.dotter/global.toml

@@ -67,14 +67,8 @@ social = "~"
 
 [writing.files]
 "writing/README.md" = { target = "~/NOWHERE", type = "symbolic", if = "false" }
-"writing/jrnl" = "~/.config/jrnl"
+"writing/.config/papis/papistui.yaml" = { target = "~/.config/papis/papistui.yaml", type = "symbolic" }
-"writing/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/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

@@ -0,0 +1,166 @@
+
+[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

@@ -0,0 +1,8 @@
+#!/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

@@ -0,0 +1,147 @@
+#!/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

@@ -0,0 +1,29 @@
+#!/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

@@ -1,15 +1,65 @@
 # Writing module
 
-This module contains everything that is specific for me writing prose, journaling and pursuing academic work.
+[bibtex](https://en.wikipedia.org/wiki/BibTeX) - plain-text reference management
-
-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)