adapted to pdf-conversion

Author: stschiff

.github/workflows/addPDF.yml

@@ -33,7 +33,7 @@ jobs:
         sed -i '1,/^\s*## Guide for/ {/## Guide for/ !d}' trident.md
         sed -i '1,/^\s*## Guide for/ {/## Guide for/ !d}' xerxes.md
         # add extra # at the beginning of janno_details.md
-        echo -e "#$(cat janno_details.md)" > janno_details.md
+        # echo -e "#$(cat janno_details.md)" > janno_details.md
 
     - name: Convert files
       run: |

janno_r_package.md

@@ -1,6 +1,6 @@
 <popup :custom-text="`<p><a href='https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024'>A short introduction to the Poseidon genotype data management framework</a> by Clemens Schmid: A Poseidon tutorial also covering <a href='https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024/spacetime.html'>the janno R package</a></p>`"></popup>
 
-# janno R package
+<h1>janno R package</h1>
 
 `janno` (formerly known as poseidonR) is an R package to simplify the interaction with `.janno` files in Poseidon packages. It provides a dedicated R S3 class `janno` that inherits from `tibble` and allows to tidily read and manipulate the context information stored in them. The code is available on [GitHub](https://github.com/poseidon-framework/janno/).
 
@@ -15,6 +15,8 @@ The guide below explains the main functions in the package. It is available in .
 
 - [🗎 Guide for the janno R package v1.0.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/janno_r_package.pdf) (shown below)
 
+# Guide for the janno R package v1.0.0
+
 ## Installation
 
 See the Poseidon website (<https://www.poseidon-adna.org/#/janno_r_package>) or the GitHub repository (<https://github.com/poseidon-framework/janno>) for up-to-date installation instructions.

pdf_conversion/pandoc_pdf_config.yml

@@ -1,5 +1,5 @@
 table-of-contents: true
-shift-heading-level-by: -2
+shift-heading-level-by: -1
 number-sections: true
 highlight-style: tango
 variables:

pdf_tests/trident.md

@@ -1,4 +1,4 @@
-# qjanno CLI software
+<h1>qjanno CLI software</h1>
 
 `qjanno` is a command line tool to run SQL queries on `.janno` (and arbitrary .csv and .tsv) files. This is an adjusted version and hard fork of the qsh package (https://github.com/itchyny/qhs). It is written in Haskell and openly available on [GitHub](https://github.com/poseidon-framework/qjanno/).
 
@@ -29,6 +29,8 @@ The guide below explains the inner workings of qjanno and gives some examples fo
 - [🗎 Guide for qjanno v1.0.0.0 to v1.0.0.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/qjanno.pdf) (shown below)
 - [🗎 Guide for qjanno v1.0.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/qjanno_guide_archive/qjanno_guide_1.0.0.pdf)
 
+# Guide for qjanno v1.0.0.0 to v1.0.0.1
+
 ## Background
 
 Qjanno started as a fork of the [qhs](https://github.com/itchyny/qhs) software tool, which was, in turn, inspired by the command line tool [q](https://github.com/harelba/q). All of them enable SQL queries on delimiter-separated text files (e.g. .csv or .tsv). For `qjanno`, we copied the source code of qhs v0.3.3 (MIT-License) and adjusted it to provide a smooth experience with a special kind of .tsv file: The Poseidon `.janno` file.

qjanno.md

@@ -1,6 +1,6 @@
 <popup :custom-text="`<p><a href='https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024'>A short introduction to the Poseidon genotype data management framework</a> by Clemens Schmid: A Poseidon tutorial showcasing the <a href='https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024/ref_pca.html'>main features of trident</a> among other things</p>`"></popup>
 
-# trident CLI software
+<h1>trident CLI software</h1>
 
 `trident` is a command line software tool to work with Poseidon packages and handle various data management tasks. It is written in Haskell and openly available on [GitHub](https://github.com/poseidon-framework/poseidon-hs/).
 
@@ -44,6 +44,8 @@ With `trident --help` and `trident <subcommand> --help` you can get information
 - [🗎 Guide for trident v0.29.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_0.29.0.pdf)
 - [🗎 Guide for trident v0.28.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_0.28.0.pdf)
 
+# Guide for trident v1.5.4.0
+
 ## Installation
 
 See the Poseidon website (<https://www.poseidon-adna.org/#/trident>) or the GitHub repository (<https://github.com/poseidon-framework/poseidon-hs>) for up-to-date installation instructions.

trident.md

@@ -1,6 +1,6 @@
 <popup :custom-text="`<p><a href='https://mpi-eva-archaeogenetics.github.io/comp_human_adna_book/fstats.html'>Introduction to F3- and F4-Statistics</a> by Stephan Schiffels: An explanation of F-Statistics and how to run them with xerxes</p>`"></popup>
 
-# xerxes CLI software
+<h1>xerxes CLI software</h1>
 
 `xerxes` is a command line software tool for population genetic analyses of Poseidon packages. It is written in Haskell and openly available on [GitHub](https://github.com/poseidon-framework/poseidon-analysis-hs/).
 
@@ -35,6 +35,8 @@ With `xerxes --help` and `xerxes <subcommand> --help` you can get information ab
 - [🗎 Guide for xerxes v1.0.0.2](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/xerxes_guide_archive/xerxes_guide_1.0.0.2.pdf)
 - [🗎 Guide for xerxes v0.2.0.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/xerxes_guide_archive/xerxes_guide_0.2.0.0.pdf)
 
+# Guide for xerxes v1.0.1.0 to v1.0.1.1
+
 ## Installation
 
 See the Poseidon website (<https://www.poseidon-adna.org/#/xerxes>) or the GitHub repository (<https://github.com/poseidon-framework/poseidon-analysis-hs>) for up-to-date installation instructions.