chore: update project structure to 45f4b1f9

Author: collijk

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/collijk/python-package-cookiecutter",
-  "commit": "cd59edc69d51f9485bca69eb940e0706bc65e9ba",
+  "commit": "45f4b1f9471d442bebcfcbc67c53bc3488de2beb",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -12,7 +12,7 @@
       "package_name": "rra_tools",
       "project_short_description": "Common utilities for IHME Rapid Response team pipelines.",
       "_template": "https://github.com/collijk/python-package-cookiecutter",
-      "_commit": "cd59edc69d51f9485bca69eb940e0706bc65e9ba"
+      "_commit": "45f4b1f9471d442bebcfcbc67c53bc3488de2beb"
     }
   },
   "directory": null

.github/workflows/cookiecutter.yml.rej

@@ -0,0 +1,10 @@
+diff a/.github/workflows/cookiecutter.yml b/.github/workflows/cookiecutter.yml	(rejected hunks)
+@@ -31,7 +31,7 @@ jobs:
+       - name: apply additional changes and fixes
+         if: steps.changes.outputs.changed > 0
+         run: |
+-          poetry lock --no-update  # add new dependencies
++          poetry lock # add new dependencies
+           poetry install
+           poetry run pre-commit run -a || true  # we have to fix other issues manually
+ 

.github/workflows/dependencies.yml.rej

@@ -0,0 +1,10 @@
+diff a/.github/workflows/dependencies.yml b/.github/workflows/dependencies.yml	(rejected hunks)
+@@ -51,7 +51,7 @@ jobs:
+ 
+       - name: Update outdated packages
+         if: ${{ steps.check_for_outdated_dependencies.outputs.body != 0 }}
+-        run: poetry lock
++        run: poetry lock --regenerate
+ 
+       # behaviour if PR already exists: https://github.com/marketplace/actions/create-pull-request#action-behaviour
+       - name: Create Pull Request

pyproject.toml.rej

@@ -0,0 +1,119 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -1,63 +1,58 @@
+-[tool.poetry]
++[project]
+ name = "rra-tools"
+ version = "0.0.1"
+ description = "Common utilities for IHME Rapid Response team pipelines."
+-authors = [
+-    "James Collins <collijk@uw.edu>",
+-]
+ license = "BSD-3-Clause"
+ readme = "README.md"
++authors = [
++    {name = "James Collins", email = "collijk@uw.edu"},
++]
++requires-python = ">=3.12"
++dependencies = [
++    "click",
++]
+ 
+-documentation = "https://collijk.github.io/rra-tools"
++[project.optional-dependencies]
++dev = [
++    "mkdocstrings[python]",
++    "mkdocs-material",
++    "mkdocs-table-reader-plugin",
++    "mkdocs-gen-files",
++    "mkdocs-literate-nav",
++    "mkdocs-section-index",
++    "mypy",
++    "pre-commit",
++    "pymdown-extensions",
++    "pytest",
++    "pytest-github-actions-annotate-failures",
++    "pytest-cov",
++    "python-kacl",
++    "ruff"
++]
++
++[project.urls]
+ homepage = "https://collijk.github.io/rra-tools"
+ repository = "https://github.com/collijk/rra-tools"
++documentation = "https://collijk.github.io/rra-tools"
+ 
+-classifiers = [
+-  "Development Status :: 4 - Beta",
+-  "Intended Audience :: Developers",
+-  "Operating System :: OS Independent",
+-  "Programming Language :: Python",
+-  "Programming Language :: Python :: 3",
+-  "Programming Language :: Python :: 3.10",
+-  "Programming Language :: Python :: 3.11",
+-  "Programming Language :: Python :: 3.12",
+-  "Topic :: Software Development :: Libraries :: Python Modules",
+-  "Typing :: Typed",
+-]
++[project.scripts]
++my-cli = "rra_tools.cli:main"
+ 
++[tool.poetry]
+ packages = [
+     { include = "rra_tools", from = "src" }
+ ]
++requires-poetry = ">=2.0"
+ 
+ [tool.poetry.dependencies]
+-python = ">=3.10, <4.0"
+-click = "*"
+-
+-[tool.poetry.group.dev.dependencies]
+-mkdocstrings = {version = "*", extras = ["python"]}
+-mkdocs-material = "*"
+-mkdocs-table-reader-plugin = "*"
+-mkdocs-gen-files = "*"
+-mkdocs-literate-nav = "*"
+-mkdocs-section-index = "*"
+-mypy = "*"
+-pre-commit = "*"
+-pymdown-extensions = "*"
+-pytest = "*"
+-pytest-github-actions-annotate-failures = "*"
+-pytest-cov = "*"
+-python-kacl = "*"
+-ruff = "*"
++python = ">=3.12, <4.0"
+ 
+ [build-system]
+-requires = ["poetry-core>=1.0.0"]
++requires = ["poetry-core>=2.0.0"]
+ build-backend = "poetry.core.masonry.api"
+ 
+-[tool.poetry.scripts]
+-my-cli = "rra_tools.cli:main"
+-
+ [tool.ruff]
+-target-version = "py310" # The lowest supported version
++target-version = "py312" # The lowest supported version
+ 
+ [tool.ruff.lint]
+ # By default, enable all the lint rules.
+@@ -117,7 +112,7 @@ exclude_lines = [
+ # This is the global mypy configuration.
+ # Avoid changing this!
+ strict = true  # See all the enabled flags `mypy --help | grep -A 10 'Strict mode'`
+-disallow_any_unimported = true
++disallow_any_unimported = false
+ 
+ # If you need to ignore something for some specific module,
+ # add overrides for them. Avoid changing the global config!
+@@ -128,9 +123,3 @@ disallow_any_unimported = true
+ #  "my_unpyted_dependency2.*"
+ # ]
+ # ignore_missing_imports = true
+-
+-# [[tool.mypy.overrides]]
+-# module = [
+-#   "tests/my_thing/test_my_thing",
+-# ]
+-# disallow_untyped_defs = false