writing: Remove bib-due scripts and update README

Removed the left-over bib-due scripts. They were neat and fun when I
wrote them but they are not useful for me anymore. Additionally they are
very brittle and I do not want to deal with fixing or updating them.

.dotter/global.toml

@@ -67,8 +67,14 @@ social = "~"
 
 [writing.files]
 "writing/README.md" = { target = "~/NOWHERE", type = "symbolic", if = "false" }
-"writing/.config/papis/papistui.yaml" = { target = "~/.config/papis/papistui.yaml", type = "symbolic" }
-"writing/.config/sioyek/prefs_user.config" = { target = "~/.config/sioyek/prefs_user.config", type = "template", prepend = "# TEMPLATED BY DOTTER\n" }
+"writing/jrnl" = "~/.config/jrnl"
+"writing/papis/papistui.yaml" = { target = "~/.config/papis/papistui.yaml", type = "symbolic" }
+"writing/papis" = "~/.config/papis"
+"writing/sioyek/prefs_user.config" = { target = "~/.config/sioyek/prefs_user.config", type = "template", prepend = "# TEMPLATED BY DOTTER\n" }
+"writing/sioyek" = "~/.config/sioyek"
+"writing/zathura" = "~/.config/zathura"
+"writing/zk" = "~/.config"
+"writing/pandoc/local" = "~/.local"
 writing = "~"
 
 # WORKSTATION: A desktop machine, with wayland environment and display attached.

writing/.config/pubs/pubsrc

@@ -1,166 +0,0 @@
-
-[main]
-
-# Where the pubs repository files (bibtex, metadata, notes) are located
-pubsdir = ~/documents/library
-
-# Where the documents files are located (default: $(pubsdir)/doc/)
-docsdir = ~/documents/library/doc
-
-# Specify if a document should be copied or moved in the docdir, or only
-# linked when adding a publication.
-doc_add = copy
-
-# the command to use when opening document files
-open_cmd = open
-
-# which editor to use when editing bibtex files.
-# if using a graphical editor, use the --wait or --block option, i.e.:
-# "atom --wait"
-# "kate --block"
-# If set to an empty string (default) pubs uses the value of the environment
-# variable $EDITOR.
-edit_cmd = ""
-
-# Which default extension to use when creating a note file.
-note_extension = md
-
-# How many authors to display when displaying a citation. If there are more
-# authors, only the first author is diplayed followed by 'et al.'.
-max_authors = 3
-
-# If true debug mode is on which means exceptions are not catched and
-# the full python stack is printed.
-debug = False
-
-# If true the citekey is normalized using the 'citekey_format' on adding new publications.
-normalize_citekey = False
-
-# String specifying how to format the citekey. All strings of
-# the form '{substitution:modifier}' and '{substitution}' will
-# be substituted with their appropriate values. The following
-# substitutions are used:
-#    author_last_name: last name of the first author
-#    year: year of publication
-#    short_title: first word of the title (excluding words such as "the", "an", ...)
-# modifiers:
-#    l: converts the text to lowercase
-#    u: converts the text to uppercase
-# examples:
-#   {author_last_name:l}{year} generates 'yang2020'
-#   {author_last_name}{year}{short_title} generates 'Yang2020Towards'
-#   {author_last_name:l}{year}{short_title:l} generates 'yang2020towards'
-#   {author_last_name:u}{year} generates 'YANG2020'
-#
-citekey_format = {author_last_name}{year}
-
-# which bibliographic fields to exclude from bibtex files. By default, none.
-# Please note that excluding critical fields such as `title` or `author`
-# will break many commands of pubs.
-exclude_bibtex_fields = ,
-
-[formating]
-
-# Enable bold formatting, if the terminal supports it.
-bold = True
-
-# Enable italics, if the terminal supports it.
-italics = True
-
-# Enable colors, if the terminal supports it.
-color = True
-
-
-[theme]
-
-# Here you can define the color theme used by pubs, if enabled in the
-# 'formating' section. Predefined theme are available at:
-# https://github.com/pubs/pubs/blob/master/extra/themes.md
-
-# Available colors are: 'black', 'red', 'green', 'yellow', 'blue', 'purple',
-# 'cyan', and 'grey'. Bold colors are available by prefixing 'b' in front of
-# the color name ('bblack', 'bred', etc.), italic colors by prefixing 'i',
-# and bold italic by prefixing 'bi'. Finally, 'bold', 'italic' and
-# 'bolditalic' can be used to apply formatting without changing the color.
-# For no color, use an empty string ''
-
-# messages
-ok = green
-warning = yellow
-error = red
-
-# ui elements
-filepath = bold
-citekey = purple
-tag = cyan
-
-# bibliographic fields
-author = bold
-title = ""
-publisher = ""
-year = bold
-volume = bold
-pages = ""
-
-
-[plugins]
-# Comma-separated list of the plugins to load.
-# Currently pubs comes with built-in plugins alias and git.
-active = alias,git
-
-[[alias]]
-# new subcommands can be defined, e.g.:
-# print = open --with lp
-# evince = open --with evince
-
-# shell commands can also be defined, by prefixing them with a bang `!`, e.g:
-# count = !pubs list -k | wc -l
-
-# aliases can also be defined with descriptions using the following configobj
-# subsectioning.  NOTE: any aliases defined this way should come after all other
-# aliases, otherwise simple aliases will be ignored.
-# [[[count]]]
-# command = !pubs list -k | wc -l
-# description = lists number of pubs in repo
-# new subcommands can be defined, e.g.:
-# print = open --with lp
-# evince = open --with evince
-
-# shell commands can also be defined, by prefixing them with a bang `!`, e.g:
-# count = !pubs list -k | wc -l
-
-# aliases can also be defined with descriptions using the following configobj
-# subsectioning.  NOTE: any aliases defined this way should come after all other
-# aliases, otherwise simple aliases will be ignored.
-# [[[count]]]
-# command = !pubs list -k | wc -l
-# description = lists number of pubs in repo
-
-# To use commas in the description, wrap them in a "" string. For example:
-# description = "lists number of pubs in repo, greets the user afterward"
-
-[[git]]
-# The git plugin will commit changes to the repository in a git repository
-# created at the root of the pubs directory. All detected changes will be
-# commited every time a change is made by a pubs command.
-# The plugin also propose the `pubs git` subcommand, to directly send git
-# commands to the pubs repository. Therefore, `pubs git status` is equivalent
-# to `git -C <pubsdir> status`, with the `-C` flag instructing
-# to invoke git as if the current directory was <pubsdir>. Note that a
-# limitation of the subcommand is that you cannot use git commands with the
-# `-c` option (pubs will interpret it first.)
-
-# if False, will display git output when automatic commit are made.
-# Invocation of `pubs git` will always have output displayed.
-quiet = True
-# if True, git will not automatically commit changes
-manual = False
-# if True, color will be conserved from git output (this add `-c color:always`
-# to the git invocation).
-force_color = True
-
-
-[internal]
-# The version of this configuration file. Do not edit.
-version = 0.9.0
-

writing/.config/sh/alias.d/pubs.sh

@@ -1,8 +0,0 @@
-#!/usr/bin/env bash
-
-pubs() {
-    command pubs --config "$XDG_CONFIG_HOME/pubs/pubsrc" "${@}"
-    if [ -f "$BIBFILE" ]; then
-        command pubs export > "$BIBFILE"
-    fi
-}

writing/.local/bin/bib-due

@@ -1,147 +0,0 @@
-#!/usr/bin/env sh
-# shows due entries of bibtex file passed in
-# HACK: brittle! will break on various bibfile abnormities (even just on due date w/o priority)
-# FIXME: reimplementation with real library needed
-#
-
-OPTIND=1 # Reset in case getopts has been used previously in the shell.
-fields="due|priority|\bauthor\b|\btitle\b"
-filterby="due"
-file="${BIBFILE}"
-until=""
-
-show_help() {
-  printf "%s\n" \
-    "" \
-    " bib-due       Show due readings from bibtex file." \
-    "" \
-    " Usage: bib-due [-hv] -i input.bib -r 'due|priority|\bauthor|\btitle' -l 'due' -u '2020-05-12'" \
-    "" \
-    " Options:" \
-    "" \
-    "     -i [bibtex-file]                    Input bibtex file to scrape and get items from." \
-    "" \
-    "     -r [fields]                         Field values to read in file." \
-    "" \
-    "     -l [filter]                         Field to use as filter entity." \
-    "                                         This field is required for the scraper to pick entries up." \
-    "" \
-    "     help    | -h | --help               Print out this help." \
-    "" \
-    " Invoked without arguments, bib-due will scrape the file defined in BIBFILE environment variable, " \
-    " filtering entries with the 'due' field, and getting the values for 'due', 'priority', 'author', " \
-    " and 'title' fields. It will then print the entries to stdout." \
-    "" \
-    " Example output line:" \
-    "" \
-    ' 2020-06-25 (1): Sergei Gerasymchuk -- “Ze” time in Ukraine (Gerasymchuk2019) ' \
-    ""
-}
-
-filter_until() {
-  # filter for dates, with line numbers
-  filtered=$(echo "$entries" | grep -noE '[[:digit:]]{4}-[[:digit:]]{2}-[[:digit:]]{2}')
-
-  # redirect entries to fifo pipe
-  mkfifo filteredentries
-  finish() {
-    rm filteredentries
-  }
-  trap finish EXIT
-  echo "$filtered" >filteredentries &
-
-  # find first date past until filter
-  lastline=""
-  while IFS= read -r line; do
-    cond=$(printf '%s' "$line" | cut -d: -f2)
-    cond=$(date -d "$cond" +%s)
-    if [ "$cond" -gt "$until" ]; then
-      lastline=$(printf '%s' "$line" | cut -d: -f1)
-      break
-    fi
-  done <filteredentries
-
-  # special cases all in filter, or none in filter
-  if [ -z "$lastline" ]; then
-    return
-  elif [ "$lastline" -eq 1 ]; then
-    entries=""
-  # filter
-  else
-    # remove lines below found
-    lastprinted="$((lastline - 1))"
-    entries=$(echo "$entries" | sed -n "1,${lastprinted}p;${lastline}q")
-  fi
-}
-
-filter_priority() {
-  priority="$1"
-  # filter for dates, with line numbers
-  # filtered=$(echo "$entries" | grep -noE '[[:digit:]]{4}-[[:digit:]]{2}-[[:digit:]]{2}')
-  filtered=""
-  while [ "$priority" -gt 0 ]; do
-    current=$(echo "$entries" | grep -E "\($priority\)")
-
-    # append found to filtered entries
-    filtered=$(printf "%s\n%s" "$filtered" "$current")
-
-    # go to next 'higher' priority
-    priority="$((priority - 1))"
-  done
-  # sort them chronologically again, remove empty lines
-  entries="$(echo "$filtered" | sed -e '/^$/d' | sort)"
-}
-
-main() {
-  if [ -z "$file" ]; then
-    echo "Requires a bibtex file as argument."
-    exit 1
-  fi
-
-  # filter all entries for those containing filterby field (default: due)
-  # retain values of all fields mentioned in fields variable
-  entries=$(grep -E "^@|$fields" "$file" | awk 1 ORS=' ' | sed -E 's/@\w+\{/\n/g' | grep "$filterby" | tail -n +2 | sed -E 's/(,\s+(\w+)\s+=\s+|,\s*$)/\t/g' | awk -F'\t' '{ print $4 "\t" $5 "\t" $2 "\t" $3 "\t" $1 }')
-
-  # prettify and sort the entries for display (remove {}, order by date,prio,author,title)
-  entries=$(echo "$entries" | awk -F'\t' '{ gsub(/{/,""); gsub(/}/,""); gsub(/prio/,"",$2) } { print $1 " (" $2 "): " $3 " -- " $4 " (" $5 ")"}' | sort)
-
-  if [ -n "$until" ]; then
-    filter_until
-  fi
-  if [ -n "$priority" ]; then
-    filter_priority "$priority"
-  fi
-
-  echo "$entries"
-}
-
-while getopts "h?i:u:r:l:p:" opt; do
-  case "$opt" in
-  h | \?)
-    show_help
-    exit 0
-    ;;
-    # v)  verbose=1
-    # ;;
-  r)
-    fields="$OPTARG"
-    ;;
-  l)
-    filterby="$OPTARG"
-    ;;
-  i)
-    file="$OPTARG"
-    ;;
-  u)
-    until="$(date -d "$OPTARG" +%s)"
-    ;;
-  p)
-    priority="$OPTARG"
-    ;;
-  esac
-done
-shift $((OPTIND - 1))
-
-[ "${1:-}" = "--" ] && shift
-
-main "$@"

writing/.local/bin/rofi-bib-due

@@ -1,29 +0,0 @@
-#!/usr/bin/env sh
-
-exist rofi normal
-
-_rofi() {
-  rofi -dmenu -no-auto-select -i -theme themes/dropdown -p "papers" -l 25 -yoffset 20 -columns 1 -u "$urgent"
-}
-
-# call for whatever file is passed in
-results="$(bib-due "$@")"
-
-# mark priority 1 items as urgent in rofi
-urgent="$(
-  # find all lines with priority 1, (marked as `(1):` );
-  # print them on 1 line, -1 since dmenu is 0 indexed
-  echo "$results" | grep -n '(1):' | cut -d: -f1 | awk '{ $0=$0-1; print $0 }' ORS=','
-)"
-
-# get user choice, exit if nothing selected
-choice=$(echo "$results" | _rofi)
-[ -z "$choice" ] && exit 0
-
-key=$(echo "$choice" | sed -E 's/.*\((\w+)\)$/\1/')
-
-# get library pdf folder (only searches for default ./pdf path)
-library="$(dirname "$(realpath "$BIBFILE")")/pdf"
-
-# find and open the key-associated pdf file
-${FILEREADER:-open} "$(find "$library" -type f -name "$key *.pdf")"

writing/README.md

@@ -1,65 +1,15 @@
 # Writing module
 
-[bibtex](https://en.wikipedia.org/wiki/BibTeX) - plain-text reference management
+This module contains everything that is specific for me writing prose, journaling and pursuing academic work.
+
+That means there are configurations for reference management (`papis`),
+for daily journaling (`jrnl`),
+for reading PDFs (`sioyek`, `zathura`)
+and for general notetaking (`zk`).
+
+[bibtex](https://en.wikipedia.org/wiki/BibTeX) - plain-text references
+[papis](https://github.com/papis/papis) - yaml-driven and bibtex-compatible reference management
+[jrnl](https://github.com/jrnl-org/jrnl) - journaling on the command line
+[zk](https://github.com/zk-org/zk) - notetaking with a 'zettelkasten' principle
 [zathura](git.pwmt.org) - keyboard-driven PDF reading
 [sioyek](http://sioyek.info/) - keyboard-driven PDF reading *and annotating*
-
-This readme is a little out of date, as are the scripts below.
-They are old, I used them during my time as a student and they are probably written terribly.
-But I still think there is value in them, hence not removing them from the repo just yet.
-
-## bib-due
-
-The `bib-due` script depends on (gnu) grep, awk, and sed, date if using date filtering capabilities. It is currently written in a rather haphazard way, and prone to breakage.
-On the other hand, it does what it's supposed to do: list bibtex entries which have their due-date coming up.
-
-The script needs bibtex entries to be marked with two fields: `due`, containing a due date (ideally in YYYY-MM-DD format, for easy sorting), and `priority` containing a read priority. It will also, by default attempt to grab the values of the fields `author` and `title`, as well as the name of the bibtex key of the entry.
-
-It can be invoked with the path to a bibtex file `bib-due path/to/library.bib`, and will gather the entries from the respective file. It can be invoked without an argument if the environment variable `$BIBFILE` is declared (pointing to a bibtex file).
-
-Example output looks as follows:
-
-![bib-due example output](.assets/bibtex/list.png)
-
-The output can then be filtered further through other programs.
-
-Bib-due itself allows 2 filtering options: *until* a certain date (`-u`), and *at least* a certain priority (`-p`).
-
-Using priority is relatively self-explanatory: 1 is the highest priority, 3 the lowest (technically, no priority is the lowest). Choosing `-p3` means priority 1, 2, and 3 will be displayed. Choosing `-p1` will only display the highest priority items.
-
-Using the date works as a cut-off for the future, and it uses gnu `date` to calculate the correct date. That makes things like `-u 'fri this week'` possible, showing only upcoming items until the end of the week. Read the `date` manual for more information.
-There will likely not be a new option for filtering dates *from* a certain point forward since I don't need it and before implementing more stuff what's there should be more solid. (and read your damn overdue texts!)
-
-Again, this script will (for now[^time]) break when bibtex files are formatted in any way other than what it expects.
-An example of a working entry:
-
-[^time]: And probably for some time since I don't see myself sinking too much more time into this in the near future. I actually need to get some of the upcoming readings done that I can now list! 🙂
-
-```
-@InBook{Borhi2016,
-  author    = {László Borhi},
-  chapter   = {1956: Self-Liberation},
-  pages     = {117--137},
-  publisher = {Indiana University Press},
-  title     = {Dealing with dictators: the {United States}, {Hungary}, and {East Central Europe}, 1942-1989},
-  year      = {2016},
-  due       = {2020-05-07},
-  file      = {:Borhi2016 - Dealing with Dictators_ the United States, Hungary, and East Central Europe, 1942 1989.pdf:PDF},
-  pagetotal = {564},
-  priority  = {prio1},
-  timestamp = {2020-05-08},
-}
-```
-
-Important fields are author, title, due, priority. These need to exist, and need to be ordered alphabetically. Otherwise there will probably be some breakage.
-
-## rofi-bib-due
-
-The `rofi-bib-due` script utilizes the `bib-due` script and depends on an existing installed `rofi` module (see [here](rofi/)).
-On invocation, it creates a list of upcoming readings, and allows selecting one of the readings. The selected reading will be passed along to `$FILEREADER` if it is declared, falling back to `xdg-open` if not.
-
-Currently, the path to the reading pdf is hard-coded to be `path/to/bibtex.bib/pdf`, and the name has to begin with the exact bibtex key; otherwise the script will not be able to find the pdf.
-
-An example of the script in action: (window size has been reduced for the recording, cutting off most entry names)
-
-![rofi-bib-due demonstration](.assets/bibtex/rofi.gif)