Merge pull request #44 from vtraag/website

Change project to website

.github/workflows/build_deploy_athenarc.yml

@@ -25,19 +25,6 @@ jobs:
       - name: Render quarto project
         uses: quarto-dev/quarto-actions/render@v2
 
-      - name: Install pagemerger
-        run: |
-          curl -OL https://github.com/tymbaca/pagemerger/releases/download/v1.0.0/pagemerger_1.0-1_amd64.deb
-          sudo dpkg -i pagemerger_1.0-1_amd64.deb
-          sudo apt-get update
-          sudo apt-get install -y aspnetcore-runtime-7.0
-          sudo chmod 755 /usr/local/bin/pagemerger
-
-      - name: Merge cover page with rendered docx
-        run: |
-          pagemerger out.docx etc/cover.docx _book/Open-Science-Indicator-Handbook.docx
-          mv out.docx _book/Open-Science-Indicator-Handbook.docx
-
       - uses: athenarc/actions-docker-build-push@master
         id: docker_build
         with:

.gitignore

@@ -1,6 +1,6 @@
 /.quarto/
 /site_libs/
-/_book/
+/_site/
 **.html
 
 /.luarc.json

_quarto.yml

@@ -1,9 +1,9 @@
 project:
-  type: book
-  output-dir: _book
+  type: website
+  output-dir: _site
   execute-dir: project
 
-book:
+website:
   title: Open Science Indicator Handbook
   reader-mode: true
 
@@ -12,93 +12,106 @@ book:
   repo-branch: main
   repo-actions: [edit, issue]
 
-  downloads: [docx]
-
   navbar:
     search: true
     logo: theme/pathos-logo.png
     logo-href: https://pathos-project.eu/
+    left:
+    - text: "Home"
+      href: index.qmd
+    - text: "Open Science"
+      href: indicator_templates/quarto/1_open_science/APC_costs.qmd
+    - text: "Academic Impact"
+      href: indicator_templates/quarto/2_academic_impact/academic_readership.qmd
+    - text: "Societal Impact"
+      href: indicator_templates/quarto/3_societal_impact/uptake_and_impact_on_societal_issues.qmd
+    - text: "Reproducibility"
+      href: reproducibility_intro.qmd
 
   sidebar:
-    collapse-level: 1
-
-  chapters:
-    - index.qmd
-
-    # - causal_intro/article/intro-causality.qmd Skip causal intro for now
-
-    - part: Open Science
-      chapters:
-        - indicator_templates/quarto/1_open_science/APC_costs.qmd
-        - indicator_templates/quarto/1_open_science/availability_data_repositories.qmd
-        - indicator_templates/quarto/1_open_science/availability_preprint_repositories.qmd
-        - indicator_templates/quarto/1_open_science/availability_publication_repositories.qmd
-        - indicator_templates/quarto/1_open_science/citizen_science.qmd
-        - indicator_templates/quarto/1_open_science/deposition_open_metadata.qmd
-        - indicator_templates/quarto/1_open_science/evaluation_open_science_in_research_assessment.qmd
-        - indicator_templates/quarto/1_open_science/open_access_journals.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_open_access_publishing.qmd
-        - indicator_templates/quarto/1_open_science/open_science_training_facilities.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_national_open_science_policies.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_open_fair_data_practices.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_open_method_practices.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_open_peer_review.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_open_science_funding_policies.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_open_science_support.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_preprinting.qmd
-        - indicator_templates/quarto/1_open_science/prevalence_replication_studies.qmd
-        - indicator_templates/quarto/1_open_science/transformative_publishing_agreements.qmd
-
-    - part: Academic Impact
-      chapters:
-        - indicator_templates/quarto/2_academic_impact/academic_readership.qmd
-        - indicator_templates/quarto/2_academic_impact/citation_impact.qmd
-        - indicator_templates/quarto/2_academic_impact/collaboration_intensity.qmd
-        - indicator_templates/quarto/2_academic_impact/diversity.qmd
-        - indicator_templates/quarto/2_academic_impact/extra-academic_collaboration.qmd
-        - indicator_templates/quarto/2_academic_impact/interdisciplinarity.qmd
-        - indicator_templates/quarto/2_academic_impact/novelty.qmd
-        - indicator_templates/quarto/2_academic_impact/use_of_code_in_research.qmd
-        - indicator_templates/quarto/2_academic_impact/use_of_data_in_research.qmd
-
-    - part: Societal Impact
-      chapters:
-        - indicator_templates/quarto/3_societal_impact/uptake_and_impact_on_societal_issues.qmd
-        - indicator_templates/quarto/3_societal_impact/uptake_by_media.qmd
-        - indicator_templates/quarto/3_societal_impact/scientific_literacy.qmd
-        - indicator_templates/quarto/3_societal_impact/uptake_by_policy_makers.qmd
-        - indicator_templates/quarto/3_societal_impact/uptake_by_patient_groups.qmd
-        - indicator_templates/quarto/3_societal_impact/uptake_in_education.qmd
-        - indicator_templates/quarto/3_societal_impact/uptake_in_medical_practice.qmd
-        - indicator_templates/quarto/3_societal_impact/uptake_in_the_legal_sector.qmd
-
-    - part: Economic Impact
-      chapters:
-        - indicator_templates/quarto/4_economic_impact/science_industry_collaboration.qmd
-        - indicator_templates/quarto/4_economic_impact/innovation_output.qmd
-        - indicator_templates/quarto/4_economic_impact/socially_relevant_products_and_processes.qmd
-        - indicator_templates/quarto/4_economic_impact/economic_growth_of_companies.qmd
-        - indicator_templates/quarto/4_economic_impact/labour_market_impacts.qmd
-        - indicator_templates/quarto/4_economic_impact/cost_savings.qmd
-
-    - part: Reproducibility
-      chapters:
-        - reproducibility_intro.qmd
-        - indicator_templates/quarto/5_reproducibility/consistency_in_reported_numbers.qmd
-        - indicator_templates/quarto/5_reproducibility/impact_of_open_code_in_research.qmd
-        - indicator_templates/quarto/5_reproducibility/impact_of_open_data_in_research.qmd
-        - indicator_templates/quarto/5_reproducibility/inclusion_in_systematic_reviews_or_meta-analyses.qmd
-        - indicator_templates/quarto/5_reproducibility/level_of_replication.qmd
-        - indicator_templates/quarto/5_reproducibility/polarity_of_publications.qmd
-        - indicator_templates/quarto/5_reproducibility/reuse_of_code_in_research.qmd
-        - indicator_templates/quarto/5_reproducibility/reuse_of_data_in_research.qmd
+    - title: Open Science
+      contents:
+        - section: Open Science
+          contents:
+            - indicator_templates/quarto/1_open_science/APC_costs.qmd
+            - indicator_templates/quarto/1_open_science/availability_data_repositories.qmd
+            - indicator_templates/quarto/1_open_science/availability_preprint_repositories.qmd
+            - indicator_templates/quarto/1_open_science/availability_publication_repositories.qmd
+            - indicator_templates/quarto/1_open_science/citizen_science.qmd
+            - indicator_templates/quarto/1_open_science/deposition_open_metadata.qmd
+            - indicator_templates/quarto/1_open_science/evaluation_open_science_in_research_assessment.qmd
+            - indicator_templates/quarto/1_open_science/open_access_journals.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_open_access_publishing.qmd
+            - indicator_templates/quarto/1_open_science/open_science_training_facilities.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_national_open_science_policies.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_open_fair_data_practices.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_open_method_practices.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_open_peer_review.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_open_science_funding_policies.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_open_science_support.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_preprinting.qmd
+            - indicator_templates/quarto/1_open_science/prevalence_replication_studies.qmd
+            - indicator_templates/quarto/1_open_science/transformative_publishing_agreements.qmd
+
+    - title: Academic Impact
+      contents:
+        - section: Academic Impact
+          contents:
+            - indicator_templates/quarto/2_academic_impact/academic_readership.qmd
+            - indicator_templates/quarto/2_academic_impact/citation_impact.qmd
+            - indicator_templates/quarto/2_academic_impact/collaboration_intensity.qmd
+            - indicator_templates/quarto/2_academic_impact/diversity.qmd
+            - indicator_templates/quarto/2_academic_impact/extra-academic_collaboration.qmd
+            - indicator_templates/quarto/2_academic_impact/interdisciplinarity.qmd
+            - indicator_templates/quarto/2_academic_impact/novelty.qmd
+            - indicator_templates/quarto/2_academic_impact/use_of_code_in_research.qmd
+            - indicator_templates/quarto/2_academic_impact/use_of_data_in_research.qmd
+
+    - title: Societal Impact
+      contents:
+        - section: Societal Impact
+          contents:
+            - indicator_templates/quarto/3_societal_impact/uptake_and_impact_on_societal_issues.qmd
+            - indicator_templates/quarto/3_societal_impact/uptake_by_media.qmd
+            - indicator_templates/quarto/3_societal_impact/scientific_literacy.qmd
+            - indicator_templates/quarto/3_societal_impact/uptake_by_policy_makers.qmd
+            - indicator_templates/quarto/3_societal_impact/uptake_by_patient_groups.qmd
+            - indicator_templates/quarto/3_societal_impact/uptake_in_education.qmd
+            - indicator_templates/quarto/3_societal_impact/uptake_in_medical_practice.qmd
+            - indicator_templates/quarto/3_societal_impact/uptake_in_the_legal_sector.qmd
+
+    - title: Economic Impact
+      contents:
+        - section: Economic Impact
+          contents:
+            - indicator_templates/quarto/4_economic_impact/science_industry_collaboration.qmd
+            - indicator_templates/quarto/4_economic_impact/innovation_output.qmd
+            - indicator_templates/quarto/4_economic_impact/socially_relevant_products_and_processes.qmd
+            - indicator_templates/quarto/4_economic_impact/economic_growth_of_companies.qmd
+            - indicator_templates/quarto/4_economic_impact/labour_market_impacts.qmd
+            - indicator_templates/quarto/4_economic_impact/cost_savings.qmd
+
+    - title: Reproducibility
+      contents:
+        - section: Reproducibility
+          contents:
+            - reproducibility_intro.qmd
+            - indicator_templates/quarto/5_reproducibility/consistency_in_reported_numbers.qmd
+            - indicator_templates/quarto/5_reproducibility/impact_of_open_code_in_research.qmd
+            - indicator_templates/quarto/5_reproducibility/impact_of_open_data_in_research.qmd
+            - indicator_templates/quarto/5_reproducibility/inclusion_in_systematic_reviews_or_meta-analyses.qmd
+            - indicator_templates/quarto/5_reproducibility/level_of_replication.qmd
+            - indicator_templates/quarto/5_reproducibility/polarity_of_publications.qmd
+            - indicator_templates/quarto/5_reproducibility/reuse_of_code_in_research.qmd
+            - indicator_templates/quarto/5_reproducibility/reuse_of_data_in_research.qmd
 
 comments:
   hypothesis:
     theme: clean
 
 format:
   html:
+    toc: true
     theme:
       - cosmo
       - theme/style.scss
@@ -109,7 +122,4 @@ format:
     author-meta: "V.A. Traag, etc..."
     callout-appearance: simple
 
-  docx:
-    reference-doc: theme/template.docx
-
 editor: visual

index.qmd

@@ -1,3 +1,7 @@
+---
+sidebar: false
+---
+
 # Introduction {.unnumbered}
 
 This is the work-in-progress Open Science Indicator Handbook by PathOS. In this handbook we cover various indicators measuring various aspects around Open Science itself, their academic, societal and economic impacts, and reproducibility.