Merge pull request #15 from s4b7r/small-fixes

Several minor fixes

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.
+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.

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

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:
 

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.
+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.

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.
+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).

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/).

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 `<workflowname>.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

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 \