workflow-nodes 0.4.1

Collection of nodes for use in workflows.

Workflow-Nodes

Workflow-Nodes is a collection of nodes usable inside a workflow written in Python 3. There are nodes to generate reports, to wrap system commands like awk and some nodes for special use cases like integrating ImageJ macros. Additionally, some nodes can interact with a Kadi4Mat instance.

Each node is an executable command line tool providing the --xmlhelp interface.

Installation

The library can be installed using pip3 (or pip, if there is no dedicated version of pip for Python 3 installed), which generally comes bundled with Python installations. Python version >= 3.6 is required.

pip3 install workflow-nodes

When installing the library from source for development instead, it is recommended to install the library in editable mode, which simply creates a link to the sources so all changes are reflected in the installed package immediately. The command will also install some additional development dependencies as defined in setup.py.

pip3 install -e .[dev]

Running the installations inside a virtual environment is recommended, see Virtualenv for more information.

After installing, make sure the workflow-nodes command is runnable from anywhere. Depending on the type of installation and if a virtual environment is used or not, the PATH system variable may need to be adapted accordingly to include the path the executable resides in. For example, the following command can be used on Linux, assuming the executable resides in ~/.local/bin:

export PATH=${HOME}/.local/bin:${PATH}

This line can also be added to .bashrc so it will be executed each time a new terminal is opened:

echo 'export PATH=${HOME}/.local/bin:${PATH}' >> ${HOME}/.bashrc

Autocomplete can be activated via

workflow-nodes config activate-autocompletion

for fish, Zsh, Bash and PowerShell.

Usage

All commands concerning different resources are available as various subcommands. For more information or to get a list of subcommands, the following commands can be used:

workflow-nodes --help

workflow-nodes --commands

To use nodes with the local workflow editor, they have to be added to the file $HOME/.pacestudio/tools.txt. Afterwards you can insert them using the "Add Tool" context menu option in the editor.

Creating new nodes

1. Create a Python file for the node in the desired package, e.g. in workflow_nodes/report/.
2. Implement the functionality of the tool. You can use other existing tools as reference.
3. Add the implemented function to a fitting subcommand group, e.g. to workflow_nodes/report/main.py.