diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml new file mode 100644 index 0000000..99bc88f --- /dev/null +++ b/.github/workflows/test.yaml @@ -0,0 +1,32 @@ +name: test + +on: push + +jobs: + test: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.10 + uses: actions/setup-python@v2 + with: + python-version: "3.10" + - name: Install poetry ${{ matrix.poetry-version }} + env: + ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true' + run: | + python -m ensurepip + python -m pip install --upgrade pip + python -m pip install poetry==1.3.2 + - name: View poetry --help + run: poetry --help + + - name: Install dependencies + shell: bash + run: python -m poetry install + + - name: Test with pytest + run: | + python3 -m poetry run pytest --cov diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..dc1b326 --- /dev/null +++ b/.gitignore @@ -0,0 +1,45 @@ + +## General pieces to ignore during git pushing, so you can use git add . without adding everything. + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ +.pytest_cache/ + +# Jupyter Notebook +.ipynb_checkpoints + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ \ No newline at end of file diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..6790723 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule ".showyourwork"] + path = .showyourwork + url = https://github.com/showyourwork/showyourwork diff --git a/.pre-commit-config.yml b/.pre-commit-config.yml new file mode 100644 index 0000000..7a05a42 --- /dev/null +++ b/.pre-commit-config.yml @@ -0,0 +1,17 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.1.0 + hooks: + - id: check-toml + - id: name-tests-test + - id: requirements-txt-fixer + - id: trailing-whitespace + - id: mixed-line-ending + - repo: https://github.com/psf/black + rev: 22.3.0 + hooks: + - id: black + - repo: https://github.com/asottile/pyupgrade + rev: v2.31.0 + hooks: + - id: pyupgrade diff --git a/.showyourwork b/.showyourwork new file mode 160000 index 0000000..bee25e5 --- /dev/null +++ b/.showyourwork @@ -0,0 +1 @@ +Subproject commit bee25e5e096fc9edaf9da7a447afdba464d5f198 diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..63b4b68 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) [year] [fullname] + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..9ae4578 --- /dev/null +++ b/README.md @@ -0,0 +1,152 @@ +This template is designed to give a framework for public distributions of "science" projects. +It is a guideline, showing the minimum things recommended to include with your public repository, +to make your results easily replicable. +It is not exhaustive by any means, nor is everything here strictly required in all cases! +Please consider this as a loose list of things considered "nice to have", and as reference material above all. + +# DeepSkies Science Repo Template +Include status links to different outside resources, such as build info, paper info, license, etc. +You can select your license from the [choose a license page.](https://choosealicense.com/licenses/), and then change the name of the license in the badge and link included. +For workflows, change the name of the repo listed in the img.shields link to point to your repo and workflows. + +[![status](https://img.shields.io/badge/arXiv-000.000-red)](arxiv link if applicable) +[![status](https://img.shields.io/badge/PyPi-0.0.0.0-blue)](pypi link if applicable) +[![status](https://img.shields.io/badge/License-MIT-lightgrey)](MIT or Apache 2.0 or another requires link changed) +![GitHub Workflow Status](https://img.shields.io/github/workflow/status/owner/repo/build-repo) +![GitHub Workflow Status](https://img.shields.io/github/workflow/status/owner/repo/test-repo?label=test) + +Your overview should contain a brief summary of the project, and figures and examples showing input and output. + +## Installation +Information about install. +We recommend publishing to pypi using a poetry package management system (described below) but we also provide instructions for using python virtual environments and showyourwork with conda integration. + +Example of what your installation instructions should look like: + +To install with pip: +> pip install git+https://github.com/DeepSkies/science_template.git +> +This will set up a virtual environment, which can b e run with on mac or linux +> source venv/bin/activate +> +Or on windows with +> venv\Scripts\activate.bat + +Verify installation is functional is all tests are passing +> pytest + +Additionally, include how to install from source (via git clone) and associated setup. + +### poetry +Poetry is our recommended method of handling a package environment as publishing and building is handled by a toml file that handles all possibly conflicting dependencies. +Full docs can be found [here](https://python-poetry.org/docs/basic-usage/). + +Install instructions: + +Add poetry to your python install +> pip install poetry + +Install the pyproject file +> poetry install + +To add another package to your environment +> poetry add (package name) + +To run within your environment +>poetry run (file).py + +If you wish to start from scratch: +> pip install poetry +> poetry init + +### virtual environment +At the bare minimum, project dependencies must be contained and strictly defined and shared for replication purposes. +The easiest way to do this is to use a python virtual environment. +Full instructions are found [here.](https://docs.python.org/3/library/venv.html) + +To initialize an environment: +> python3 -m venv /path/to/env +> +To activate it: +Linux and Mac: +> source venv/bin/activate +> +Windows: +> venv\Scripts\activate.bat + +And use pip as normal to install packages. + +In order to produce a file to share with your version of dependencies, produce a requirements.txt. +This can later be installed in full to a new system using `pip install -r requirements.txt`. +Note that this does not manage any versioning conflicts and can very quickly become depreciated. +> pip freeze >requirements.txt + +### show your work with conda +We also supply a ["show your work"](https://github.com/showyourwork/showyourwork) workflow to use with a conda venv which can compile the example tex file in `DeepTemplate-Science/src/tex/ms.tex` + +To execute this workflow: +>showyourwork build + +This will build your project and install the conda venv associated with the project (or just compile the document if you haven't been using it) and output the document as a pdf. +If you would like to integrate with overleaf to push your work remotely, you can do that by adding the following lines to your showyourwork.yml file: +> +> overleaf: +> +> id: URL identifying your project +> push: +> - src/tex/figures +> - src/tex/output +> pull: +> - src/tex/ms.tex +> - src/tex/bib.bib + +And adding the system variables `$OVERLEAF_EMAIL` and `$OVERLEAF_PASSWORD` with your credentials. +To do this, use a bash terminal to input the command `export OVERLEAF_EMAIL='youremail@server.org`, and do the same for your password. +To verify these are set correctly, run `echo $OVERLEAF_EMAIL`and `echo $OVERLEAF_PASSWORD`. +To complete this setup, run `showyourwork build` as if you were compiling a project. +The above snippet of the yaml file will then push anything in the `src/tex/figures` and `src/tex/output` folders to the remote, under the `images` folder. + +The existing yaml file is set up to modify the [template project](*https://www.overleaf.com/read/fsjwntpjmdzw). +The differences in the ID in the template and the url you'll see is due to the fact that only project owners have access to that ID (even if I want to share). +This limits the person who can build the project to the person that owns the overleaf page, at least until Latex sets up token authentication. +The workaround for this is account sharing, but this is not recommended. + +For more information please see the [showyourwork page on the topic](https://show-your.work/en/latest/overleaf/). + + + +## Quickstart +Description of the immediate steps to replicate your results, pointing to a script with cli execution. +You can also point to a notebook if your results are highly visual and showing plots in line with code is desired. + +Example: + +To run full model training: +> python3 train.py --data /path/to/data/folder + +To evaluate a single ""data format of choice"" +> python3 eval.py --data /path/to/data + +## Documentation +Please include any further information needed to understand your work. +This can include an explanation of different notebooks, basic code diagrams, conceptual explanations, etc. +If you have a folder of documentation, summarize it here and point to it. + +## Citation +Include a link to your bibtex citation for others to use. + +``` +@article{key , + author = {You :D}, + title = {title}, + journal = {journal}, + volume = {v}, + year = {20XX}, + number = {X}, + pages = {XX--XX} +} + +``` + +## Acknowledgement +Include any acknowledgements for research groups, important collaborators not listed as a contributor, institutions, etc. diff --git a/Snakefile b/Snakefile new file mode 100644 index 0000000..e69de29 diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..bdd8ef1 --- /dev/null +++ b/environment.yml @@ -0,0 +1,10 @@ +## THIS IS FOR SHOW YOUR WORK - 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+pyyaml = ">=6.0,<7.0" + +[metadata] +lock-version = "2.0" +python-versions = "^3.9" +content-hash = "6562be89be482fa5dcbefcb4629368ce8b9c044ead733ccfcbbc1c044b5b2f58" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..6d90ccf --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,21 @@ +[tool.poetry] +name = "deeptemplate-science" +version = "0.1.0" +description = "a template for a science motivated project, focus on ease of reproducablity" +authors = ["voetberg "] +license = "MIT" + +[tool.poetry.dependencies] +python = "^3.9" + +[tool.poetry.dev-dependencies] +showyourwork = "^0.4.2" +pytest = "^7.3.2" + +[tool.poetry.group.dev.dependencies] +pre-commit = "^3.3.2" +pytest-cov = "^4.1.0" + +[build-system] +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" diff --git a/showyourwork.yml b/showyourwork.yml new file mode 100644 index 0000000..206454e --- /dev/null +++ b/showyourwork.yml @@ -0,0 +1,7 @@ +version: 0.3.0 + +overleaf: + id: 62defbc43013ada57aa4c153 + push: + - src/tex/figures + - src/tex/output \ No newline at end of file diff --git a/src/scripts/__init__.py b/src/scripts/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/scripts/__version__.py b/src/scripts/__version__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/scripts/evaluate.py b/src/scripts/evaluate.py new file mode 100644 index 0000000..664d20e --- /dev/null +++ b/src/scripts/evaluate.py @@ -0,0 +1,46 @@ +""" +Simple stub functions to use in inference +""" + +import argparse + + +def load_model(checkpoint_path): + """ + Load the entire model for prediction with an input + + :param checkpoint_path: location + :return: loaded model object that can be used with the predict function + """ + pass + + +def predict(input, model): + """ + + :param input: loaded object used for inference + :param model: loaded model + :return: Prediction + """ + return 0 + +def load_inference_object(input_path): + """ + + :param input_path: path to the object you want to predict + :return: loaded object + """ + return 0 + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument("--checkpoint", type=str, help="Checkpoint to unloaded model checkpoint, either weights or the compressed model object") + parser.add_argument("--input", type=str, help="path to object to predict quality of") + args = parser.parse_args() + + model = load_model(args.checkpoint) + pred_obj = load_inference_object(args.input) + + prediction = predict(pred_obj, model) + print(prediction) diff --git a/src/scripts/paths.py b/src/scripts/paths.py new file mode 100644 index 0000000..8c9434e --- /dev/null +++ b/src/scripts/paths.py @@ -0,0 +1,29 @@ +""" +Exposes common paths useful for manipulating datasets and generating figures. + +""" +from pathlib import Path + +# Absolute path to the top level of the repository +root = Path(__file__).resolve().parents[2].absolute() + +# Absolute path to the `src` folder +src = root / "src" + +# Absolute path to the `src/data` folder (contains datasets) +data = src / "data" + +# Absolute path to the `src/static` folder (contains static images) +static = src / "static" + +# Absolute path to the `src/scripts` folder (contains figure/pipeline scripts) +scripts = src / "scripts" + +# Absolute path to the `src/tex` folder (contains the manuscript) +tex = src / "tex" + +# Absolute path to the `src/tex/figures` folder (contains figure output) +figures = tex / "figures" + +# Absolute path to the `src/tex/output` folder (contains other user-defined output) +output = tex / "output" \ No newline at end of file diff --git a/src/scripts/train.py b/src/scripts/train.py new file mode 100644 index 0000000..a24465b --- /dev/null +++ b/src/scripts/train.py @@ -0,0 +1,39 @@ +""" +Simple stubs to use for re-train of the final model +Can leave a default data source, or specify that 'load data' loads the dataset used in the final version +""" +import argparse + + +def architecture(): + """ + :return: compiled architecture of the model you want to have trained + """ + return 0 + +def load_data(data_source): + """ + :return: data loader or full training data, split in val and train + """ + return 0, 0 + +def train_model(data_source, n_epochs): + """ + :param data_source: + :param n_epochs: + :return: trained model, or simply None, but saved trained model + """ + data = load_data(data_source) + model = architecture() + + return 0 + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--data_source", type=str, help="Data used to train the model") + parser.add_argument("--n_epochs", type=int, help='Integer number of epochs to train the model') + + args = parser.parse_args() + + train_model(data_source=args.data_source, n_epochs=args.n_epochs) diff --git a/src/static/.gitignore b/src/static/.gitignore new file mode 100644 index 0000000..e167a34 --- /dev/null +++ b/src/static/.gitignore @@ -0,0 +1,2 @@ +# Anything is game in this folder +!* diff --git a/src/tex/.gitignore b/src/tex/.gitignore new file mode 100644 index 0000000..841b7c7 --- /dev/null +++ b/src/tex/.gitignore @@ -0,0 +1,2 @@ +# Don't track TeX temporaries +*latexindent* \ No newline at end of file diff --git a/src/tex/bib.bib b/src/tex/bib.bib new file mode 100644 index 0000000..5ca6881 --- /dev/null +++ b/src/tex/bib.bib @@ -0,0 +1,37 @@ +@article{Hunter:2007, + Author = {Hunter, J. D.}, + Title = {Matplotlib: A 2D graphics environment}, + Journal = {Computing in Science \& Engineering}, + Volume = {9}, + Number = {3}, + Pages = {90--95}, + abstract = {Matplotlib is a 2D graphics package used for Python for + application development, interactive scripting, and publication-quality + image generation across user interfaces and operating systems.}, + publisher = {IEEE COMPUTER SOC}, + doi = {10.1109/MCSE.2007.55}, + year = 2007 + } + +@article{ harris2020array, + title = {Array programming with {NumPy}}, + author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J. + van der Walt and Ralf Gommers and Pauli Virtanen and David + Cournapeau and Eric Wieser and Julian Taylor and Sebastian + Berg and Nathaniel J. Smith and Robert Kern and Matti Picus + and Stephan Hoyer and Marten H. van Kerkwijk and Matthew + Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del + R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre + G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and + Warren Weckesser and Hameer Abbasi and Christoph Gohlke and + Travis E. Oliphant}, + year = {2020}, + month = sep, + journal = {Nature}, + volume = {585}, + number = {7825}, + pages = {357--362}, + doi = {10.1038/s41586-020-2649-2}, + publisher = {Springer Science and Business Media {LLC}}, + url = {https://doi.org/10.1038/s41586-020-2649-2} +} \ No newline at end of file diff --git a/src/tex/figures/.gitignore b/src/tex/figures/.gitignore new file mode 100644 index 0000000..9d0f65c --- /dev/null +++ b/src/tex/figures/.gitignore @@ -0,0 +1,5 @@ +# Nothing should be tracked in this folder... +* + +# Except the gitignore file itself! +!.gitignore \ No newline at end of file diff --git a/src/tex/ms.tex b/src/tex/ms.tex new file mode 100644 index 0000000..ad2222b --- /dev/null +++ b/src/tex/ms.tex @@ -0,0 +1,254 @@ + +\documentclass[twocolumn]{aastex631} + +% Import showyourwork magic +\usepackage{showyourwork} + +\usepackage[utf8]{inputenc} +\usepackage{amsmath} +\usepackage{unicode-math} + + +% Recommended, but optional, packages for figures and better typesetting: +\usepackage{microtype} +\usepackage{graphicx} +\usepackage{subfigure} +\usepackage{booktabs} % for professional tables +\usepackage{multirow} + +% hyperref makes hyperlinks in the resulting PDF. +% xurl can wrap the link if it spans a column (especially in citations). +\usepackage{hyperref} +\usepackage{xurl} + + +% This command creates a new command \editor{} that highlights any of the text in {} with a maroon color, so it can easily be spotted during internal review + +\usepackage[textsize=tiny]{todonotes} +\newcommand{\editor}[1]{{\color{purple} #1}} + +\begin{document} + +\title{DeepSkies - Template} % Define the title itself, so it may be used in headers + +\author{Author 1 \thanks{Corresponding Author, email@domain.com}} + + +\begin{abstract} + This document is meant to be used as a lose guide. + It includes useful and basic packages and formatting tips to keep you from hunting for formatting code while writing. + Please use this as a reference, and especially while writing without a specific journal already in mind. + This will not be the format all journals accept, so please use their defined style guides when work on your draft. + % Additionally, it's very nice to keep all your sentences on different lines. + % It makes editing a lot easier. +\end{abstract} + +\section{Basic Format and Style} + +\subsection{Format} + +The specific format of the paper if between you and your journal and your editors. +However, it is a good idea to include the basic sections of "Introduction, Methods, Conclusions". + +\subsection{Style} + +Names of coding packages denoted with: \texttt{Package}. + + + +\editor{Here is an quick comment that may appear, indicating an addition by an editor.} + +\subsubsection{Tables} + +Tables should act as summaries, and include error bars when applicable. Captions should draw attention to the main takeaway and can provide analysis, but not necessary give a full summary. +Please view sample table formats in the appendix ~\ref{tab:two_column} + + + + +\subsubsection{Plots and other graphics} + +When making graphics, please keep accessibility in mind. +All plots should be understandable in both black and white and color. +This requires things like using color blind friendly color packages (matplotlib's virdis for example), and changing line and marker styles for different elements of a graph. +Plots also must be clearly labeled and include legends where applicable. +Captions should both describe what the figure contains and its significance. + +When referencing a figure in the main text, please refer to it with \verb|~\ref{figure label}|. +Please view different figure layouts in the appendix ~\ref{fig:single_graphic_figure}. + + + +\subsubsection{Equations} + +Large equations should be numbered and included in an equation block such that +\begin{align} + E=mc^2 \label{eq:1} \\ + F=ma \label{eq:2} +\end{align} + + +Intermediate steps can not include numbers such that +\begin{align*} + A = \pi r^2 +\end{align*} + +Or by using: + +\begin{align} + A + &=B \label{eq:3}\\ + &=B \notag\\ + A + &=BCD \label{eq:4}\\ + &=B \notag +\end{align} + + +Labels are used so that they can be referenced later on using the command \verb|~\ref{eq:equation label}|. Singular symbols can be added into the middle of sentences using \verb|$\symbol$|, such that \verb|\pi| becomes $\pi$. + +\section {Acknowledgements} + +Make sure to cite \cite{harris2020array} all of your sources \cite{Hunter:2007}. + + +You can also optionally provide contributions by person: + +\paragraph{Author 1} +Author 1 contributed X Y and Z + +\paragraph{Author 2} +Author 2 contributed A B and C + +If you work with the DeepSkies research group; please include the following text: + +\emph{We acknowledge the Deep Skies Lab as a community of multi-domain experts and collaborators who’ve facilitated an environment of open discussion, idea-generation, and collaboration. This community was important for the development of this project.} + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% bibliography +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +% Style of the bib may change based on the publications requirements + +\bibliography{bib} + + + % Ending the multicol format before the appendix + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% APPENDIX +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +\newpage +\appendix +\section{Appendix} +You may include an appendix, it contains extra tables not required to understand the main body, but helpful references. + +\subsection{Figure References} +\begin{figure}[h] + \centering + \includegraphics[scale=.1] + {figures/frog.jpg} + \caption{ + This is a figure (containing a cute, although not colorblind friendly, frog) with a single graphic. + Because the original image is very large, it is resized with a smaller scale. + } + \label{fig:single_graphic_figure} +\end{figure} + + +\begin{figure}[h] + \begin{center} + \begin{minipage}{.35\linewidth} + \includegraphics[width=\linewidth]{figures/frog2.jpg} + + \caption{An example of using minipage to caption each image in a combined figure separately.} + \end{minipage}\hfill + + \begin{minipage}{.35\linewidth} + \includegraphics[width=\linewidth]{figures/frog3.jpg} + + \caption{This frog has it's own caption, so they can be referred to separately If you were heartless enough to separate them.} + \end{minipage} + \label{multifigAB} + + \end{center} + +\end{figure} + +% Todo Example of running show your work function within the tex to produce table + +\subsection{Table References} + +\begin{figure}[h] + \centering + \mbox{\subfigure{\includegraphics[width=.35\linewidth]{figures/frog2.jpg}}\quad + \subfigure{\includegraphics[width=.35\linewidth]{figures/frog3.jpg} }} + \caption{An example showing two images with a shared caption using subfigure. Now the frogs cannot be separated.} + \label{fig:multifigC} +\end{figure} + +\begin{table}[h] + \centering + \caption{Sample table with two columns and a header, with the caption placed on top.} + \label{tab:two_column} + \vspace{.2in} + \begin{tabular}{c | c} + \toprule + Header 1 & Header 2 \\ + \midrule + Entry 1 & 0 $\pm$ 0.001 \\ + Entry 2 & 1 $\pm$ 0.001 \\ + Entry 3 & 2 $\pm$ 0.001 \\ + \bottomrule + \end{tabular} +\end{table} + +\begin{table}[h] + \centering + \caption{A Table displaying multi-rows. Horizontal lines can be removed, but tend to lead to confusing tables.} + \vspace{.2in} + \label{tab:multirow} + \begin{tabular}{c|c|c} + + \toprule + Header 1 & Header 2 & Header 3 \\ + \midrule + + \multirow{2}*{Multi-Row} + & Row 1 & Row 1 \\ + \cline{2-3} % \cline{n_rows-n_columns} + & Row 2 & Row 2 \\ + + + \hline + Single-Row & Row 3 & Row 3\\ + \bottomrule + \end{tabular} + +\end{table} + +\begin{table}[h] + \centering + \caption{A Table with multiple columns.} + \label{tab:multicol} + \vspace{.2in} + + \begin{tabular}{c|c|c} + \toprule + \multicolumn{2}{c|}{Multi-Column} & Column 3 \\ + \midrule + Column 1 & Column 2 & Column 3 \\ + Column 1 & Column 2 & Column 3 \\ + \bottomrule + \end{tabular} +\end{table} + +% Todo: Show your work table drawing results from a function + +\end{document} diff --git a/src/tex/output/.gitignore b/src/tex/output/.gitignore new file mode 100644 index 0000000..9d0f65c --- /dev/null +++ b/src/tex/output/.gitignore @@ -0,0 +1,5 @@ +# Nothing should be tracked in this folder... +* + +# Except the gitignore file itself! +!.gitignore \ No newline at end of file diff --git a/src/tex/showyourwork.sty b/src/tex/showyourwork.sty new file mode 100644 index 0000000..8432d72 --- /dev/null +++ b/src/tex/showyourwork.sty @@ -0,0 +1,13 @@ +\NeedsTeXFormat{LaTeX2e} +\ProvidesPackage{showyourwork}[2022/01/12 Open source science articles] + +\IfFileExists{./showyourwork.tex}{ + \input{showyourwork.tex} +}{ + \newcommand\GitHubURL{} + \newcommand\GitHubSHA{} + \newcommand\GitHubIcon{} + \newcommand\showyourwork{} + \newcommand\script[1]{} + \newcommand\variable[1]{} +} \ No newline at end of file diff --git a/test/test_example.py b/test/test_example.py new file mode 100644 index 0000000..897c195 --- /dev/null +++ b/test/test_example.py @@ -0,0 +1,23 @@ +""" +Example of pytest functionality + +Goes over some basic assert examples +""" +import pytest + + +def test_example_assert_equal(): + assert 0 == 0 + + +def test_example_assert_no_equal(): + assert 0 != 1 + + +def test_example_assert_almost_equal(): + assert 1.0 == pytest.approx(1.01, .1) + + +""" +To run this suite of tests, run 'pytest' in the main directory +""" \ No newline at end of file