Fix GitHub doc build issue due to ImageMagick security policy blockin…

…g conversion (#178) * Minor fix in docs. * Add Makefile entry for converting generated images to png via pdftoppm. * Install poppler-utils in Documenter workflow. * Use pdftocairo instead of poppler-utils. * Fix last commit (pdftocairo actually is part of poppler-utils). * Fix pdftocairo calls. * Increase size thresholds for Documenter HTML output.
JuliaGNI · Oct 9, 2023 · f576a49 · f576a49
1 parent 6eeecba
commit f576a49
Show file tree

Hide file tree

Showing 15 changed files with 43 additions and 15 deletions.
diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -24,10 +24,12 @@ jobs:
             Pkg.build()
             Pkg.precompile()'
           sudo apt-get install imagemagick
+          sudo apt-get install poppler-utils
           sudo apt-get install texlive-xetex
       - name: Generate Images
         run: |
           make all   -C src/images
+          make png   -C src/images
           make clean -C src/images
         working-directory: docs
       - uses: julia-actions/julia-buildpkg@v1

diff --git a/docs/make.jl b/docs/make.jl
@@ -21,6 +21,8 @@ makedocs(
     warnonly = Documenter.except(:autodocs_block, :cross_references, :docs_block, :doctest, :eval_block, :example_block, :footnote, :linkcheck_remotes, :linkcheck, :meta_block, :parse_error, :setup_block),
     format = Documenter.HTML(
                prettyurls = get(ENV, "CI", nothing) == "true",
+               size_threshold = 524288,
+               size_threshold_warn = 262144,
                mathengine = MathJax3(Dict(
                  :tex => Dict(
                    :macros => Dict(

diff --git a/docs/src/GeometricIntegrators.bib b/docs/src/GeometricIntegrators.bib
@@ -357,7 +357,7 @@ @article{McLachlanQuispel:2002
     doi     = {10.1017/S0962492902000053}
 }
 
-@article{OberBlobaum:2014,
+@article{OberBloebaum:2014,
     author  = {Ober-Blöbaum, Sina and Saake, Nils},
     title   = {Construction and analysis of higher order Galerkin variational integrators},
     journal = {Advances in Computational Mathematics},

diff --git a/docs/src/images/Makefile b/docs/src/images/Makefile
@@ -1,5 +1,4 @@
-
-all:
+pdf:
 	xelatex -shell-escape commuting-diagram
 	xelatex -shell-escape omega-orthogonal-projection
 	xelatex -shell-escape post-projection
@@ -11,13 +10,28 @@ all:
 	xelatex -shell-escape variation-continuous
 	xelatex -shell-escape variation-discrete
 
+png:
+	pdftocairo  -png -r 150 -transp -singlefile  commuting-diagram.pdf               commuting-diagram              
+	pdftocairo  -png -r 150 -transp -singlefile  omega-orthogonal-projection.pdf     omega-orthogonal-projection    
+	pdftocairo  -png -r 150 -transp -singlefile  post-projection.pdf                 post-projection                
+	pdftocairo  -png -r 150 -transp -singlefile  post-projection-unstable.pdf        post-projection-unstable       
+	pdftocairo  -png -r 150 -transp -singlefile  standard-projection.pdf             standard-projection            
+	pdftocairo  -png -r 150 -transp -singlefile  symmetric-projection-minus.pdf      symmetric-projection-minus     
+	pdftocairo  -png -r 150 -transp -singlefile  symmetric-projection-plus.pdf       symmetric-projection-plus      
+	pdftocairo  -png -r 150 -transp -singlefile  symplectic-projection-unstable.pdf  symplectic-projection-unstable 
+	pdftocairo  -png -r 150 -transp -singlefile  variation-continuous.pdf            variation-continuous           
+	pdftocairo  -png -r 150 -transp -singlefile  variation-discrete.pdf              variation-discrete             
+
 clean:
 	rm -f *.aux
 	rm -f *.fdb_latexmk
 	rm -f *.fls
 	rm -f *.log
 	rm -f *.pdf
+	rm -f *.xdv
 
 empty: clean
 	rm -f *.png
 	rm -f *.svg
+
+all: pdf
diff --git a/docs/src/images/commuting-diagram.tex b/docs/src/images/commuting-diagram.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/omega-orthogonal-projection.tex b/docs/src/images/omega-orthogonal-projection.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/post-projection-unstable.tex b/docs/src/images/post-projection-unstable.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/post-projection.tex b/docs/src/images/post-projection.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/standard-projection.tex b/docs/src/images/standard-projection.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/symmetric-projection-minus.tex b/docs/src/images/symmetric-projection-minus.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/symmetric-projection-plus.tex b/docs/src/images/symmetric-projection-plus.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/symplectic-projection-unstable.tex b/docs/src/images/symplectic-projection-unstable.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{amsmath}
 \usepackage{amsfonts}

diff --git a/docs/src/images/variation-continuous.tex b/docs/src/images/variation-continuous.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{fontspec}
 \usepackage{amsmath}

diff --git a/docs/src/images/variation-discrete.tex b/docs/src/images/variation-discrete.tex
@@ -1,4 +1,5 @@
-\documentclass[12pt,convert={density=150}]{standalone}
+%\documentclass[12pt,convert={density=150}]{standalone}
+\documentclass[12pt]{standalone}
 
 \usepackage{fontspec}
 \usepackage{amsmath}

diff --git a/docs/src/integrators/cgvi.md b/docs/src/integrators/cgvi.md
@@ -1,6 +1,6 @@
 # [Continuous Galerkin Variational Integrators](@id cgvi)
 
-In the following, we first present the Galerkin framework for variational integrators [[Leok:2004](@cite), [Leok:2011](@cite), [Campos:2014](@cite), [Campos:2015](@cite), [OberBlobaum:2014](@cite), [OberBloebaum:2016](@cite)] where the space of curves $\mf{Q}$ that connect two points in $\mf{M}$ is approximated by a finite-dimensional subspace (Galerkin integrators of 0th kind).
+In the following, we first present the Galerkin framework for variational integrators [[Leok:2004](@cite), [Leok:2011](@cite), [Campos:2014](@cite), [Campos:2015](@cite), [OberBloebaum:2014](@cite), [OberBloebaum:2016](@cite)] where the space of curves $\mf{Q}$ that connect two points in $\mf{M}$ is approximated by a finite-dimensional subspace (Galerkin integrators of 0th kind).
 We use Lagrange polynomials to approximate the trajectories albeit other choices are possible.
 Alternatively, we can approximate the generalised velocities 
 (Galerkin integrators of 1st kind), which leads us to variational-partitioned Runge-Kutta methods.
@@ -47,7 +47,7 @@ It should be made clear, that $\mf{Q}_d$ is an approximation of $\mf{Q}$, but no
 $\mf{Q}_h$, however, is a subspace of $\mf{Q}$ (although it can be broken).
 The connection between $\mf{Q}_h$ and $\mf{Q}_d$ is made by the continuity constraints (which for
 Lagrange polynomials and sequences of nodes which include the boundaries, i.e., $c_1=0$
-and $c_s=1$, is automatically satisfied).
+and $c_s=1$, is automatically satisfied -> this is not true).
 In this context we also need to discuss that curves in $\mf{Q}(\mf{M})$ are assumed to be $C^2$,
 which is not required by the curves in $\mf{Q}_h$.*