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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
parent c40d138563
commit 978101f9c2
3 changed files with 24 additions and 77 deletions
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42
README.md
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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). 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** 3. **PSI Network Access**
@ -44,9 +44,9 @@ For **Windows** users, the following are required:
### Download DIMA ### 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 ```bash
cd path/to/Gitea cd path/to/Gitea
@ -54,46 +54,42 @@ Navigate to your `Gitea` folder, clone the repository, and navigate to the `dima
cd dima 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 ```bash
cd path/to/GitLab/dima cd path/to/Gitea/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
conda env create --file environment.yml conda env create --file environment.yml
``` ```
3. Activate the Environment
```bash
conda activate dima_env
```
<details> ### Working with Jupyter Notebooks
<summary> <b> Working with Jupyter Notebooks </b> </summary> We now make the previously installed Python environment `dima_env` selectable as a kernel in Jupyter's interface.
We now make the previously installed Python environment `multiphase_chemistry_env` selectable as a kernel in Jupyter's interface.
1. Open an Anaconda Prompt, check if the environment exists, and activate it: 1. Open an Anaconda Prompt, check if the environment exists, and activate it:
``` ```
conda env list conda env list
conda activate multiphase_chemistry_env conda activate dima_env
``` ```
2. Register the environment in Jupyter: 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: 3. Start a Jupyter Notebook by running the command:
``` ```
jupyter notebook 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 ## Repository Structure and Software arquitecture

4
environment.yml
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@ -1,8 +1,6 @@
name: pyenv5505 name: dima_env
#prefix: ./envs/pyenv5505 # Custom output folder
channels: channels:
- conda-forge - conda-forge
- defaults
dependencies: dependencies:
- python=3.11 - python=3.11
- jupyter - jupyter

47
setup_env.sh
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@ -1,47 +0,0 @@
#!/bin/bash
# Define the name of the environment
ENV_NAME="multiphase_chemistry_env"
# Check if mamba is available and use it instead of conda for faster installation
if command -v mamba &> /dev/null; then
CONDA_COMMAND="mamba"
else
CONDA_COMMAND="conda"
fi
# Create the conda environment with all dependencies, resolving from conda-forge and defaults
$CONDA_COMMAND create -y -n "$ENV_NAME" -c conda-forge -c defaults python=3.11 \
jupyter numpy h5py pandas matplotlib plotly=5.24 scipy pip
# Check if the environment was successfully created
if [ $? -ne 0 ]; then
echo "Failed to create the environment '$ENV_NAME'. Please check the logs above for details."
exit 1
fi
# Activate the new environment
if source activate "$ENV_NAME" 2>/dev/null || conda activate "$ENV_NAME" 2>/dev/null; then
echo "Environment '$ENV_NAME' activated successfully."
else
echo "Failed to activate the environment '$ENV_NAME'. Please check your conda setup."
exit 1
fi
# Install additional pip packages only if the environment is activated
echo "Installing additional pip packages..."
pip install pybis==1.35 igor2 ipykernel sphinx
# Check if pip installations were successful
if [ $? -ne 0 ]; then
echo "Failed to install pip packages. Please check the logs above for details."
exit 1
fi
# Optional: Export the environment to a YAML file (commented out)
# $CONDA_COMMAND env export -n "$ENV_NAME" > "$ENV_NAME-environment.yaml"
# Print success message
echo "Environment '$ENV_NAME' created and configured successfully."
# echo "Environment configuration saved to '$ENV_NAME-environment.yaml'."