Add working link checker workflow using lychee

.github/workflows/link-check.yaml

@@ -0,0 +1,171 @@
+name: Link Checker
+
+# =======================
+# Website Link Validation
+# =======================
+# Purpose: Downloads the latest built site and checks all links (internal + external)
+# Triggers: Weekly on Mondays at 01:30 UTC or manual dispatch
+# Reports: Creates a GitHub issue with label "link-check" when broken links are found
+# Config: See .lychee.toml for exclusion patterns and request settings
+
+on:
+  schedule:
+    # Runs at 01:30 UTC every Monday
+    - cron: '30 1 * * 1'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  issues: write
+  actions: read
+
+concurrency:
+  group: link-check-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  link-check:
+    name: Check Links
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Download latest build artifact
+        uses: dawidd6/action-download-artifact@07ab29fd4a977ae4d2b275087cf67563dfdf0295
+        with:
+          workflow: deploy.yaml
+          name: forrt-website-.*
+          name_is_regexp: true
+          path: /tmp/site
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          search_artifacts: true
+          if_no_artifact_found: fail
+
+      - name: Run lychee link checker
+        id: lychee
+        uses: lycheeverse/lychee-action@v2
+        with:
+          args: "--config .lychee.toml --base-url https://forrt.org /tmp/site"
+          output: /tmp/lychee/out.md
+          fail: false
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Process lychee output
+        if: steps.lychee.outputs.exit_code != 0
+        run: |
+          python3 << 'PYEOF'
+          import re
+
+          with open("/tmp/lychee/out.md") as f:
+              content = f.read()
+
+          lines = content.split("\n")
+
+          # Keep the summary table (everything before "## Errors per input")
+          summary_lines = []
+          error_lines = []
+          in_errors = False
+          for line in lines:
+              if line.startswith("## Errors per input"):
+                  in_errors = True
+                  continue
+              if in_errors:
+                  error_lines.append(line)
+              else:
+                  summary_lines.append(line)
+
+          # Parse errors, tracking which pages each URL appears on
+          # url -> {"status": str, "pages": [str]}
+          url_info = {}
+          main_errors = {}    # non-403
+          forbidden_errors = {}  # 403
+          current_page = ""
+
+          for line in error_lines:
+              # Track section headers (### Errors in /tmp/site/.../index.html)
+              page_match = re.match(r"^### Errors in /tmp/site/[^/]+/(.+)", line)
+              if page_match:
+                  # Convert file path to URL path
+                  path = page_match.group(1)
+                  path = re.sub(r"/index\.html$", "/", path)
+                  current_page = f"/{path}"
+                  continue
+
+              m = re.match(r"^\* \[(\w+)\] <([^>]+)>", line)
+              if not m:
+                  continue
+              status, url = m.group(1), m.group(2)
+
+              target = forbidden_errors if status == "403" else main_errors
+              if url not in target:
+                  target[url] = {"status": status, "pages": []}
+              if current_page and current_page not in target[url]["pages"]:
+                  target[url]["pages"].append(current_page)
+
+          # Build output
+          output = "\n".join(summary_lines).rstrip()
+          output += "\n\n## Broken links\n\n"
+
+          if main_errors:
+              for url, info in main_errors.items():
+                  pages = info["pages"]
+                  page_str = f" (in {pages[0]})" if len(pages) == 1 else f" (in {len(pages)} pages)"
+                  output += f"* [{info['status']}] <{url}>{page_str}\n"
+          else:
+              output += "No broken links found (excluding 403s).\n"
+
+          if forbidden_errors:
+              output += f"\n<details>\n<summary>403 Forbidden ({len(forbidden_errors)} URLs — likely bot-blocking, not broken)</summary>\n\n"
+              output += "These sites block automated requests. The links may still be valid.\n"
+              output += "Showing first 100 — see workflow logs for full list.\n\n"
+              for i, (url, info) in enumerate(forbidden_errors.items()):
+                  if i >= 100:
+                      output += f"\n*... and {len(forbidden_errors) - 100} more*"
+                      break
+                  output += f"* <{url}>\n"
+              output += "\n</details>\n"
+
+          with open("/tmp/lychee/out.md", "w") as f:
+              f.write(output)
+          PYEOF
+
+      - name: Find publisher URLs that should use doi.org
+        id: doi-check
+        run: |
+          # Search source markdown files (excluding glossary, which is auto-generated)
+          # for direct publisher URLs that should use https://doi.org/ instead.
+          PUBLISHERS='(journals\.sagepub|tandfonline|psycnet\.apa|onlinelibrary\.wiley|link\.springer|academic\.oup|sciencedirect|jstor\.org|journals\.lww|royalsocietypublishing)\.(com|org)'
+          # Extract just file:line and the URL itself (not full line content)
+          MATCHES=$(grep -rno --include='*.md' -E \
+            "https?://[^ )\"']*(${PUBLISHERS})/[^ )\"']*(doi/|article|fulltext)[^ )\"']*" \
+            content/ --exclude-dir=content/glossary | sort -u || true)
+          if [ -n "$MATCHES" ]; then
+            COUNT=$(echo "$MATCHES" | wc -l)
+            {
+              echo ""
+              echo "## Publisher URLs that should use doi.org ($COUNT found)"
+              echo ""
+              echo "The following links point directly to publisher websites instead of using"
+              echo "\`https://doi.org/{DOI}\` format. Publishers often block automated requests,"
+              echo "making these URLs uncheckable. Please replace them with doi.org links."
+              echo "If the DOI is not visible in the URL, look it up on https://search.crossref.org"
+              echo ""
+              echo '```'
+              echo "$MATCHES"
+              echo '```'
+            } >> /tmp/lychee/out.md
+            echo "found=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "found=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Create issue from lychee output
+        if: steps.lychee.outputs.exit_code != 0 || steps.doi-check.outputs.found == 'true'
+        uses: peter-evans/create-issue-from-file@v5
+        with:
+          title: "Link Checker Report"
+          content-filepath: /tmp/lychee/out.md
+          labels: link-check
+          token: ${{ secrets.GITHUB_TOKEN }}

.lychee.toml

@@ -0,0 +1,50 @@
+# Lychee link checker configuration
+# https://lychee.cli.rs/usage/config/
+#
+# Used by the link-check GitHub Actions workflow.
+# Checks all links (internal + external) in the built HTML files.
+
+# ---------------------
+# Exclusions
+# ---------------------
+# Patterns to exclude from link checking (common false positives)
+exclude = [
+  # Internal links — already verified as local files in the build artifact
+  "forrt\\.org",
+
+  # Placeholder / example domains
+  "example\\.com",
+  "localhost",
+  "127\\.0\\.0\\.1",
+
+  # Social media sites that block automated requests
+  "linkedin\\.com",
+  "twitter\\.com",
+  "x\\.com",
+
+  # Web Archive — often slow or flaky
+  "web\\.archive\\.org",
+
+  # GitHub edit links with templated paths
+  "github\\.com/.*/edit/",
+]
+
+# ---------------------
+# Request settings
+# ---------------------
+# Accept 2xx/3xx and 429 (rate limiting)
+# Note: 403 is NOT accepted — those are separated into a collapsed section
+# by the workflow's post-processing step, since many publishers block bots.
+accept = ["100..=399", "429"]
+
+# Timeout per request in seconds
+timeout = 30
+
+# Maximum number of retries per link
+max_retries = 3
+
+# Maximum concurrent requests
+max_concurrency = 16
+
+# Do not show progress bar (cleaner CI output)
+no_progress = true

content/authors/berit-t-barthelmes-msc/_index.md

@@ -4,7 +4,7 @@ name: "Berit T. Barthelmes, M.Sc."
 
 # Username (this should match the folder name)
 authors:
-- Name "Berit T. Barthelmes, M.Sc."
+- "Berit T. Barthelmes, M.Sc."
 
 # Is this the primary user of the site?
 superuser: false

content/clusters/cluster3.md

@@ -164,7 +164,7 @@ PsuTeachR's [Data Skills for Reproducible Science](https://psyteachr.github.io/m
 
 ***Includes tools such as statcheck.io, GRIM, and SPRITE***
 
-* Brown, N. J., & Heathers, J. A. (2016). The GRIM test: A simple technique detects numerous anomalies in the reporting of results in psychology. Social Psychological and Personality Science, 1948550616673876. http://journals.sagepub.com/doi/pdf/10.1177/1948550616673876
+* Brown, N. J., & Heathers, J. A. (2016). The GRIM test: A simple technique detects numerous anomalies in the reporting of results in psychology. Social Psychological and Personality Science, 1948550616673876. https://doi.org/10.1177/1948550616673876
 
 * Nuijten, M. B., Van Assen, M. A. L. M., Hartgerink, C. H. J., Epskamp, S., & Wicherts, J. M. (2017). The validity of the tool “statcheck” in discovering statistical reporting inconsistencies. Preprint retrieved from https://psyarxiv.com/tcxaj/.
 

content/educators-corner/004-Teaching-why-how-replication/index.md

@@ -121,7 +121,7 @@ As another example, when I illustrate the smallest-effect-size-of-interest workf
 ![Notes](fig9.webp "Notes")
 
 
-One last issue that comes out of the simulations is the number of assumptions that one must make in the process of doing a simulation study. This includes both statistical assumptions, such as the size of the standard deviation of the outcome measure, and non-statistical assumptions, such as the length of time it takes for a typical participate in the study (a fact that is necessary to accurately estimate the number of participants who can participate in a lab-based study, for example). I argue that pilot studies are useful for developing good values for these assumptions. Pilot studies are _not_ useful for directly estimating the value of the target effect size itself ([Albers & Lakens, 2018](https://www.sciencedirect.com/science/article/pii/S002210311630230X?casa_token=OETt_Sm5VFEAAAAA:-9rK8QScds9e0A1siznusvdtvl0-yC2WpBVWe7ztdGkZ8eVILbyqWMC5WmcsAxHWp6X7X7voPeA)); in any case it is better to power to a smallest effect size of interest than the expected effect size.
+One last issue that comes out of the simulations is the number of assumptions that one must make in the process of doing a simulation study. This includes both statistical assumptions, such as the size of the standard deviation of the outcome measure, and non-statistical assumptions, such as the length of time it takes for a typical participate in the study (a fact that is necessary to accurately estimate the number of participants who can participate in a lab-based study, for example). I argue that pilot studies are useful for developing good values for these assumptions. Pilot studies are _not_ useful for directly estimating the value of the target effect size itself ([Albers & Lakens, 2018](https://www.sciencedirect.com/science/article/pii/S002210311630230X)); in any case it is better to power to a smallest effect size of interest than the expected effect size.
 
 ![Workflow 2](fig10.webp "Workflow 2")
 

content/educators-corner/006-qualitative-OS-practices/index.md

@@ -46,7 +46,7 @@ We thus gathered people interested in qualitative open science research in educa
 ![Criteria for Reporting Qualitative Studies](Fig1.webp "Criteria for Reporting Qualitative Studies")
 
 
-3. **Open Materials.** Thanks to the internet, researchers have websites and repositories where they can upload the tools for others to access. In qualitative research, this might mean interview protocols, memos, coding notebooks, tools (such as Nvivo or R packages), or even the data itself. This provides a sort of audit trail so others can verify the results of the research. There is no all or nothing here; open materials, much like the rest of these open science practices, exist along a spectrum. Not only what researchers share is on a spectrum; researchers can also dictate who may access the open materials. Perhaps it’s the entire public, but it could just be people who want to verify findings (i.e., dissertation committees, participants, reviewers). Below you can see how [Bowman and Keene (2018)](https://www.tandfonline.com/doi/pdf/10.1080/08824096.2018.1513273) described open science practices as a layered onion with the innermost layer being the most transparent. However, no matter what or to whom materials are shared, researchers must include their plan within their consent procedures and IRB protocols to not violate any ethical boundaries. 
+3. **Open Materials.** Thanks to the internet, researchers have websites and repositories where they can upload the tools for others to access. In qualitative research, this might mean interview protocols, memos, coding notebooks, tools (such as Nvivo or R packages), or even the data itself. This provides a sort of audit trail so others can verify the results of the research. There is no all or nothing here; open materials, much like the rest of these open science practices, exist along a spectrum. Not only what researchers share is on a spectrum; researchers can also dictate who may access the open materials. Perhaps it’s the entire public, but it could just be people who want to verify findings (i.e., dissertation committees, participants, reviewers). Below you can see how [Bowman and Keene (2018)](https://doi.org/10.1080/08824096.2018.1513273) described open science practices as a layered onion with the innermost layer being the most transparent. However, no matter what or to whom materials are shared, researchers must include their plan within their consent procedures and IRB protocols to not violate any ethical boundaries. 
 
 
 ![Conceptual Onion of Open Science Practices](Fig2.webp "Conceptual Onion of Open Science Practices")

content/educators-corner/010-Neurodiversity/index.md

@@ -58,7 +58,7 @@ People with disabilities are more likely to be excluded from the academic workfo
 
 Many gatekeepers determine whether an individual is neurodivergent and these processes are driven by individuals who are neurotypical. As a result, referral time for these services vary widely, from 4 weeks to 201 weeks within the UK (Lloyd, 2019) and if a person does not fit the criteria, the individual can be ignored and may not receive the much-needed help that they require. This can lead to poor self-esteem, unemployment (e.g. around 22% in autistic people are in any type of employment; see Figure 2 in [fact sheet](https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/disability/articles/outcomesfordisabledpeopleintheuk/2020)). As a result, neurodivergent individuals may blame themselves for the difficulties they encounter, as opposed to the barriers that society has placed on them. 
 
-Despite this, people of different neurodivergent conditions or families of the people with the conditions have begun meeting and talking to each other about their experiences and one common shared experience is a  history of misinterpretation and mistreatment by the dominant neurotypical cultures and its institutions such as academia. As a result of centuries of oppression of disabled people worldwide and a hyper-normalised environment, in addition to seeing the disproportionate impact of the coronavirus pandemic on disabled students (see this amazing [paper ](https://link.springer.com/article/10.1007/s10639-021-10559-3)by Dr Joanna Zawadka), many neurodivergent and disabled staff feel discouraged in an environment that should aim to support them. They do not feel like they belong, their differences are seen as an impairment and their voice does not seem to matter. They do not see themselves represented in psychological science, academia, business, teaching or elsewhere.
+Despite this, people of different neurodivergent conditions or families of the people with the conditions have begun meeting and talking to each other about their experiences and one common shared experience is a  history of misinterpretation and mistreatment by the dominant neurotypical cultures and its institutions such as academia. As a result of centuries of oppression of disabled people worldwide and a hyper-normalised environment, in addition to seeing the disproportionate impact of the coronavirus pandemic on disabled students (see this amazing [paper ](https://doi.org/10.1007/s10639-021-10559-3)by Dr Joanna Zawadka), many neurodivergent and disabled staff feel discouraged in an environment that should aim to support them. They do not feel like they belong, their differences are seen as an impairment and their voice does not seem to matter. They do not see themselves represented in psychological science, academia, business, teaching or elsewhere.
 
 We are a group of early-career neurotypical and neurodivergent researchers that are a part of the Framework of Open Reproducible Research and Training (FORRT) community, aiming to make academia and the open scholarship community more open to neurodiversity. Everyone, no matter what they identify with, is welcome in this group.  We aim to discuss how open scholarship can be intersected with the neurodiversity movement, and emphasise how differences should be highlighted and accepted, whilst supporting  the idea of accessibility. Our neurodiversity team is a group that currently consists of individuals that have autism, dyspraxia/DCD, speech-language differences, ADHD, dyslexia, or are neurotypical allies. If you have these or other neurominorities and wish to be part of the team, you are more than welcome to join!