Merge pull request #79 from revbayes/checked_snippet

Add a snippet tag that checks the snippet against a file.

Author: bredelings

_plugins/snippet.rb

@@ -0,0 +1,53 @@
+module Liquid
+	class Snippet < Block
+		def initialize(tag_name, markup, options)
+			super
+                        @filename = markup.strip
+		end
+
+		def render(context)
+                        code_block = super.strip
+                        code_lines = code_block.lines.map{ |l| l.strip }
+
+                        # Site source directory (so we don't need absolute paths)
+                        current_page_path = context.registers[:page]["path"]    # e.g., "docs/example.md"
+                        page_dir = File.dirname(current_page_path)               # => "docs"
+
+                        # Resolve snippet file relative to the document
+                        site_source = context.registers[:site].source
+                        file_path = File.expand_path(File.join(site_source, page_dir, @filename))
+  
+                        unless File.exist?(file_path)
+#                          return "❌ Error: File '#{@filename}' not found at #{file_path}."
+                          raise IOError, "❌ Error: File '#{@filename}' not found at #{file_path}."
+                        end
+
+                        file_lines = File.readlines(file_path).map{ |l| l.strip }
+
+                        # Search for exact match of code_lines in file_lines
+                        match_found = false
+                        (0..(file_lines.length - code_lines.length)).each do |start_idx|
+                          if file_lines[start_idx, code_lines.length] == code_lines
+                            match_found = true
+                            break
+                          end
+                        end
+
+                        unless match_found
+#                          return "❌ Error: Code block not found in file `#{@filename}`:\n\n#{code_block}"
+                          raise RuntimeError, "❌ Error: Code block not found in file `#{@filename}`:\n\n#{code_block}"
+                        end
+
+                        <<~MARKDOWN
+
+
+                        ```
+                        #{code_block}
+                        ```
+
+                        MARKDOWN
+		end
+	end
+end
+
+Liquid::Template.register_tag('snippet', Liquid::Snippet)

tutorials/biogeo/tests.txt

@@ -2,4 +2,4 @@ run_simple.Rev
 run_simple_phy.Rev
 run_epoch.Rev
 run_epoch_phy.Rev
-mcmc_primates_bg_simple.Rev
+

tutorials/chromo/index.md

@@ -281,25 +281,29 @@ model, run the MCMC analysis, and summarize the results.
 First, we'll read in the phylogeny. In this example the phylogeny is
 assumed known. In further examples we'll jointly estimate chromosome
 evolution and the phylogeny.
-```
+
+{% snippet scripts/ChromEvol_simple.Rev %}
 phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
-```
+{% endsnippet %}
+
 We need to limit the maximum number of chromosomes allowed in our model,
 so here we use the largest observed chromosome count plus 10. This is an
 arbitrary limit on the size of the state space that could be increased
 if necessary.
-```
+
+{% snippet scripts/ChromEvol_simple.Rev %}
 max_chromo = 26
-```
+{% endsnippet %}
+
 Now we get the observed chromosome counts from a tab-delimited file.
-```
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
-```
+{% snippet scripts/ChromEvol_simple.Rev %}
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
+{% endsnippet %}
 Finally, we initialize a variable for our vector of moves and monitors.
-```
+{% snippet scripts/ChromEvol_simple.Rev %}
 moves    = VectorMoves()
 monitors = VectorMonitors()
-```
+{% endsnippet %}
 
 ### The Chromosome Evolution Model
 

tutorials/chromo/scripts/BiChroM.Rev

@@ -52,7 +52,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_bichrom_counts.tsv", stateLabels=2*(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_bichrom_counts.tsv", stateLabels=2*(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromEvol_clado.Rev

@@ -37,7 +37,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromEvol_joint.Rev

@@ -35,7 +35,7 @@ monitors = VectorMonitors()
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 # Get the DNA sequence alignment for the matK chloroplast gene.
 dna_seq = readDiscreteCharacterData("data/aristolochia_matK.fasta")

tutorials/chromo/scripts/ChromEvol_simmap.Rev

@@ -34,7 +34,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/scripts/ChromEvol_simple.Rev

@@ -35,7 +35,7 @@ phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################
@@ -133,3 +133,4 @@ ancestralStateTree(phylogeny, anc_state_trace, "output/ChromEvol_simple_final.tr
 # using the RevGadgets R package.
 #
 #########################################################################################################
+q()

tutorials/chromo/scripts/ChromoSSE_simple.Rev

@@ -35,7 +35,7 @@ phylogeny <- readTrees("data/aristolochia-bd.tree")[1]
 max_chromo = 26
 
 # Get the chromosome counts from a tab-delimited file.
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", headers=FALSE)
+chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
 
 
 #########################

tutorials/chromo/tests.txt

@@ -0,0 +1 @@
+ChromEvol_simple.Rev