Installation of TurboWorkflows

Requirements

Python 3.8 or later
TurboRVB
TurboGenius

Please install TurboRVB and TurboGenius according to their installation instructions.

It is convenient to have conda for managing Python execution environments.

Conda (optional, recommended for Python environment management)

The following Python packages are used. These are automatically installed together with TurboWorkflows.

paramiko
paradag
pyyaml
toml
pandas
graphviz
setuptools_scm

The following is also required when running tutorials.

PySCF
trexio
trexio-tools

Installation Procedure

If you created a conda environment when installing TurboGenius, activate it.
```
conda activate turborvb
```

Obtain the source files from the GitHub repository.

cd ~/applications
git clone https://github.com/kousuke-nakano/turboworkflows.git

Install using pip.
```
cd turboworkflows
pip install -e .
```
Note

-e is for installation in develop mode

Note

To explicitly install in a local environment, for example when permission-related errors occur, add –user.

On the first run of the turbo-jobmanager command, configuration files will be copied to .turbofilemanager_config in the home directory.

turbo-jobmanager --help

The yaml file=/home/user/.turbofilemanager_config/machine_data.yaml is not found!!
/home/user/.turbofilemanager_config is not found. Probably, this is the first run.
/home/user/.turbofilemanager_config has been generated.
plz. edit /home/user/.turbofilemanager_config/machine_data.yaml

Edit the configuration files. For details, see Environment Configuration.
Run the turbo-jobmanager command again.
```
turbo-jobmanager --help
```
If the help message is displayed, the installation has completed successfully.

Upgrade and Uninstallation

Upgrade

To upgrade to the latest version, execute the following commands.
```
cd ~/applications/turboworkflows
git pull
pip install -e . --upgrade
```
Note

Configuration files are not automatically updated. Please update them manually if necessary.
Uninstallation

To uninstall TurboWorkflows, execute the following command.
```
pip uninstall turboworkflows
```
Note

Configuration files (~/.turbofilemanager_config) are not deleted. To completely remove them, please delete them manually.
Backup configuration files

It is recommended to back up configuration files before upgrading or uninstalling.
```
cp -r ~/.turbofilemanager_config ~/.turbofilemanager_config.backup
```