Initial QA setup

Author: davidorme

.gitignore

@@ -1,3 +1,15 @@
+# Data files - we do not want to populate data files into this repository.
+*.nc
+*.ncdf
+*.tiff
+*.tif
+*.geotiff
+*.xlsx
+*.xls
+*.csv
+*.dat
+*.txt
+
 # History files
 .Rhistory
 .Rapp.history

.lintr

@@ -0,0 +1,4 @@
+linters: linters_with_defaults(
+    cyclocomp_linter(complexity_limit = 10L),
+    indentation_linter(indent = 4L)
+  )

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    # These are generic hooks to keep files clean and tidy
+    rev: v5.0.0
+    hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files
+    - id: check-merge-conflict
+    - id: debug-statements
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # This is python specific linting and formatting using ruff
+    rev: v0.9.3
+    hooks:
+    - id: ruff                                  # Run the linter.
+      args: [--fix, --exit-non-zero-on-fix]
+    - id: ruff-format                           # Run the formatter.
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    # This is markdown linting
+    rev: v0.44.0
+    hooks:
+    - id: markdownlint
+  - repo: https://github.com/lorenzwalthert/precommit
+    # These are R specific tools to format and lint the code and check for common errors 
+    rev: v0.4.3.9003
+    hooks: 
+    - id: style-files
+      args: [--style_pkg=styler, --indent_by=4, --style_fun=tidyverse_style]
+    - id: lintr
+    - id: readme-rmd-rendered
+    - id: parsable-R
+    - id: no-browser-statement
+    - id: no-debug-statement
+    - id: deps-in-desc

.vscode/extensions.json

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+{
+	// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
+	// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
+	// List of extensions which should be recommended for users of this workspace.
+	"recommendations": [
+		"ms-python.python",
+		"ms-toolsai.jupyter",
+		"davidanson.vscode-markdownlint",
+		"executablebookproject.myst-highlight",
+		"reditorsupport.r"
+	],
+	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
+	"unwantedRecommendations": []
+}

README.md

@@ -1,3 +1,39 @@
 # The Virtual Ecosystem data science repository
 
-This repository is the data science repository for the Virtual Ecosystem project. It is used to store all the research and analysis being used to parameterise and run the Virtual Ecosystem model.
+This repository is the data science repository for the Virtual Ecosystem project. It is
+used to store all the research and analysis being used to parameterise and run the
+Virtual Ecosystem model.
+
+## Getting started with the repository
+
+The first step is to clone the repository
+
+```sh
+git clone https://github.com/ImperialCollegeLondon/ve_data_science.git
+```
+
+That gives you a complete copy of all of the current files across all branches and all
+of the changes ever made to those files.
+
+However, we use a number of quality assurance tools (QA) to help manage the code files
+and documents within this repository. You also need to do the following to get this set
+up working:
+
+1. Install python
+
+2. Install `poetry`: `pip install poetry`
+
+3. Run `poetry install`
+
+4. Set the interpreter path
+    * Run `poetry env list --full-path`, copy the result and add `/bin/python` to the
+      end. For example:
+      `/Users/dorme/Library/Caches/pypoetry/virtualenvs/ve-data-science-ND1juKN--py3.12/bin/python`
+    * In the menus, select View > Command Palette and then enter `interpreter` in the
+      box to find the `Python: Select Interpreter` command. Click on `Enter interpreter
+      path` and paste in the path from above.
+
+5. Run `poetry run pre-commit install`
+
+6. Whenever you are working in the repo, use `poetry shell` to start up the environment
+   first.