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Refactor README to use Miniforge and conda-forge for env setup; remove unreliable shell script instructions

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florez_j
2025-06-29 07:53:20 +02:00
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@ -30,7 +30,7 @@ For **Windows** users, the following are required:
1. **Git Bash**: Install [Git Bash](https://git-scm.com/downloads) to run shell scripts (`.sh` files).
2. **Conda**: Install [Anaconda](https://www.anaconda.com/products/individual) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
2. **Miniforge**: Install [Miniforge](https://conda-forge.org/download/).
3. **PSI Network Access**
@ -44,56 +44,52 @@ For **Windows** users, the following are required:
### Download DIMA
Open a **Git Bash** terminal.
Open a **Git Bash** terminal (or a terminal of your choice).
Navigate to your `Gitea` folder, clone the repository, and navigate to the `dima` folder as follows:
Navigate to your `Gitea` folder, clone the repository, and move into the `dima` directory:
```bash
cd path/to/Gitea
git clone --recurse-submodules https://gitea.psi.ch/5505-public/dima.git
cd dima
```bash
cd path/to/Gitea
git clone --recurse-submodules https://gitea.psi.ch/5505-public/dima.git
cd dima
```
### Install Python Interpreter
### Install Python Environment Using Miniforge and conda-forge
Open **Git Bash** terminal.
We recommend using Miniforge to manage your conda environments. Miniforge ensures compatibility with packages from the conda-forge channel.
**Option 1**: Install a suitable conda environment `multiphase_chemistry_env` inside the repository `dima` as follows:
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/GitLab/dima
Bash setup_env.sh
```
Open **Anaconda Prompt** or a terminal with access to conda.
**Option 2**: Install conda enviroment from YAML file as follows:
```bash
cd path/to/GitLab/dima
cd path/to/Gitea/dima
conda env create --file environment.yml
```
3. Activate the Environment
```bash
conda activate dima_env
```
<details>
<summary> <b> Working with Jupyter Notebooks </b> </summary>
We now make the previously installed Python environment `multiphase_chemistry_env` selectable as a kernel in Jupyter's interface.
### Working with Jupyter Notebooks
We now make the previously installed Python environment `dima_env` selectable as a kernel in Jupyter's interface.
1. Open an Anaconda Prompt, check if the environment exists, and activate it:
```
conda env list
conda activate multiphase_chemistry_env
conda activate dima_env
```
2. Register the environment in Jupyter:
```
python -m ipykernel install --user --name multiphase_chemistry_env --display-name "Python (multiphase_chemistry_env)"
python -m ipykernel install --user --name dima_env --display-name "Python (dima_env)"
```
3. Start a Jupyter Notebook by running the command:
```
jupyter notebook
```
and select the `multiphase_chemistry_env` environment from the kernel options.
and select the `dima_env` environment from the kernel options.
</details>
## Repository Structure and Software arquitecture