Fix replace linkcheck with https://linkchecker.github.io

.github/workflows/linkcheck.yml

@@ -7,15 +7,13 @@ jobs:
     runs-on: ubuntu-latest
     name: Check for broken links
     steps:
-    - name: Check for broken links
-      id: link-report
-      uses: celinekurpershoek/link-checker@v1.0.2
+    - name: Setup Python
+      uses: actions/setup-python@v5
       with:
-        # Required:
-        url: 'https://hupo-psi.github.io/mzQC/'
-        # optional:
-        honorRobotExclusions: false
-        ignorePatterns: 'github,google,channel'
-        recursiveLinks: false # Check all URLs on all reachable pages (could take a while)
+        python-version: '3.10'
+    - run: pip3 install linkchecker
+    - name: Link Checker
+      id: link-report
+      run: linkchecker -ofailures --check-extern --ignore-url="\s*\.md" https://hupo-psi.github.io/mzQC/
     - name: Get the result
-      run: echo "${{steps.link-report.outputs.result}}"
+      run: echo linkchecker/failures

docs/pages/use-case-stories/mzQC_for_analytical_chemists.md

@@ -17,7 +17,7 @@ While many of the papers describing QC metrics for mass spectrometry have been b
 4. What fraction of MS/MS scans came from +2 precursor ions?
     _63.67%_
 
-Naturally, it’s much easier if you use software to produce these values.  In this case, I am using values reported by the QuaMeter software[1] in “IDFree” mode.
+Naturally, it’s much easier if you use software to produce these values.  In this case, I am using values reported by the QuaMeter software [1](#bumbershoot) in “IDFree” mode.
 
 
 ## Format metrics in JSON
@@ -124,5 +124,5 @@ Choosing JSON rather than XML is intended to reduce the effort required to write
 
 
 ---
-[1]: Bumbershoot from proteowizard.sourceforge.net.  X. Wang et al. Anal. Chem.. (2014) 86: 2497
+<a id="bumbershoot">[1]</a>: Bumbershoot from proteowizard.sourceforge.net.  X. Wang et al. Anal. Chem.. (2014) 86: 2497
 Original draft: https://docs.google.com/document/d/16b1n_LXYWsxLK2PQfXWj_WvtiwJOXu2EZx1Q8WzZNlc/edit#

docs/pages/use-cases.md

@@ -6,13 +6,13 @@ permalink: /use-cases/
 This page should give you a (non-exclusive) overview over the use cases covered by mzQC:
 
 ## Handover Format
-It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/individual-runs/).
+It is easy with **mzQC** to get relevant QC info, easy to put your data into context (of measurement realities). That makes it a preferred medium to handover quality information. Read more about it in [mzQC at a glance](at-a-glance/) and explore [a small mzQC example](../examples/intro_run/).
 
 ## Quality Reports
 With JSON at its core, mzQC follows a '_works online, works everywhere_' approach. Even for single spectra, as we show with the [universal spectrum identifier example](../examples/USI-example/).
 
 ## Archival
-The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/qc-sample-run/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzML-mzQC/).
+The format is an optimal QC tool for the analytical chemist and instrument operators keeping track (and archive) instrument performance. Read on with an [introduction to mzQC for anlytical chemists](analytical-chemists/) or explore our [QC sample example](../examples/QC2-sample-example/). You can even embed mzQC in mzML, should you choose to. [View an example here](../examples/mzml-mzqc-example/).
 
 ## Common currency
 With mzQC for archival, quality reports, and as handover format, [mzQC can serve as a common currency](mzQC-common-currency/) for data repositories, journals, and collaborators.

docs/pages/worked-examples/QC2-sample-example.mzQC.md

@@ -53,4 +53,4 @@ Since each column is in turn defined by a cv term, the column can also be assign
 
 
 ### This is the mzQC file once again, in full:
-**[QC2-sample-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/QC2-sample-example.mzQC)**
+**[QC2-sample-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/QC2-sample-example.mzQC)**

docs/pages/worked-examples/USI-example.mzQC.md

@@ -53,4 +53,4 @@ Each row represents one spectrum that can be directly looked up, in the case of
 [even directly from the web](https://www.proteomicsdb.org/use/?usi=mzspec:PXD000966:CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09:scan:2).
 
 ### This is the mzQC file once again, in full:
-**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/USI-example.mzQC)**
+**[USI-example.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/USI-example.mzQC)**

docs/pages/worked-examples/metabo-batches.mzQC.md

@@ -87,4 +87,4 @@ before | after
 
 
 ### This is the mzQC file once again, in full:
-**[metabo-batches.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/metabo-batches.mzQC)**
+**[metabo-batches.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/metabo-batches.mzQC)**

docs/pages/worked-examples/mzml-mzqc-example.md

@@ -84,4 +84,4 @@ The `<cv>` elements are again very similar to the respective entries in _mzQC_,
 Note that you should also add your software to `<software>` and `<dataProcessing>`.
 
 ### This is the mzQC file once again, in full:
-**[mzml-mzqc-example.mzML](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/mzml-mzqc-example.mzML)**
+**[mzml-mzqc-example.mzML](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/mzml-mzqc-example.mzML)**

docs/pages/worked-examples/set-of-runs.mzQC.md

@@ -456,4 +456,4 @@ On the other hand, ommitting the `healthy`/`diseased` setQualities is not sensib
 }
 ```
 ### This is the mzQC file once again, in full:
-**[sets-of-runs.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/draft_v1/examples/set-of-runs.mzQC)**
+**[sets-of-runs.mzQC](https://github.com/HUPO-PSI/mzQC/tree/main/specification_documents/examples/set-of-runs.mzQC)**