functionsPython

Python library to work with XPS data campaigns, encoded in HDF5 files.

TODO

• Talk to Thorsten about rga txt files. Example folder contains incosistent rga txt files, there is no unique column separator (, or )

Installation

Follow these steps to install and set up the project:

1. Download our GitLab repository in your GitLab folder, or alternatively open a Git Bash terminal and run the following commands

cd Path/to/GitLab
git clone https://gitlab.psi.ch/5505/functionspython.git

2. Open an Anaconda Prompt (Anaconda3) as administrator, and set the current directory to the path of the project's folder.

3. Create the project's environment multiphase_chemistry_env by running the following command:

conda env create -f environment.yml

4. Activate the created environment by running the appropriate command based on your preferred Python IDE or terminal:

• Jupyter Notebook/Lab: When starting a new notebook, select the multiphase_chemistry_env environment from the kernel options.

• Visual Studio Code (VS Code): After opening your project in VS Code, click on the Python interpreter in the status bar and choose the multiphase_chemistry_env environment.

Getting started

To make it easy for you to get started with GitLab, here's a list of recommended next steps.

Already a pro? Just edit this README.md and make it your own. Want to make it easy? Use the template at the bottom!

Add your files

• Create or upload files
• Add files using the command line or push an existing Git repository with the following command:

cd existing_repo
git remote add origin https://gitlab.psi.ch/5505/functionspython.git
git branch -M main
git push -uf origin main

Data integration workflow

Metadata review workflow

- review through branches
- updating files with metadata in Openbis

Specifying a compound attribute in yaml language.

Consider the compound attribute relative_humidity, which has subattributes value, units, range, and definition. The yaml description of such an attribute is as follows:

relative_humidity:
  value: 65
  units: percentage
  range: '[0,100]'
  definition: 'Relative humidity represents the amount of water vapor present in the air relative to the maximum amount of water vapor the air can hold at a given temperature.'  

Deleting or renaming a compound attribute in yaml language.

• Assume the attribute relative_humidity already exists. Then it should be displayed as follows with the subattribute rename_as. This can be set differently to suggest a renaming of the attribute.
• To suggest deletion of an attribute, we are required to add a subattribute delete with value as true. Below for example, the attribute relative_ humidity is suggested to be deleted. Otherwise if delete is set as false, it will have no effect.

relative_humidity:
  delete: true # we added this line in the review process
  rename_as: relative_humidity
  value: 65
  units: percentage
  range: '[0,100]'
  definition: 'Relative humidity represents the amount of water vapor present in the air relative to the maximum amount of water vapor the air can hold at a given temperature.'

cd existing_repo
git remote add origin https://gitlab.psi.ch/5505/functionspython.git
git branch -M main
git push -uf origin main

Integrate with your tools

Integrate with your tools

• Set up project integrations

Collaborate with your team

• Invite team members and collaborators
• Create a new merge request
• Automatically close issues from merge requests
• Enable merge request approvals
• Automatically merge when pipeline succeeds

Test and Deploy

Use the built-in continuous integration in GitLab.

• Get started with GitLab CI/CD
• Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)
• Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy
• Use pull-based deployments for improved Kubernetes management
• Set up protected environments

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Editing this README

When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to makeareadme.com for this template.

Suggestions for a good README

Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.

Name

Choose a self-explaining name for your project.

Description

Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.

Badges

On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.

Visuals

Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.

Installation

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Usage

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Support

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Roadmap

If you have ideas for releases in the future, it is a good idea to list them in the README.

Contributing

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You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.

Authors and acknowledgment

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License

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Project status

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