Flesh out tempalte

Author: TomDonoghue

.gitignore

@@ -1,3 +1,6 @@
+# List any files that should be ignored from the repository here
+# Some standard files to ignore are already included
+
 # Ignore notebook checkpoint files
 .ipynb_checkpoints
 

README.md

@@ -1,3 +1,56 @@
 # ProjectTemplate
 
-Project description.
+A generic template for an analysis project repository.
+
+## Overview
+
+This repository is a template for scientific analysis projects.
+
+## Files & Folders
+
+This template lays out a set of recommended folders for organizing files in the project.
+
+These folders are:
+
+- `custom/` custom code for the project
+- `notebooks/` Jupyter notebooks that do or illustrate parts of the project
+- `scripts/` scripts that run parts of the project
+- `figures/` any figures from the project that are included in the repository
+- `data/` any data from the project that are included in the repository
+
+In addition, the repository should include the following files:
+
+- A LICENSE file, indicating the LICENSE that the code is shared under
+- A requirements.txt file, listing out any dependencies
+
+## README Outline
+
+The repository should include a descriptive README in the base folder.
+
+Suggested sections in the README are as follows:
+
+#### Overview
+
+_A brief description of the project._
+
+#### Project Guide
+
+_A note on how to interact with this project._
+_For example, this could guide people interested in the project to start with the notebooks._
+
+#### Reference
+
+_Links to the reference for the project, such as a preprint or paper._
+
+#### Requirements
+
+_Notes on what requirements there are to run this project._
+
+_This should include programming language, major version required, and any dependencies._
+
+#### Repository Layout
+
+_A brief description of the repository layout and contents._
+
+_This should be a list of all subfolders, and a quick description of what they contain._
+_This list folder can be adapted from the `Files & Folders` list above._

custom/README.md

@@ -0,0 +1,5 @@
+This folder should include any custom code for the project, organized into a mini-module.
+
+This code should be organized into functions and classes and so on that can be imported by scripts or notebooks that need them.
+
+Any general settings for the project can also be collected into a `settings.py` file, to be imported and used wherever they are needed.

custom/funcs.py

@@ -7,3 +7,8 @@ def do_things():
     """Helper function to do things."""
 
     print('Things have been done.')
+
+def do_more_things():
+    """Helper function to do things."""
+
+    print('More things have been done.')

custom/settings.py

@@ -0,0 +1,12 @@
+"""Any general settings for the project can be defined here."""
+
+###################################################################################################
+###################################################################################################
+
+# Set up some settings
+SETTING_ONE = [1, 2, 3]
+SETTING_TWO = True
+
+# Set up some other settings
+DO_X = True
+DO_Y = False

data/README.md

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+This folder should include any data included in the project repository.
+
+If there are folders from different analyses or aspects of the project, this folder can contain sub-folders, and the structure can be described in this README.

figures/README.md

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+This folder should include any figures included in the project repository.
+
+If there are folders from different analyses or aspects of the project, this folder can contain sub-folders, and the structure can be described in this README.

notebooks/README.md

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+This folder should contain any notebooks included in the project.
+
+If notebooks are ordered, there file names should be numbered, for example, as:
+
+- `01-DoFirstThing.ipynb`
+- `02-NowDoSecondThing.ipynb`
+
+This README can be used to include a brief description of the notebooks.

requirements.txt

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+List any required packages for the project here.

scripts/README.md

@@ -0,0 +1 @@
+This folder should contain any scripts included in the project.