aurora-biologic 0.2.1__tar.gz

aurora_biologic-0.2.1/.github/workflows/test.yml

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+name: CI
+
+on:
+  push:
+    branches: [ "main" ]
+    tags:
+      - v[0-9]+.[0-9]+.[0-9]+*
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Test with Pytest
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version:
+          - "3.10"
+          - "3.13"
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python-version }}
+    
+      - name: Install
+        run: |
+          uv pip install ruff pytest pytest-cov
+          uv pip install -e .
+      - name: Lint with ruff
+        run: |
+          ruff check --select=F,E9,B
+  
+      - name: Test with pytest
+        run: |
+          pytest --cov=aurora_biologic --cov-report=term
+
+  # Publish to PyPI if tagged and tests pass
+  publish:
+    name: Publish to PyPI
+    needs: test
+    if: startsWith(github.ref, 'refs/tags/v') && github.repository == 'empaeconversion/aurora-biologic'
+    runs-on: windows-latest
+    permissions:
+      id-token: write
+      contents: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install flit
+        run: pip install flit~=3.12
+
+      - name: Publish to PyPI
+        run: flit publish
+        env:
+          FLIT_USERNAME: __token__
+          FLIT_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+
+      - name: Create GitHub release
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

aurora_biologic-0.2.1/.gitignore

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+# Python-generated files
+__pycache__/
+*.py[oc]
+build/
+dist/
+wheels/
+*.egg-info
+
+# Virtual environments
+.venv
+
+# UV lock file
+uv.lock

aurora_biologic-0.2.1/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.4
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--select=F,E9,B"]
+      - id: ruff-format

aurora_biologic-0.2.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: aurora-biologic
+Version: 0.2.1
+Summary: Python API for Biologic EC-lab potentiostats
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Dist: comtypes>=1.4.11
+Requires-Dist: platformdirs>=4.3.8
+Requires-Dist: pre-commit>=4.3.0
+Requires-Dist: psutil>=7.0.0
+Requires-Dist: typer>=0.16.0
+Requires-Dist: bumpver>=2025.1131 ; extra == "dev"
+Requires-Dist: pytest>=8.4.1 ; extra == "dev"
+Requires-Dist: ruff>=0.12.3 ; extra == "dev"
+Provides-Extra: dev
+
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/0caae30d-92cf-4964-b95d-c84d59041a78#gh-light-mode-only" width="500" align="center" alt="aurora-biologic logo">
+  <img src="https://github.com/user-attachments/assets/7a32e5f4-f2a7-4ef4-83b1-50e9e10ff4fb#gh-dark-mode-only" width="500" align="center" alt="aurora-biologic logo">
+</p>
+
+</br>
+
+## Overview
+`aurora-biologic` provides a standalone Python API and command line interface (CLI) to control Biologic cyclers.
+
+It is designed and tested on MPG2 cyclers using EC-lab 11.52 and 11.61.
+
+## Features
+- CLI and Python API
+- Connect to EC-lab cyclers
+- Retrieve status of channels
+- Load protocols onto channels
+- Start and stop experiments
+
+For parsing binary data from Biologic, we recommend [`yadg`](https://github.com/dgbowl/yadg).
+
+## Installation
+Install on a Windows PC with EC-lab >11.52 installed.
+> [!IMPORTANT]
+> EC-lab must have OLE/COM activated
+
+OLE/COM is a Windows interface for programs to expose their functionality to third-parties, which is supported by EC-lab.
+
+Open a terminal as administrator, go to your folder containing `EClab.exe` and register the server:
+
+`cmd`
+```cmd
+cd "C:/Program files (x86)/EC-lab"
+eclab \regserver
+```
+
+`powershell`
+```powershell
+cd "C:/Program files (x86)/EC-lab"
+.\eclab \\regserver
+```
+
+You can also deregister in the same way with `/unregserver`.
+
+Next, install this package with
+```bash
+pip install aurora-biologic
+```
+
+To see commands, use
+```bash
+biologic --help
+```
+
+The first time you run the command line, a config file is generated at:
+
+`C:\Users\<user>\AppData\Local\aurora-biologic\aurora-biologic\config.json`
+
+which will look like:
+```json
+{
+    "serial_to_name": {
+        "12345": "MPG2-1",
+        "12346": "MPG2-2"
+    },
+    "eclab_path": "C:/Program Files (x86)/EC-Lab/EClab.exe"
+}
+```
+Rename your devices according to their serial number, and make sure the EC-lab executable path is correct and the same as the executable registered in the first step.
+
+## CLI usage
+
+Make sure EC-lab is running.
+
+You can check what devices and channels were found with
+```bash
+biologic pipelines
+```
+The pipeline ID is made up of the `{device name}-{channel index}`, such as `MPG2-1-7`
+
+These IDs are used for other functions, for example to see the status of that channel use
+```bash
+biologic status MPG2-1-7
+```
+
+>[!TIP]
+>See all commands with `biologic --help`.
+>
+>See details of a command with `biologic [command] --help` e.g. `biologic status --help`.
+
+## API usage
+
+Commands can also be run using Python.
+
+Make sure EC-lab is running.
+
+Then commands can be run using the BiologicAPI object
+```python
+from aurora_biologic import BiologicAPI
+with BiologicAPI() as bio:
+    bio.start(
+        "my_pipeline_id",
+        "path/to/my_experiment.mps",
+        "path/to/an/output.mpr",
+    )
+```
+
+## Using commands over SSH
+>[!WARNING]
+>OLE/COM requires an interactive session to function.
+>
+>Standard command line functions will not work in non-interactive session, such as normal SSH from a terminal.
+
+To use the CLI over SSH you must start a listener daemon in an interactive terminal.
+
+On the PC with EC-lab, start the listener with:
+```bash
+biologic daemon
+```
+
+Then from the SSH session use normal CLI commands with the `--ssh` option, e.g.
+```bash
+biologic status --ssh
+```
+
+Instead of trying to run OLE/COM commands directly in the non-interactive session, it will send commands to the daemon, which will execute and reply.
+
+## Contributors
+
+- [Graham Kimbell](https://github.com/g-kimbell)
+
+## Acknowledgements
+
+Special thanks to Julian Diener from Biologic for their advice and support.
+
+This software was developed at the Laboratory of Materials for Energy Conversion at Empa, the Swiss Federal Laboratories for Materials Science and Technology, and supported by funding from the [IntelLiGent](https://heuintelligent.eu/) project from the European Union’s research and innovation program under grant agreement No. 101069765, and from the Swiss State Secretariat for Education, Research, and Innovation (SERI) under contract No. 22.001422.
+
+<img src="https://github.com/user-attachments/assets/373d30b2-a7a4-4158-a3d8-f76e3a45a508#gh-light-mode-only" height="100" alt="IntelLiGent logo">
+<img src="https://github.com/user-attachments/assets/9d003d4f-af2f-497a-8560-d228cc93177c#gh-dark-mode-only" height="100" alt="IntelLiGent logo">&nbsp;&nbsp;&nbsp;&nbsp;
+<img src="https://github.com/user-attachments/assets/1d32a635-703b-432c-9d42-02e07d94e9a9" height="100" alt="EU flag">&nbsp;&nbsp;&nbsp;&nbsp;
+<img src="https://github.com/user-attachments/assets/cd410b39-5989-47e5-b502-594d9a8f5ae1" height="100" alt="Swiss secretariat">
+

aurora_biologic-0.2.1/README.md

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+<p align="center">
+  <img src="https://github.com/user-attachments/assets/0caae30d-92cf-4964-b95d-c84d59041a78#gh-light-mode-only" width="500" align="center" alt="aurora-biologic logo">
+  <img src="https://github.com/user-attachments/assets/7a32e5f4-f2a7-4ef4-83b1-50e9e10ff4fb#gh-dark-mode-only" width="500" align="center" alt="aurora-biologic logo">
+</p>
+
+</br>
+
+## Overview
+`aurora-biologic` provides a standalone Python API and command line interface (CLI) to control Biologic cyclers.
+
+It is designed and tested on MPG2 cyclers using EC-lab 11.52 and 11.61.
+
+## Features
+- CLI and Python API
+- Connect to EC-lab cyclers
+- Retrieve status of channels
+- Load protocols onto channels
+- Start and stop experiments
+
+For parsing binary data from Biologic, we recommend [`yadg`](https://github.com/dgbowl/yadg).
+
+## Installation
+Install on a Windows PC with EC-lab >11.52 installed.
+> [!IMPORTANT]
+> EC-lab must have OLE/COM activated
+
+OLE/COM is a Windows interface for programs to expose their functionality to third-parties, which is supported by EC-lab.
+
+Open a terminal as administrator, go to your folder containing `EClab.exe` and register the server:
+
+`cmd`
+```cmd
+cd "C:/Program files (x86)/EC-lab"
+eclab \regserver
+```
+
+`powershell`
+```powershell
+cd "C:/Program files (x86)/EC-lab"
+.\eclab \\regserver
+```
+
+You can also deregister in the same way with `/unregserver`.
+
+Next, install this package with
+```bash
+pip install aurora-biologic
+```
+
+To see commands, use
+```bash
+biologic --help
+```
+
+The first time you run the command line, a config file is generated at:
+
+`C:\Users\<user>\AppData\Local\aurora-biologic\aurora-biologic\config.json`
+
+which will look like:
+```json
+{
+    "serial_to_name": {
+        "12345": "MPG2-1",
+        "12346": "MPG2-2"
+    },
+    "eclab_path": "C:/Program Files (x86)/EC-Lab/EClab.exe"
+}
+```
+Rename your devices according to their serial number, and make sure the EC-lab executable path is correct and the same as the executable registered in the first step.
+
+## CLI usage
+
+Make sure EC-lab is running.
+
+You can check what devices and channels were found with
+```bash
+biologic pipelines
+```
+The pipeline ID is made up of the `{device name}-{channel index}`, such as `MPG2-1-7`
+
+These IDs are used for other functions, for example to see the status of that channel use
+```bash
+biologic status MPG2-1-7
+```
+
+>[!TIP]
+>See all commands with `biologic --help`.
+>
+>See details of a command with `biologic [command] --help` e.g. `biologic status --help`.
+
+## API usage
+
+Commands can also be run using Python.
+
+Make sure EC-lab is running.
+
+Then commands can be run using the BiologicAPI object
+```python
+from aurora_biologic import BiologicAPI
+with BiologicAPI() as bio:
+    bio.start(
+        "my_pipeline_id",
+        "path/to/my_experiment.mps",
+        "path/to/an/output.mpr",
+    )
+```
+
+## Using commands over SSH
+>[!WARNING]
+>OLE/COM requires an interactive session to function.
+>
+>Standard command line functions will not work in non-interactive session, such as normal SSH from a terminal.
+
+To use the CLI over SSH you must start a listener daemon in an interactive terminal.
+
+On the PC with EC-lab, start the listener with:
+```bash
+biologic daemon
+```
+
+Then from the SSH session use normal CLI commands with the `--ssh` option, e.g.
+```bash
+biologic status --ssh
+```
+
+Instead of trying to run OLE/COM commands directly in the non-interactive session, it will send commands to the daemon, which will execute and reply.
+
+## Contributors
+
+- [Graham Kimbell](https://github.com/g-kimbell)
+
+## Acknowledgements
+
+Special thanks to Julian Diener from Biologic for their advice and support.
+
+This software was developed at the Laboratory of Materials for Energy Conversion at Empa, the Swiss Federal Laboratories for Materials Science and Technology, and supported by funding from the [IntelLiGent](https://heuintelligent.eu/) project from the European Union’s research and innovation program under grant agreement No. 101069765, and from the Swiss State Secretariat for Education, Research, and Innovation (SERI) under contract No. 22.001422.
+
+<img src="https://github.com/user-attachments/assets/373d30b2-a7a4-4158-a3d8-f76e3a45a508#gh-light-mode-only" height="100" alt="IntelLiGent logo">
+<img src="https://github.com/user-attachments/assets/9d003d4f-af2f-497a-8560-d228cc93177c#gh-dark-mode-only" height="100" alt="IntelLiGent logo">&nbsp;&nbsp;&nbsp;&nbsp;
+<img src="https://github.com/user-attachments/assets/1d32a635-703b-432c-9d42-02e07d94e9a9" height="100" alt="EU flag">&nbsp;&nbsp;&nbsp;&nbsp;
+<img src="https://github.com/user-attachments/assets/cd410b39-5989-47e5-b502-594d9a8f5ae1" height="100" alt="Swiss secretariat">

aurora_biologic-0.2.1/aurora_biologic/__init__.py

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+"""Biologic API for Python."""
+
+from .biologic import BiologicAPI
+from .version import __version__
+
+__all__ = [
+    "BiologicAPI",
+    "__version__",
+]