Based on hank

.copier-answers.yml

@@ -0,0 +1,12 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 2024.08.19
+_src_path: gh:scientific-python/cookie
+backend: hatch
+email: alujan@jhu.edu
+full_name: Alan Lujan
+license: MIT
+org: alanlujan91
+project_name: SequentialEGM
+project_short_description: A great package.
+url: https://github.com/alanlujan91/SequentialEGM
+vcs: true

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/CONTRIBUTING.md

@@ -45,7 +45,7 @@ py -m venv .venv
 py -m install -v -e .[dev]
 ```
 
-# Post setup
+# Pre-commit
 
 You should prepare pre-commit, which will help you by checking that commits pass
 required checks:
@@ -87,15 +87,3 @@ You can see a preview with:
 ```bash
 nox -s docs -- --serve
 ```
-
-# Pre-commit
-
-This project uses pre-commit for all style checking. While you can run it with
-nox, this is such an important tool that it deserves to be installed on its own.
-Install pre-commit and run:
-
-```bash
-pre-commit run -a
-```
-
-to check all files.

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/cd.yml

@@ -15,6 +15,8 @@ concurrency:
   cancel-in-progress: true
 
 env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
   FORCE_COLOR: 3
 
 jobs:
@@ -35,6 +37,8 @@ jobs:
     environment: pypi
     permissions:
       id-token: write
+      attestations: write
+      contents: read
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
 
@@ -44,8 +48,12 @@ jobs:
           name: Packages
           path: dist
 
+      - name: Generate artifact attestation for sdist and wheel
+        uses: actions/attest-build-provenance@v1.4.1
+        with:
+          subject-path: "dist/*"
+
       - uses: pypa/gh-action-pypi-publish@release/v1
-        if: github.event_name == 'release' && github.event.action == 'published'
         with:
           # Remember to tell (test-)pypi about this repo before publishing
           # Remove this line to publish to PyPI

.github/workflows/ci.yml

@@ -12,6 +12,8 @@ concurrency:
   cancel-in-progress: true
 
 env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
   FORCE_COLOR: 3
 
 jobs:
@@ -29,9 +31,7 @@ jobs:
         with:
           extra_args: --hook-stage manual --all-files
       - name: Run PyLint
-        run: |
-          echo "::add-matcher::$GITHUB_WORKSPACE/.github/matchers/pylint.json"
-          pipx run nox -s pylint
+        run: pipx run nox -s pylint -- --output-format=github
 
   checks:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
@@ -40,11 +40,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.12"]
-        runs-on: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.13"]
+        runs-on: [ubuntu-latest, windows-latest, macos-14]
 
         include:
-          - python-version: pypy-3.10
+          - python-version: "pypy-3.10"
             runs-on: ubuntu-latest
 
     steps:
@@ -66,4 +66,6 @@ jobs:
           --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v4.0.2
+        uses: codecov/codecov-action@v4.5.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/deploy.yml

@@ -0,0 +1,46 @@
+# This file was created automatically with `myst init --gh-pages` 🪄 💚
+
+name: MyST GitHub Pages Deploy
+on:
+  push:
+    # Runs on pushes targeting the default branch
+    branches: [main]
+env:
+  # `BASE_URL` determines the website is served from, including CSS & JS assets
+  # You may need to change this to `BASE_URL: ''`
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 18.x
+      - name: Install MyST Markdown
+        run: npm install -g mystmd
+      - name: Build HTML Assets
+        run: myst build --html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: "./_build/html"
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

@@ -138,7 +138,7 @@ dmypy.json
 cython_debug/
 
 # setuptools_scm
-code/*/_version.py
+src/*/_version.py
 
 
 # ruff
@@ -157,6 +157,5 @@ Thumbs.db
 *~
 *.swp
 
-*_build
-*_pdf_logs
-*_pdf_tex
+# MyST build outputs
+_build

.pre-commit-config.yaml

@@ -2,12 +2,14 @@ ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
 
+exclude: ^.cruft.json|.copier-answers.yml$
+
 repos:
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.16.0"
+    rev: "1.18.0"
     hooks:
       - id: blacken-docs
-        additional_dependencies: [black==23.*]
+        additional_dependencies: [black==24.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: "v4.6.0"
@@ -32,38 +34,38 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v4.0.0-alpha.8"
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.3.3"
     hooks:
       - id: prettier
         types_or: [yaml, html, css, scss, javascript, json]
         args: [--prose-wrap=always]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.4.10"
+    rev: "v0.6.1"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
 
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: "v1.8.0"
-  #   hooks:
-  #     - id: mypy
-  #       files: code|tests
-  #       args: []
-  #       additional_dependencies:
-  #         - pytest
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.11.1"
+    hooks:
+      - id: mypy
+        files: src|tests
+        args: []
+        additional_dependencies:
+          - pytest
 
-  # - repo: https://github.com/codespell-project/codespell
-  #   rev: "v2.2.6"
-  #   hooks:
-  #     - id: codespell
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
 
-  # - repo: https://github.com/shellcheck-py/shellcheck-py
-  #   rev: "v0.9.0.6"
-  #   hooks:
-  #     - id: shellcheck
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
 
   - repo: local
     hooks:
@@ -74,13 +76,13 @@ repos:
         exclude: .pre-commit-config.yaml
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: "v0.18"
+    rev: "v0.19"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.28.5"
+    rev: "0.29.1"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

.readthedocs.yaml

@@ -0,0 +1,17 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv venv
+    - uv pip install .[docs]
+    - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D
+      language=en docs $READTHEDOCS_OUTPUT/html

README.md

@@ -1,14 +1,4 @@
----
-title: "EGMⁿ: The Sequential Endogenous Grid Method"
-author: "Alan Lujan"
-date: 2023/02/15
----
-
-# EGMⁿ: The Sequential Endogenous Grid Method
-
-## Abstract
-
-Heterogeneous agent models with multiple decisions are often solved using inefficient grid search methods that require a large number of points and are time intensive. This paper provides a novel method for solving such models using an extension of the endogenous grid method (EGM) that uses Gaussian Process Regression (GPR) to interpolate functions on unstructured grids. First, separating models into smaller, sequential problems allows the problems to be more tractable and easily analyzed. Second, using an exogenous grid of post-decision states and solving for an endogenous grid of pre-decision states that obey a first order condition greatly speeds up the solution process. Third, since the resulting endogenous grid can often be curvilinear at best and unstructured at worst, GPR provides an efficient and accurate method for interpolating the value, marginal value, and policy functions. Applied sequentially to each decision within the overarching problem, the method is able to solve heterogeneous agent models with multiple decisions in a fraction of the time and with less computational resources than are required by standard grid search methods currently used. This paper also illustrates how this method can be applied to a number of increasingly complex models. Software is provided in the form of a Python module under the `HARK` package.
+# SequentialEGM
 
 [![Actions Status][actions-badge]][actions-link]
 [![Documentation Status][rtd-badge]][rtd-link]

build.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Run reproduce_paper.py and check if it was successful
-if python3 code/reproduce_paper.py; then
+if python3 src/reproduce_paper.py; then
     echo "reproduce_paper.py ran successfully. Now running myst build..."
 
     # Run myst build command and check if it was successful