PEAR-2035 update pdf generation

The old way to building PDFs was unsupported and did not work with Python 3. Instead, we moved to a mkdocs plugin, mkdocs-with-pdf, that does the conversion as part of the mkdocs build.
NCIP · Aug 1, 2024 · dd33d8b · dd33d8b
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diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,4 @@ site/
 .DS_Store
 venv*/
 .vscode/
+docs/*/PDF/*.pdf
diff --git a/API_UG.yml b/API_UG.yml
@@ -1,30 +1,64 @@
+---
 #
 # GDC Docs - Config
 #
 
 site_name: GDC Docs
-site_url: http://gdc-docs.nci.nih.gov
+site_url: https://docs.gdc.cancer.gov
 repo_url: https://github.com/NCI-GDC/gdc-docs
-copyright: "&copy; 2015-2016"
-theme_dir: theme
-pages:
-- API:
-  - Getting Started: 'API/Users_Guide/Getting_Started.md'
-  - Search and Retrieval: 'API/Users_Guide/Search_and_Retrieval.md'
-  - Downloading Files: 'API/Users_Guide/Downloading_Files.md'
-  - Data Analysis: API/Users_Guide/Data_Analysis.md
-  - BAM Slicing: 'API/Users_Guide/BAM_Slicing.md'
-  - Submission: 'API/Users_Guide/Submission.md'
-  - Python Examples: 'API/Users_Guide/Python_Examples.md'
-  - GraphQL Examples: 'API/Users_Guide/GraphQL_Examples.md'
-  - System Information: 'API/Users_Guide/System_Information.md'
-  - Additional Examples: 'API/Users_Guide/Additional_Examples.md'
-  - "Appendix A: Available Fields": 'API/Users_Guide/Appendix_A_Available_Fields.md'
-  - "Appendix B: Key Terms": 'API/Users_Guide/Appendix_B_Key_Terms.md'
-  - "Appendix C: Format of Submission Queries and Responses": 'API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses.md'
-  - Release Notes: 'API/Release_Notes/API_Release_Notes.md'
+copyright: '&copy; 2015-2024'
+nav:
+  - API:
+      - Home: index.md
+      - Getting Started: API/Users_Guide/Getting_Started.md
+      - Search and Retrieval: API/Users_Guide/Search_and_Retrieval.md
+      - Downloading Files: API/Users_Guide/Downloading_Files.md
+      - Data Analysis: API/Users_Guide/Data_Analysis.md
+      - BAM Slicing: API/Users_Guide/BAM_Slicing.md
+      - Submission: API/Users_Guide/Submission.md
+      - Python Examples: API/Users_Guide/Python_Examples.md
+      - GraphQL Examples: API/Users_Guide/GraphQL_Examples.md
+      - System Information: API/Users_Guide/System_Information.md
+      - Additional Examples: API/Users_Guide/Additional_Examples.md
+      - 'Appendix A: Available Fields': API/Users_Guide/Appendix_A_Available_Fields.md
+      - 'Appendix B: Key Terms': API/Users_Guide/Appendix_B_Key_Terms.md
+      - 'Appendix C: Format of Submission Queries and Responses': API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses.md
+      - Release Notes: API/Release_Notes/API_Release_Notes.md
 extra:
-  project_root_dir: '/'
-  project_org: 'GDC'
-  project_description: 'GDC Docs'
+  project_root_dir: /
+  project_org: GDC
+  project_description: GDC Docs
   version: 1.0
+theme:
+  custom_dir: overrides
+  favicon: images/favicon.ico
+  features:
+    - navigation.tabs
+    - navigation.tabs.sticky
+  logo: images/nih-header-logo-color.png
+  name: material
+  palette:
+    primary: white
+    scheme: gdc-accessible
+markdown_extensions:
+  - tables
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      combine_header_slug: true
+      alternate_style: true
+      slugify: !!python/object/apply:pymdownx.slugs.slugify
+        kwds:
+          case: lower
+  - pymdownx.details
+plugins:
+  - with-pdf:
+      author: NCI GDC
+      cover_title: GDC API User's Guide
+      cover_subtitle: NCI Genomic Data Commons (GDC)
+      cover_logo: docs/images/nih-header-logo-color.png
+      toc_level: 3
+      exclude_pages:
+        - ^$
+      enabled_if_env: ENABLE_PDF_EXPORT
+      render_js: false
+      output_path: ../docs/API/PDF/API_UG.pdf
diff --git a/Data_Portal_UG.yml b/Data_Portal_UG.yml
@@ -1,34 +1,67 @@
+---
 #
 # GDC Docs - Config
 #
 
 site_name: GDC Docs
-site_url: http://docs.gdc.cancer.gov
+site_url: https://docs.gdc.cancer.gov
 repo_url: https://github.com/NCI-GDC/gdc-docs
-copyright: "&copy; 2015-2016"
-theme_dir: theme
-pages:
-- Data Portal:
-  - Getting Started: 'Data_Portal/Users_Guide/getting_started.md'
-  - Quick Start: 'Data_Portal/Users_Guide/quick_start.md'
-  - Cohort Builder: 'Data_Portal/Users_Guide/cohort_builder.md'
-  - Analysis Center: 'Data_Portal/Users_Guide/analysis_center.md'
-  - Repository: 'Data_Portal/Users_Guide/Repository.md'
-  - Projects: 'Data_Portal/Users_Guide/Projects.md'
-  - BAM Slicing: 'Data_Portal/Users_Guide/BAMslicing.md'
-  - Clinical Data Analysis: 'Data_Portal/Users_Guide/clinical_data_analysis.md'
-  - Cohort Comparison: 'Data_Portal/Users_Guide/cohort_comparison.md'
-  - Cohort Level MAF: 'Data_Portal/Users_Guide/cohortMAF.md'
-  - Gene Expression Clustering: 'Data_Portal/Users_Guide/gene_expression_clustering.md'
-  - Mutation Frequency: 'Data_Portal/Users_Guide/mutation_frequency.md'
-  - OncoMatrix: 'Data_Portal/Users_Guide/oncomatrix.md'
-  - ProteinPaint: 'Data_Portal/Users_Guide/proteinpaint_lollipop.md'
-  - Sequence Reads: 'Data_Portal/Users_Guide/proteinpaint_bam.md'
-  - Set Operations: 'Data_Portal/Users_Guide/set_operations.md'
-  - For Developers: 'Data_Portal/Users_Guide/Developers_Guide.md'
-  - Release Notes: 'Data_Portal/Release_Notes/Data_Portal_Release_Notes.md'
+copyright: '&copy; 2015-2024'
+nav:
+  - Data Portal:
+      - Getting Started: Data_Portal/Users_Guide/getting_started.md
+      - Quick Start: Data_Portal/Users_Guide/quick_start.md
+      - Cohort Builder: Data_Portal/Users_Guide/cohort_builder.md
+      - Analysis Center: Data_Portal/Users_Guide/analysis_center.md
+      - Repository: Data_Portal/Users_Guide/Repository.md
+      - Projects: Data_Portal/Users_Guide/Projects.md
+      - BAM Slicing: Data_Portal/Users_Guide/BAMslicing.md
+      - Clinical Data Analysis: Data_Portal/Users_Guide/clinical_data_analysis.md
+      - Cohort Comparison: Data_Portal/Users_Guide/cohort_comparison.md
+      - Cohort Level MAF: Data_Portal/Users_Guide/cohortMAF.md
+      - Gene Expression Clustering: Data_Portal/Users_Guide/gene_expression_clustering.md
+      - Mutation Frequency: Data_Portal/Users_Guide/mutation_frequency.md
+      - OncoMatrix: Data_Portal/Users_Guide/oncomatrix.md
+      - ProteinPaint: Data_Portal/Users_Guide/proteinpaint_lollipop.md
+      - Sequence Reads: Data_Portal/Users_Guide/proteinpaint_bam.md
+      - Set Operations: Data_Portal/Users_Guide/set_operations.md
+      - For Developers: Data_Portal/Users_Guide/Developers_Guide.md
+      - Release Notes: Data_Portal/Release_Notes/Data_Portal_Release_Notes.md
 extra:
-  project_root_dir: '/'
-  project_org: 'GDC'
-  project_description: 'GDC Docs'
+  project_root_dir: /
+  project_org: GDC
+  project_description: GDC Docs
   version: 1.0
+theme:
+  custom_dir: overrides
+  favicon: images/favicon.ico
+  features:
+    - navigation.tabs
+    - navigation.tabs.sticky
+  logo: images/nih-header-logo-color.png
+  name: material
+  palette:
+    primary: white
+    scheme: gdc-accessible
+markdown_extensions:
+  - tables
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      combine_header_slug: true
+      alternate_style: true
+      slugify: !!python/object/apply:pymdownx.slugs.slugify
+        kwds:
+          case: lower
+  - pymdownx.details
+plugins:
+  - with-pdf:
+      author: NCI GDC
+      cover_title: GDC Data Portal User's Guide
+      cover_subtitle: NCI Genomic Data Commons (GDC)
+      cover_logo: docs/images/nih-header-logo-color.png
+      toc_level: 3
+      exclude_pages:
+        - ^$
+      enabled_if_env: ENABLE_PDF_EXPORT
+      render_js: false
+      output_path: ../docs/Data_Portal/PDF/Data_Portal_UG.pdf
diff --git a/Data_Submission_Portal_UG.yml b/Data_Submission_Portal_UG.yml
@@ -1,23 +1,56 @@
+---
 #
 # GDC Docs - Config
 #
 
 site_name: GDC Docs
-site_url: http://docs.gdc.cancer.gov
+site_url: https://docs.gdc.cancer.gov
 repo_url: https://github.com/NCI-GDC/gdc-docs
-copyright: "&copy; 2015-2016"
-theme_dir: theme
-pages:
-- Data Submission Portal:
-  - Before Submitting Data to the GDC Portal: 'Data_Submission_Portal/Users_Guide/Checklist.md'
-  - Data Submission Overview: 'Data_Submission_Portal/Users_Guide/Data_Submission_Overview.md'
-  - Data Submission Portal: 'Data_Submission_Portal/Users_Guide/Data_Submission_Process.md'
-  - Data Upload Walkthrough: 'Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md'
-  - Pre-Release Data Portal: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
-  - Release Notes: 'Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md'
+copyright: '&copy; 2015-2024'
+nav:
+  - Data Submission Portal:
+      - Before Submitting Data to the GDC Portal: Data_Submission_Portal/Users_Guide/Checklist.md
+      - Data Submission Overview: Data_Submission_Portal/Users_Guide/Data_Submission_Overview.md
+      - Data Submission Portal: Data_Submission_Portal/Users_Guide/Data_Submission_Process.md
+      - Data Upload Walkthrough: Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md
+      - Pre-Release Data Portal: Data_Submission_Portal/Users_Guide/Pre_Release_QC.md
+      - Release Notes: Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md
 
 extra:
-  project_root_dir: '/'
-  project_org: 'GDC'
-  project_description: 'GDC Docs'
+  project_root_dir: /
+  project_org: GDC
+  project_description: GDC Docs
   version: 1.0
+theme:
+  custom_dir: overrides
+  favicon: images/favicon.ico
+  features:
+    - navigation.tabs
+    - navigation.tabs.sticky
+  logo: images/nih-header-logo-color.png
+  name: material
+  palette:
+    primary: white
+    scheme: gdc-accessible
+markdown_extensions:
+  - tables
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      combine_header_slug: true
+      alternate_style: true
+      slugify: !!python/object/apply:pymdownx.slugs.slugify
+        kwds:
+          case: lower
+  - pymdownx.details
+plugins:
+  - with-pdf:
+      author: NCI GDC
+      cover_title: GDC Data Submission Portal User's Guide
+      cover_subtitle: NCI Genomic Data Commons (GDC)
+      cover_logo: docs/images/nih-header-logo-color.png
+      toc_level: 3
+      exclude_pages:
+        - ^$
+      enabled_if_env: ENABLE_PDF_EXPORT
+      render_js: false
+      output_path: ../docs/Data_Submission_Portal/PDF/Data_Submission_Portal_UG.pdf
diff --git a/Data_Transfer_Tool_UG.yml b/Data_Transfer_Tool_UG.yml
@@ -1,23 +1,56 @@
+---
 #
 # GDC Docs - Config
 #
 
 site_name: GDC Docs
-site_url: http://docs.gdc.cancer.gov
+site_url: https://docs.gdc.cancer.gov
 repo_url: https://github.com/NCI-GDC/gdc-docs
-copyright: "&copy; 2015-2016"
-theme_dir: theme
-pages:
-- Data Transfer Tool:
-  - Getting Started: 'Data_Transfer_Tool/Users_Guide/Getting_Started.md'
-  - Preparing for Data Download and Upload: 'Data_Transfer_Tool/Users_Guide/Preparing_for_Data_Download_and_Upload.md'
-  - Data Transfer Tool Command Line Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
-  - Release Notes - Command Line: 'Data_Transfer_Tool/Release_Notes/DTT_Release_Notes.md'
-  - Data Transfer Tool UI Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_DTT_UI.md'
-  - Release Notes - UI: 'Data_Transfer_Tool/Release_Notes/DTT_UI_Release_Notes.md'
+copyright: '&copy; 2015-2024'
+nav:
+  - Data Transfer Tool:
+      - Getting Started: Data_Transfer_Tool/Users_Guide/Getting_Started.md
+      - Preparing for Data Download and Upload: Data_Transfer_Tool/Users_Guide/Preparing_for_Data_Download_and_Upload.md
+      - Data Transfer Tool Command Line Documentation: Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md
+      - Release Notes - Command Line: Data_Transfer_Tool/Release_Notes/DTT_Release_Notes.md
+      - Data Transfer Tool UI Documentation: Data_Transfer_Tool/Users_Guide/Data_Download_DTT_UI.md
+      - Release Notes - UI: Data_Transfer_Tool/Release_Notes/DTT_UI_Release_Notes.md
 
 extra:
-  project_root_dir: '/'
-  project_org: 'GDC'
-  project_description: 'GDC Docs'
+  project_root_dir: /
+  project_org: GDC
+  project_description: GDC Docs
   version: 1.0
+theme:
+  custom_dir: overrides
+  favicon: images/favicon.ico
+  features:
+    - navigation.tabs
+    - navigation.tabs.sticky
+  logo: images/nih-header-logo-color.png
+  name: material
+  palette:
+    primary: white
+    scheme: gdc-accessible
+markdown_extensions:
+  - tables
+  - pymdownx.superfences
+  - pymdownx.tabbed:
+      combine_header_slug: true
+      alternate_style: true
+      slugify: !!python/object/apply:pymdownx.slugs.slugify
+        kwds:
+          case: lower
+  - pymdownx.details
+plugins:
+  - with-pdf:
+      author: NCI GDC
+      cover_title: GDC Data Transfer Tool User's Guide
+      cover_subtitle: NCI Genomic Data Commons (GDC)
+      cover_logo: docs/images/nih-header-logo-color.png
+      toc_level: 3
+      exclude_pages:
+        - ^$
+      enabled_if_env: ENABLE_PDF_EXPORT
+      render_js: false
+      output_path: ../docs/Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf