Merge pull request #80 from revbayes/checked_snippet

Allow lines to match non-continuously, and require indentation.

Author: bredelings

_plugins/snippet.rb

@@ -1,3 +1,15 @@
+def lines_match_in_order?(snippet_lines, file_lines)
+  i = 0
+  snippet_lines.each do |snippet_line|
+    while i < file_lines.length && file_lines[i].strip != snippet_line.strip
+      i += 1
+    end
+    return false if i == file_lines.length
+    i += 1
+  end
+  true
+end
+
 module Liquid
 	class Snippet < Block
 		def initialize(tag_name, markup, options)
@@ -6,7 +18,8 @@ def initialize(tag_name, markup, options)
 		end
 
 		def render(context)
-                        code_block = super.strip
+                        code_block = super
+
                         code_lines = code_block.lines.map{ |l| l.strip }
 
                         # Site source directory (so we don't need absolute paths)
@@ -18,32 +31,21 @@ def render(context)
                         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
+                        match_found = lines_match_in_order?(code_lines, file_lines)
 
                         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

tutorials/chromo/index.md

@@ -283,7 +283,7 @@ 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]
+    phylogeny <- readBranchLengthTrees("data/aristolochia.tree")[1]
 {% endsnippet %}
 
 We need to limit the maximum number of chromosomes allowed in our model,
@@ -292,17 +292,17 @@ arbitrary limit on the size of the state space that could be increased
 if necessary.
 
 {% snippet scripts/ChromEvol_simple.Rev %}
-max_chromo = 26
+    max_chromo = 26
 {% endsnippet %}
 
 Now we get the observed chromosome counts from a tab-delimited file.
 {% snippet scripts/ChromEvol_simple.Rev %}
-chromo_data = readCharacterDataDelimited("data/aristolochia_chromosome_counts.tsv", stateLabels=(max_chromo + 1), type="NaturalNumbers", delimiter="\t", header=FALSE)
+    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()
+    moves    = VectorMoves()
+    monitors = VectorMonitors()
 {% endsnippet %}
 
 ### The Chromosome Evolution Model

tutorials/clocks/index.md

@@ -229,9 +229,11 @@ age being younger than 38 Mya is equal to 0, using this value to offset
 a prior distribution on the root-age.
 
 First specify the occurrence-time of the fossil.
-```
-tHesperocyon <- 38.0
-```
+
+{% snippet scripts/m_BDP_bears.Rev %}
+    tHesperocyon <- 38.0
+{% endsnippet %}
+
 We will assume a lognormal prior on the root age that is offset by the
 observed age of *Hesperocyon gregarius*. We can use the previous
 analysis by {% cite DosReis2012 %} to parameterize the lognormal prior on the root
@@ -241,22 +243,28 @@ distribution to equal $49 - 38 = 11$ Mya. Given the expected value of
 the lognormal (`mean_ra`) and a standard deviation (`stdv_ra`), we can
 also compute the location parameter of the lognormal (`mu_ra`).
 
+{% snippet scripts/m_BDP_bears.Rev %}
     mean_ra <- 11.0
     stdv_ra <- 0.25
     mu_ra <- ln(mean_ra) - ((stdv_ra*stdv_ra) * 0.5)
+{% endsnippet %}
 
 With these parameters we can instantiate the root age stochastic node
 with the offset value.
 
+{% snippet scripts/m_BDP_bears.Rev %}
     root_time ~ dnLognormal(mu_ra, stdv_ra, offset=tHesperocyon)
+{% endsnippet %}
 
 ### Time Tree Stochastic Node
 
 Now that we have specified all of the parameters of the birth-death
 process, we can create our stochastic node representing the tree
 topology and divergence times.
 
+{% snippet scripts/m_BDP_bears.Rev %}
     timetree ~ dnBDP(lambda=birth_rate, mu=death_rate, rho=rho, rootAge=root_time, samplingStrategy="uniform", condition="nTaxa", taxa=taxa)
+{% endsnippet %}
 
 ### Creating a Node-Age Variable
 
@@ -267,27 +275,35 @@ taxa using the `clade()` function. This will not restrict this node to
 be monophyletic, but just create a node that is the MRCA of the taxa
 listed (even if that node has descendants that are not named).
 
-    clade_Ursidae <- clade("Ailuropoda_melanoleuca","Tremarctos_ornatus","Helarctos_malayanus", "Ursus_americanus","Ursus_thibetanus","Ursus_arctos","Ursus_maritimus","Melursus_ursinus")
+{% snippet scripts/m_BDP_bears.Rev %}
+    clade_Ursidae <- clade("Ailuropoda_melanoleuca","Tremarctos_ornatus","Helarctos_malayanus","Ursus_americanus","Ursus_thibetanus","Ursus_arctos","Ursus_maritimus","Melursus_ursinus")
+{% endsnippet %}
 
 Once we have defined the node, we can create a deterministic node to
 monitor its age.
 
+{% snippet scripts/m_BDP_bears.Rev %}
     tmrca_Ursidae := tmrca(timetree,clade_Ursidae)
+{% endsnippet %}
 
 ### Proposals on the Time Tree
 
 Next, create the vector of moves. These tree moves act on node ages:
 
-    moves.append( mvNodeTimeSlideUniform(timetree, weight=30.0) ) )
+{% snippet scripts/m_BDP_bears.Rev %}
+    moves.append( mvNodeTimeSlideUniform(timetree, weight=30.0 ) )
     moves.append( mvSlide(root_time, delta=2.0, tune=true, weight=10.0) )
     moves.append( mvScale(root_time, lambda=2.0, tune=true, weight=10.0) )
     moves.append( mvTreeScale(tree=timetree, rootAge=root_time, delta=1.0, tune=true, weight=3.0) )
+{% endsnippet %}
 
 Then, we will add moves that will propose changes to the tree topology.
 
+{% snippet scripts/m_BDP_bears.Rev %}
     moves.append( mvNNI(timetree, weight=8.0) )
     moves.append( mvNarrow(timetree, weight=8.0) )
     moves.append( mvFNPR(timetree, weight=8.0) )
+{% endsnippet %}
 
 Now save and close the file. This file, with all the model
 specifications will be loaded by other `Rev` files.

tutorials/clocks/scripts/m_BDP_bears.Rev

@@ -52,12 +52,11 @@ mean_ra <- 11.0
 stdv_ra <- 0.25
 ### the lognormal distribution is parameterized by mu which is a function of the mean and standard deviation
 mu_ra <- ln(mean_ra) - ((stdv_ra*stdv_ra) * 0.5)
-root_time ~ dnLnorm(mu_ra, stdv_ra, offset=tHesperocyon)
+root_time ~ dnLognormal(mu_ra, stdv_ra, offset=tHesperocyon)
 
 
 ### the time tree is a stochastic node modeled by the constant rate birth-death process (dnBDP)
-timetree ~ dnBDP(lambda=birth_rate, mu=death_rate, rho=rho, rootAge=root_time, 
-	samplingStrategy="uniform", condition="nTaxa", taxa=taxa)
+timetree ~ dnBDP(lambda=birth_rate, mu=death_rate, rho=rho, rootAge=root_time, samplingStrategy="uniform", condition="nTaxa", taxa=taxa)
 
 
 ### If you would like to specify a starting tree, simply use the .setValue() method
@@ -70,9 +69,7 @@ timetree ~ dnBDP(lambda=birth_rate, mu=death_rate, rho=rho, rootAge=root_time,
 ### then a deterministic node for the age. This does not create a monophyletic constraint.
 
 ### The clade() function specifies the node that is the MRCA of all listed taxa
-clade_Ursidae <- clade("Ailuropoda_melanoleuca","Tremarctos_ornatus","Helarctos_malayanus",
-                        "Ursus_americanus","Ursus_thibetanus","Ursus_arctos","Ursus_maritimus",
-                        "Melursus_ursinus")
+clade_Ursidae <- clade("Ailuropoda_melanoleuca","Tremarctos_ornatus","Helarctos_malayanus","Ursus_americanus","Ursus_thibetanus","Ursus_arctos","Ursus_maritimus","Melursus_ursinus")
 
 
 ### A deterministic node for a given "clade" will report the age of that node (even if they are not
@@ -82,12 +79,12 @@ tmrca_Ursidae := tmrca(timetree,clade_Ursidae)
 ####### Tree Moves #######
 
 ### add moves on the tree node times, including the root time, which is outside of the timetree 
-moves.append(mvNodeTimeSlideUniform(timetree, weight=30.0))
-moves.append(mvTreeScale(tree=timetree, rootAge=root_time, delta=1.0, tune=true, weight=3.0))
-moves.append(mvSlide(root_time, delta=2.0, tune=true, weight=10.0))
-moves.append(mvScale(root_time, lambda=2.0, tune=true, weight=10.0))
+moves.append( mvNodeTimeSlideUniform(timetree, weight=30.0 ) )
+moves.append( mvSlide(root_time, delta=2.0, tune=true, weight=10.0) )
+moves.append( mvScale(root_time, lambda=2.0, tune=true, weight=10.0) )
+moves.append( mvTreeScale(tree=timetree, rootAge=root_time, delta=1.0, tune=true, weight=3.0) )
 
 ### and moves for the tree topology
-moves.append(mvNNI(timetree, weight=8.0))
-moves.append(mvNarrow(timetree, weight=8.0))
-moves.append(mvFNPR(timetree, weight=8.0))
+moves.append( mvNNI(timetree, weight=8.0) )
+moves.append( mvNarrow(timetree, weight=8.0) )
+moves.append( mvFNPR(timetree, weight=8.0) )