diff --git a/docs/pages/additional_considerations/documentation.md b/docs/pages/additional_considerations/documentation.md index 4f94b91..7765d28 100644 --- a/docs/pages/additional_considerations/documentation.md +++ b/docs/pages/additional_considerations/documentation.md @@ -6,6 +6,6 @@ parent: Additional Considerations grand_parent: Contributor QuickStart Guide --- -## Documentation: +## Documentation -Write detailed documentation for your code. Use a tool like Sphinx to generate documentation from docstrings. Place the documentation in the `docs/` folder. \ No newline at end of file +Write detailed documentation for your code. Use a tool like [Sphinx](https://www.sphinx-doc.org) to generate documentation from docstrings. Place the documentation in the `docs/` folder. diff --git a/docs/pages/additional_considerations/package.md b/docs/pages/additional_considerations/package.md index b01eebf..af83325 100644 --- a/docs/pages/additional_considerations/package.md +++ b/docs/pages/additional_considerations/package.md @@ -8,7 +8,7 @@ grand_parent: Contributor QuickStart Guide ## Package Your Code: -Create a `setup.py` file for packaging your code. Include necessary metadata like name, version, author, and dependencies. Example: +Create a `setup.py` file for packaging your code. Include necessary metadata like name, [version](../versioning), [author](/workflow-store/#5-add-citation-info-optional), and [dependencies](../python_environments). Example: ```python from setuptools import setup, find_packages diff --git a/docs/pages/additional_considerations/readme.md b/docs/pages/additional_considerations/readme.md index 563a34d..a457c83 100644 --- a/docs/pages/additional_considerations/readme.md +++ b/docs/pages/additional_considerations/readme.md @@ -6,20 +6,20 @@ parent: Additional Considerations grand_parent: Contributor QuickStart Guide --- -## README.md: +## README.md Write a comprehensive README.md file to provide an overview of your project. Include the following: - Title - Badges (e.g., Travis CI, Codecov) - Project description - Installation instructions - Usage examples - Citation information - Configuration options - Contribution guidelines - Code of conduct - License information +- Title +- Badges (e.g., Travis CI, Codecov) +- Project description +- Installation instructions +- Usage examples +- Configuration options +- Citation information +- Contribution guidelines +- Code of conduct +- License information Example README.md template: diff --git a/docs/pages/additional_considerations/release.md b/docs/pages/additional_considerations/release.md index cfa5ce3..4588f30 100644 --- a/docs/pages/additional_considerations/release.md +++ b/docs/pages/additional_considerations/release.md @@ -8,4 +8,4 @@ grand_parent: Contributor QuickStart Guide ## Release Workflow: -Consider using a tool like `twine` to upload your package to the Python Package Index (PyPI). Create a release workflow that includes updating version numbers, creating tags, and publishing the package. \ No newline at end of file +Consider using a tool like `twine` to upload your package to the Python Package Index (PyPI). Create a release workflow that includes [updating version numbers](../versioning), [creating tags](/workflow-store/#6-create-a-releasetag), and publishing the package. diff --git a/docs/pages/additional_considerations/versioning.md b/docs/pages/additional_considerations/versioning.md index d701aeb..613806a 100644 --- a/docs/pages/additional_considerations/versioning.md +++ b/docs/pages/additional_considerations/versioning.md @@ -6,6 +6,6 @@ parent: Additional Considerations grand_parent: Contributor QuickStart Guide --- -## Choose proper version numbers: +## Choose proper version numbers -Follow semantic versioning (SemVer) for versioning your project (major.minor.patch). Update the version number in your setup.py file when releasing a new version. \ No newline at end of file +Follow [semantic versioning (SemVer)](https://semver.org/) for versioning your project (major.minor.patch). Update the version number in your [meta.json](/workflow-store/#2-add-meta-information), [CITATION.cff](/workflow-store/#4-add-a-license-optional), [setup.py](../package), etc. files when releasing a new version. Then [create a new tag and release](/workflow-store/#6-create-a-releasetag) and [upload it to the workflow store](/workflow-store/#7-upload-to-the-workflow-store). diff --git a/docs/pages/index.md b/docs/pages/index.md index 7324ce6..2cdf535 100644 --- a/docs/pages/index.md +++ b/docs/pages/index.md @@ -48,12 +48,13 @@ Sample `meta.json`: } ``` -Full info on the file format [here](https://workflows.material-digital.de/info/). +Full info on the file format [here](pages/detailed_instructions/metadata). ### 3. Add a README (optional) -Add a Readme instructions/installation/tips/FAQs.-> section Readme +Add a Readme with instructions and tips on setup and useage of your workflow. +[Further suggestions on creating your Readme](pages/additional_considerations/readme) ### 4. Add a License (optional) @@ -68,14 +69,14 @@ Author Name *et al.* (2023) *"Title of publication."* Journal [Vol], p1-10 DOI:. #### Citation File (optional) The prefered method to add citations is to include - a [`CREDENTIALS.cff` file](https://citation-file-format.github.io/) in your repository. +a [`CREDENTIALS.cff` file](https://citation-file-format.github.io/) in your repository. ### 6. Create a release/tag Commit all required files and create a release with an associated [release tag](https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository#creating-a-release) ### 7. Upload to the Workflow Store -1. Login to the [workflow Store](https://workflows.material-digital.de/) +1. Login to the [workflow Store](https://workflows.material-digital.de/) (via the button in the top right) 2. [Upload your workflow](https://workflows.material-digital.de/upload_workflow/) -Detailed instructions including information on how to add private repositories are provided in the [upload workflow section]() +Detailed instructions including information on how to add private repositories are provided in the [upload workflow section](pages/detailed_instructions/upload/). diff --git a/docs/pages/user-guide/execute-workflow.md b/docs/pages/user-guide/execute-workflow.md index 52ee9c0..4df4ad4 100644 --- a/docs/pages/user-guide/execute-workflow.md +++ b/docs/pages/user-guide/execute-workflow.md @@ -5,8 +5,9 @@ nav_order: 2 parent: User Guide --- -### Quickstart-guide for executing a workflow -#### pyiron +# Quickstart Guide for Executing a Workflow + +## pyiron - ensure you have access to unix-like environment: - Linux & macOS will work right away 1. install conda [link to conda](https://conda.io/projects/conda/en/latest/user-guide/install/index.html). We suggest to install the [miniforge distribution](https://github.com/conda-forge/miniforge), but any conda/mamba installation will work just fine. @@ -16,6 +17,6 @@ parent: User Guide 5. open the notebook `.ipynb` and execute the workflow (i.e. run the notebook cells). - windows: use wsl or [anacondaprompt](https://conda.io/projects/conda/en/latest/user-guide/install/windows.html). *It's strongly suggested to use wsl, as it will ensure you can use all of the following instructions & suggestions right away.* With wsl, follow the linux instructions from above. If you choose to use anacondaprompt, you already have access to a conda installation and may start from step 2 onward. -#### simstack: +### SimStack: - [install](https://simstack.readthedocs.io/en/latest/installation/index.html) - download and unpack diff --git a/docs/pages/user-guide/find-and-download.md b/docs/pages/user-guide/find-and-download.md index a011e96..fdd97f2 100644 --- a/docs/pages/user-guide/find-and-download.md +++ b/docs/pages/user-guide/find-and-download.md @@ -5,22 +5,22 @@ nav_order: 1 parent: User Guide --- +# Find and Download Workflows -### Login -- log in using your material-digital account +## Login +- log in [via the button in the top right](https://workflows.material-digital.de) using your material-digital account -### Find and download workflows -#### Using the website's UI +## Using the Website - browse the inventory or use the search feature - select a workflow you are interested in. *Note that each workflow requires one of the workflow environments supported by the PMD: pyiron or simstack* - Click on download. You will recieve a zip-archive. Unpack it to your preferred destination. -#### Using the API +## Using the API - make sure you are logged in - click on 'User details' or navigate your browser to [https://workflows.material-digital.de/auth/user_details](https://workflows.material-digital.de/auth/user_details) - click on 'Generate token' or directly navigate to [https://workflows.material-digital.de/get-token](https://workflows.material-digital.de/get-token) in your browser -##### Get all workflows +### Get All Workflows **Bash** ```bash curl -X GET \ @@ -55,7 +55,7 @@ Result: ] ``` -##### Download a single workflow +### Download a Single Workflow **Bash** ```bash curl -X GET \