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nfdi4cat · Oct 12, 2024 · d92402b · d92402b
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diff --git a/.buildinfo b/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 97df74e32765a91deeb228a735f7bda8
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/docs_maintenance/creating-docs-locally.doctree b/.doctrees/docs_maintenance/creating-docs-locally.doctree
diff --git a/.doctrees/docs_maintenance/handling-ID-requests.doctree b/.doctrees/docs_maintenance/handling-ID-requests.doctree
diff --git a/.doctrees/docs_usage/about.doctree b/.doctrees/docs_usage/about.doctree
diff --git a/.doctrees/docs_usage/guidelines.doctree b/.doctrees/docs_usage/guidelines.doctree
diff --git a/.doctrees/docs_usage/how-to-contribute.doctree b/.doctrees/docs_usage/how-to-contribute.doctree
diff --git a/.doctrees/docs_usage/how-to-use.doctree b/.doctrees/docs_usage/how-to-use.doctree
diff --git a/.doctrees/docs_usage/published-guidelines-v2.doctree b/.doctrees/docs_usage/published-guidelines-v2.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/404.html b/404.html
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+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="" xml:lang="">
+<head>
+  <meta charset="utf-8" />
+  <meta name="generator" content="pandoc" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+  <title>404</title>
+  <style>
+    h1 {
+      color: #005A9C;
+      font: 200% sans-serif;
+      text-align: center
+    }
+    body {
+      padding: 2em;
+      font-family: sans-serif;
+      text-align: center;
+    }
+  </style>
+</head>
+<body>
+  <h1 id="section">404</h1>
+  <p>We couldn’t find the page you are looking for.</p>
+  <p>Check out:</p>
+  <p>
+    <a href="https://nfdi4cat.github.io/voc4cat/"><img src="https://img.shields.io/static/v1?label=voc4cat&amp;message=index%20of%20pages&amp;color=green&amp;logo=github"   alt="voc4cat - index of pages" /></a>
+    <a href="https://github.com/nfdi4cat/voc4cat"><img src="https://img.shields.io/static/v1?label=voc4cat&amp;message=repository&amp;color=blue&amp;logo=github" alt="voc4cat - repository" /></a>
+  </p>
+  </body>
+</html>
diff --git a/_images/cc-by-license.png b/_images/cc-by-license.png
diff --git a/_images/contributions-steps.png b/_images/contributions-steps.png
diff --git a/_images/dechema.png b/_images/dechema.png
diff --git a/_images/dfg.png b/_images/dfg.png
diff --git a/_images/nfdi4cat-partners.png b/_images/nfdi4cat-partners.png
diff --git a/_images/referenced-in-qrcodes.png b/_images/referenced-in-qrcodes.png
diff --git a/_images/voc4cat-concept-sheet.webp b/_images/voc4cat-concept-sheet.webp
diff --git a/_images/voc4cat-pylode-docs.webp b/_images/voc4cat-pylode-docs.webp
diff --git a/_images/workflow.png b/_images/workflow.png
diff --git a/_images/xlsx-icon-on-concept-sheet.webp b/_images/xlsx-icon-on-concept-sheet.webp
diff --git a/_sources/docs_maintenance/creating-docs-locally.md.txt b/_sources/docs_maintenance/creating-docs-locally.md.txt
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+# Building the documentation locally
+
+You need a recent Python version on your computer and a local clone of the repository.
+
+The following commands should be run from the root directory of the clone.
+
+First, install the required packages into a virtual environment. The documentation is build with Sphinx and MyST for markdown support.
+
+```bat
+py -m venv .venv
+.venv\Scripts\activate
+pip install -r docs\requirements.txt
+```
+
+Navigate to the docs-directory and build the documentation:
+
+```bat
+cd docs
+make html
+```
+
+The documentation is created in `docs/_build` and can be previewed by opening the file `docs\_build\html\index.html` in a web browser.
diff --git a/_sources/docs_maintenance/handling-ID-requests.md.txt b/_sources/docs_maintenance/handling-ID-requests.md.txt
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+# Handling ID-requests
+
+```{note} This guide is only relevant for maintainers with commit rights.
+```
+
+To update or create ID-ranges for people use the following workflow.
+It is written for using git from the command line.
+
+**Step 1**: Navigate to the folder on your computer with a local clone of the voc4cat-repo:
+
+```bat
+C:\Users\dlinke\MyProg_local
+λ cd gh-nfdi4cat\voc4cat
+```
+
+Make sure you are on the main branch. If not switch to the main branch with `git switch main`.
+
+**Step 2**: Pull the latest changes into the local repo.
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(main -> origin)
+λ git pull
+remote: Enumerating objects: 33, done.
+remote: Counting objects: 100% (33/33), done.
+remote: Compressing objects: 100% (23/23), done.
+remote: Total 33 (delta 10), reused 30 (delta 10), pack-reused 0
+Unpacking objects: 100% (33/33), 100.81 KiB | 291.00 KiB/s, done.
+From https://github.com/nfdi4cat/voc4cat
+   9d78e5a..d0f2cd7  main       -> origin/main
+ + f9c7ee0...01421a8 gh-pages   -> origin/gh-pages  (forced update)
+Updating 9d78e5a..d0f2cd7
+Fast-forward
+ vocabularies/voc4cat/0007018.ttl        |  2 +-
+ vocabularies/voc4cat/0007101.ttl        | 18 ++++++++++++++++++
+(...)
+```
+
+**Step 3**: Create a feature branch with a reasonable name (here the IDs were requested in issue #79).
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(main -> origin)
+λ git switch -c issue79-id-request
+Switched to a new branch 'issue79-id-request'
+```
+
+**Step 4**: Open an editor and update the `idranges.toml` file based on the request.
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request)
+λ code .
+```
+
+**Step 5**: Push the changes to GitHub. This involves, adding the changed file, setting the remote branch and pushing the changes.
+
+First it is a good idea to check the status of the git repository.
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request)
+λ git status
+On branch issue79-id-request
+Changes not staged for commit:
+  (use "git add <file>..." to update what will be committed)
+  (use "git restore <file>..." to discard changes in working directory)
+        modified:   idranges.toml
+
+no changes added to commit (use "git add" and/or "git commit -a")
+```
+
+If there is just `idrange.toml` changed (as expected) we proceed:
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request)
+λ git add idranges.toml
+
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request)
+λ git commit -m "Add idrange for philippstangl"
+[issue79-id-request c9f6770] Add idrange for philippstangl
+ 1 file changed, 7 insertions(+)
+
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request)
+λ git push --set-upstream origin issue79-id-request
+Enumerating objects: 5, done.
+Counting objects: 100% (5/5), done.
+Delta compression using up to 4 threads
+Compressing objects: 100% (3/3), done.
+Writing objects: 100% (3/3), 395 bytes | 79.00 KiB/s, done.
+Total 3 (delta 2), reused 0 (delta 0), pack-reused 0
+remote: Resolving deltas: 100% (2/2), completed with 2 local objects.
+remote:
+remote: Create a pull request for 'issue79-id-request' on GitHub by visiting:
+remote:      https://github.com/nfdi4cat/voc4cat/pull/new/issue79-id-request
+remote:
+To https://github.com/nfdi4cat/voc4cat.git
+ * [new branch]      issue79-id-request -> issue79-id-request
+branch 'issue79-id-request' set up to track 'origin/issue79-id-request'.
+
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request -> origin)
+```
+
+**Step 6**: Create a pull request on GitHub.
+
+To do this open the the [voc4cat-repo](https://github.com/nfdi4cat/voc4cat). GitHub will automatically offer you to create a PR from the branch just pushed.
+
+You can also use the the link provided in the command line output.
+
+**Step 7**: Accept the PR in GitHub GUI (needs approval by another developer/curator).
+
+After the successful merge, delete the feature branch in the PR-page on GitHub (there is a button for it).
+
+**Step 8**: Clean up your local repo.
+
+Switch back to main in the local repo and pull the latest changes:
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(issue79-id-request)
+λ git switch main
+Switched to branch 'main'
+Your branch is up to date with 'origin/main'.
+
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(main -> origin)
+λ git pull
+remote: Enumerating objects: 5, done.
+remote: Counting objects: 100% (5/5), done.
+remote: Compressing objects: 100% (1/1), done.
+remote: Total 3 (delta 2), reused 2 (delta 2), pack-reused 0
+Unpacking objects: 100% (3/3), 409 bytes | 20.00 KiB/s, done.
+From https://github.com/nfdi4cat/voc4cat
+   d0f2cd7..d634f60  main       -> origin/main
+Updating d0f2cd7..d634f60
+Fast-forward
+ idranges.toml | 7 +++++++
+ 1 file changed, 7 insertions(+)
+```
+
+Finally, you may want to delete the feature branch to keep your local repo clean.
+
+```bat
+C:\Users\dlinke\MyProg_local\gh-nfdi4cat\voc4cat(main -> origin)
+λ git branch -d issue79-id-request
+warning: deleting branch 'issue79-id-request' that has been merged to
+         'refs/remotes/origin/issue79-id-request', but not yet merged to HEAD
+Deleted branch issue79-id-request (was 7a74c4d).
+```
diff --git a/_sources/docs_usage/about.md.txt b/_sources/docs_usage/about.md.txt
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+# About Voc4Cat
+
+Voc4Cat is an example for applying *open data, open code, and open infrastructure (O3)* to create community-curated scientific resources that can outlast funding.
+For more information on the *O3* idea, see [C. Hoyt and B. Gyori, 2024](https://doi.org/10.1038/s41597-024-03406-w).
+
+```{todo} Add contributors, maintainers, citation, licence etc. - review which parts from about-guidelines and main project README.md should move here.
+```
+
+**FUNDING**
+
+<img src="./media/dfg.png" alt="DFG logo" />
+
+This work was funded by the German Research Foundation (DFG) through the project "[NFDI4Cat](https://nfdi4cat.org/) - NFDI for Catalysis-Related
+Sciences" (DFG project no. [441926934](https://gepris.dfg.de/gepris/projekt/441926934)),
+within the National Research Data Infrastructure ([NFDI](https://www.nfdi.de/)) programme of the Joint Science Conference (GWK).
+
+**CONTACT for NFDI4Cat**
+
+<img src="./media/dechema.png" alt="DECHEMA e.V. logo" />
+
+DECHEMA Gesellschaft für Chemische Technik und Biotechnologie e.V.
+Theodor-Heuss-Allee 25
+D–60486 Frankfurt am Main
+
+Phone: 0049-69-7564-0
+Fax: 0049-69-7564-117
+
+Dr. Sara Espinoza
+
+e-mail: [email protected]  
+Internet: https://www.dechema.de