\input texinfo    @c -*- texinfo -*-
@c %**start of header
@setfilename gnosis.info
@settitle Gnosis User Manual
@documentencoding UTF-8
@documentlanguage en
@set MAINTAINERSITE @uref{https://thanosapollo.org,maintainer webpage}
@set MAINTAINER Thanos Apollo
@set MAINTAINEREMAIL @email{public@thanosapollo.org}
@set MAINTAINERCONTACT @uref{mailto:public@thanosapollo.org,contact the maintainer}
@c %**end of header

@dircategory Emacs misc features
@direntry
* Gnosis: (gnosis).     Spaced Repetition System.
@end direntry

@finalout
@titlepage
@title Gnosis User Manual
@author Thanos Apollo (@email{public@@thanosapollo.org})
@end titlepage

@ifnottex
@node Top
@top Gnosis User Manual

Gnosis is a customizable spaced repetition system designed to enhance
memory retention through active recall.  It allows users to set
specific review intervals for note decks & tags, creating an optimal
learning environment tailored to each specific topic/subject.

@noindent
This manual is written for Gnosis version 0.5.0, released on 2025-06-17.

@itemize
@item
Manual:
@itemize
@item
@uref{https://elpa.nongnu.org/nongnu/doc/gnosis.html}
@item
@uref{https://thanosapollo.org/projects/gnosis/} (Mirror)
@end itemize
@item
Git repositories:
@itemize
@item
@uref{https://git.thanosapollo.org/gnosis}
@item
@uref{https://codeberg.org/thanosapollo/emacs-gnosis} (Mirror)
@item
@uref{https://git.savannah.gnu.org/cgit/emacs/nongnu.git/?h=elpa/gnosis} (Mirror)
@end itemize
@end itemize

@insertcopying

@end ifnottex

@menu
* Introduction::
* Getting started::
* Note Types::
* Linking gnosis notes to org-gnosis content::
* Customization::
* Gnosis Algorithm::
* Editing notes::
* Sync between devices::
* Interactions with other software::
* Contributing::

@detailmenu
--- The Detailed Node Listing ---

Getting started

* Gnosis Dashboard::

Note Types

* Cloze::
* MCQ::

Cloze

* Default cloze format::
* Using anki-like syntax::

Customization

* Typos | String Comparison::

Gnosis Algorithm

* Anagnosis Event::
* Lethe event::
* Proto::

Interactions with other software

* emacs-no-littering::

Contributing

* How to create a patch::

@end detailmenu
@end menu

@node Introduction
@chapter Introduction

Gnosis (γνῶσις) is a spaced repetition system that enhances memory
retention through active recall. It employs a Q&A format, where each
gnosis consists of a question, answer, and explanation.

Gnosis algorithm is highly adjustable, allowing users to set specific
values not just for note decks but for tags as well.  Gnosis'
adjustability allows users to fine-tune settings not only for entire
note collections but also for specific tagged topics, thereby creating
a personalized learning environment for each topic.  Read more on
@ref{Gnosis Algorithm}

@node Getting started
@chapter Getting started

To follow this tutorial, clone the demo deck available at codeberg

Demo Deck: @uref{https://codeberg.org/thanosapollo/gnosis-demo}

Import it to your gnosis collection via @kbd{M-x gnosis-import-deck}

@menu
* Gnosis Dashboard::
@end menu

@node Gnosis Dashboard
@section Gnosis Dashboard

The first thing new users should familiarize themselves with is
@samp{gnosis-dashboard}, which you can access via @kbd{M-x gnosis-dashboard}.

From there you have access to your review stats & history as well as
your gnosis contents.

You can start a review session from the dashboard or with @kbd{M-x gnosis-review}.

NOTE: Gnosis supports reviewing specifics topics for notes of
@samp{org-gnosis} with @kbd{M-x gnosis-review-topic}

You can add new gnosis from the dashboard or with @kbd{M-x gnosis-add-note}

@node Note Types
@chapter Note Types

Each note is a @strong{thema} consisting of the following components:

@itemize
@item
@strong{Keimenon}; The main text or question.
@item
@strong{Hypothesis}; Assumptions/hints for the text to guide to the right answer
@itemize
@item
For example this is used as hints for cloze type or as choices in MCQs
@end itemize
@item
@strong{Answer}; The correct response or solution to the keimenon.
@item
@strong{Parathema}; expansion of keimenon, that can include links to e.g
org-gnosis topics or even files, serving as a way to link org-gnosis
topics to current thema.
@end itemize

Optionally, you can use also add tags for each note.

Notes/themas can have multiple hypotheses and answers (@strong{depending on
their type}), separated by @samp{gnosis-export-separator}, which defaults to
@samp{"\n-"} @emph{(a new line followed by a dash)}.

@menu
* Cloze::
* MCQ::
@end menu

@node Cloze
@section Cloze

A cloze note type is a format where you create sentences or paragraphs
with ``missing'' words.  A fill-in-the-blanks question.  

You can create a cloze note type using @samp{M-x gnosis-add-note} and
selecting @code{Cloze}.

Example format:

@menu
* Default cloze format::
* Using anki-like syntax::
@end menu

@node Default cloze format
@subsection Default cloze format

@example
* Thema                      :pharmacology:antimicrobials:penicillin:
:PROPERTIES:
:GNOSIS_ID: NEW
:GNOSIS_TYPE: cloze
:END:
** Keimenon 
What is the treatment for Actinomyces infection?

Penicillin

** Hypothesis 
- drug type

** Answer 
- Penicillin

** Parathema 
Sulfonamides → Nocardia
Actinomyces → [[id:680ca944-8ee9-4513-92d6-25696ee01f48][Penicillin]] 
(treatment is a SNAP)
@end example

@node Using anki-like syntax
@subsection Using anki-like syntax

@example
* Thema                      :pharmacology:antimicrobials:penicillin:
:PROPERTIES:
:GNOSIS_ID: NEW
:GNOSIS_TYPE: cloze
:END:
** Keimenon 
@{c1:Cyproheptadine::drug name@} is a(n) @{c2:5-HT2@} receptor antagonist used to treat @{c2:serotonin syndrome@}

** Hypothesis 
- 

** Answer 
- 

** Parathema 

@end example


You can format clozes like Anki if you so prefer with hints; e.g @code{@{@{c1::Cyproheptadine::drug name@}@}}
@itemize
@item
You can use the keyword @samp{::} to indicate a hint.
@end itemize

@itemize
@item
For each cX-tag there will be created a cloze type note, the above
example creates 2 cloze type notes.

@item
Each cX tag can have multiple clozes, but each cloze must be a
@strong{UNIQUE} word, or a unique combination of words, in given note.

@itemize
@item
If a cloze is repeated, such as in phrases with ``acetyl'' &
acetylcholine, include whitespace in the cloze to denote a single
word.
@end itemize
@end itemize

@node MCQ
@section MCQ

Example format:
@example

* Thema                                                            :clinical:
:PROPERTIES:
:GNOSIS_ID: NEW
:GNOSIS_TYPE: mcq
:END:
** Keimenon
A 60-year-old man comes to the physician with chills, nausea, and
diffuse muscle aches for 3 days. His niece had similar symptoms 2
weeks ago and H3N2 influenza strain was isolated from her respiratory
secretions. He received his influenza vaccination 2 months ago. His
temperature is 38.5°C. A rapid influenza test is
positive. Which of the following mechanisms best explains this
patient's infection despite vaccination?

** Hypothesis
- Random point mutations within viral genome
- Complementing with functional viral proteins
- Exchange of viral genes between chromosomes
- Reassortment of viral RNA segments
- Acquisition of viral surface proteins

** Answer
- Random point mutations within viral genome

** Parathema
Random point mutations within the viral genome are responsible for
antigenic drift, which creates a new virus strain.

@end example

@node Linking gnosis notes to org-gnosis content
@chapter Linking gnosis notes to org-gnosis content

@emph{org-gnosis is the note taking module of gnosis}

@itemize
@item
You can create notes using @samp{M-x org-gnosis-find}, to link them to a
gnosis thema use @samp{M-x org-gnosis-insert} to insert a link of said
topic, either on the keimenon or parathema.

@item
You can review gnosis questions that are linked to a topic by using
@samp{M-x gnosis-review-topic}.
@end itemize

@node Customization
@chapter Customization

@menu
* Typos | String Comparison::
@end menu

@node Typos | String Comparison
@section Typos | String Comparison

You can adjust @samp{gnosis-string-difference}, this is a threshold value
for string comparison that determines the maximum acceptable
Levenshtein distance between two strings, which identifies their
similarity

Let's illustrate with an example:
@lisp
(setf gnosis-string-difference 1)
@end lisp

In this scenario, we set @samp{gnosis-string-difference} to 1. This implies
that two strings will be recognized as similar if they exhibit a
difference of at most one character edit.

To demonstrate, 'example' and 'examples' will be recognized as
similar, considering that the latter involves just one additional
character."

@node Gnosis Algorithm
@chapter Gnosis Algorithm

Each gnosis note has a gnosis score, which is a list of 3 values,
(gnosis-plus gnosis-minus gnosis-synolon/total).  Gnosis-synolon is
what is used to determine the next interval upon a successful recall,
gnosis-plus is added to gnosis-synolon upon a successful recall as
well, gnosis-minus is subtracted from gnosis-synolon upon failing to
recall a note's answer.

Gnosis has 2 special events, one is @code{anagnosis} @emph{ανάγνωση} and @code{lethe} @emph{λήθη}.

@menu
* Anagnosis Event::
* Lethe event::
* Proto::
@end menu

@node Anagnosis Event
@section Anagnosis Event

@code{Anagnosis}, which means comprehension & recognition of knowledge, is
triggered when the consecutive successful or failed recalls are equal
or greater to anagnosis value.

When @code{anagnosis} is triggered by consecutive @strong{successful} recalls,
@code{epignosis} value is added to gnosis-plus.  @emph{Epignosis means accuracy of knowledge}.

When @code{anagnosis} is triggered by consecutive @strong{failed} recalls,
@code{agnoia} value is added to gnosis-minus. @emph{Agnoia means lack of knowledge}

You can set specific values for each deck and tag of the variables
mentioned above by adjusting @samp{gnosis-custom-values}.

@node Lethe event
@section Lethe event

The @code{Lethe} event triggers after a certain number of consecutive
failures to recall an answer correctly.

When this threshold is reached, the next interval is reset to 0.

For example, with lethe value of 2, upon having 2 consecutive failed
recalls the next review will be set for the current day.

@node Proto
@section Proto

The default initial interval is defined at
@samp{gnosis-algorithm-proto}, you can define a custom initial interval
for each deck as well.

@samp{gnosis-algorithm-interval} is a list of numbers, representing the
first initial intervals for successful reviews.  There is no limit on
the length of the list.

Example:

@lisp
(setq gnosis-algorithm-interval '(0 1 2 30))
@end lisp

Upon each successful note review, the algorithm will increment to the
next interval value: 0 days (0), 1 day later (1), 2 days later
(2), and 30 days later.

Upon failing to review a note without completing it's proto successful reviews,
it's next review date will be on the same date.

@node Editing notes
@chapter Editing notes

@itemize
@item
Currently there are 2 ways for editing notes:

@itemize
@item
You can edit a note after review by pressing @code{e}
@item
Open @samp{gnosis-dashboard} with @samp{M-x gnosis-dashboard}, find the note you want to edit and press @code{e}
@end itemize
@end itemize

@node Sync between devices
@chapter Sync between devices

Gnosis uses git to maintain data integrity and facilitate
synchronization across devices.

You will need to configure your remote manually.

Example:

@example
cd ~/.emacs.d/gnosis # default location for gnosis, no-littering is ~/.emacs.d/var/gnosis
git init # After completing your first review session, a git repo should have been initialized automatically.
git remote add origin <remote_url>
git push --set-upstream origin master
@end example


You can interactively use @samp{gnosis-vc-push} & @samp{gnosis-vc-pull}. As the
name suggests, they rely on @samp{vc} to work properly.

Depending on your setup, @samp{vc} might require an external package for
the ssh passphrase dialog, such as @code{x11-ssh-askpass}.

To automatically push changes after a review session, add this to your configuration:
@lisp
(setf gnosis-vc-auto-push t)
(gnosis-vc-pull) ;; Run vc-pull for gnosis on startup
@end lisp

@node Interactions with other software
@chapter Interactions with other software

@menu
* emacs-no-littering::
@end menu

@node emacs-no-littering
@section emacs-no-littering

If you are a user of @uref{https://github.com/emacscollective/no-littering, emacs-no-littering}, you can theme Gnosis to fit
its standards by adding the following snippet to your configuration:

@lisp
(setq gnosis-dir (no-littering-expand-var-file-name "gnosis/"))
@end lisp

This sets @samp{gnosis-dir} to @samp{~/.emacs.d/var/gnosis}, in line with the folders of other packages.

@node Contributing
@chapter Contributing

Thank you for considering contributing back to gnosis.  You can
contribute by submitting a pull request on the codeberg mirror
repository, or directly sending me patch via email.

@menu
* How to create a patch::
@end menu

@node How to create a patch
@section How to create a patch

@emph{Example:}

@example
$ git clone https://git.thanosapollo.com/gnosis.git && cd gnosis
$ emacs something
$ git add something
$ git commit -m "Fix something"
$ git format-patch HEAD^1
0001-Fix-something.patch
@end example

You can sent the patch to ``Thanos Apollo'', the email of which you can
find on the git log.

@bye
