# HG changeset patch
# User Henry S Thompson <ht@inf.ed.ac.uk>
# Date 1723722251 -3600
# Node ID 19b134ea79c85d2e973dd77d00a2138de93eed1b
# Parent  f5509fb303f65acf06b9e4e05494a7a9de52f5ec
cctest version from 2022-06-29

diff -r f5509fb303f6 -r 19b134ea79c8 cc.def
--- a/cc.def	Thu Aug 15 12:43:22 2024 +0100
+++ b/cc.def	Thu Aug 15 12:44:11 2024 +0100
@@ -2,16 +2,33 @@
 From: debian:bullseye
 
 %post
+    sed 's/PS1/PSone/' -i .singularity.d/env/99-base.sh
+
     sed '2s/main/main contrib non-free/' -i /etc/apt/sources.list
     apt-get -y update
     apt-get -y install locales
     sed '/en_GB.UTF/s/# //;/en_US.UTF/s/# //' -i /etc/locale.gen
     locale-gen
     apt-get -y install apt-utils python3 python3-pip isal less git ack procps psmisc
-    apt-get -y install man-db gdb gcc
+    apt-get -y install man-db gdb emacs xemacs21 sqlite3
+    apt-get -y install moreutils
+    # do this after the above in order to
+    # hide the moreutils version of parallel as moreutils.parallel
+    apt-get -y install parallel
 
     pip3 install six isal regex chardet stopit urllib3 cryptography
     
+    cd /usr/local/src
+    git clone https://github.com/htInEdin/pdfminer.six.git
+    git clone https://github.com/htInEdin/pdfx.git
+    cd pdfminer.six
+    git checkout preferLoggingToWarning
+    cd ../pdfx
+    git checkout tidy_up_link_extraction
+    cd /usr/local/lib/python3.9/dist-packages/
+    ln -s /usr/local/src/pdfx/pdfx .
+    ln -s /usr/local/src/pdfminer.six/pdfminer .
+
     sed '8i\
   if [ "$WSHARED" ]\
   then\
@@ -30,7 +47,7 @@
 export PS1='\[\033[1m\]sing\[\033[0m\]<\!>: '
 
 %runscript
-#!/bin/bash
+v#!/bin/bash
 if [ -f $WSHARED/.bash_extras ]
 then
  . $WSHARED/.bash_extras