Update README.md with conda forge install instructions and input data format. Add environment.yml to construct comp env based on conda forge.

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2025-07-04 14:52:29 +02:00
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---
### Input Format
The ACSM data integration pipeline reads data from an **input directory** and an **instrument folder** specified in the `campaignDescriptor.yaml` file with key-value pairs as follows:
```yaml
input_file_directory : NETWORK_MOUNT/Data/JFJ/
instrument_datafolder: ACSM_TOFWARE/2024/
```
Make sure the combined path contains the following structure and files:
```swift
NETWORK_MOUNT/Data/JFJ/ACSM_TOFWARE/2024/
├── ACSM_JFJ_2024_meta.txt
├── ACSM_JFJ_2024_timeseries.txt
├── CH0001G.20240101000000...lev1.nas
├── Org_data_valid.csv
├── Org_err_valid.csv
├── Org_mz_valid.csv
├── Org_time_valid.csv
└── params/
├── calibration_params.yaml
├── limits_of_detection.yaml
└── validity_thresholds.yaml
```
### Output Formats
- **NAS EBAS-compliant files**, structured and metadata-rich for archive submission
@ -79,7 +103,7 @@ For Windows users, the following are required:
2. **Git Bash**: Used to run shell scripts (`.sh` files).
3. **Conda (Optional)**: Required only if you plan to run the toolkit **outside of Docker**. You can install [Anaconda](https://www.anaconda.com/products/distribution) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
3. **Miniforge (Optional)**: Install [Miniforge](https://conda-forge.org/download/). Required only if you plan to run the toolkit **outside of Docker**.
4. **PSI Network Access** *(for data retrieval)*: Needed only if accessing live data from a PSI network-mounted drive.
@ -142,11 +166,40 @@ This toolkit includes a containerized JupyterLab environment for executing the d
> Required only if you plan to run the toolkit outside of Docker
If **Git Bash** lacks a suitable Python interpreter, run:
### Install Python Environment Using Miniforge and conda-forge
```bash
bash env_setup.sh
```
We recommend using Miniforge to manage your conda environments. Miniforge ensures compatibility with packages from the conda-forge channel.
1. Make sure you have installed **Miniforge**.
2. Create the Environment from `environment.yml`
After installing Miniforge, open **Miniforge Prompt** or a terminal with access to conda and run:
```bash
cd path/to/Gitea/acsmnode
conda env create --file environment.yml
```
3. Activate the Environment
```bash
conda activate acsmnode_env
```
### Working with Jupyter Notebooks
We now make the previously installed Python environment `acsmnode_env` selectable as a kernel in Jupyter's interface.
1. Open an **Miniforge Prompt**, check if the environment exists, and activate it:
```
conda env list
conda activate acsmnode_env
```
2. Register the environment in Jupyter:
```
python -m ipykernel install --user --name acsmnode_env --display-name "Python (acsmnode_env)"
```
3. Start a Jupyter Notebook by running the command:
```
jupyter notebook
```
and select the `acsmnode_env` environment from the kernel options.
## (Optional) Run the Dashboard App

22
environment.yml Normal file
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name: acsmnode_env
channels:
- conda-forge
dependencies:
- python=3.11
- jupyter
- numpy
- h5py
- pandas
- matplotlib
- plotly=5.24
- scipy
- sphinx
- pip
- pip:
# - h5py==3.10
- pybis==1.35
- igor2
- ipykernel
- dash
- dash-bootstrap-components
- graphviz