PEAR-2035 upgrade build encyclopedia script

In addition to upgrading the script, I also commited the
resulting encyclopidia changes to mkdocs.yml

buildencyclopedia.py

@@ -4,24 +4,43 @@
 import os
 import yaml
 
+try:
+    from yaml import CLoader as Loader, CDumper as Dumper
+except ImportError:
+    from yaml import Loader, Dumper
+
 ABSFILEPATH = os.path.dirname(os.path.realpath(__file__))
-FILEARRAY = os.listdir(ABSFILEPATH + '/docs/Encyclopedia/pages')
+FILEARRAY = os.listdir(ABSFILEPATH + "/docs/Encyclopedia/pages")
 FILEARRAY = sorted(FILEARRAY, key=str.lower)
 
-with open(ABSFILEPATH + '/mkdocs.yml', 'r') as f:
-    doc = yaml.load(f)
+with open(ABSFILEPATH + "/mkdocs.yml", "r") as f:
+    doc = yaml.load(f, Loader=Loader)
 
-encycdict = next(d for (index, d) in enumerate(doc['pages']) \
-             if d.get('EncyclopediaEntries', False) != False)
+encycdict = next(
+    d for (index, d) in enumerate(doc["nav"]) if d.get("Encyclopedia", False) != False
+)
 
 newlist = []
 
 for x in range(len(FILEARRAY)):
     if FILEARRAY[x][-3:] == ".md":
-        tempdict = {FILEARRAY[x][:-3].replace("_"," "):"".join(['Encyclopedia/pages/', FILEARRAY[x][:-3], '.md'])}
+        tempdict = {
+            FILEARRAY[x][:-3].replace("_", " "): "".join(
+                ["Encyclopedia/pages/", FILEARRAY[x][:-3], ".md"]
+            )
+        }
         newlist.append(tempdict)
 
-encycdict['EncyclopediaEntries'] = newlist
-
-with open(ABSFILEPATH + '/mkdocs.yml', 'w+') as f:
-    f.write(yaml.dump(doc, default_flow_style=False))
+encycdict["Encyclopedia"] = newlist
+
+with open(ABSFILEPATH + "/mkdocs.yml", "w+") as f:
+    f.write(
+        yaml.dump(
+            doc,
+            default_flow_style=False,
+            explicit_start=True,
+            indent=2,
+            width=80,
+            Dumper=Dumper,
+        )
+    )

mkdocs.yml

@@ -26,10 +26,6 @@ markdown_extensions:
         kwds:
           case: lower
   - pymdownx.details
-  # - BSCodeTabExtension:
-  #     animate_tab_transitions: false
-  #     default_lang: Source
-  #     show_all_code_as_folders: true
 nav:
   - Home: index.md
   - API:
@@ -109,15 +105,23 @@ nav:
       - Release Notes: Data/Release_Notes/Data_Release_Notes.md
       - fa-file-text Download PDF /Data/PDF/Data_UG.pdf: Data/PDF/index.md
   - Encyclopedia:
-      - Index: Encyclopedia/index.md
+      - ABSOLUTE LiftOver: Encyclopedia/pages/ABSOLUTE_LiftOver.md
       - Affymetrix SNP 6.0: Encyclopedia/pages/Affymetrix_SNP_6.0.md
       - Aggregated Somatic Mutation: Encyclopedia/pages/Aggregated_Somatic_Mutation.md
       - Aligned Reads: Encyclopedia/pages/Aligned_Reads.md
       - Aliquot: Encyclopedia/pages/Aliquot.md
+      - Aliquot Ensemble Somatic Variant Merging and Masking: Encyclopedia/pages/Aliquot_Ensemble_Somatic_Variant_Merging_and_Masking.md
       - Analyte: Encyclopedia/pages/Analyte.md
       - Annotations: Encyclopedia/pages/Annotations.md
       - Annotations TCGA: Encyclopedia/pages/Annotations_TCGA.md
+      - Arriba: Encyclopedia/pages/Arriba.md
+      - ASCAT2: Encyclopedia/pages/ASCAT2.md
+      - ASCAT3: Encyclopedia/pages/ASCAT3.md
+      - AscatNGS: Encyclopedia/pages/AscatNGS.md
+      - BCGSC miRNA Profiling: Encyclopedia/pages/BCGSC_miRNA_Profiling.md
       - Biospecimen Data: Encyclopedia/pages/Biospecimen_Data.md
+      - Birdseed: Encyclopedia/pages/Birdseed.md
+      - BRASS: Encyclopedia/pages/BRASS.md
       - Cancer Genomics Hub: Encyclopedia/pages/Cancer_Genomics_Hub.md
       - Case: Encyclopedia/pages/Case.md
       - Center for Cancer Genomics: Encyclopedia/pages/Center_for_Cancer_Genomics.md
@@ -128,8 +132,13 @@ nav:
       - Data Submitter: Encyclopedia/pages/Data_Submitter.md
       - dbGaP: Encyclopedia/pages/dbGaP.md
       - Entity: Encyclopedia/pages/Entity.md
+      - FM Simple Somatic Mutation: Encyclopedia/pages/FM_Simple_Somatic_Mutation.md
+      - FoundationOne Annotation: Encyclopedia/pages/FoundationOne_Annotation.md
+      - FoundationOne Variant Aggregation and Masking: Encyclopedia/pages/FoundationOne_Variant_Aggregation_and_Masking.md
       - FPKM-UQ: Encyclopedia/pages/FPKM-UQ.md
       - FPKM: Encyclopedia/pages/FPKM.md
+      - GATK4 MuTect2 Tumor-Only: Encyclopedia/pages/GATK4_MuTect2_Tumor-Only.md
+      - GATK4 MuTect2 Tumor-Only Annotation: Encyclopedia/pages/GATK4_MuTect2_Tumor-Only_Annotation.md
       - GDC API: Encyclopedia/pages/GDC_API.md
       - GDC Data Portal: Encyclopedia/pages/GDC_Data_Portal.md
       - GDC Data Submission Portal: Encyclopedia/pages/GDC_Data_Submission_Portal.md
@@ -142,29 +151,45 @@ nav:
       - Latest Data: Encyclopedia/pages/Latest_Data.md
       - Manifest File: Encyclopedia/pages/Manifest_File.md
       - MD5 Checksum: Encyclopedia/pages/MD5_Checksum.md
+      - MuSE: Encyclopedia/pages/MuSE.md
+      - MuSE Annotation: Encyclopedia/pages/MuSE_Annotation.md
       - Mutation Annotation Format: Encyclopedia/pages/Mutation_Annotation_Format.md
       - Mutation Annotation Format TCGAv2: Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2.md
+      - MuTect2: Encyclopedia/pages/MuTect2.md
+      - MuTect2 Annotation: Encyclopedia/pages/MuTect2_Annotation.md
+      - Pindel: Encyclopedia/pages/Pindel.md
+      - Pindel Annotation: Encyclopedia/pages/Pindel_Annotation.md
       - Redaction: Encyclopedia/pages/Redaction.md
       - Release Number: Encyclopedia/pages/Release_Number.md
       - REST API: Encyclopedia/pages/REST_API.md
       - RNA-Seq: Encyclopedia/pages/RNA-Seq.md
+      - SeSAMe Methylation Beta Estimation: Encyclopedia/pages/SeSAMe_Methylation_Beta_Estimation.md
+      - Seurat 10x Chromium: Encyclopedia/pages/Seurat_10x_Chromium.md
       - SNP Array-Based Data: Encyclopedia/pages/SNP_Array-Based_Data.md
+      - STAR-Fusion: Encyclopedia/pages/STAR-Fusion.md
+      - STAR 2-Pass Chimeric: Encyclopedia/pages/STAR_2-Pass_Chimeric.md
+      - STAR 2-Pass Genome: Encyclopedia/pages/STAR_2-Pass_Genome.md
+      - STAR 2-Pass Transcriptome: Encyclopedia/pages/STAR_2-Pass_Transcriptome.md
+      - STAR Counts: Encyclopedia/pages/STAR_Counts.md
       - TCGA Barcode: Encyclopedia/pages/TCGA_Barcode.md
       - TCGA VCF 1.1v2: Encyclopedia/pages/TCGA_VCF_1.1v2.md
       - TCIA: Encyclopedia/pages/TCIA.md
       - UUID: Encyclopedia/pages/UUID.md
       - Variant Call Format: Encyclopedia/pages/Variant_Call_Format.md
       - Variant Type: Encyclopedia/pages/Variant_Type.md
+      - VarScan2: Encyclopedia/pages/VarScan2.md
+      - VarScan2 Annotation: Encyclopedia/pages/VarScan2_Annotation.md
+      - VCF LiftOver: Encyclopedia/pages/VCF_LiftOver.md
 site_name: GDC Docs
 site_url: http://docs.gdc.cancer.gov
 theme:
-  name: material
-  logo: images/nih-header-logo-color.png
+  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
-  custom_dir: overrides

requirements.in

@@ -1,2 +1,3 @@
 mkdocs>=1.6.0
 mkdocs-material>=9.5.26
+pyyaml>=6.0.1

requirements.txt

@@ -6,7 +6,7 @@
 #
 babel==2.15.0
     # via mkdocs-material
-certifi==2024.6.2
+certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
     # via requests
@@ -41,7 +41,7 @@ mkdocs==1.6.0
     #   mkdocs-material
 mkdocs-get-deps==0.2.0
     # via mkdocs
-mkdocs-material==9.5.26
+mkdocs-material==9.5.30
     # via -r requirements.in
 mkdocs-material-extensions==1.3.1
     # via mkdocs-material
@@ -55,25 +55,26 @@ platformdirs==4.2.2
     # via mkdocs-get-deps
 pygments==2.18.0
     # via mkdocs-material
-pymdown-extensions==10.8.1
+pymdown-extensions==10.9
     # via mkdocs-material
 python-dateutil==2.9.0.post0
     # via ghp-import
 pyyaml==6.0.1
     # via
+    #   -r requirements.in
     #   mkdocs
     #   mkdocs-get-deps
     #   pymdown-extensions
     #   pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
-regex==2024.5.15
+regex==2024.7.24
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
 six==1.16.0
     # via python-dateutil
-urllib3==2.2.1
+urllib3==2.2.2
     # via requests
 watchdog==4.0.1
     # via mkdocs