Initial commit

.github/workflows/test.yaml

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+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

.gitignore

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+
+## 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/

.gitmodules

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+[submodule ".showyourwork"]
+	path = .showyourwork
+	url = https://github.com/showyourwork/showyourwork

.pre-commit-config.yml

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+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

LICENSE.txt

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+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.

README.md

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+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='[email protected]`, 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. 

environment.yml

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+## THIS IS FOR SHOW YOUR WORK - DO NOT USE IT FOR YOUR PROJECT PLEASE
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - numpy=1.19.2
+  - pip=21.0.1
+  - python=3.9
+  - pip:
+      - matplotlib==3.4.3