Refactor README to use Miniforge and conda-forge for env setup; remove unreliable shell script instructions
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42
README.md
42
README.md
@ -30,7 +30,7 @@ For **Windows** users, the following are required:
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1. **Git Bash**: Install [Git Bash](https://git-scm.com/downloads) to run shell scripts (`.sh` files).
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2. **Conda**: Install [Anaconda](https://www.anaconda.com/products/individual) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html).
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2. **Miniforge**: Install [Miniforge](https://conda-forge.org/download/).
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3. **PSI Network Access**
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@ -44,9 +44,9 @@ For **Windows** users, the following are required:
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### Download DIMA
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Open a **Git Bash** terminal.
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Open a **Git Bash** terminal (or a terminal of your choice).
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Navigate to your `Gitea` folder, clone the repository, and navigate to the `dima` folder as follows:
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Navigate to your `Gitea` folder, clone the repository, and move into the `dima` directory:
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```bash
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cd path/to/Gitea
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@ -54,46 +54,42 @@ Navigate to your `Gitea` folder, clone the repository, and navigate to the `dima
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cd dima
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```
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### Install Python Interpreter
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### Install Python Environment Using Miniforge and conda-forge
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Open **Git Bash** terminal.
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We recommend using Miniforge to manage your conda environments. Miniforge ensures compatibility with packages from the conda-forge channel.
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**Option 1**: Install a suitable conda environment `multiphase_chemistry_env` inside the repository `dima` as follows:
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1. Make sure you have installed **Miniforge**.
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2. Create the Environment from `environment.yml`
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After installing Miniforge, open **Miniforge Prompt** or a terminal with access to conda and run:
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```bash
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cd path/to/GitLab/dima
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Bash setup_env.sh
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```
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Open **Anaconda Prompt** or a terminal with access to conda.
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**Option 2**: Install conda enviroment from YAML file as follows:
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```bash
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cd path/to/GitLab/dima
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cd path/to/Gitea/dima
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conda env create --file environment.yml
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```
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3. Activate the Environment
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```bash
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conda activate dima_env
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```
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<details>
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<summary> <b> Working with Jupyter Notebooks </b> </summary>
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We now make the previously installed Python environment `multiphase_chemistry_env` selectable as a kernel in Jupyter's interface.
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### Working with Jupyter Notebooks
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We now make the previously installed Python environment `dima_env` selectable as a kernel in Jupyter's interface.
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1. Open an Anaconda Prompt, check if the environment exists, and activate it:
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```
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conda env list
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conda activate multiphase_chemistry_env
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conda activate dima_env
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```
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2. Register the environment in Jupyter:
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```
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python -m ipykernel install --user --name multiphase_chemistry_env --display-name "Python (multiphase_chemistry_env)"
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python -m ipykernel install --user --name dima_env --display-name "Python (dima_env)"
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```
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3. Start a Jupyter Notebook by running the command:
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```
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jupyter notebook
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```
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and select the `multiphase_chemistry_env` environment from the kernel options.
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and select the `dima_env` environment from the kernel options.
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</details>
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## Repository Structure and Software arquitecture
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@ -1,8 +1,6 @@
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name: pyenv5505
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#prefix: ./envs/pyenv5505 # Custom output folder
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name: dima_env
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python=3.11
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- jupyter
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47
setup_env.sh
47
setup_env.sh
@ -1,47 +0,0 @@
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#!/bin/bash
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# Define the name of the environment
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ENV_NAME="multiphase_chemistry_env"
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# Check if mamba is available and use it instead of conda for faster installation
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if command -v mamba &> /dev/null; then
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CONDA_COMMAND="mamba"
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else
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CONDA_COMMAND="conda"
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fi
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# Create the conda environment with all dependencies, resolving from conda-forge and defaults
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$CONDA_COMMAND create -y -n "$ENV_NAME" -c conda-forge -c defaults python=3.11 \
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jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip
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# Check if the environment was successfully created
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if [ $? -ne 0 ]; then
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echo "Failed to create the environment '$ENV_NAME'. Please check the logs above for details."
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exit 1
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fi
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# Activate the new environment
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if source activate "$ENV_NAME" 2>/dev/null || conda activate "$ENV_NAME" 2>/dev/null; then
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echo "Environment '$ENV_NAME' activated successfully."
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else
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echo "Failed to activate the environment '$ENV_NAME'. Please check your conda setup."
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exit 1
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fi
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# Install additional pip packages only if the environment is activated
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echo "Installing additional pip packages..."
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pip install pybis==1.35 igor2 ipykernel sphinx
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# Check if pip installations were successful
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if [ $? -ne 0 ]; then
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echo "Failed to install pip packages. Please check the logs above for details."
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exit 1
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fi
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# Optional: Export the environment to a YAML file (commented out)
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# $CONDA_COMMAND env export -n "$ENV_NAME" > "$ENV_NAME-environment.yaml"
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# Print success message
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echo "Environment '$ENV_NAME' created and configured successfully."
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# echo "Environment configuration saved to '$ENV_NAME-environment.yaml'."
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