Merge pull request #24 from trigaten/docs_site

Docs site

.github/workflows/gh-pages.yml

@@ -0,0 +1,29 @@
+name: Deploy
+on:
+  push:
+    branches: [main, docs_site]
+
+jobs:
+  docs:
+    name: Generate Website
+    runs-on: ubuntu-latest
+    env:
+      SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+
+      - name: Install dependencies
+        run: pip install -r requirements.txt && git clone https://github.com/trigaten/Prompt_Systematic_Review.git
+
+      - name: Build
+        run: sphinx-build -b dirhtml -v docs/ build
+
+      - name: Upload to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./build/
+
+    permissions: 
+      contents: write

.gitignore

@@ -1,2 +1,5 @@
 __pycache__
-*.egg-info/
+_build
+.DS_Store
+build/
+*.egg-info/

docs/Makefile

@@ -0,0 +1,24 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+github:
+	@make html
+	@cp -a build/html/. ./docs
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,33 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+import renku_sphinx_theme
+
+project = "Prompt Systematic Review"
+copyright = "2023, Schulhoff et al."
+author = "Schulhoff et al."
+release = "0.0.1"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "renku_sphinx_theme",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+
+html_theme = "renku"
+html_static_path = ["_static"]

docs/how_to_research.rst

@@ -0,0 +1,41 @@
+=========================
+How to Research
+=========================
+
+It can be difficult to know where to start researching a topic, especially as an undergrad with little or no experience. 
+I had to figure this out a few years, so let me save you some time :)
+
+
+The Beginning
+=========================
+
+At the beginning of the research process, you want to go broad in your subject. For example, if you are researching Gen AI Security,
+you might look up "Generative AI Security review" (or overview), "Generative AI Security survey", and similar terms. If you can find
+a review paper, great, read it. If not, start with the most relevant paper, read the abstract/conclusion, then jump to *related work*.
+Most papers have a related work section; it discusses papers related to that one in the field. 
+
+Use **Google Scholar**/ArXiv/Semantic Scholar
+
+
+How to Read a Paper
+=========================
+If you need to understand a technique proposed by a paper (rather than just learn broadly about the field), do this:
+
+I am using the Chain of thought paper as an example: https://arxiv.org/pdf/2201.11903.pdf
+
+- Read the abstract+conclusion
+- Read the description of the proposed method/analysis
+- Look at any images (usually exclude graphs)
+- Skip related work
+- Skip experimental setup
+- Skip ablations
+- Read the conclusion, and perhaps some discussion
+
+You will usually only want to read the sections I said to skip if you *really* need to understand the technique (for example, if you are comparing it to other techniques).
+
+How to keep track of information
+==================================================
+
+Do whatever your project lead suggests. The way I keep track of info is by adding the citation to the Overleaf 
+bibliography file (read the on Overleaf), then writing comments above it as my notes. I try to just started writing in the regular tex
+file as soon as I get a decent understanding of the field.

docs/index.rst

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+.. Prompt Systematic Review documentation master file, created by
+   sphinx-quickstart on Thu Nov  2 15:25:04 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Documentation for the Systematic Prompt Review Project
+====================================================
+
+This website contains all the information you need to understand the research process for this project. The first three sections
+are about how to do research and use LaTeX/Github. The fourth section is an autogenerated API reference for our codebase. 
+Make sure to write Sphinx-style docstrings (look this up).
+
+Quick Info:
+
+- Github: https://github.com/trigaten/Prompt_Systematic_Review
+- Overleaf: DM Sander or sub-team leader
+- The plan document: check announcements in slack
+- Main contact: [email protected]
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   how_to_research
+   using_latex
+   using_github
+   prompt_systematic_review
+
+
+
+.. Indices and tables
+.. ==================
+
+.. * :ref:`genindex`
+.. * :ref:`modindex`
+.. * :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/prompt_systematic_review.rst

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+prompt_systematic_review
+========
+
+.. automodule:: prompt_systematic_review.arxiv_source
+    :members:
+
+
+.. automodule:: prompt_systematic_review.paperSource
+    :members:
+
+.. automodule:: prompt_systematic_review.utils
+    :members:

docs/using_github.rst

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+=========================
+Using Git/Github
+=========================
+
+Git and Github are important tools for collaborative coding projects. Here's a basic guide:
+
+1. **Git Basics**: Git is a version control system that helps you track changes in your code. You need to have Git installed on your computer. Learn a few commands like `git clone` (to get a copy of the project), `git pull` (to get the latest changes), `git push` (to share your changes), and `git commit` (to save your work).
+
+2. **Github**: Github is a platform where we store our code, which is based on Git.
+
+3. **Cloning a Repository**: To start working on a project, use `git clone https://github.com/trigaten/Prompt_Systematic_Review.git` to bring the project to your computer. 
+
+4. **Branches and Pull Requests**: When you want to change something in the project, create a "branch." It's like creating a separate workspace for your ideas. After you're done, you can ask others to review your work by making a "pull request." It's like getting feedback from others before your changes become part of the main project.
+
+5. **Commit Messages**: When you make changes, write clear and simple messages about what you did. Use [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/).
+
+If you have any questions, feel free to ask me or your sub-team leader.
+
+For more help, you can check out the Github Help website: [Github Quickstart](https://docs.github.com/en/get-started/quickstart/hello-world).
+
+Note that our Github repo has a CI pipeline, which automatically runs tests, style checks, and more when you request you merge new code.
+This helps ensure that broken code does not get merged in.

docs/using_latex.rst

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+=========================
+Using LaTeX
+=========================
+
+LaTeX is a typesetting language commonly used for creating documents with complex formatting, such as research papers 
+and scientific articles. For our collaborative document editing, we will be using Overleaf, an online LaTeX editor that 
+allows multiple people to work on a document simultaneously. If you need access to the LaTeX repository for our project, 
+please don't hesitate to reach out to me or your sub team lead.
+
+Here are some basic formatting tips with LaTeX:
+
+1. **Section Headings**: You can create section headings using LaTeX by starting a line with a series of `#` symbols. The number of `#` symbols determines the section level. For example, `#` is a top-level section, `##` is a subsection, and so on.
+
+2. **Italics and Bold**: To make text italic, you can use `\textit{}` and to make text bold, you can use `\textbf{}`. For example, `\textit{italic text}` and `\textbf{bold text}`.
+
+Learn more here: [Link to LaTeX Documentation](https://www.overleaf.com/learn)

requirements.txt

@@ -7,4 +7,7 @@ huggingface_hub
 pytest
 jellyfish
 black
+sphinx
+renku-sphinx-theme
+sphinx-autobuild
 -e .