chore: update project structure to 0a6fca5a

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/collijk/python-package-cookiecutter",
-  "commit": "7e9285f84cc6b52165dbc97b9a0d4f059d0f6818",
+  "commit": "0a6fca5a3df116e2596adc8e8c7a0e5899e72352",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -11,7 +11,8 @@
       "project_slug": "climate-data",
       "package_name": "climate_data",
       "project_short_description": "Pipelines to extract, format, and downscale ERA5 and CMIP6 data.",
-      "_template": "https://github.com/collijk/python-package-cookiecutter"
+      "_template": "https://github.com/collijk/python-package-cookiecutter",
+      "_commit": "0a6fca5a3df116e2596adc8e8c7a0e5899e72352"
     }
   },
   "directory": null

.github/alternative_workflows/build_docs.yml

@@ -0,0 +1,21 @@
+name: Build and Deploy Docs
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+    types:
+      - closed
+
+jobs:
+  build-and-deploy-docs:
+    if: ${{ github.event.pull_request.merged }} or ${{ github.event_name == 'workflow_dispatch' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GH_TOKEN }}
+      - uses: ./.github/actions/python-poetry-env
+      - name: Deploy docs
+        run: poetry run mkdocs gh-deploy --force

.pre-commit-config.yaml.rej

@@ -0,0 +1,13 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -25,11 +25,6 @@ repos:
+         # Add --fix, in case you want it to autofix when this hook runs
+         entry: poetry run ruff check --force-exclude --fix
+         require_serial: true
+-      - id: ruff
+-        name: ruff
+-        # Add --fix, in case you want it to autofix when this hook runs
+-        entry: poetry run ruff check --force-exclude
+-        require_serial: true
+         language: system
+         types: [ python ]
+       - id: mypy

mkdocs.yml.rej

@@ -0,0 +1,34 @@
+diff a/mkdocs.yml b/mkdocs.yml	(rejected hunks)
+@@ -14,9 +14,9 @@ theme:
+         name: Switch to light mode
+
+ nav:
+-  - Introduction: 'index.md'
+-  - api_docs.md
+-  - changelog.md
++  - Home: 'index.md'
++  - Code Reference: reference/
++  - Changelog: changelog.md
+
+ watch:
+   - src/climate_data
+@@ -61,6 +61,12 @@ markdown_extensions:
+ plugins:
+   - table-reader
+   - search
++  - gen-files:
++      scripts:
++        - scripts/gen_ref_pages.py
++  - literate-nav:
++      nav_vile: SUMMARY.md
++  - section-index
+   - mkdocstrings:
+       default_handler: python
+       handlers:
+@@ -73,5 +79,5 @@ extra_javascript:
+   - https://unpkg.com/[email protected]/dist/tablesort.min.js
+   - _javascript/tablesort.js
+   - _javascript/mathjax.js
+-  - https://polyfill.io/v3/polyfill.min.js?features=es6
++  - https://cdnjs.cloudflare.com/polyfill/v3/polyfill.min.js?features=es6
+   - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js

pyproject.toml.rej

@@ -0,0 +1,50 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -34,9 +34,12 @@ python = ">=3.10, <4.0"
+ click = "*"
+
+ [tool.poetry.group.dev.dependencies]
+-mkdocstrings = {version = ">=0.23", extras = ["python"]}
++mkdocstrings = {version = "*", extras = ["python"]}
+ mkdocs-material = "*"
+ mkdocs-table-reader-plugin = "*"
++mkdocs-gen-files = "*"
++mkdocs-literate-nav = "*"
++mkdocs-section-index = "*"
+ mypy = "*"
+ pre-commit = "*"
+ pymdown-extensions = "*"
+@@ -44,13 +47,13 @@ pytest = "*"
+ pytest-github-actions-annotate-failures = "*"
+ pytest-cov = "*"
+ python-kacl = "*"
+-ruff = ">=0.2.0"
++ruff = "*"
+
+ [build-system]
+ requires = ["poetry-core>=1.0.0"]
+ build-backend = "poetry.core.masonry.api"
+
+-[project.scripts]
++[tool.poetry.scripts]
+ my-cli = "climate_data.cli:main"
+
+ [tool.ruff]
+@@ -78,6 +81,9 @@ ignore = [
+     "ARG",      # "Unused function argument". Fixtures are often unused.
+     "S105",     # "Possible hardcoded password".
+ ]
++"scripts/**" = [
++    "INP001",   # "Scripts are not part of a package."
++]
+
+ [tool.ruff.lint.mccabe]
+ max-complexity = 10
+@@ -90,7 +96,7 @@ classmethod-decorators = [
+ ]
+
+ [tool.ruff.lint.flake8-tidy-imports]
+-ban-relative-imports = true
++ban-relative-imports = "all"
+
+ [tool.pytest.ini_options]
+ addopts = """\

src/climate_data/cli_options.py

@@ -236,36 +236,36 @@ def with_overwrite() -> ClickOption[_P, _T]:
 
 
 __all__ = [
-    "VALID_HISTORY_YEARS",
-    "VALID_REFERENCE_YEARS",
-    "VALID_FORECAST_YEARS",
-    "VALID_MONTHS",
-    "VALID_DRAWS",
-    "VALID_ERA5_VARIABLES",
-    "VALID_ERA5_DATASETS",
-    "VALID_CMIP6_SOURCES",
-    "VALID_CMIP6_EXPERIMENTS",
-    "STRIDE",
     "LATITUDES",
     "LONGITUDES",
-    "with_year",
-    "with_month",
+    "RUN_ALL",
+    "STRIDE",
+    "VALID_CMIP6_EXPERIMENTS",
+    "VALID_CMIP6_SOURCES",
+    "VALID_DRAWS",
+    "VALID_ERA5_DATASETS",
+    "VALID_ERA5_VARIABLES",
+    "VALID_FORECAST_YEARS",
+    "VALID_HISTORY_YEARS",
+    "VALID_MONTHS",
+    "VALID_REFERENCE_YEARS",
+    "ClickOption",
+    "with_choice",
+    "with_cmip6_experiment",
+    "with_cmip6_source",
+    "with_debugger",
     "with_draw",
-    "with_era5_variable",
     "with_era5_dataset",
-    "with_cmip6_source",
-    "with_cmip6_experiment",
+    "with_era5_variable",
+    "with_input_directory",
     "with_lat_start",
     "with_lon_start",
+    "with_month",
+    "with_num_cores",
     "with_output_directory",
+    "with_overwrite",
+    "with_progress_bar",
     "with_queue",
     "with_verbose",
-    "with_debugger",
-    "with_input_directory",
-    "with_num_cores",
-    "with_progress_bar",
-    "RUN_ALL",
-    "ClickOption",
-    "with_choice",
-    "with_overwrite",
+    "with_year",
 ]