aind-clabe 0.5.0__tar.gz

aind_clabe-0.5.0/.flake8

@@ -0,0 +1,8 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    .venv,
+    build
+max-complexity = 10
+max-line-length = 120

aind_clabe-0.5.0/.gitattributes

@@ -0,0 +1,4 @@
+* text=auto
+*.cmd text eol=crlf
+*.bat text eol=crlf
+*.bonsai text

aind_clabe-0.5.0/.github/workflows/ci.yml

@@ -0,0 +1,26 @@
+name: ci/cd
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+      - dev
+  push:
+    branches:
+      - main
+      - dev
+
+jobs:
+
+  python-linting:
+    uses: AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/python-linting.yml@main
+    with:
+        runs-on: windows-latest
+
+  aind-behavior-framework-testing:
+    uses: AllenNeuralDynamics/Aind.Behavior.GitHubActions/.github/workflows/python-unit-test.yml@main
+    with:
+        python-version-path: .python-version
+        runs-on: windows-latest
+        run-coverage: true

aind_clabe-0.5.0/.github/workflows/docs.yml

@@ -0,0 +1,31 @@
+name: deploy-docs
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv sync --extra docs
+  
+      - name: Configure Git user
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          
+      - name: Deploy documentation
+        run: uv run mkdocs gh-deploy --force

aind_clabe-0.5.0/.github/workflows/tag_and_publish.yml

@@ -0,0 +1,68 @@
+name: Tag and Publish
+
+on:
+  workflow_dispatch:
+    inputs:
+      publish:
+        type: boolean
+        description: 'Whether to publish the package to PyPI'
+        required: false
+        default: true
+
+jobs:
+  tag:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v3
+      with:
+        enable-cache: true
+    - name: Set up Python
+      run: uv python install
+
+    - name: Extract version from __init__.py and package name from pyproject.toml
+      id: get_version_and_name
+      run: |
+        version=$(uv run python -c "import re; 
+        with open(f'./src/clabe/__init__.py', 'r') as f: 
+          content = f.read();
+          match = re.search(r'__version__\s*=\s*[\'\"]([^\'\"]+)[\'\"]', content); 
+          print(match.group(1)) if match else exit(1)")
+        echo "PACKAGE_NAME=aind-clabe" >> $GITHUB_ENV
+        echo "PACKAGE_VERSION=$version" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Create Git tag
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+        git tag -a v${{ env.PACKAGE_VERSION }} -m "v${{ env.PACKAGE_VERSION }}"
+        git push origin v${{ env.PACKAGE_VERSION }}
+
+    - name: Create GitHub Release
+      uses: softprops/action-gh-release@v2
+      with:
+        tag_name: v${{ env.PACKAGE_VERSION }}
+        name: Release v${{ env.PACKAGE_VERSION }}
+        generate_release_notes: true
+
+  publish:
+    needs: tag
+    if: github.event_name == 'workflow_dispatch' && inputs.publish || github.event_name == 'push'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+
+      - name: Set up Python
+        run: uv python install
+
+      - name: Build
+        run: uv build
+
+      - name: Publish
+        run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }}
+      - name: Publish
+        run: uv publish --token ${{ secrets.AIND_PYPI_TOKEN }}

aind_clabe-0.5.0/.gitignore

@@ -0,0 +1,82 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Sphinx documentation
+docs/_build/
+
+# Mkdocs
+docs/site/
+site/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# vscode
+.vscode/
+
+# venv
+.venv/
+
+# pycharm
+.idea/
+
+local

aind_clabe-0.5.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "tests/assets/Aind.Behavior.curriculumTemplate"]
+	path = tests/assets/Aind.Behavior.curriculumTemplate
+	url = https://github.com/AllenNeuralDynamics/Aind.Behavior.curriculumTemplate

aind_clabe-0.5.0/.python-version

@@ -0,0 +1,3 @@
+3.11
+3.12
+3.13

aind_clabe-0.5.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Allen Institute for Neural Dynamics
+
+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.

aind_clabe-0.5.0/PKG-INFO

@@ -0,0 +1,121 @@
+Metadata-Version: 2.4
+Name: aind-clabe
+Version: 0.5.0
+Summary: A library for a minimal framework that can be used to build experimental interfaces.
+Author-email: Bruno Cruz <bruno.cruz@alleninstitute.org>
+License-Expression: MIT
+Project-URL: Documentation, https://allenneuraldynamics.github.io/clabe/
+Project-URL: Repository, https://github.com/AllenNeuralDynamics/clabe/
+Project-URL: Issues, https://github.com/AllenNeuralDynamics/clabe/issues
+Project-URL: Changelog, https://github.com/AllenNeuralDynamics/clabe/releases
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Operating System :: Microsoft :: Windows
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic>=2.7
+Requires-Dist: pydantic-settings
+Requires-Dist: gitpython
+Requires-Dist: semver
+Requires-Dist: rich
+Requires-Dist: aind_behavior_services<1
+Provides-Extra: aind-services
+Requires-Dist: aind-slims-api; extra == "aind-services"
+Requires-Dist: aind-watchdog-service; extra == "aind-services"
+Requires-Dist: aind-data-schema<2; extra == "aind-services"
+Requires-Dist: ms-active-directory; extra == "aind-services"
+Requires-Dist: cryptography; extra == "aind-services"
+Requires-Dist: winkerberos; sys_platform == "win32" and extra == "aind-services"
+Requires-Dist: ldap3; sys_platform == "win32" and extra == "aind-services"
+Provides-Extra: dev
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: codespell; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: aind-clabe[aind-services]; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: aind-clabe[aind-services]; extra == "docs"
+Requires-Dist: mkdocs; extra == "docs"
+Requires-Dist: mkdocs-material; extra == "docs"
+Requires-Dist: mkdocstrings[python]; extra == "docs"
+Requires-Dist: pymdown-extensions; extra == "docs"
+Requires-Dist: ruff; extra == "docs"
+Dynamic: license-file
+
+<div align="center">
+
+<pre>
+ ██████╗██╗      █████╗ ██████╗ ███████╗
+██╔════╝██║     ██╔══██╗██╔══██╗██╔════╝
+██║     ██║     ███████║██████╔╝█████╗  
+██║     ██║     ██╔══██║██╔══██╗██╔══╝  
+╚██████╗███████╗██║  ██║██████╔╝███████╗
+ ╚═════╝╚══════╝╚═╝  ╚═╝╚═════╝ ╚══════╝
+
+Command-line-interface Launcher for AIND Behavior Experiments
+</pre>
+</div>
+
+
+
+![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.ExperimentLauncher/actions/workflows/ci.yml/badge.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/aind-clabe)](https://pypi.org/project/aind-clabe/)
+[![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)
+
+# clabe
+
+A library for building workflows for behavior experiments.
+
+> ⚠️ **Caution:**  
+> This repository is currently under active development and is subject to frequent changes. Features and APIs may evolve without prior notice.
+
+## Installing and Upgrading
+
+If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:
+
+```bash
+pip install .
+```
+
+Otherwise, you can use pip:
+
+```bash
+pip install aind-clabe
+```
+
+## Getting started and API usage
+
+The library provides a main class "Launcher" that can be used to create a linear workflow for behavior experiments. These workflows rely on modular interfaces that can be used to interact with various components of the experiment and other services.
+Some of these services are specific for AIND:
+
+- [aind-data-schema](https://github.com/AllenNeuralDynamics/aind-data-schema)
+- [aind-data-schema-models](https://github.com/AllenNeuralDynamics/aind-data-schema-models)
+- [aind-watchdog-service](https://github.com/AllenNeuralDynamics/aind-watchdog-service)
+- [aind-slims-api](https://github.com/AllenNeuralDynamics/aind-slims-api)
+- [aind-data-mapper](https://github.com/AllenNeuralDynamics/aind-metadata-mapper)
+
+We will also try to scope all dependencies of the related to AIND Services to its own optional dependency list in the `./pyproject.toml` file of this repository. Therefore, in order to use this module, you will need to install these optional dependencies by running:
+
+```uv sync --extra aind-services```
+
+A basic example of how to use the Launcher class can be found in the `examples` directory of this repository.
+
+## Contributors
+
+Contributions to this repository are welcome! However, please ensure that your code adheres to the recommended DevOps practices below:
+
+### Linting
+
+We use [ruff](https://docs.astral.sh/ruff/) as our primary linting tool.
+
+### Testing
+
+Attempt to add tests when new features are added.
+To run the currently available tests, run `uv run -m unittest` from the root of the repository.
+
+### Lock files
+
+We use [uv](https://docs.astral.sh/uv/) to manage our lock files and therefore encourage everyone to use uv as a package manager as well.

aind_clabe-0.5.0/README.md

@@ -0,0 +1,76 @@
+<div align="center">
+
+<pre>
+ ██████╗██╗      █████╗ ██████╗ ███████╗
+██╔════╝██║     ██╔══██╗██╔══██╗██╔════╝
+██║     ██║     ███████║██████╔╝█████╗  
+██║     ██║     ██╔══██║██╔══██╗██╔══╝  
+╚██████╗███████╗██║  ██║██████╔╝███████╗
+ ╚═════╝╚══════╝╚═╝  ╚═╝╚═════╝ ╚══════╝
+
+Command-line-interface Launcher for AIND Behavior Experiments
+</pre>
+</div>
+
+
+
+![CI](https://github.com/AllenNeuralDynamics/Aind.Behavior.ExperimentLauncher/actions/workflows/ci.yml/badge.svg)
+[![PyPI - Version](https://img.shields.io/pypi/v/aind-clabe)](https://pypi.org/project/aind-clabe/)
+[![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)
+
+# clabe
+
+A library for building workflows for behavior experiments.
+
+> ⚠️ **Caution:**  
+> This repository is currently under active development and is subject to frequent changes. Features and APIs may evolve without prior notice.
+
+## Installing and Upgrading
+
+If you choose to clone the repository, you can install the package by running the following command from the root directory of the repository:
+
+```bash
+pip install .
+```
+
+Otherwise, you can use pip:
+
+```bash
+pip install aind-clabe
+```
+
+## Getting started and API usage
+
+The library provides a main class "Launcher" that can be used to create a linear workflow for behavior experiments. These workflows rely on modular interfaces that can be used to interact with various components of the experiment and other services.
+Some of these services are specific for AIND:
+
+- [aind-data-schema](https://github.com/AllenNeuralDynamics/aind-data-schema)
+- [aind-data-schema-models](https://github.com/AllenNeuralDynamics/aind-data-schema-models)
+- [aind-watchdog-service](https://github.com/AllenNeuralDynamics/aind-watchdog-service)
+- [aind-slims-api](https://github.com/AllenNeuralDynamics/aind-slims-api)
+- [aind-data-mapper](https://github.com/AllenNeuralDynamics/aind-metadata-mapper)
+
+We will also try to scope all dependencies of the related to AIND Services to its own optional dependency list in the `./pyproject.toml` file of this repository. Therefore, in order to use this module, you will need to install these optional dependencies by running:
+
+```uv sync --extra aind-services```
+
+A basic example of how to use the Launcher class can be found in the `examples` directory of this repository.
+
+## Contributors
+
+Contributions to this repository are welcome! However, please ensure that your code adheres to the recommended DevOps practices below:
+
+### Linting
+
+We use [ruff](https://docs.astral.sh/ruff/) as our primary linting tool.
+
+### Testing
+
+Attempt to add tests when new features are added.
+To run the currently available tests, run `uv run -m unittest` from the root of the repository.
+
+### Lock files
+
+We use [uv](https://docs.astral.sh/uv/) to manage our lock files and therefore encourage everyone to use uv as a package manager as well.

aind_clabe-0.5.0/docs/_regenerate_api.py

@@ -0,0 +1,159 @@
+import logging
+import shutil
+from pathlib import Path
+from typing import Any, Dict, List, Union
+
+import yaml
+
+ROOT_DIR = Path(__file__).parent.parent
+PACKAGE_NAME = "clabe"
+SRC_DIR = ROOT_DIR / "src" / PACKAGE_NAME
+DOCS_DIR = ROOT_DIR / "docs"
+API_DIR = DOCS_DIR / "api"
+MKDOCS_YML = ROOT_DIR / "mkdocs.yml"
+API_LABEL = "API Reference"
+INCLUDE_PRIVATE_MODULES = False
+
+TO_COPY = ["assets", "examples", "LICENSE"]
+log = logging.getLogger("mkdocs")
+
+
+def discover_python_modules(package_root: Path, include_private: bool = False) -> List[str]:
+    modules = []
+
+    def _find_modules(current_path: Path, prefix: str = "") -> None:
+        if not current_path.exists() or not current_path.is_dir():
+            return
+
+        for item in current_path.iterdir():
+            if not item.is_dir():
+                continue
+            if not (item / "__init__.py").exists():
+                continue
+
+            if item.name.startswith("_") and not include_private:
+                continue
+
+            module_name = f"{prefix}{item.name}" if prefix else item.name
+            modules.append(module_name)
+
+            # Recursively search subdirectories for nested modules
+            _find_modules(item, f"{module_name}.")
+
+    _find_modules(package_root)
+    return sorted(modules)
+
+
+def discover_module_files(module_path: Path, include_private: bool = False) -> List[str]:
+    files = []
+
+    def _find_files(current_path: Path, prefix: str = "") -> None:
+        if not current_path.exists() or not current_path.is_dir():
+            return
+
+        for item in current_path.iterdir():
+            if item.is_file() and item.suffix == ".py":
+                if item.name.startswith("_") and not include_private:
+                    continue
+                file_name = f"{prefix}{item.stem}" if prefix else item.stem
+                files.append(file_name)
+            elif item.is_dir() and not item.name.startswith("__"):
+                if item.name.startswith("_") and not include_private:
+                    continue
+                # Recursively search subdirectories
+                _find_files(item, f"{prefix}{item.name}." if prefix else f"{item.name}.")
+
+    _find_files(module_path)
+    return sorted(files)
+
+
+def on_pre_build(config: Dict[str, Any]) -> None:
+    """Mkdocs pre-build hook."""
+    for file_or_dir in TO_COPY:
+        src: Path = ROOT_DIR / file_or_dir
+        dest: Path = 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()
+
+
+def generate_api_structure() -> Dict[str, List[Dict[str, str]]]:
+    api_structure: Dict[str, List[Dict[str, str]]] = {}
+    modules = discover_python_modules(SRC_DIR, INCLUDE_PRIVATE_MODULES)
+
+    for module_name in modules:
+        module_structure: List[Dict[str, str]] = []
+        module_path = SRC_DIR / module_name.replace(".", "/")
+
+        # Add the module's __init__.py as the main module entry
+        safe_module_name = module_name.replace(".", "_")
+        module_structure.append({module_name: f"api/{safe_module_name}/{safe_module_name}.md"})
+
+        module_files = discover_module_files(module_path, INCLUDE_PRIVATE_MODULES)
+        for file_name in module_files:
+            safe_file_name = file_name.replace(".", "_")
+            module_structure.append({file_name: f"api/{safe_module_name}/{safe_file_name}.md"})
+
+        (API_DIR / safe_module_name).mkdir(parents=True, exist_ok=True)
+
+        with open(DOCS_DIR / f"api/{safe_module_name}/{safe_module_name}.md", "w") as f:
+            f.write(f"# {module_name}\n\n")
+            f.write(f"::: {PACKAGE_NAME}.{module_name}\n")
+
+        for file_name in module_files:
+            safe_file_name = file_name.replace(".", "_")
+            with open(DOCS_DIR / f"api/{safe_module_name}/{safe_file_name}.md", "w") as f:
+                f.write(f"# {module_name}.{file_name}\n\n")
+                f.write(f"::: {PACKAGE_NAME}.{module_name}.{file_name}\n")
+
+        api_structure[module_name] = module_structure
+
+    return api_structure
+
+
+def update_mkdocs_yml(api_structure: Dict[str, List[Dict[str, str]]]) -> None:
+    with open(MKDOCS_YML, "r") as f:
+        config: Dict[str, Any] = yaml.safe_load(f)
+
+    nav: List[Union[str, Dict[str, Any]]] = config.get("nav", [])
+
+    for entry in nav:
+        if isinstance(entry, dict) and API_LABEL in entry:
+            api_ref: List[Union[str, Dict[str, List[Dict[str, str]]]]] = ["api/index.md"]
+
+            for module_name, module_content in api_structure.items():
+                api_ref.append({module_name.capitalize().replace("_", " "): module_content})
+
+            entry[API_LABEL] = api_ref
+
+    with open(MKDOCS_YML, "w") as f:
+        yaml.dump(config, f, sort_keys=False, default_flow_style=False)
+
+
+def main() -> None:
+    log.info("Regenerating API documentation...")
+
+    # Generate API structure
+    api_structure: Dict[str, List[Dict[str, str]]] = generate_api_structure()
+
+    # Update mkdocs.yml
+    update_mkdocs_yml(api_structure)
+
+    log.info("API documentation regenerated successfully.")
+
+
+if __name__ == "__main__":
+    main()

aind_clabe-0.5.0/docs/api/index.md

@@ -0,0 +1,3 @@
+# API Reference
+
+The `clabe` package