Fix workflows

For some reason, it is different. See:
https://www.mff.cuni.cz/cs/vnitrni-zalezitosti/predpisy/opatreni-dekana/opatreni-dekana-c-27-2023

.github/workflows/main.yml

@@ -15,7 +15,9 @@ jobs:
     container: { image: 'aergus/latex' }
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Install nodejs
+        run: apt-get update && apt-get install -y nodejs
+      - uses: https://gitea.com/ScMi1/checkout@v1
       - name: Build the thesis
         run: latexmk thesis && latexmk abstract-cz && latexmk abstract-en
       - name: Upload artifacts
@@ -32,7 +34,9 @@ jobs:
     container: { image: 'ghcr.io/mff-cuni-cz/cuni-thesis-validator' }
 
     steps:
+      - name: Install nodejs
+        run: apt-get update && apt-get upgrade -y && apt-get install -y curl && curl -fsSL https://deb.nodesource.com/setup_16.x | bash - && apt-get install -y nodejs
       - name: Get PDFs
-        uses: actions/download-artifact@v3
+        uses: https://gitea.com/actions/download-artifact@v3
       - name: Run VeraPDF
-        run: verify Thesis/*.pdf | tee /dev/stderr | grep -qE 'nonCompliant="0"'
+        run: verify Thesis/*.pdf | tee /dev/stderr | grep -qE 'nonCompliant="0" failedJobs="0"'

.github/workflows/pages.yml

@@ -11,7 +11,9 @@ jobs:
     container: { image: 'aergus/latex' }
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Install nodejs
+        run: apt-get update && apt-get install -y nodejs
+      - uses: https://gitea.com/ScMi1/checkout@v1
       - name: Build the thesis
         run: latexmk thesis && latexmk abstract-cz && latexmk abstract-en
       - name: Prepare a website directory
@@ -24,8 +26,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           cd public
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
+          git config --global user.name "$GITHUB_ACTOR"
+          git config --global user.email "$GITHUB_ACTOR@users.noreply.github.com"
           GIT_WORK_TREE=. git checkout --orphan gh-pages
           GIT_WORK_TREE=. git add .
           GIT_WORK_TREE=. git commit -m 'pages'

.latexmkrc

@@ -0,0 +1 @@
+$pdf_mode = 4

Makefile

@@ -1,6 +1,6 @@
 NAME=thesis
 ABSTRACT=abstract
-LATEXMKOPTS=#-pdf #enable for forcing pdflatex
+LATEXMKOPTS=-pdflua #you can also use -pdf for forcing pdflatex, if required
 LATEXMK=latexmk $(LATEXMKOPTS)
 
 all:

README.md

@@ -60,7 +60,7 @@ docker run -u $UID -ti --rm -v $PWD:/th -w /th aergus/latex make
 
 ## PDF/A
 
-With a bit of luck, you should get a valid PDF/A right out of LaTeX. If you are using GitHub actions or GitLab CI, the CI will run the PDF/A verifier automatically for you.
+With a bit of luck, you should get a valid PDF/A right out of LaTeX. Remember that you should use a well-maintained PDF-capable TeX engine, which currently means `lualatex` and may possibly also include `xelatex`. Older `pdflatex` might work, but you may hit problems (e.g. using "small caps" feature with the default Libertinus font triggers glyph validation errors). If you are using GitHub actions or GitLab CI, the CI will run the PDF/A verifier automatically for you.
 
 A PDF/A validator that can point out exact problems is available here: https://github.com/mff-cuni-cz/cuni-thesis-validator
 

abstract-cz.tex

@@ -2,8 +2,6 @@
 
 \usepackage[a-2u]{pdfx}
 \usepackage[czech,shorthands=off]{babel}
-\usepackage[utf8]{inputenc}
-\usepackage[T1]{fontenc}
 
 \usepackage{lmodern}
 

abstract-en.tex

@@ -1,8 +1,6 @@
 \documentclass[12pt]{report}
 
 \usepackage[a-2u]{pdfx}
-\usepackage[utf8]{inputenc}
-\usepackage[T1]{fontenc}
 
 \usepackage{lmodern}
 

ch1.tex

@@ -54,7 +54,7 @@ As an usual example, \xxx{\textit{`The sentence, which I wrote, seemed ugly.'}}
 \paragraph{Nouns}
 Every noun needs a determiner (`a', `the', `my', `some', \dots); the exceptions to this rule, such as non-adjectivized names and indeterminate plural, are relatively scarce. Without a determiner, a noun can be easily mistaken for something completely different, such as an adjective or a verb.
 
-Name all things with appropriate nouns to help both the reader and yourself, and do not hesitate to invent good names and labels for anything that you will refer to more than once. Proper naming will save you a lot of writing effort because you will not have to repeat descriptions such as \xxx{\textit{`the third output of the second benchmarked method of the improved set,'}} instead you may introduce a labeling that will allow you to say just something like \textit{`output M2\textsuperscript{+}-3'}. At the same time, this will reduce the risk that the reader will confuse the object with another one --- for illustration, the long version of the previous example might very easily confuse with the second output of the third method. The same also applies to methods descriptions, algorithms, programs, testing datasets, theorems, use-cases, challenges and other things. As an example, \xxx{\textit{`the algorithm that organizes the potatoes into appropriate buckets'}} shortens nicely as \textit{`the potato bucketer'} and may be labeled as a procedure \textsc{BucketPotatoes()}, and \xxx{\textit{`the issue where the robot crashes into a wall and takes significant time to return to the previous task'}} may be called just \textit{`the crash-recovery lag'}.
+Name all things with appropriate nouns to help both the reader and yourself, and do not hesitate to invent good names and labels for anything that you will refer to more than once. Proper naming will save you a lot of writing effort because you will not have to repeat descriptions such as \xxx{\textit{`the third output of the second benchmarked method of the improved set,'}} instead you may introduce a labeling that will allow you to say just something like \textit{`output M2\textsuperscript{+}-3'}. At the same time, this will reduce the risk that the reader will confuse the object with another one --- for illustration, the long version of the previous example might very easily confuse with the second output of the third method. The same also applies to methods descriptions, algorithms, programs, testing datasets, theorems, use-cases, challenges and other things. As an example, \xxx{\textit{`the algorithm that organizes the potatoes into appropriate buckets'}} shortens nicely as \textit{`the potato bucketer'} and may be labeled as a procedure \textsc{BucketPotatoes()}, and \xxx{\textit{`the issue where the robot crashes into a wall and takes significant time to return to the previous task'}} may be called just \textit{`the crash--recovery lag'}.
 
 \paragraph{Verbs}
 Although English can express a whopping 65 base verb tenses and their variants, scientific literature often suppresses this complexity and uses only several basic tenses where the meaning is clearly defined. Typically, you state facts in present simple (\textit{`Theorem 1 proves that Gadget B works as intended.'}), talk about previous work and experiments done in past simple (\textit{`We constructed Gadget B from Gizmo C, which was previously prepared by Tinkerer et al.'}), and identify achieved results in present perfect (\textit{`We have constructed Technology T.'}). Avoid using future tense, except for sections that explicitly describe future work --- as a typical mistake, if you state that the thesis \emph{will} describe something in later chapters, you imply that the description is not present there yet.

docker/Dockerfile

@@ -17,6 +17,7 @@ RUN apt-get -qq update && apt-get install -y \
   texlive-science \
   texlive \
   ghostscript \
+  latexmk \
   make
 
 RUN rm -fr /var/lib/apt /var/cache/apt

pdfa.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 # Use this script to convert random PDFs to PDF/A (e.g. figures).
-# Unfortunately, ghostscript can not retain the PDF/A metadata. In result, if
+# Unfortunately, ghostscript cannot retain the PDF/A metadata. In result, if
 # you use this on the thesis, it _will_ become PDF/A compliant (and SIS will
 # accept it), but won't contain the magic PDF/A "stamp" and will show only as
 # normal PDF-1.4. :(
@@ -17,7 +17,7 @@ gs -dPDFA=1 \
 # Notes:
 #
 # PDFACompatibilityPolicy=3 actually doesn't exist. A bug in ghostscript
-# interprets is as something between 1 and 2, without unnecessary failing on
+# interprets it as something between 1 and 2, without unnecessarily failing on
 # various dumb errors.
 #
 # Add -dNoOutputFonts if you absolutely totally need to get rid of fonts in a

thesis.tex

@@ -6,8 +6,6 @@
 \usepackage[a-2u]{pdfx}
 
 \ifEN\else\usepackage[czech,shorthands=off]{babel}\fi
-\usepackage[utf8]{inputenc}
-\usepackage[T1]{fontenc}
 
 % See https://en.wikipedia.org/wiki/Canons_of_page_construction before
 % modifying the size of printable area. LaTeX defaults are great.
@@ -16,31 +14,24 @@
 % The official recommendation expands the area quite a bit (looks pretty harsh):
 %\usepackage[textwidth=145mm,textheight=247mm]{geometry}
 
-%%% FONTS %%%
-\usepackage{lmodern} % TeX "original" (this sets up the latin mono)
+%%% TYPICAL FONT CHOICES (uncomment what you like) %%%
+% Recommended combo: Libertinus (autoselects Biolinum for sans) and everything
+% else (math+tt) comes from Latin Modern)
+\usepackage{lmodern}
+\usepackage[mono=false]{libertinus}
 
-% Optionally choose an override for the main font for typesetting:
-\usepackage[mono=false]{libertinus} % popular for comp-sci (ACM uses this)
-%\usepackage{tgschola} % Schoolbook-like (gives a bit of historic feel)
-%\usepackage[scale=0.96]{tgpagella} % Palladio-like (popular in formal logic).
-% IBM Plex font suite is nice but requires us to fine-tune the sizes, also note
-% that it does not directly support small caps (\textsc) and requires lualatex:
+% For the "classic" LaTeX fonts (very good for pure math theses), simply
+% comment out the libertinus package above.
+
+% IBM Plex font suite: nice, but requires us to fine-tune the sizes and does
+% not directly support small caps (\textsc):
 %\usepackage[usefilenames,RM={Scale=0.88},SS={Scale=0.88},SScon={Scale=0.88},TT={Scale=0.88},DefaultFeatures={Ligatures=Common}]{plex-otf}
 
-% Optionally, choose a custom sans-serif fonts (e.g. for figures and tables).
-% Default sans-serif font is usually Latin Modern Sans. Some font packages
-% (e.g. libertinus) replace that with a better matching sans-serif font.
-%\usepackage{tgheros} % recommended and very readable (Helvetica-like)
-%\usepackage{FiraSans} % looks great
-% DO NOT typeset the main text in sans-serif font!
-% The serifs make the text easily readable on the paper.
-
-
-% IMPORTANT FONT NOTE: Some fonts require additional PDF/A conversion using
-% the pdfa.sh script. These currently include only 'tgpagella'; but various
-% other fonts from the texlive distribution need that too (mainly the Droid
-% font family).
-
+% TeX Gyre combo (Pagella+Heros+Cursor)
+%\usepackage{fontspec}
+%\setmainfont{TeX Gyre Pagella}
+%\setsansfont{TeX Gyre Heros}
+%\setmonofont{TeX Gyre Cursor}
 
 % some useful packages
 \usepackage{microtype}
@@ -51,25 +42,33 @@
 \usepackage{caption}
 \usepackage{floatrow}
 
-% load bibliography tools
-\usepackage[backend=bibtex,natbib,style=numeric,sorting=none]{biblatex}
-% alternative with alphanumeric citations (more informative than numbers):
-%\usepackage[backend=bibtex,natbib,style=alphabetic]{biblatex}
+% Bibliography formatting.
+% CHECK THE REQUIREMENTS OF YOUR DEPARTMENT AND FACULTY ON THE CITATION FORMAT!
 %
-% alternatives that conform to iso690
-% (iso690 is not formally required on MFF, but may help elsewhere):
-%\usepackage[backend=bibtex,natbib,style=iso-numeric,sorting=none]{biblatex}
-%\usepackage[backend=bibtex,natbib,style=iso-alphabetic]{biblatex}
+% These are relatively "safe" default options that most people use:
+\usepackage[natbib,style=numeric,sorting=none]{biblatex}
+% alternative with alphanumeric citations (more informative than numbers, and
+% more common in computer science journals):
+%\usepackage[natbib,style=alphabetic]{biblatex}
 %
-% additional option choices:
+% ALTERNATIVES THAT CONFORM TO ISO690
+% ISO690 is not the greatest citation format ever, but may be formally
+% required at Charles University, depending on your faculty and department.
+%\usepackage[natbib,style=iso-numeric,sorting=none]{biblatex}
+%\usepackage[natbib,style=iso-alphabetic]{biblatex}
+% You might want to add extra options such as `maxbibnames=6,maxcitenames=2`
+% here to further conform to some of the formatting requirements (see below for
+% details). Again, consult your faculty rules.
+%
+% Additional option choices:
 %  - add `giveninits=true` to typeset "E. A. Poe" instead of full Edgar Allan
 %  - `terseinits=true` additionaly shortens it to nature-like "Poe EA"
 %  - add `maxnames=10` to limit (or loosen) the maximum number of authors in
 %    bibliography entry before shortening to `et al.` (useful when referring to
 %    book collections that may have hundreds of authors)
-%  - for additional flexibility (e.g. multiple reference sections, etc.),
-%    remove `backend=bibtex` and compile with `biber` instead of `bibtex` (see
-%    Makefile)
+%  - use `maxcitenames=2` to finetune the amount of authors listed in text-cite
+%    commands (\citet). Corresponding option that only affects the bibliography
+%    is `maxbibnames=10`.
 %  - `sorting=none` causes the bibliography list to be ordered by the order of
 %    citation as they appear in the text, which is usually the desired behavior
 %    with numeric citations. Additionally you can use a style like
@@ -85,7 +84,7 @@
 %\DeclareNameAlias{default}{family-given}
 
 % load the file with bibliography entries
-\addbibresource{refs}
+\addbibresource{refs.bib}
 
 % remove this if you won't use fancy verbatim environments
 \usepackage{fancyvrb}

title.tex

@@ -72,28 +72,10 @@
 
 \ifEN
 \noindent
-I declare that I carried out this \ThesisAccusative thesis independently, and only with the cited
-sources, literature and other professional sources. It has not been used to obtain another
-or the same degree.
+I declare that I carried out this \ThesisAccusative thesis on my own, and only with the cited sources, literature and other professional sources. I understand that my work relates to the rights and obligations under the Act No. 121/2000 Sb., the Copyright Act, as amended, in particular the fact that the Charles University has the right to conclude a license agreement on the use of this work as a school work pursuant to Section 60 subsection 1 of the Copyright Act.
 \else
 \noindent
-Prohlašuji, že jsem tuto \ThesisAccusative práci vypracoval(a) samostatně a výhradně
-s~použitím citovaných pramenů, literatury a dalších odborných zdrojů.
-Tato práce nebyla využita k získání jiného nebo stejného titulu.
-\fi
-
-\ifEN
-\medskip\noindent
-I understand that my work relates to the rights and obligations under the Act No.~121/2000 Sb.,
-the Copyright Act, as amended, in particular the fact that the Charles
-University has the right to conclude a license agreement on the use of this
-work as a school work pursuant to Section 60 subsection 1 of the Copyright~Act.
-\else
-\medskip\noindent
-Beru na~vědomí, že se na moji práci vztahují práva a povinnosti vyplývající
-ze zákona č. 121/2000 Sb., autorského zákona v~platném znění, zejména skutečnost,
-že Univerzita Karlova má právo na~uzavření licenční smlouvy o~užití této
-práce jako školního díla podle §60 odst. 1 autorského zákona.
+Prohlašuji, že jsem tuto \ThesisAccusative práci vypracoval(a) samostatně a~výhradně s~použitím citovaných pramenů, literatury a~dalších odborných zdrojů. Beru na vědomí, že se na moji práci vztahují práva a~povinnosti vyplývající ze zákona č.~121/2000 Sb., autorského zákona v platném znění, zejména skutečnost, že Univerzita Karlova má právo na uzavření licenční smlouvy o~užití této práce jako školního díla podle § 60 odst. 1 autorského zákona.
 \fi
 
 \vspace{10mm}