Merge pull request #2 from daskol/style/neurips2023

Add NeurIPS 2023 template

.gitignore

@@ -0,0 +1,6 @@
+# Ignore LaTeX output files.
+*.aux
+*.bbl
+*.bst
+*.log
+*.out

README.md

@@ -12,6 +12,19 @@ template for ICML and are going to add templates for other conferences and
 journals during calendar year.
 
 - [International Conference on Machine Learning (ICML)](icml).
-- Neural Information Processing System (NeurIPS).
+- [Neural Information Processing System (NeurIPS)](neurips).
 - International Conference on Learning Representations (ICLR).
 - Association for the Advancement of Artificial Intelligence (AAAI).
+
+## Utilities
+
+Typst of version 0.10.0 does not produce colored annotations. In order to
+mitigate the issue, we add [a simple script](colorize-annotations.py) to the
+repository. The script is plain and simple. One can use it as follows.
+
+```shell
+./colorize-annotations.py \
+    neurips/example-paper.typst.pdf neurips/example-paper-colored.typst.pdf
+```
+
+It is written with PyMuPDF library and inserts colored annotation.

colorize-annotations.py

@@ -0,0 +1,169 @@
+#!/usr/bin/env python
+"""Simple script based on MuPDF bindings for colorizing annotation in documents
+produced by Typst v0.10.0 (or may be newer).
+"""
+
+from argparse import ArgumentParser, Namespace
+from dataclasses import astuple, dataclass
+from os import unlink
+from pathlib import Path
+from shutil import move
+from tempfile import NamedTemporaryFile
+from typing import Any, Self
+
+import fitz
+from fitz import Document, Page
+
+DEFAULT_STROKE_CYAN = (0.0, 1.0, 1.0)
+
+DEFAULT_STROKE_RED = (1.0, 0.0, 0.0)
+
+parser = ArgumentParser(description=__doc__)
+parser.add_argument('source', type=Path, help='path to original document')
+parser.add_argument('target', type=Path, help='path to output document')
+
+
+@dataclass
+class Point:
+
+    x: float
+
+    y: float
+
+    def __add__(self, other: Self) -> Self:
+        return self.__class__(self.x + other.x, self.y + other.y)
+
+    def __iadd__(self, other: Self) -> Self:
+        self.x += other.x
+        self.y += other.y
+        return self
+
+
+@dataclass
+class Rect:
+
+    top_left: Point
+
+    bot_right: Point
+
+    @classmethod
+    def from_points(cls, x0: float, y0: float, x1: float, y1: float) -> Self:
+        return cls(Point(x0, y0), Point(x1, y1))
+
+    @classmethod
+    def from_postscript(cls, value: str) -> Self:
+        points = [float(x) for x in value[1:-1].split()]
+        return cls.from_points(*points)
+
+    def __add__(self, other) -> Self:
+        return self.__class__(self.top_left + other.top_left,
+                              self.bot_right + other.bot_right)
+
+    def __iadd__(self, other) -> Self:
+        self.top_left += other.top_left
+        self.bot_right += other.bot_right
+        return self
+
+    def to_points(self) -> tuple[float, float, float, float]:
+        return astuple(self.top_left) + astuple(self.bot_right)
+
+    def to_postscript(self) -> str:
+        points = self.to_points()
+        coords = ' '.join(f'{point:g}' for point in points)
+        return f'[{coords}]'
+
+
+DEFAULT_SPACING = Rect.from_points(-0.5, -2.5, 0.5, 1.5)
+
+
+@dataclass
+class Style:
+
+    stroke: tuple[float, float, float]
+
+    spacing: Rect
+
+
+DEFAULT_STYLES = {
+    'external': Style(stroke=DEFAULT_STROKE_CYAN, spacing=DEFAULT_SPACING),
+    'internal': Style(stroke=DEFAULT_STROKE_RED, spacing=DEFAULT_SPACING),
+}
+
+
+def enumerate_links(doc: Document):
+    page: Page
+    for ix, page in enumerate(doc):
+        for link in page.get_links():
+            yield ix, page, link
+
+
+def colorize_link(doc: Document, link: dict[str, Any], styles=None):
+    # If there is no valid xref then it is embedded annotation. Skip it.
+    if (xref := link['xref']) is None or xref <= 0:
+        return
+
+    styles = styles or DEFAULT_STYLES
+    if 'uri' in link:
+        style = styles['external']
+    else:
+        style = styles['internal']
+
+    stroke_str = ' '.join(f'{x:g}' for x in style.stroke)
+    doc.xref_set_key(xref, 'H', '/I')
+    doc.xref_set_key(xref, 'C', f'[{stroke_str}]')
+    doc.xref_set_key(xref, 'BS', '<< /W 1 /S /S >>')
+
+    # Adjust bounding box of annotation.
+    type_, value = doc.xref_get_key(xref, 'Rect')
+    if type_ != 'array':
+        print(f'Attribute `Rect` of xref={xref} is not array.')
+        return
+    rect = Rect.from_postscript(value)
+    rect += style.spacing
+    doc.xref_set_key(xref, 'Rect', rect.to_postscript())
+
+
+def colorize(source: Path, target: Path, styles=None):
+    doc: Document = fitz.open(source)
+
+    # Enumerate all available links and create new link with the same
+    # attributes. The issue is that Typst writes embeddable annotations which
+    # does not have xref. This makes impossible to modify annotation attributes
+    # inplace.
+    for _, page, link in enumerate_links(doc):
+        new_link = {**link}
+        new_link.pop('xref', None)
+        new_link.pop('zoom', None)
+        new_link.pop('id', None)
+        page.insert_link(new_link)
+
+    # As we duplicated annotations, we can update their appearence.
+    total_pages = len(doc)
+    for ix, page in enumerate(doc, 1):
+        print(f'{ix}/{total_pages}: {page}')
+        for link in page.links():
+            colorize_link(doc, link, styles)
+
+    # If source and target pathes are equal then write to temporary and then
+    # replace the original one.
+    if target != source:
+        target.parent.mkdir(exist_ok=True, parents=True)
+        doc.save(target, garbage=3, deflate=True)
+        doc.close()
+    else:
+        prefix = '.' + target.name.removesuffix('.pdf') + '-'
+        with NamedTemporaryFile(mode='w', dir=target.parent, prefix=prefix,
+                                suffix='.pdf', delete=False) as tempfile:
+            unlink(tempfile.name)
+            doc.save(tempfile.name, garbage=3, deflate=True)
+            doc.close()
+            move(tempfile.name, source)  # Copy back.
+
+
+def main():
+    ns: Namespace = parser.parse_args()
+    colorize(ns.source, ns.target)
+
+
+if __name__ == '__main__':
+    main()

neurips/README.md

@@ -0,0 +1,53 @@
+# Neural Information Processing Systems (NeurIPS) 2023
+
+## Example Papers
+
+Here are an example paper in [LaTeX][1] and in [Typst][2].
+
+## Issues
+
+- The biggest and the most important issues is related to line ruler. We are
+  not aware of universal method for numbering lines in the main body of a
+  paper.
+
+- There is an issue in Typst with spacing between figures and between figure
+  with floating placement. The issue is that there is no way to specify gap
+  between subsequent figures. In order to have behaviour similar to original
+  LaTeX template, one should consider direct spacing adjacemnt with `v(-1em)`
+  as follows.
+
+  ```typst
+  #figure(
+    rect(width: 4.25cm, height: 4.25cm, stroke: 0.4pt),
+    caption: [Sample figure caption.#v(-1em)],
+    placement: top,
+  )
+  #figure(
+    rect(width: 4.25cm, height: 4.25cm, stroke: 0.4pt),
+    caption: [Sample figure caption.],
+    placement: top,
+  )
+  ```
+
+- Another issue is related to Typst's inablity to produce colored annotation.
+  In order to mitigte the issue, we add a script which modifies annotations and
+  make them colored.
+
+  ```shell
+  ../colorize-annotations.py \
+      example-paper.typst.pdf example-paper-colored.typst.pdf
+  ```
+
+  See [README.md][3] for details.
+
+- NeurIPS 2023 instructions discuss bibliography in vague terms. Namely, there
+  is not specific requirements. Thus we stick to `ieee` bibliography style
+  since we found it in several accepted papers and it is similar to that in the
+  example paper.
+
+- It is unclear how to render notice in the bottom of the title page in case of
+  final (`accepted: true`) or preprint (`accepted: none`) submission.
+
+[1]: example-paper.latex.pdf
+[2]: example-paper.typst.pdf
+[3]: ../#colored-annotations

neurips/logo.typ

@@ -0,0 +1,18 @@
+#let kern(length) = h(length, weak: true)
+#let TeX = style(styles => {
+  let e = measure(text("E"), styles)
+  let T = "T"
+  let E = text(baseline: e.height / 2, "E")
+  let X = "X"
+  box(T + kern(-0.1667em) + E + kern(-0.125em) + X)
+})
+#let LaTeX = style(styles => {
+  let l = measure(text(10pt, "L"), styles)
+  let a = measure(text(7pt, "A"), styles)
+  let L = "L"
+  let A = text(7pt, baseline: a.height - l.height, "A")
+  box(L + kern(-0.36em) + A + kern(-0.15em) + TeX)
+})
+#let LaTeXe = style(styles => {
+  box(LaTeX + sym.space.sixth + [2#text(baseline: 0.3em, $epsilon$)])
+})

neurips/main.bib

@@ -0,0 +1,25 @@
+@article{alexander1994template,
+  title={Template-based algorithms for connectionist rule extraction},
+  author={Alexander, Jay and Mozer, Michael C},
+  journal={Advances in neural information processing systems},
+  volume={7},
+  year={1994}
+}
+
+@book{bower2012book,
+  title={The book of GENESIS: exploring realistic neural models with the GEneral NEural SImulation System},
+  author={Bower, James M and Beeman, David},
+  year={2012},
+  publisher={Springer Science \& Business Media}
+}
+
+@article{hasselmo1995dynamics,
+  title={Dynamics of learning and recall at excitatory recurrent synapses and cholinergic modulation in rat hippocampal region CA3},
+  author={Hasselmo, Michael E and Schnell, Eric and Barkai, Edi},
+  journal={Journal of Neuroscience},
+  volume={15},
+  number={7},
+  pages={5249--5262},
+  year={1995},
+  publisher={Soc Neuroscience}
+}