/examples/contract.md docs/doc_examples/contract.mddocs/examples/contract.md renamed to docs/doc_examples/contract.md

@@ -1,6 +1,6 @@
 # Quality Control Examples
 
-This page demonstrates how to use the Quality Control (QC) module in AIND Behavior Core Analysis.
+This page demonstrates how to use the Quality Control (qc) module.
 
 ## Example Code
 

docs/examples/qc.md docs/doc_examples/qc.mddocs/examples/qc.md renamed to docs/doc_examples/qc.md

@@ -4,17 +4,17 @@
 from aind_behavior_services.session import AindBehaviorSessionModel
 from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel
 
-from aind_behavior_core_analysis.contract import Dataset, DataStreamCollection
-from aind_behavior_core_analysis.contract.camera import Camera
-from aind_behavior_core_analysis.contract.csv import Csv
-from aind_behavior_core_analysis.contract.harp import (
+from contraqctor.contract import Dataset, DataStreamCollection
+from contraqctor.contract.camera import Camera
+from contraqctor.contract.csv import Csv
+from contraqctor.contract.harp import (
     DeviceYmlByFile,
     HarpDevice,
 )
-from aind_behavior_core_analysis.contract.json import PydanticModel, SoftwareEvents
-from aind_behavior_core_analysis.contract.mux import MapFromPaths
-from aind_behavior_core_analysis.contract.text import Text
-from aind_behavior_core_analysis.contract.utils import print_data_stream_tree
+from contraqctor.contract.json import PydanticModel, SoftwareEvents
+from contraqctor.contract.mux import MapFromPaths
+from contraqctor.contract.text import Text
+from contraqctor.contract.utils import print_data_stream_tree
 
 dataset_root = Path(r"path_to_data")
 my_dataset = Dataset(