change to pyproject.toml and add pre-commit to CI

.github/workflows/tests.yaml

@@ -41,6 +41,13 @@ jobs:
            python - V
            python -m pip install -e . --no-deps --force-reinstall
 
+      - name: pre-commit
+        shell: micromamba-shell {0}
+        run: |
+          pip install pre-commit
+          pre-commit install --install-hooks
+          pre-commit run --all-files
+
       - name: Running Tests
         shell: bash -l {0}
         run: |

.pre-commit-config.yaml

@@ -17,28 +17,18 @@ repos:
     # Ruff version.
     rev: "v0.4.7"
     hooks:
-      # Run the linter.
       - id: ruff
-        args: [ --fix ]
-      # Run the formatter.
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.10.0
     hooks:
       - id: mypy
-        # Copied from setup.cfg
-        exclude: "properties|asv_bench|docs"
         additional_dependencies: [
-            # Type stubs
-            types-python-dateutil,
-            types-pkg_resources,
-            types-PyYAML,
-            types-pytz,
-            # Dependencies that are typed
-            numpy,
-            typing-extensions>=4.1.0,
-          ]
+        "types-python-dateutil",
+        "types-PyYAML",
+        "types-pytz"
+      ]        
 
   - repo: https://github.com/MarcoGorelli/absolufy-imports
     rev: v0.3.1

pyproject.toml

@@ -0,0 +1,60 @@
+[project]
+name = "cstar"
+version = "0.0.0"
+description = "Computational systems for tracking ocean carbon"
+readme = "README.md"
+urls = { repository = "https://github.com/CWorthy-ocean/C-Star", homepage = "https://www.cworthy.org" }
+
+authors = [
+    { name = "Dafydd Stephenson", email = "[email protected]" },
+    { name = "Thomas Nicholas", email = "[email protected]" },
+    { name = "Nora Loose", email = "[email protected]" },
+    { name = "Matt Long", email = "[email protected]" }
+]
+license = { text = "GPL-3.0-only" }
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Oceanography"
+]
+requires-python = ">=3.10"
+
+dependencies = [
+    "python-dateutil>=2.8.2",
+    "PyYAML==6.0.2",
+    "pooch>=1.8.1"
+]
+
+keywords = ["MCDR", "CDR", "ocean carbon", "climate"]
+
+[build-system]
+requires = ["setuptools>=42", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project.optional-dependencies]
+dev = []
+
+# Configuration for mypy type checker
+[tool.mypy]
+ignore_missing_imports = true 
+exclude = "properties|asv_bench|docs"
+
+# Configuration for ruff linter and formatter
+[tool.ruff]
+fix = true
+
+[tool.pre-commit]
+config = ".pre-commit-config.yaml"
+
+[tool.setuptools.packages.find]
+# Automatically find the packages
+where = ["."]
+include = ["cstar"]
+exclude = ["tests*", "docs*", "examples*"]
+
+[tool.setuptools]
+include-package-data = true