From a7833aab17dbada9022bc38604874d66f43ebac9 Mon Sep 17 00:00:00 2001
From: Cordero Core <127983572+uwcdc@users.noreply.github.com>
Date: Thu, 31 Oct 2024 19:54:25 +0000
Subject: [PATCH] chore: Add pixi, Codespaces, and pre-commit support

---
 .coveragerc                |  3 ++
 .devcontainer/postBuild.sh |  0
 .gitattributes             |  2 +
 .github/dependabot.yml     | 11 +++++
 .gitignore                 |  5 +-
 .pre-commit-config.yaml    | 97 ++++++++++++++++++++++++++++++++++++++
 pixi.toml                  | 11 +++++
 7 files changed, 128 insertions(+), 1 deletion(-)
 create mode 100644 .coveragerc
 create mode 100644 .devcontainer/postBuild.sh
 create mode 100644 .gitattributes
 create mode 100644 .github/dependabot.yml
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 pixi.toml

diff --git a/.coveragerc b/.coveragerc
new file mode 100644
index 0000000..bb5cdb2
--- /dev/null
+++ b/.coveragerc
@@ -0,0 +1,3 @@
+[run]
+omit =
+    */version.py
\ No newline at end of file
diff --git a/.devcontainer/postBuild.sh b/.devcontainer/postBuild.sh
new file mode 100644
index 0000000..e69de29
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..07fe41c
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 0000000..4556ff4
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 5ecd3fc..9287c8d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -138,4 +138,7 @@ dmypy.json
 version.py
 
 # data
-*.nc
\ No newline at end of file
+*.nc
+# pixi environments
+.pixi
+*.egg-info
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 0000000..3cfda96
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,97 @@
+exclude: |
+  (?x)^(
+    docs/conf.py
+  )
+
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.18.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v4.0.0-alpha.8"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.5.5"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.11.0"
+    hooks:
+      - id: mypy
+        files: src|tests
+        args: []
+        additional_dependencies:
+          - pytest
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.18"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.29.1"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: "2024.04.23"
+    hooks:
+      - id: sp-repo-review
\ No newline at end of file
diff --git a/pixi.toml b/pixi.toml
new file mode 100644
index 0000000..5f014f0
--- /dev/null
+++ b/pixi.toml
@@ -0,0 +1,11 @@
+[project]
+authors = ["Cordero Core <127983572+uwcdc@users.noreply.github.com>"]
+channels = ["conda-forge"]
+description = "Add a short description here"
+name = "biodiversity-horizons"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]