Update docs, Automate pdf and html regeneration

Author: telatin

Makefile

@@ -10,10 +10,14 @@ build:
 
 .PHONY: docs
 
-docs: docs/pdf/abif.pdf docs/pdf/abi2fq.pdf docs/pdf/abimetadata.pdf
+
+docs: docs/theindex.html docs/pdf/abif.pdf docs/pdf/abi2fq.pdf docs/pdf/abimetadata.pdf docs/pdf/abichromatogram.pdf
 	find src/htmldocs/ -type f | xargs rm -v
 	echo "All documentation generated."
 
+docs/theindex.html:
+	nimble docs
+
 docs/pdf/%.pdf: src/%.nim
 	@echo "Generating documentation for $<"
 	nim doc2tex $<
@@ -25,6 +29,8 @@ docs: $(patsubst src/%.nim,docs/pdf/%.pdf,$(wildcard src/*.nim))
 
 # Make clean should remove bin/* and all the binaries (not .nim!) in tests 
 clean:
+	find docs/ -name "*.idx" | xargs rm -v
+	find docs/ -name "theindex.html" | xargs rm -v
 	find . -name abif.log -delete
 	find bin/  -type f  | xargs rm -v
 	find tests -type f -name "test_*" ! -name '*.nim' | xargs rm -v

abif.nimble

@@ -90,10 +90,11 @@ let isNim2OrLater = versionAtLeast(nimVersion, 2, 0, 0)
 task docs, "Generate documentation":
 
   if isNim2OrLater:
-    exec "nim doc --project --out:docs src/abif.nim"
-    exec "nim doc --project --out:docs src/abi2fq.nim"
-    exec "nim doc --project --out:docs src/abimerge.nim"
-    exec "nim doc --project --out:docs src/abimetadata.nim"
+    exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --index:on --project --out:docs src/abif.nim"
+    exec "nim doc  --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abi2fq.nim"
+    exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abimerge.nim"
+    exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abimetadata.nim"
+    exec "nim doc --git.url:https://github.com/quadram-institute-bioscience/nim-abif/ --git.commit:main --project --out:docs src/abichromatogram.nim"
 
 task buildbin, "Build all binaries to bin/ directory":
     exec "mkdir -p bin"

docs/abi2fq.html

@@ -103,7 +103,9 @@ <h1 class="title">src/abi2fq</h1>
 
   </div>
   <div class="nine columns" id="content">
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L1" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L1" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
     <div id="tocRoot"></div>
 
     <p class="module-desc"><p>This module provides a command-line tool for converting ABIF files to FASTQ format with optional quality trimming.</p>
@@ -147,7 +149,9 @@ <h1><a class="toc-backref" href="#7">Types</a></h1>
   <dd>
 
     Configuration for the abi2fq tool. Contains command-line options and settings.
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L37" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L37" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
   </dd>
 </div>
 
@@ -165,7 +169,9 @@ <h1><a class="toc-backref" href="#12">Procs</a></h1>
     <p>Main entry point for the abi2fq program.</p>
 <p>Handles command-line parsing, reads the input ABIF file, performs quality trimming if enabled, and outputs the result in FASTQ format.</p>
 
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L206" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L206" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
   </dd>
 </div>
 
@@ -185,7 +191,9 @@ <h1><a class="toc-backref" href="#12">Procs</a></h1>
 </ul>
 <p>Returns: A Config object with settings based on command-line arguments</p>
 
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L69" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L69" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
   </dd>
 </div>
 
@@ -196,7 +204,9 @@ <h1><a class="toc-backref" href="#12">Procs</a></h1>
   <dd>
 
     Displays the help message for the abi2fq tool. Exits the program after displaying the message.
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L48" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L48" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
   </dd>
 </div>
 
@@ -213,7 +223,9 @@ <h1><a class="toc-backref" href="#12">Procs</a></h1>
 <p>Parameters: sequence: The DNA sequence to trim qualities: Quality scores for each base in the sequence windowSize: Size of the sliding window for quality assessment threshold: Quality threshold (bases with qualities below this are trimmed)</p>
 <p>Returns: A tuple containing the trimmed sequence and its quality values</p>
 
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L132" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L132" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
   </dd>
 </div>
 
@@ -229,7 +241,9 @@ <h1><a class="toc-backref" href="#12">Procs</a></h1>
 <p>If outFile is empty, the FASTQ data is written to stdout.</p>
 <p>Parameters: sequence: The DNA sequence to write qualities: Quality scores for each base in the sequence name: The sample name for the FASTQ header outFile: Path to the output file (empty string for stdout)</p>
 
-    
+    <a href="https://github.com/quadram-institute-bioscience/nim-abif//tree/main/src/abi2fq.nim#L182" class="link-seesrc" target="_blank">Source</a>&nbsp;&nbsp;
+<a href="https://github.com/quadram-institute-bioscience/nim-abif//edit/devel/src/abi2fq.nim#L182" class="link-seesrc" target="_blank" >Edit</a>&nbsp;&nbsp;
+
   </dd>
 </div>
 
@@ -244,7 +258,7 @@ <h1><a class="toc-backref" href="#12">Procs</a></h1>
       <div class="twelve-columns footer">
         <span class="nim-sprite"></span>
         <br>
-        <small style="color: var(--hint);">Made with Nim. Generated: 2025-04-26 09:24:11 UTC</small>
+        <small style="color: var(--hint);">Made with Nim. Generated: 2025-04-26 09:58:55 UTC</small>
       </div>
     </div>
   </div>