From 14e3bbf5e8fc628ca4a112a4059906972233f8c5 Mon Sep 17 00:00:00 2001
From: Stella <30465823+stellaprins@users.noreply.github.com>
Date: Mon, 13 Jan 2025 11:55:28 +0000
Subject: [PATCH] Add pre-commit configuration and pyproject.toml and update
 gitignore

---
 .gitignore              |  1 +
 .pre-commit-config.yaml | 50 +++++++++++++++++++++++++++++++++++++++++
 pyproject.toml          | 24 ++++++++++++++++++++
 3 files changed, 75 insertions(+)
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 pyproject.toml

diff --git a/.gitignore b/.gitignore
index e837a44d..0b8437e8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,6 +36,7 @@ arm64
 /SBML/ex9.csv
 /SBML/hr.csv
 /test_suite/semantic/
+/test_suite/SBML_test_suite/
 /test_suite/semantic_tests_with_sedml_and_graphs.v*.zip*
 .vscode
 /BioModels/cache
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..67bb961e
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,50 @@
+# Formatting shouldn't be applied to auto generated files,
+# or files taken verbatim from external resources.
+exclude: |-
+  (?x)^(
+      LEMS/.*|
+      Brian/.*|
+      NEURON/.*|
+      NeuroML2/.*|
+      tellurium/simple.py*|
+      .*\.xml$|
+      .*\.sedml$|
+      .*\.sbml$|
+      .*\.omex$|
+      .*\.json$|
+      .*\.md$|
+  )$
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.1
+    hooks:
+      - id: ruff
+      - id: ruff-format
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.24.2
+    hooks:
+      - id: toml-sort-fix
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+      - id: prettier
+        args:
+          - --quote-props=as-needed
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args:
+          - --fix=lf
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/mirrors-isort
+    rev: v5.10.1
+    hooks:
+      - id: isort
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..ba965d1b
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools>=42", "wheel", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "SBMLShowcase"
+dynamic = ["version"]
+requires-python = ">=3.9"
+dependencies = [
+  "pyNeuroML[annotations]",
+  "python-libsedml",
+  "tellurium",
+  "pymetadata>=0.4.2",
+  "docker",
+  "requests<2.32.0"
+]
+
+[project.optional-dependencies]
+dev = [
+  "pre-commit"
+]
+
+[tool.setuptools]
+packages = []