From 769a543e5560b8f9ae814e1537c8c7c4c4be79bd Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 5 Dec 2023 13:38:25 -0500
Subject: [PATCH 01/16] upgrade python version

---
 CONTRIBUTING.rst                                   |  2 +-
 README.rst                                         |  6 +++---
 .../.github/workflows/deploy.yml                   |  4 ++--
 .../.github/workflows/docs.yml                     |  2 +-
 .../.github/workflows/tests.yml                    |  2 +-
 {{cookiecutter.repository_name}}/.travis.yml       | 12 ++++++------
 {{cookiecutter.repository_name}}/README.md         |  4 ++--
 {{cookiecutter.repository_name}}/setup.py          |  8 ++++----
 {{cookiecutter.repository_name}}/tox.ini           | 14 +++++++-------
 9 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index a145395..56c9a79 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -135,7 +135,7 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 
-3. The pull request should work for Python 2.7, 3.5, 3.6 and 3.7, and for PyPy. Check
+3. The pull request should work for Python 2.7, 3.8, 3.9, 3.10, and 3.11, and for PyPy. Check
    https://travis-ci.org/audreyr/cookiecutter-pypackage/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
diff --git a/README.rst b/README.rst
index f19945f..c01904e 100644
--- a/README.rst
+++ b/README.rst
@@ -19,7 +19,7 @@ Features
 * Testing setup with ``unittest`` and ``pytest``
 * Github-Actions_: Ready for Github Actions Continuous Integration testing
 * Travis-CI_: Ready for Travis Continuous Integration testing
-* Tox_ testing: Setup to easily test for Python 2.7, 3.5, 3.6, 3.7, 3.8
+* Tox_ testing: Setup to easily test for Python 2.7, 3.8, 3.9, 3.10, 3.11
 * Sphinx_ docs: Documentation ready for generation, automatic building and deploying to gh-pages (strongly recommended)
 * Bumpversion_: Pre-configured version bumping with a single command
 * Auto-release to PyPI_ when you push a new tag to master (strongly recommended)
@@ -199,8 +199,8 @@ things are files and folders and I'll give you a quick overview of what they
 are/do.
 
 * Tox_ (tox.ini): A system that can run all kinds of tests for you. For
-  instance, you can test your code on various versions (Python 2.7, 3.5,
-  3.6, 3.7, 3.8) and test your code on linters as well.
+  instance, you can test your code on various versions (Python 2.7, 3.8,
+  3.9, 3.10, 3.11) and test your code on linters as well.
 
 * Travis-CI_ (travis.yml): A continuous integration system. That means every
   time you push a commit it will simulate downloading your project, installing
diff --git a/{{cookiecutter.repository_name}}/.github/workflows/deploy.yml b/{{cookiecutter.repository_name}}/.github/workflows/deploy.yml
index 42e5abc..bb09311 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/deploy.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/deploy.yml
@@ -16,10 +16,10 @@ jobs:
 
     steps:
       - uses: actions/checkout@v1
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.8
 
       - name: Install dependencies
         run: |
diff --git a/{{cookiecutter.repository_name}}/.github/workflows/docs.yml b/{{cookiecutter.repository_name}}/.github/workflows/docs.yml
index b11e9d7..b9f8856 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/docs.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/docs.yml
@@ -14,7 +14,7 @@ jobs:
     - name: Python
       uses: actions/setup-python@v1
       with:
-        python-version: '3.7'
+        python-version: '3.8'
 
     - name: Build
       run: |
diff --git a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
index 9ee10bf..acbac3a 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-latest, macos-latest]
 
     steps:
diff --git a/{{cookiecutter.repository_name}}/.travis.yml b/{{cookiecutter.repository_name}}/.travis.yml
index 2a9287a..88ad41d 100644
--- a/{{cookiecutter.repository_name}}/.travis.yml
+++ b/{{cookiecutter.repository_name}}/.travis.yml
@@ -3,16 +3,16 @@ dist: trusty
 language: python
 python:
   - 3.8
-  - 3.7
-  - 3.6
-  - 3.5
+  - 3.9
+  - 3.10
+  - 3.11
 {%- if cookiecutter.support_py2 == 'y' %}
   - 2.7
 {%- endif %}
 
 matrix:
   include:
-    - python: 3.7
+    - python: 3.8
       dist: xenial
       sudo: required
 
@@ -46,7 +46,7 @@ deploy:
     on:
       tags: true
       repo: {{ cookiecutter.github_owner }}/{{ cookiecutter.repository_name }}
-      python: 3.7
+      python: 3.8
 {%- endif %}
 {% if cookiecutter.use_ghpages_with_ci == 'y' %}
   # Automatically build and deploy documentation to GitHub Pages after every
@@ -62,5 +62,5 @@ deploy:
     target-branch: gh-pages
     on:
       branch: master
-      python: 3.7
+      python: 3.8
 {%- endif %}
diff --git a/{{cookiecutter.repository_name}}/README.md b/{{cookiecutter.repository_name}}/README.md
index fe9ecf1..22216ff 100644
--- a/{{cookiecutter.repository_name}}/README.md
+++ b/{{cookiecutter.repository_name}}/README.md
@@ -36,13 +36,13 @@ TODO: Provide a short overview of the project here.
 
 ## Requirements
 
-**{{ cookiecutter.project_name }}** has been developed and tested on [Python {% if cookiecutter.support_py2 == 'y' %}2.7, {% endif %}3.5, 3.6, 3.7 and 3.8](https://www.python.org/downloads/)
+**{{ cookiecutter.project_name }}** has been developed and tested on [Python {% if cookiecutter.support_py2 == 'y' %}2.7, {% endif %}3.8, 3.9, 3.10 and 3.11](https://www.python.org/downloads/)
 
 Also, although it is not strictly required, the usage of a [virtualenv](https://virtualenv.pypa.io/en/latest/)
 is highly recommended in order to avoid interfering with other software installed in the system
 in which **{{ cookiecutter.project_name }}** is run.
 
-These are the minimum commands needed to create a virtualenv using python3.6 for **{{ cookiecutter.project_name }}**:
+These are the minimum commands needed to create a virtualenv using python3.8 for **{{ cookiecutter.project_name }}**:
 
 ```bash
 pip install virtualenv
diff --git a/{{cookiecutter.repository_name}}/setup.py b/{{cookiecutter.repository_name}}/setup.py
index b35fc60..cf584ca 100644
--- a/{{cookiecutter.repository_name}}/setup.py
+++ b/{{cookiecutter.repository_name}}/setup.py
@@ -77,10 +77,10 @@
         'Programming Language :: Python :: 2.7',
 {%- endif %}
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
     ],
     description='{{ cookiecutter.project_short_description.replace("\'", "\\\'") }}',
     {%- if 'no' not in cookiecutter.command_line_interface|lower %}
@@ -108,7 +108,7 @@
 {%- if cookiecutter.support_py2 == 'y' %}
     python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*',
 {%- else %}
-    python_requires='>=3.5',
+    python_requires='>=3.8',
 {%- endif %}
     setup_requires=setup_requires,
     test_suite='tests',
diff --git a/{{cookiecutter.repository_name}}/tox.ini b/{{cookiecutter.repository_name}}/tox.ini
index 53accf0..fbb39d7 100644
--- a/{{cookiecutter.repository_name}}/tox.ini
+++ b/{{cookiecutter.repository_name}}/tox.ini
@@ -1,14 +1,14 @@
 [tox]
-envlist = {% if cookiecutter.support_py2 == 'y' %}py27, {% endif %}py35, py36, py37, py38, lint, docs
+envlist = {% if cookiecutter.support_py2 == 'y' %}py27, {% endif %}py38, py39, py310, py311, lint, docs
 
 
 {%- if cookiecutter.ci_provider == 'Travis CI' %}
 [travis]
 python =
     3.8: py38
-    3.7: py37, docs, lint
-    3.6: py36
-    3.5: py35
+    3.9: py39, docs, lint
+    3.10: py310
+    3.11: py311
 {%- if cookiecutter.support_py2 == 'y' %}
     2.7: py27
 {%- endif %}
@@ -18,9 +18,9 @@ python =
 [gh-actions]
 python =
     3.8: py38
-    3.7: py37, docs, lint
-    3.6: py36
-    3.5: py35
+    3.9: py39, docs, lint
+    3.10: py310
+    3.11: py311
 {%- if cookiecutter.support_py2 == 'y' %}
     2.7: py27
 {%- endif %}

From 2fb99464cbf999e894acd5059f4dddb0c94d70b1 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 5 Dec 2023 16:37:01 -0500
Subject: [PATCH 02/16] update package

---
 cookiecutter.json                             |   2 +-
 .../.github/workflows/tests.yml               | 116 +++++++++++++---
 {{cookiecutter.repository_name}}/Makefile     | 109 +++++++++++++--
 {{cookiecutter.repository_name}}/setup.py     |   2 +
 {{cookiecutter.repository_name}}/tasks.py     | 127 ++++++++++++++++++
 {{cookiecutter.repository_name}}/tox.ini      |  38 ++++--
 6 files changed, 349 insertions(+), 45 deletions(-)
 create mode 100644 {{cookiecutter.repository_name}}/tasks.py

diff --git a/cookiecutter.json b/cookiecutter.json
index 68ca7c5..d6e5ebd 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -2,7 +2,7 @@
   "full_name": "Your Name",
   "email": "email@mit.edu",
   "github_username": "username",
-  "github_owner": ["DAI-Lab", "HDI-Project", "D3-AI", "data-dev", "sdv-dev", "{{ cookiecutter.github_username }}"],
+  "github_owner": ["DAI-Lab", "HDI-Project", "D3-AI", "data-dev", "sdv-dev", "sintel-dev", "{{ cookiecutter.github_username }}"],
   "project_name": "Python Boilerplate",
   "package_name": "{{ cookiecutter.project_name.lower().replace(' ', '-') }}",
   "project_slug": "{{ cookiecutter.package_name.replace('-', '_') }}",
diff --git a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
index acbac3a..46a0654 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
@@ -1,3 +1,6 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
 name: Run Tests
 
 on:
@@ -7,32 +10,109 @@ on:
     branches: [ master ]
 
 jobs:
-  build:
-    runs-on: {{ '${{ matrix.os }}' }}
+  lint:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.8]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package
+      run: pip install invoke .[dev]
+    - name: invoke lint
+      run: invoke lint
+
+
+  docs:
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11']
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-20.04]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package
+      run: pip install .[dev]
+    - name: make docs
+      run: make docs
+
 
+  readme:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python {{ '${{ matrix.python-version }}' }}
-      uses: actions/setup-python@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
       with:
-        python-version: {{ '${{ matrix.python-version }}' }}
-        
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox tox-gh-actions
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install invoke rundoc .
+    - name: invoke readme
+      run: invoke readme
 
-    - name: Test with tox
-      run: tox
 
-{%- if cookiecutter.use_codecov_with_ci == 'y' %}
+  unit:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-20.04, macos-latest, windows-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install invoke .[test]
+    - name: invoke pytest
+      run: invoke pytest
 
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+
+  minimum:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-20.04, macos-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install invoke .[test]
+    - name: invoke minimum
+      run: invoke minimum
+
+
+  tutorials:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-20.04, macos-latest, windows-latest]
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
       with:
-        file: ./coverage.xml
-{%- endif %}
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: pip install invoke jupyter matplotlib .
+    - name: invoke tutorials
+      run: invoke tutorials
diff --git a/{{cookiecutter.repository_name}}/Makefile b/{{cookiecutter.repository_name}}/Makefile
index 2cd2faa..195928e 100644
--- a/{{cookiecutter.repository_name}}/Makefile
+++ b/{{cookiecutter.repository_name}}/Makefile
@@ -29,6 +29,9 @@ BROWSER := python -c "$$BROWSER_PYSCRIPT"
 help:
 	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
 
+
+# INSTALL TARGETS
+
 .PHONY: install
 install: clean-build clean-pyc ## install the package to the active Python's site-packages
 	pip install .
@@ -37,29 +40,67 @@ install: clean-build clean-pyc ## install the package to the active Python's sit
 install-test: clean-build clean-pyc ## install the package and test dependencies
 	pip install .[test]
 
-.PHONY: test
-test: ## run tests quickly with the default Python
-	python -m pytest --basetemp=${ENVTMPDIR} --cov={{ cookiecutter.project_slug }} --cov-report xml
+.PHONY: install-develop
+install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
+	pip install -e .[dev]
+
+MINIMUM := $(shell sed -n '/install_requires = \[/,/]/p' setup.py | grep -v -e '[][]' | sed 's/ *\(.*\),$?$$/\1/g' | tr '>' '=')
+
+.PHONY: install-minimum
+install-minimum: ## install the minimum supported versions of the package dependencies
+	pip install $(MINIMUM)
+
+.PHONY: check-dependencies
+check-dependencies: ## test if there are any broken dependencies
+	pip check
+
+
+# LINT TARGETS
 
 .PHONY: lint
+lint: ## check style with flake8 and isort
+	invoke lint
+
+.PHONY: lint-{{ cookiecutter.project_slug }}
 lint: ## check style with flake8 and isort
 	flake8 {{ cookiecutter.project_slug }} tests
 	isort -c --recursive {{ cookiecutter.project_slug }} tests
 
-.PHONY: install-develop
-install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
-	pip install -e .[dev]
-
-.PHONY: test-all
-test-all: ## run tests on every Python version with tox
-	tox -r -p auto
-
 .PHONY: fix-lint
 fix-lint: ## fix lint issues using autoflake, autopep8, and isort
 	find {{ cookiecutter.project_slug }} tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
 	autopep8 --in-place --recursive --aggressive {{ cookiecutter.project_slug }} tests
 	isort --apply --atomic --recursive {{ cookiecutter.project_slug }} tests
 
+
+# TEST TARGETS
+
+.PHONY: test-unit
+test-unit: ## run tests quickly with the default Python
+	invoke unit
+
+.PHONY: test-readme
+test-readme: ## run the readme snippets
+	invoke readme
+
+.PHONY: test-tutorials
+test-tutorials: ## run the tutorial notebooks
+	invoke tutorials
+
+.PHONY: test
+test: test-unit test-readme test-tutorials ## test everything that needs test dependencies
+
+.PHONY: test-minimum
+test-minimum: install-minimum check-dependencies test ## run tests using the minimum supported dependencies
+
+.PHONY: test-{{ cookiecutter.project_slug }}
+test: ## run tests quickly with the default Python
+	python -m pytest --basetemp=${ENVTMPDIR} --cov={{ cookiecutter.project_slug }} --cov-report xml
+
+.PHONY: test-all
+test-all: ## run tests on every Python version with tox
+	tox -r -p auto
+
 .PHONY: coverage
 coverage: ## check code coverage quickly with the default Python
 	coverage run --source {{ cookiecutter.project_slug }} -m pytest
@@ -67,6 +108,9 @@ coverage: ## check code coverage quickly with the default Python
 	coverage html
 	$(BROWSER) htmlcov/index.html
 
+
+# DOCS TARGETS
+
 .PHONY: docs
 docs: clean-docs ## generate Sphinx HTML documentation, including API docs
 	sphinx-apidoc --separate --no-toc -o docs/api/ {{ cookiecutter.project_slug }}
@@ -80,27 +124,44 @@ view-docs: docs ## view docs in browser
 serve-docs: view-docs ## compile the docs watching for changes
 	watchmedo shell-command -W -R -D -p '*.rst;*.md' -c '$(MAKE) -C docs html' .
 
+
+# RELEASE TARGETS
+
 .PHONY: dist
 dist: clean ## builds source and wheel package
 	python setup.py sdist
 	python setup.py bdist_wheel
 	ls -l dist
 
+.PHONY: publish-confirm
+publish-confirm:
+	@echo "WARNING: This will irreversibly upload a new version to PyPI!"
+	@echo -n "Please type 'confirm' to proceed: " \
+		&& read answer \
+		&& [ "$${answer}" = "confirm" ]
+
 .PHONY: test-publish
 test-publish: dist ## package and upload a release on TestPyPI
 	twine upload --repository-url https://test.pypi.org/legacy/ dist/*
 
 .PHONY: publish
-publish: dist ## package and upload a release
+publish: dist publish-confirm ## package and upload a release
 	twine upload dist/*
 
 .PHONY: bumpversion-release
 bumpversion-release: ## Merge master to stable and bumpversion release
-	git checkout stable
+	git checkout stable || git checkout -b stable
 	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
 	bumpversion release
 	git push --tags origin stable
 
+.PHONY: bumpversion-release-test
+bumpversion-release-test: ## Merge master to stable and bumpversion release
+	git checkout stable || git checkout -b stable
+	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
+	bumpversion release --no-tag
+	@echo git push --tags origin stable
+
 .PHONY: bumpversion-patch
 bumpversion-patch: ## Merge stable to master and bumpversion patch
 	git checkout master
@@ -120,9 +181,21 @@ bumpversion-major: ## Bump the version the next major skipping the release
 bumpversion-candidate: ## Bump the version to the next candidate
 	bumpversion candidate --no-tag
 
+.PHONY: bumpversion-revert
+bumpversion-revert: ## Undo a previous bumpversion-release
+	git checkout master
+	git branch -D stable
+
+CLEAN_DIR := $(shell git status --short | grep -v ??)
 CURRENT_BRANCH := $(shell git rev-parse --abbrev-ref HEAD 2>/dev/null)
 CHANGELOG_LINES := $(shell git diff HEAD..origin/stable HISTORY.md 2>&1 | wc -l)
 
+.PHONY: check-clean
+check-clean: ## Check if the directory has uncommitted changes
+ifneq ($(CLEAN_DIR),)
+	$(error There are uncommitted changes)
+endif
+
 .PHONY: check-master
 check-master: ## Check if we are in master branch
 ifneq ($(CURRENT_BRANCH),master)
@@ -137,19 +210,29 @@ endif
 
 .PHONY: check-release
 check-release: check-master check-history ## Check if the release can be made
+	@echo "A new release can be made"
 
 .PHONY: release
 release: check-release bumpversion-release publish bumpversion-patch
 
+.PHONY: release-test
+release-test: check-release bumpversion-release-test publish-test bumpversion-revert
+
 .PHONY: release-candidate
 release-candidate: check-master publish bumpversion-candidate
 
+.PHONY: release-candidate-test
+release-candidate-test: check-clean check-master publish-test
+
 .PHONY: release-minor
 release-minor: check-release bumpversion-minor release
 
 .PHONY: release-major
 release-major: check-release bumpversion-major release
 
+
+# CLEAN TARGETS
+
 .PHONY: clean
 clean: clean-build clean-pyc clean-test clean-coverage clean-docs ## remove all build, test, coverage, docs and Python artifacts
 
diff --git a/{{cookiecutter.repository_name}}/setup.py b/{{cookiecutter.repository_name}}/setup.py
index cf584ca..ef6fb80 100644
--- a/{{cookiecutter.repository_name}}/setup.py
+++ b/{{cookiecutter.repository_name}}/setup.py
@@ -23,6 +23,7 @@
 tests_require = [
     'pytest>=3.4.2',
     'pytest-cov>=2.6.0',
+    'rundoc>=0.4.3',
 ]
 
 development_requires = [
@@ -52,6 +53,7 @@
     # Advanced testing
     'coverage>=4.5.1',
     'tox>=2.9.1',
+    'invoke',
 ]
 
 {%- set license_classifiers = {
diff --git a/{{cookiecutter.repository_name}}/tasks.py b/{{cookiecutter.repository_name}}/tasks.py
new file mode 100644
index 0000000..5ad19ba
--- /dev/null
+++ b/{{cookiecutter.repository_name}}/tasks.py
@@ -0,0 +1,127 @@
+import glob
+import operator
+import os
+import pkg_resources
+import platform
+import re
+import shutil
+import stat
+from pathlib import Path
+
+from invoke import task
+
+
+COMPARISONS = {
+    '>=': operator.ge,
+    '>': operator.gt,
+    '<': operator.lt,
+    '<=': operator.le
+}
+
+
+@task
+def check_dependencies(c):
+    c.run('python -m pip check')
+
+
+@task
+def unit(c):
+    c.run('python -m pytest --cov={{cookiecutter.repository_name}} --cov-report=xml')
+
+
+def _validate_python_version(line):
+    is_valid = True
+    for python_version_match in re.finditer(r"python_version(<=?|>=?|==)\'(\d\.?)+\'", line):
+        python_version = python_version_match.group(0)
+        comparison = re.search(r'(>=?|<=?|==)', python_version).group(0)
+        version_number = python_version.split(comparison)[-1].replace("'", "")
+        comparison_function = COMPARISONS[comparison]
+        is_valid = is_valid and comparison_function(
+            pkg_resources.parse_version(platform.python_version()),
+            pkg_resources.parse_version(version_number),
+        )
+
+    return is_valid
+
+
+@task
+def install_minimum(c):
+    with open('setup.py', 'r') as setup_py:
+        lines = setup_py.read().splitlines()
+
+    versions = []
+    started = False
+    for line in lines:
+        if started:
+            if line == ']':
+                started = False
+                continue
+
+            line = line.strip()
+            if _validate_python_version(line):
+                requirement = re.match(r'[^>]*', line).group(0)
+                requirement = re.sub(r"""['",]""", '', requirement)
+                version = re.search(r'>=?(\d\.?)+\w*', line).group(0)
+                if version:
+                    version = re.sub(r'>=?', '==', version)
+                    version = re.sub(r"""['",]""", '', version)
+                    requirement += version
+                versions.append(requirement)
+
+        elif (line.startswith('install_requires = [')):
+            started = True
+
+    c.run(f'python -m pip install {" ".join(versions)}')
+
+
+@task
+def minimum(c):
+    install_minimum(c)
+    check_dependencies(c)
+    unit(c)
+
+
+@task
+def readme(c):
+    test_path = Path('tests/readme_test')
+    if test_path.exists() and test_path.is_dir():
+        shutil.rmtree(test_path)
+
+    cwd = os.getcwd()
+    os.makedirs(test_path, exist_ok=True)
+    shutil.copy('README.md', test_path / 'README.md')
+    os.chdir(test_path)
+    c.run('rundoc run --single-session python3 -t python3 README.md')
+    os.chdir(cwd)
+    shutil.rmtree(test_path)
+
+
+@task
+def tutorials(c):
+    for ipynb_file in glob.glob('tutorials/*.ipynb'):
+        if '.ipynb_checkpoints' not in ipynb_file:
+            c.run((
+                'jupyter nbconvert --execute --ExecutePreprocessor.timeout=3600 '
+                f'--to=html --stdout {ipynb_file}'
+            ), hide='out')
+
+
+@task
+def lint(c):
+    check_dependencies(c)
+    c.run('flake8 {{cookiecutter.repository_name}} tests')
+    c.run('isort -c --recursive {{cookiecutter.repository_name}} tests')
+
+
+def remove_readonly(func, path, _):
+    "Clear the readonly bit and reattempt the removal"
+    os.chmod(path, stat.S_IWRITE)
+    func(path)
+
+
+@task
+def rmdir(c, path):
+    try:
+        shutil.rmtree(path, onerror=remove_readonly)
+    except PermissionError:
+        pass
\ No newline at end of file
diff --git a/{{cookiecutter.repository_name}}/tox.ini b/{{cookiecutter.repository_name}}/tox.ini
index fbb39d7..3a79706 100644
--- a/{{cookiecutter.repository_name}}/tox.ini
+++ b/{{cookiecutter.repository_name}}/tox.ini
@@ -12,19 +12,6 @@ python =
 {%- if cookiecutter.support_py2 == 'y' %}
     2.7: py27
 {%- endif %}
-{%- endif %}
-
-{%- if cookiecutter.ci_provider == 'Github Actions' %}
-[gh-actions]
-python =
-    3.8: py38
-    3.9: py39, docs, lint
-    3.10: py310
-    3.11: py311
-{%- if cookiecutter.support_py2 == 'y' %}
-    2.7: py27
-{%- endif %}
-{%- endif %}
 
 [testenv]
 passenv = CI TRAVIS TRAVIS_*
@@ -47,3 +34,28 @@ skipsdist = true
 extras = dev
 commands =
     /usr/bin/env make docs
+{%- endif %}
+
+{%- if cookiecutter.ci_provider == 'Github Actions' %}
+[testenv]
+skipsdist = false
+skip_install = false
+deps =
+    invoke
+    readme: rundoc
+    tutorials: jupyter
+extras =
+    lint: dev
+    docs: dev
+    unit: test
+    minimum: test
+commands =
+    docs: /usr/bin/env make docs
+    lint: invoke lint
+    readme: invoke readme
+    unit: invoke unit
+    minimum: invoke minimum
+    tutorials: invoke tutorials
+    invoke rmdir --path {envdir}
+{%- endif %}
+{%- endif %}
\ No newline at end of file

From 7d2b8d5920e9026e8ab320a3722dbe10034d01b7 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 5 Dec 2023 16:46:41 -0500
Subject: [PATCH 03/16] remove empty lines

---
 {{cookiecutter.repository_name}}/tox.ini | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/tox.ini b/{{cookiecutter.repository_name}}/tox.ini
index 3a79706..c84920f 100644
--- a/{{cookiecutter.repository_name}}/tox.ini
+++ b/{{cookiecutter.repository_name}}/tox.ini
@@ -12,7 +12,6 @@ python =
 {%- if cookiecutter.support_py2 == 'y' %}
     2.7: py27
 {%- endif %}
-
 [testenv]
 passenv = CI TRAVIS TRAVIS_*
 setenv =
@@ -20,15 +19,11 @@ setenv =
 extras = test
 commands =
     /usr/bin/env make test
-
-
 [testenv:lint]
 skipsdist = true
 extras = dev
 commands =
     /usr/bin/env make lint
-
-
 [testenv:docs]
 skipsdist = true
 extras = dev
@@ -58,4 +53,4 @@ commands =
     tutorials: invoke tutorials
     invoke rmdir --path {envdir}
 {%- endif %}
-{%- endif %}
\ No newline at end of file
+{%- endif %}

From 01964d88c9546d4c38188c1ad6274920834d0030 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 5 Dec 2023 16:54:16 -0500
Subject: [PATCH 04/16] remove extra if statement

---
 {{cookiecutter.repository_name}}/tox.ini | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/tox.ini b/{{cookiecutter.repository_name}}/tox.ini
index c84920f..185e71b 100644
--- a/{{cookiecutter.repository_name}}/tox.ini
+++ b/{{cookiecutter.repository_name}}/tox.ini
@@ -12,6 +12,7 @@ python =
 {%- if cookiecutter.support_py2 == 'y' %}
     2.7: py27
 {%- endif %}
+
 [testenv]
 passenv = CI TRAVIS TRAVIS_*
 setenv =
@@ -19,11 +20,13 @@ setenv =
 extras = test
 commands =
     /usr/bin/env make test
+
 [testenv:lint]
 skipsdist = true
 extras = dev
 commands =
     /usr/bin/env make lint
+
 [testenv:docs]
 skipsdist = true
 extras = dev
@@ -52,5 +55,4 @@ commands =
     minimum: invoke minimum
     tutorials: invoke tutorials
     invoke rmdir --path {envdir}
-{%- endif %}
-{%- endif %}
+{%- endif %}
\ No newline at end of file

From 9d91b4d80bb836f45366b42394ecc8c68bc93510 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 5 Dec 2023 17:02:49 -0500
Subject: [PATCH 05/16] fix tests

---
 .../.github/workflows/tests.yml               | 49 +++++++++++--------
 1 file changed, 28 insertions(+), 21 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
index 46a0654..b9b8413 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
@@ -11,17 +11,17 @@ on:
 
 jobs:
   lint:
-    runs-on: ${{ matrix.os }}
+    runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
         python-version: [3.8]
         os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python {{ '${{ matrix.python-version }}' }}
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: {{ '${{ matrix.python-version }}' }}
     - name: Install package
       run: pip install invoke .[dev]
     - name: invoke lint
@@ -29,17 +29,17 @@ jobs:
 
 
   docs:
-    runs-on: ${{ matrix.os }}
+    runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python {{ '${{ matrix.python-version }}' }}
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: {{ '${{ matrix.python-version }}' }}
     - name: Install package
       run: pip install .[dev]
     - name: make docs
@@ -47,17 +47,17 @@ jobs:
 
 
   readme:
-    runs-on: ${{ matrix.os }}
+    runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python {{ '${{ matrix.python-version }}' }}
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: {{ '${{ matrix.python-version }}' }}
     - name: Install package and dependencies
       run: pip install invoke rundoc .
     - name: invoke readme
@@ -65,35 +65,42 @@ jobs:
 
 
   unit:
-    runs-on: ${{ matrix.os }}
+    runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python {{ '${{ matrix.python-version }}' }}
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: {{ '${{ matrix.python-version }}' }}
     - name: Install package and dependencies
       run: pip install invoke .[test]
-    - name: invoke pytest
-      run: invoke pytest
+    - name: invoke unit
+      run: invoke unit
+
+{%- if cookiecutter.use_codecov_with_ci == 'y' %}
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        file: ./coverage.xml
+{%- endif %}
 
 
   minimum:
-    runs-on: ${{ matrix.os }}
+    runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python {{ '${{ matrix.python-version }}' }}
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: {{ '${{ matrix.python-version }}' }}
     - name: Install package and dependencies
       run: pip install invoke .[test]
     - name: invoke minimum
@@ -101,18 +108,18 @@ jobs:
 
 
   tutorials:
-    runs-on: ${{ matrix.os }}
+    runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ubuntu-20.04, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python {{ '${{ matrix.python-version }}' }}
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: {{ '${{ matrix.python-version }}' }}
     - name: Install package and dependencies
       run: pip install invoke jupyter matplotlib .
     - name: invoke tutorials
-      run: invoke tutorials
+      run: invoke tutorials
\ No newline at end of file

From bc32c23802b9d196a169c709aca98bfa63d88155 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Mon, 13 Jan 2025 18:09:06 -0500
Subject: [PATCH 06/16] migrate setup to pyproject.toml

---
 .../pyproject.toml                            | 190 ++++++++++++++++++
 {{cookiecutter.repository_name}}/ruff.toml    |   0
 {{cookiecutter.repository_name}}/setup.cfg    |  50 -----
 {{cookiecutter.repository_name}}/setup.py     | 121 -----------
 4 files changed, 190 insertions(+), 171 deletions(-)
 create mode 100644 {{cookiecutter.repository_name}}/pyproject.toml
 create mode 100644 {{cookiecutter.repository_name}}/ruff.toml
 delete mode 100644 {{cookiecutter.repository_name}}/setup.cfg
 delete mode 100644 {{cookiecutter.repository_name}}/setup.py

diff --git a/{{cookiecutter.repository_name}}/pyproject.toml b/{{cookiecutter.repository_name}}/pyproject.toml
new file mode 100644
index 0000000..154641a
--- /dev/null
+++ b/{{cookiecutter.repository_name}}/pyproject.toml
@@ -0,0 +1,190 @@
+[build-system]
+requires = ['setuptools', 'wheel']
+build-backend = 'setuptools.build_meta'
+
+[project]
+name = '{{ cookiecutter.project_slug }}'
+version = '{{ cookiecutter.version }}'
+description = '{{ cookiecutter.project_short_description.replace("\'", "\\\'") }}'
+readme = 'README.md'
+authors = [
+  {name = '{{ cookiecutter.license_owner }}', email = '{{ cookiecutter.license_owner_email }}'}
+]
+{%- set license_classifiers = {
+    'MIT license': 'License :: OSI Approved :: MIT License',
+    'BSD license': 'License :: OSI Approved :: BSD License',
+    'ISC license': 'License :: OSI Approved :: ISC License (ISCL)',
+    'Apache Software License 2.0': 'License :: OSI Approved :: Apache Software License',
+    'GNU General Public License v3': 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)'
+} %}
+classifiers = [
+    'Development Status :: 2 - Pre-Alpha',
+    'Intended Audience :: Developers',
+{%- if cookiecutter.open_source_license in license_classifiers %}
+    '{{ license_classifiers[cookiecutter.open_source_license] }}',
+{%- endif %}
+    'Natural Language :: English',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+]
+license = {text = '{{ cookiecutter.open_source_license }}'}
+dependencies = [
+    {%- if cookiecutter.command_line_interface|lower == 'click' %}'Click>=6.0',{%- endif %}
+]
+
+[project.optional-dependencies]
+tests = [
+    'pytest>=3.4.2',
+    'pytest-cov>=2.6.0',
+    'pytest-runner>=2.11.1',
+]
+
+dev = [
+    '{{ cookiecutter.project_slug }}[test]',
+
+    # general
+    'bumpversion>=0.5.3',
+    'pip>=9.0.1',
+    'watchdog>=0.8.3',
+
+    # docs
+    'm2r>=0.2.0,<0.3',
+    'Sphinx>=1.7.1,<3',
+    'sphinx_rtd_theme>=0.2.4,<0.5',
+    'autodocsumm>=0.1.10',
+
+    # style check
+    'ruff>=0.4.5',
+
+    # distribute on PyPI
+    'twine>=1.10.0',
+    'wheel>=0.30.0',
+
+    # Advanced testing
+    'coverage>=4.5.1',
+    'tox>=2.9.1',
+]
+
+[project.urls]
+homepage = 'https://github.com/{{ cookiecutter.github_owner }}/{{ cookiecutter.repository_name }}'
+
+[project.entry-points]
+{{ cookiecutter.project_slug }} = { main = '{{ cookiecutter.project_slug }}.cli.__main__:main' }
+
+{% if cookiecutter.command_line_interface == 'Yes' %}
+[project.scripts]
+{{ cookiecutter.project_slug }} = '{{ cookiecutter.project_slug }}.cli:app'
+{% endif %}
+
+[tool.setuptools]
+include-package-data = true
+license-files = ['LICENSE']
+
+[tool.setuptools.packages.find]
+include = ['{{ cookiecutter.project_slug }}', '{{ cookiecutter.project_slug }}.*']
+namespaces = false
+
+[tool.setuptools.package-data]
+"*" = ["*.*"]
+
+[tool.setuptools.exclude-package-data]
+'*' = [
+    '* __pycache__',
+]
+
+[tool.setuptools.dynamic]
+version = {attr = '{{ cookiecutter.project_slug }}.__version__'}
+
+[tool.bumpversion]
+current_version = '{{ cookiecutter.version }}'
+parse = '(?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<candidate>\d+))?'
+serialize = [
+    '{major}.{minor}.{patch}.{release}{candidate}',
+	'{major}.{minor}.{patch}'
+]
+search = '{current_version}'
+replace = '{new_version}'
+regex = false
+ignore_missing_version = false
+tag = true
+sign_tags = false
+tag_name = 'v{new_version}'
+tag_message = 'Bump version: {current_version} → {new_version}'
+allow_dirty = false
+commit = true
+message = 'Bump version: {current_version} → {new_version}'
+commit_args = ''
+
+[tool.bumpversion.parts.release]
+first_value = 'dev'
+optional_value = 'release'
+values = [
+    'dev',
+    'release'
+]
+
+[[tool.bumpversion.files]]
+filename = "{{ cookiecutter.project_slug }}/__init__.py"
+search = "__version__ = '{current_version}'"
+replace = "__version__ = '{new_version}'"
+
+[tool.pytest.ini_options]
+addopts = "--ignore=pyproject.toml"
+
+# linting
+[tool.ruff]
+preview = true
+line-length = 99
+indent-width = 4
+src = ['{{ cookiecutter.project_slug }}']
+exclude = [
+    "docs",
+    ".tox",
+    ".git",
+    "__pycache__",
+    "*.ipynb",
+    ".ipynb_checkpoints",
+]
+
+[tool.ruff.lint]
+select = [
+    "F", # Pyflakes
+    "E", # pycodestyle
+    "W", # pycodestyle
+    "D", # pydocstyle
+    "I001", # isort
+    "T201", # print statements
+]
+ignore = [
+    # pydocstyle
+    "D107",  # Missing docstring in __init__
+    "D417",   # Missing argument descriptions in the docstring
+    "PD901",
+    "PD101",
+]
+
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
+preview = true
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
+
+[tool.ruff.lint.isort]
+known-first-party = ['{{ cookiecutter.project_slug }}']
+lines-between-types = 0
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["F401", "E402", "F403", "F405", "E501", "I001"]
+"tests/**.py" = ["D"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.ruff.lint.pycodestyle]
+max-doc-length = 99
+max-line-length = 99
\ No newline at end of file
diff --git a/{{cookiecutter.repository_name}}/ruff.toml b/{{cookiecutter.repository_name}}/ruff.toml
new file mode 100644
index 0000000..e69de29
diff --git a/{{cookiecutter.repository_name}}/setup.cfg b/{{cookiecutter.repository_name}}/setup.cfg
deleted file mode 100644
index f3bb7de..0000000
--- a/{{cookiecutter.repository_name}}/setup.cfg
+++ /dev/null
@@ -1,50 +0,0 @@
-[bumpversion]
-current_version = {{ cookiecutter.version }}
-commit = True
-tag = True
-parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<candidate>\d+))?
-serialize =
-	{major}.{minor}.{patch}.{release}{candidate}
-	{major}.{minor}.{patch}
-
-[bumpversion:part:release]
-optional_value = release
-first_value = dev
-values =
-	dev
-	release
-
-[bumpversion:part:candidate]
-
-[bumpversion:file:setup.py]
-search = version='{current_version}'
-replace = version='{new_version}'
-
-[bumpversion:file:{{ cookiecutter.project_slug }}/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
-
-[bdist_wheel]
-universal = 1
-
-[flake8]
-max-line-length = 99
-exclude = docs, .tox, .git, __pycache__, .ipynb_checkpoints
-# Ignore W503 (line break before binary operator)
-# Line breaks should occur before the binary operator because it keeps all operators aligned.
-# Please discuss with the group before adding other ignores. 
-ignore = W503  
-
-[isort]
-include_trailing_comma = True
-line_length=99
-lines_between_types = 0
-multi_line_output = 4
-not_skip = __init__.py
-use_parentheses = True
-
-[aliases]
-test = pytest
-
-[tool:pytest]
-collect_ignore = ['setup.py']
diff --git a/{{cookiecutter.repository_name}}/setup.py b/{{cookiecutter.repository_name}}/setup.py
deleted file mode 100644
index ef6fb80..0000000
--- a/{{cookiecutter.repository_name}}/setup.py
+++ /dev/null
@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-"""The setup script."""
-
-from setuptools import setup, find_packages
-
-with open('README.md', encoding='utf-8') as readme_file:
-    readme = readme_file.read()
-
-with open('HISTORY.md', encoding='utf-8') as history_file:
-    history = history_file.read()
-
-install_requires = [
-    {%- if cookiecutter.command_line_interface|lower == 'click' %}'Click>=6.0',{%- endif %}
-    {%- if cookiecutter.support_py2 == 'y' %}'six',{%- endif %}
-]
-
-setup_requires = [
-    'pytest-runner>=2.11.1',
-]
-
-tests_require = [
-    'pytest>=3.4.2',
-    'pytest-cov>=2.6.0',
-    'rundoc>=0.4.3',
-]
-
-development_requires = [
-    # general
-    'bumpversion>=0.5.3',
-    'pip>=9.0.1',
-    'watchdog>=0.8.3',
-
-    # docs
-    'm2r>=0.2.0,<0.3',
-    'Sphinx>=1.7.1,<3',
-    'sphinx_rtd_theme>=0.2.4,<0.5',
-    'autodocsumm>=0.1.10',
-
-    # style check
-    'flake8>=3.7.7',
-    'isort>=4.3.4',
-
-    # fix style issues
-    'autoflake>=1.2',
-    'autopep8>=1.4.3',
-
-    # distribute on PyPI
-    'twine>=1.10.0',
-    'wheel>=0.30.0',
-
-    # Advanced testing
-    'coverage>=4.5.1',
-    'tox>=2.9.1',
-    'invoke',
-]
-
-{%- set license_classifiers = {
-    'MIT license': 'License :: OSI Approved :: MIT License',
-    'BSD license': 'License :: OSI Approved :: BSD License',
-    'ISC license': 'License :: OSI Approved :: ISC License (ISCL)',
-    'Apache Software License 2.0': 'License :: OSI Approved :: Apache Software License',
-    'GNU General Public License v3': 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)'
-} %}
-
-setup(
-    author='{{ cookiecutter.license_owner }}',
-    author_email='{{ cookiecutter.license_owner_email }}',
-    classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers',
-{%- if cookiecutter.open_source_license in license_classifiers %}
-        '{{ license_classifiers[cookiecutter.open_source_license] }}',
-{%- endif %}
-        'Natural Language :: English',
-{%- if cookiecutter.support_py2 == 'y' %}
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 2.7',
-{%- endif %}
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-        'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
-    ],
-    description='{{ cookiecutter.project_short_description.replace("\'", "\\\'") }}',
-    {%- if 'no' not in cookiecutter.command_line_interface|lower %}
-    entry_points={
-        'console_scripts': [
-            '{{ cookiecutter.package_name }}={{ cookiecutter.project_slug }}.cli:main',
-        ],
-    },
-    {%- endif %}
-    extras_require={
-        'test': tests_require,
-        'dev': development_requires + tests_require,
-    },
-    install_package_data=True,
-    install_requires=install_requires,
-{%- if cookiecutter.open_source_license in license_classifiers %}
-    license='{{ cookiecutter.open_source_license }}',
-{%- endif %}
-    long_description=readme + '\n\n' + history,
-    long_description_content_type='text/markdown',
-    include_package_data=True,
-    keywords='{{ cookiecutter.project_slug }} {{ cookiecutter.package_name }} {{ cookiecutter.project_name }}',
-    name='{{ cookiecutter.package_name }}',
-    packages=find_packages(include=['{{ cookiecutter.project_slug }}', '{{ cookiecutter.project_slug }}.*']),
-{%- if cookiecutter.support_py2 == 'y' %}
-    python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*',
-{%- else %}
-    python_requires='>=3.8',
-{%- endif %}
-    setup_requires=setup_requires,
-    test_suite='tests',
-    tests_require=tests_require,
-    url='https://github.com/{{ cookiecutter.github_owner }}/{{ cookiecutter.repository_name }}',
-    version='{{ cookiecutter.version }}',
-    zip_safe=False,
-)

From c68a234f9de8b59e59c5948f5f7018519078c764 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Mon, 13 Jan 2025 18:20:39 -0500
Subject: [PATCH 07/16] remove python 2 option

---
 cookiecutter.json | 1 -
 1 file changed, 1 deletion(-)

diff --git a/cookiecutter.json b/cookiecutter.json
index d6e5ebd..53abb56 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -12,7 +12,6 @@
   "license_owner_email": "{{ 'dailabmit@gmail.com' if cookiecutter.github_username != cookiecutter.github_owner else cookiecutter.email }}",
   "pypi_username": "{{ 'mit_dai_lab' if cookiecutter.github_username != cookiecutter.github_owner else cookiecutter.github_username }}",
   "version": "0.1.0.dev0",
-  "support_py2": "n",
   "ci_provider": ["Github Actions", "Travis CI", "No continuous integration"],
   "use_pypi_with_ci": "n",
   "use_ghpages_with_ci": "y",

From 951ff269efc5fae8be0cc75e3109c3b7b5e87fd5 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Mon, 13 Jan 2025 18:33:33 -0500
Subject: [PATCH 08/16] add python 3.12

---
 CONTRIBUTING.rst                                |  2 +-
 README.rst                                      |  6 +++---
 .../.github/workflows/tests.yml                 | 15 ++++++++-------
 {{cookiecutter.repository_name}}/.travis.yml    |  4 +---
 {{cookiecutter.repository_name}}/README.md      |  2 +-
 {{cookiecutter.repository_name}}/tox.ini        | 17 +++++++++++++----
 6 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 56c9a79..dcd77df 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -135,7 +135,7 @@ Before you submit a pull request, check that it meets these guidelines:
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
 
-3. The pull request should work for Python 2.7, 3.8, 3.9, 3.10, and 3.11, and for PyPy. Check
+3. The pull request should work for Python 3.8, 3.9, 3.10, 3.11 and 3.12, and for PyPy. Check
    https://travis-ci.org/audreyr/cookiecutter-pypackage/pull_requests
    and make sure that the tests pass for all supported Python versions.
 
diff --git a/README.rst b/README.rst
index c01904e..07db73d 100644
--- a/README.rst
+++ b/README.rst
@@ -19,7 +19,7 @@ Features
 * Testing setup with ``unittest`` and ``pytest``
 * Github-Actions_: Ready for Github Actions Continuous Integration testing
 * Travis-CI_: Ready for Travis Continuous Integration testing
-* Tox_ testing: Setup to easily test for Python 2.7, 3.8, 3.9, 3.10, 3.11
+* Tox_ testing: Setup to easily test for Python 3.8, 3.9, 3.10, 3.11, 3.12
 * Sphinx_ docs: Documentation ready for generation, automatic building and deploying to gh-pages (strongly recommended)
 * Bumpversion_: Pre-configured version bumping with a single command
 * Auto-release to PyPI_ when you push a new tag to master (strongly recommended)
@@ -199,8 +199,8 @@ things are files and folders and I'll give you a quick overview of what they
 are/do.
 
 * Tox_ (tox.ini): A system that can run all kinds of tests for you. For
-  instance, you can test your code on various versions (Python 2.7, 3.8,
-  3.9, 3.10, 3.11) and test your code on linters as well.
+  instance, you can test your code on various versions (Python 3.8,
+  3.9, 3.10, 3.11, 3.12) and test your code on linters as well.
 
 * Travis-CI_ (travis.yml): A continuous integration system. That means every
   time you push a commit it will simulate downloading your project, installing
diff --git a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
index b9b8413..7f9f3a2 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
@@ -32,8 +32,9 @@ jobs:
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        os: [ubuntu-20.04]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        os: [ubuntu-latest, macos-latest]
+
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python {{ '${{ matrix.python-version }}' }}
@@ -50,7 +51,7 @@ jobs:
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
@@ -68,7 +69,7 @@ jobs:
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-20.04, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
@@ -93,7 +94,7 @@ jobs:
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-20.04, macos-latest]
     steps:
     - uses: actions/checkout@v1
@@ -111,7 +112,7 @@ jobs:
     runs-on: {{ '${{ matrix.os }}' }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: [ubuntu-20.04, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
@@ -122,4 +123,4 @@ jobs:
     - name: Install package and dependencies
       run: pip install invoke jupyter matplotlib .
     - name: invoke tutorials
-      run: invoke tutorials
\ No newline at end of file
+      run: invoke tutorials
diff --git a/{{cookiecutter.repository_name}}/.travis.yml b/{{cookiecutter.repository_name}}/.travis.yml
index 88ad41d..474ff64 100644
--- a/{{cookiecutter.repository_name}}/.travis.yml
+++ b/{{cookiecutter.repository_name}}/.travis.yml
@@ -6,9 +6,7 @@ python:
   - 3.9
   - 3.10
   - 3.11
-{%- if cookiecutter.support_py2 == 'y' %}
-  - 2.7
-{%- endif %}
+  - 3.12
 
 matrix:
   include:
diff --git a/{{cookiecutter.repository_name}}/README.md b/{{cookiecutter.repository_name}}/README.md
index 22216ff..e6803db 100644
--- a/{{cookiecutter.repository_name}}/README.md
+++ b/{{cookiecutter.repository_name}}/README.md
@@ -36,7 +36,7 @@ TODO: Provide a short overview of the project here.
 
 ## Requirements
 
-**{{ cookiecutter.project_name }}** has been developed and tested on [Python {% if cookiecutter.support_py2 == 'y' %}2.7, {% endif %}3.8, 3.9, 3.10 and 3.11](https://www.python.org/downloads/)
+**{{ cookiecutter.project_name }}** has been developed and tested on [Python 3.8, 3.9, 3.10, 3.11 and 3.12](https://www.python.org/downloads/)
 
 Also, although it is not strictly required, the usage of a [virtualenv](https://virtualenv.pypa.io/en/latest/)
 is highly recommended in order to avoid interfering with other software installed in the system
diff --git a/{{cookiecutter.repository_name}}/tox.ini b/{{cookiecutter.repository_name}}/tox.ini
index 185e71b..4d28466 100644
--- a/{{cookiecutter.repository_name}}/tox.ini
+++ b/{{cookiecutter.repository_name}}/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = {% if cookiecutter.support_py2 == 'y' %}py27, {% endif %}py38, py39, py310, py311, lint, docs
+envlist = py38, py39, py310, py311, py312, lint, docs
 
 
 {%- if cookiecutter.ci_provider == 'Travis CI' %}
@@ -9,8 +9,17 @@ python =
     3.9: py39, docs, lint
     3.10: py310
     3.11: py311
-{%- if cookiecutter.support_py2 == 'y' %}
-    2.7: py27
+    3.12: py312
+{%- endif %}
+
+{%- if cookiecutter.ci_provider == 'Github Actions' %}
+[gh-actions]
+python =
+    3.8: py38
+    3.9: py39, docs, lint
+    3.10: py310
+    3.11: py311
+    3.12: py312
 {%- endif %}
 
 [testenv]
@@ -55,4 +64,4 @@ commands =
     minimum: invoke minimum
     tutorials: invoke tutorials
     invoke rmdir --path {envdir}
-{%- endif %}
\ No newline at end of file
+{%- endif %}

From e869f7215d49187b494add915a6e448ae3359973 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 14 Jan 2025 10:26:45 -0500
Subject: [PATCH 09/16] fix tox issue and remove ruff.toml

---
 {{cookiecutter.repository_name}}/ruff.toml |  0
 {{cookiecutter.repository_name}}/tox.ini   | 26 +---------------------
 2 files changed, 1 insertion(+), 25 deletions(-)
 delete mode 100644 {{cookiecutter.repository_name}}/ruff.toml

diff --git a/{{cookiecutter.repository_name}}/ruff.toml b/{{cookiecutter.repository_name}}/ruff.toml
deleted file mode 100644
index e69de29..0000000
diff --git a/{{cookiecutter.repository_name}}/tox.ini b/{{cookiecutter.repository_name}}/tox.ini
index 4d28466..54846f9 100644
--- a/{{cookiecutter.repository_name}}/tox.ini
+++ b/{{cookiecutter.repository_name}}/tox.ini
@@ -40,28 +40,4 @@ commands =
 skipsdist = true
 extras = dev
 commands =
-    /usr/bin/env make docs
-{%- endif %}
-
-{%- if cookiecutter.ci_provider == 'Github Actions' %}
-[testenv]
-skipsdist = false
-skip_install = false
-deps =
-    invoke
-    readme: rundoc
-    tutorials: jupyter
-extras =
-    lint: dev
-    docs: dev
-    unit: test
-    minimum: test
-commands =
-    docs: /usr/bin/env make docs
-    lint: invoke lint
-    readme: invoke readme
-    unit: invoke unit
-    minimum: invoke minimum
-    tutorials: invoke tutorials
-    invoke rmdir --path {envdir}
-{%- endif %}
+    /usr/bin/env make docs
\ No newline at end of file

From f616b9498072664327bc1b6679a00a12cd1b3c39 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 14 Jan 2025 12:26:56 -0500
Subject: [PATCH 10/16] add ruff commands

---
 {{cookiecutter.repository_name}}/Makefile | 13 ++++++++-----
 {{cookiecutter.repository_name}}/tasks.py | 11 +++++++++--
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/Makefile b/{{cookiecutter.repository_name}}/Makefile
index 195928e..1832fa1 100644
--- a/{{cookiecutter.repository_name}}/Makefile
+++ b/{{cookiecutter.repository_name}}/Makefile
@@ -63,14 +63,17 @@ lint: ## check style with flake8 and isort
 
 .PHONY: lint-{{ cookiecutter.project_slug }}
 lint: ## check style with flake8 and isort
-	flake8 {{ cookiecutter.project_slug }} tests
-	isort -c --recursive {{ cookiecutter.project_slug }} tests
+	ruff check {{ cookiecutter.project_slug }}/
+	ruff format --check --diff {{ cookiecutter.project_slug }}/
+
+.PHONY: lint-tests
+lint: ## check style with flake8 and isort
+	ruff check tests/
+	ruff format --check --diff tests/
 
 .PHONY: fix-lint
 fix-lint: ## fix lint issues using autoflake, autopep8, and isort
-	find {{ cookiecutter.project_slug }} tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
-	autopep8 --in-place --recursive --aggressive {{ cookiecutter.project_slug }} tests
-	isort --apply --atomic --recursive {{ cookiecutter.project_slug }} tests
+	invoke fix-lint
 
 
 # TEST TARGETS
diff --git a/{{cookiecutter.repository_name}}/tasks.py b/{{cookiecutter.repository_name}}/tasks.py
index 5ad19ba..ffbacca 100644
--- a/{{cookiecutter.repository_name}}/tasks.py
+++ b/{{cookiecutter.repository_name}}/tasks.py
@@ -109,8 +109,15 @@ def tutorials(c):
 @task
 def lint(c):
     check_dependencies(c)
-    c.run('flake8 {{cookiecutter.repository_name}} tests')
-    c.run('isort -c --recursive {{cookiecutter.repository_name}} tests')
+    c.run('ruff check .')
+    c.run('ruff format --check --diff .')
+
+
+@task
+def fix_lint(c):
+    check_dependencies(c)
+    c.run('ruff check --fix .')
+    c.run('ruff format .')
 
 
 def remove_readonly(func, path, _):

From 36cdbc61e2d2a2ca8a1167c933aec25ecda0d9ca Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 14 Jan 2025 16:38:57 -0500
Subject: [PATCH 11/16] fix small issues

---
 {{cookiecutter.repository_name}}/MANIFEST.in    | 13 -------------
 {{cookiecutter.repository_name}}/Makefile       |  5 ++---
 {{cookiecutter.repository_name}}/pyproject.toml |  1 +
 {{cookiecutter.repository_name}}/tasks.py       |  6 +++---
 4 files changed, 6 insertions(+), 19 deletions(-)
 delete mode 100644 {{cookiecutter.repository_name}}/MANIFEST.in

diff --git a/{{cookiecutter.repository_name}}/MANIFEST.in b/{{cookiecutter.repository_name}}/MANIFEST.in
deleted file mode 100644
index 9c2f658..0000000
--- a/{{cookiecutter.repository_name}}/MANIFEST.in
+++ /dev/null
@@ -1,13 +0,0 @@
-{% if cookiecutter.create_author_file == 'y' -%}
-include AUTHORS.rst
-{% endif -%}
-include CONTRIBUTING.rst
-include HISTORY.md
-include LICENSE
-include README.md
-
-recursive-include tests *
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-recursive-include docs *.md *.rst conf.py Makefile make.bat *.jpg *.png *.gif
diff --git a/{{cookiecutter.repository_name}}/Makefile b/{{cookiecutter.repository_name}}/Makefile
index 1832fa1..33028f0 100644
--- a/{{cookiecutter.repository_name}}/Makefile
+++ b/{{cookiecutter.repository_name}}/Makefile
@@ -44,7 +44,7 @@ install-test: clean-build clean-pyc ## install the package and test dependencies
 install-develop: clean-build clean-pyc ## install the package in editable mode and dependencies for development
 	pip install -e .[dev]
 
-MINIMUM := $(shell sed -n '/install_requires = \[/,/]/p' setup.py | grep -v -e '[][]' | sed 's/ *\(.*\),$?$$/\1/g' | tr '>' '=')
+MINIMUM := $(shell sed -n '/dependencies = \[/,/]/p' pyproject.toml | grep -v -e '[][]' | sed 's/ *\(.*\),$?$$/\1/g' | tr '>' '=')
 
 .PHONY: install-minimum
 install-minimum: ## install the minimum supported versions of the package dependencies
@@ -132,8 +132,7 @@ serve-docs: view-docs ## compile the docs watching for changes
 
 .PHONY: dist
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m build --wheel --sdist
 	ls -l dist
 
 .PHONY: publish-confirm
diff --git a/{{cookiecutter.repository_name}}/pyproject.toml b/{{cookiecutter.repository_name}}/pyproject.toml
index 154641a..19abf56 100644
--- a/{{cookiecutter.repository_name}}/pyproject.toml
+++ b/{{cookiecutter.repository_name}}/pyproject.toml
@@ -148,6 +148,7 @@ exclude = [
     "__pycache__",
     "*.ipynb",
     ".ipynb_checkpoints",
+    "tasks.py"
 ]
 
 [tool.ruff.lint]
diff --git a/{{cookiecutter.repository_name}}/tasks.py b/{{cookiecutter.repository_name}}/tasks.py
index ffbacca..5bceda8 100644
--- a/{{cookiecutter.repository_name}}/tasks.py
+++ b/{{cookiecutter.repository_name}}/tasks.py
@@ -46,8 +46,8 @@ def _validate_python_version(line):
 
 @task
 def install_minimum(c):
-    with open('setup.py', 'r') as setup_py:
-        lines = setup_py.read().splitlines()
+    with open('pyproject.toml', 'r') as pyproject_file:
+        lines = pyproject_file.read().splitlines()
 
     versions = []
     started = False
@@ -68,7 +68,7 @@ def install_minimum(c):
                     requirement += version
                 versions.append(requirement)
 
-        elif (line.startswith('install_requires = [')):
+        elif (line.startswith('dependencies = [')):
             started = True
 
     c.run(f'python -m pip install {" ".join(versions)}')

From 461adc5a2c073f068494d572f6b816c484bc110e Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Tue, 14 Jan 2025 18:34:41 -0500
Subject: [PATCH 12/16] edit bumpversion commands

---
 {{cookiecutter.repository_name}}/Makefile       | 12 ++++++------
 {{cookiecutter.repository_name}}/pyproject.toml | 16 +++++++++-------
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/Makefile b/{{cookiecutter.repository_name}}/Makefile
index 33028f0..23f1f55 100644
--- a/{{cookiecutter.repository_name}}/Makefile
+++ b/{{cookiecutter.repository_name}}/Makefile
@@ -154,34 +154,34 @@ publish: dist publish-confirm ## package and upload a release
 bumpversion-release: ## Merge master to stable and bumpversion release
 	git checkout stable || git checkout -b stable
 	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
-	bumpversion release
+	bump-my-version bump release
 	git push --tags origin stable
 
 .PHONY: bumpversion-release-test
 bumpversion-release-test: ## Merge master to stable and bumpversion release
 	git checkout stable || git checkout -b stable
 	git merge --no-ff master -m"make release-tag: Merge branch 'master' into stable"
-	bumpversion release --no-tag
+	bump-my-version bump release --no-tag
 	@echo git push --tags origin stable
 
 .PHONY: bumpversion-patch
 bumpversion-patch: ## Merge stable to master and bumpversion patch
 	git checkout master
 	git merge stable
-	bumpversion --no-tag patch
+	bump-my-version bump --no-tag patch
 	git push
 
 .PHONY: bumpversion-minor
 bumpversion-minor: ## Bump the version the next minor skipping the release
-	bumpversion --no-tag minor
+	bump-my-version bump --no-tag minor
 
 .PHONY: bumpversion-major
 bumpversion-major: ## Bump the version the next major skipping the release
-	bumpversion --no-tag major
+	bump-my-version bump --no-tag major
 
 .PHONY: bumpversion-candidate
 bumpversion-candidate: ## Bump the version to the next candidate
-	bumpversion candidate --no-tag
+	bump-my-version bump candidate --no-tag
 
 .PHONY: bumpversion-revert
 bumpversion-revert: ## Undo a previous bumpversion-release
diff --git a/{{cookiecutter.repository_name}}/pyproject.toml b/{{cookiecutter.repository_name}}/pyproject.toml
index 19abf56..302ad41 100644
--- a/{{cookiecutter.repository_name}}/pyproject.toml
+++ b/{{cookiecutter.repository_name}}/pyproject.toml
@@ -1,12 +1,6 @@
-[build-system]
-requires = ['setuptools', 'wheel']
-build-backend = 'setuptools.build_meta'
-
 [project]
 name = '{{ cookiecutter.project_slug }}'
-version = '{{ cookiecutter.version }}'
 description = '{{ cookiecutter.project_short_description.replace("\'", "\\\'") }}'
-readme = 'README.md'
 authors = [
   {name = '{{ cookiecutter.license_owner }}', email = '{{ cookiecutter.license_owner_email }}'}
 ]
@@ -31,7 +25,11 @@ classifiers = [
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
 ]
+keywords = '{{ cookiecutter.project_slug }} {{ cookiecutter.package_name }} {{ cookiecutter.project_name }}'
+dynamic = ['version']
 license = {text = '{{ cookiecutter.open_source_license }}'}
+requires-python = '>=3.8,<3.13'
+readme = 'README.md'
 dependencies = [
     {%- if cookiecutter.command_line_interface|lower == 'click' %}'Click>=6.0',{%- endif %}
 ]
@@ -47,7 +45,7 @@ dev = [
     '{{ cookiecutter.project_slug }}[test]',
 
     # general
-    'bumpversion>=0.5.3',
+    'bump-my-version>=0.18.3',
     'pip>=9.0.1',
     'watchdog>=0.8.3',
 
@@ -80,6 +78,10 @@ homepage = 'https://github.com/{{ cookiecutter.github_owner }}/{{ cookiecutter.r
 {{ cookiecutter.project_slug }} = '{{ cookiecutter.project_slug }}.cli:app'
 {% endif %}
 
+[build-system]
+requires = ['setuptools', 'wheel']
+build-backend = 'setuptools.build_meta'
+
 [tool.setuptools]
 include-package-data = true
 license-files = ['LICENSE']

From 5b3ea097f8511446524ef43c11707c2696f885dd Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Wed, 15 Jan 2025 09:57:18 -0500
Subject: [PATCH 13/16] add build dependency and update ubuntu image in tests

---
 .../.github/workflows/tests.yml                           | 8 ++++----
 {{cookiecutter.repository_name}}/pyproject.toml           | 1 +
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
index 7f9f3a2..7a97372 100644
--- a/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
+++ b/{{cookiecutter.repository_name}}/.github/workflows/tests.yml
@@ -52,7 +52,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        os: [ubuntu-20.04, macos-latest]
+        os: [ubuntu-latest, macos-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python {{ '${{ matrix.python-version }}' }}
@@ -70,7 +70,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        os: [ubuntu-20.04, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python {{ '${{ matrix.python-version }}' }}
@@ -95,7 +95,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        os: [ubuntu-20.04, macos-latest]
+        os: [ubuntu-latest, macos-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python {{ '${{ matrix.python-version }}' }}
@@ -113,7 +113,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        os: [ubuntu-20.04, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
     - uses: actions/checkout@v1
     - name: Set up Python {{ '${{ matrix.python-version }}' }}
diff --git a/{{cookiecutter.repository_name}}/pyproject.toml b/{{cookiecutter.repository_name}}/pyproject.toml
index 302ad41..7b6c20a 100644
--- a/{{cookiecutter.repository_name}}/pyproject.toml
+++ b/{{cookiecutter.repository_name}}/pyproject.toml
@@ -45,6 +45,7 @@ dev = [
     '{{ cookiecutter.project_slug }}[test]',
 
     # general
+    'build>=1.0.0,<2',
     'bump-my-version>=0.18.3',
     'pip>=9.0.1',
     'watchdog>=0.8.3',

From eedf8b82fd1d6a3cea82cf61b6201d2ec3ba6da4 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <sarahalnegheimish@gmail.com>
Date: Wed, 15 Jan 2025 10:02:29 -0500
Subject: [PATCH 14/16] remove sdv-dev and rename D3-AI to sintel-dev

---
 cookiecutter.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cookiecutter.json b/cookiecutter.json
index 53abb56..05c256a 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -2,7 +2,7 @@
   "full_name": "Your Name",
   "email": "email@mit.edu",
   "github_username": "username",
-  "github_owner": ["DAI-Lab", "HDI-Project", "D3-AI", "data-dev", "sdv-dev", "sintel-dev", "{{ cookiecutter.github_username }}"],
+  "github_owner": ["DAI-Lab", "HDI-Project", "sintel-dev", "data-dev", "{{ cookiecutter.github_username }}"],
   "project_name": "Python Boilerplate",
   "package_name": "{{ cookiecutter.project_name.lower().replace(' ', '-') }}",
   "project_slug": "{{ cookiecutter.package_name.replace('-', '_') }}",

From d476ed0acb507f559a02d233352e3b594187519f Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <40212131+sarahmish@users.noreply.github.com>
Date: Fri, 17 Jan 2025 16:57:44 -0500
Subject: [PATCH 15/16] update keywords to be a list

---
 {{cookiecutter.repository_name}}/pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{cookiecutter.repository_name}}/pyproject.toml b/{{cookiecutter.repository_name}}/pyproject.toml
index 7b6c20a..eb6bcdf 100644
--- a/{{cookiecutter.repository_name}}/pyproject.toml
+++ b/{{cookiecutter.repository_name}}/pyproject.toml
@@ -25,7 +25,7 @@ classifiers = [
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
 ]
-keywords = '{{ cookiecutter.project_slug }} {{ cookiecutter.package_name }} {{ cookiecutter.project_name }}'
+keywords = ['{{ cookiecutter.project_slug }}','{{ cookiecutter.package_name }}','{{ cookiecutter.project_name }}']
 dynamic = ['version']
 license = {text = '{{ cookiecutter.open_source_license }}'}
 requires-python = '>=3.8,<3.13'
@@ -191,4 +191,4 @@ convention = "google"
 
 [tool.ruff.lint.pycodestyle]
 max-doc-length = 99
-max-line-length = 99
\ No newline at end of file
+max-line-length = 99

From 6b6bde5da6a06e1778c15b120aa8ae28097e5c41 Mon Sep 17 00:00:00 2001
From: Sarah Alnegheimish <40212131+sarahmish@users.noreply.github.com>
Date: Sun, 19 Jan 2025 10:11:29 -0500
Subject: [PATCH 16/16] fix typo 'tests' -> 'test'

---
 {{cookiecutter.repository_name}}/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.repository_name}}/pyproject.toml b/{{cookiecutter.repository_name}}/pyproject.toml
index eb6bcdf..dd9f04e 100644
--- a/{{cookiecutter.repository_name}}/pyproject.toml
+++ b/{{cookiecutter.repository_name}}/pyproject.toml
@@ -35,7 +35,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-tests = [
+test = [
     'pytest>=3.4.2',
     'pytest-cov>=2.6.0',
     'pytest-runner>=2.11.1',