Change setup to pyproject.toml (#29)

* migrate to pyproject toml

* fix lint test

* fix docs

* change python version tests

* remove python 3.8

* fix tests

* use 20.04 image of ubuntu

* downgrade pip

Author: sarahmish

.github/workflows/docs.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Python
       uses: actions/setup-python@v1
       with:
-        python-version: '3.8'
+        python-version: '3.9'
 
     - name: Build
       run: |

.github/workflows/tests.yml

@@ -11,94 +11,72 @@ on:
 
 jobs:
   lint:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        python-version: [3.8]
-        os: [macos-13]
+    runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install package
+        python-version: '3.9'
+    - name: Install dependencies
       run: |
-          python -m pip install --upgrade pip
-          python -m pip install invoke .[dev]
-    - name: invoke lint
+        pip install --upgrade "pip<=24.1" setuptools wheel
+        python -m pip install invoke .[dev]
+    - name: Run lint checks
       run: invoke lint
 
 
-  # docs:
-  #   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 }}
-  #     uses: actions/setup-python@v2
-  #     with:
-  #       python-version: ${{ matrix.python-version }}
-  #   - name: Install package
-  #     run: pip install .[dev]
-  #   - name: make docs
-  #     run: make docs
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .[dev]
+    - name: Build docs
+      run: make docs
 
 
   unit:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        os: [ubuntu-latest, macos-13, windows-latest]
+        python-version: ['3.9', '3.10', '3.11']
+        os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install package and dependencies
       run: |
           python -m pip install --upgrade pip
           python -m pip install invoke .[test]
-    - name: invoke unit
+    - name: Run unit tests
       run: invoke unit
 
 
   # minimum:
   #   runs-on: ${{ matrix.os }}
   #   strategy:
   #     matrix:
-  #       python-version: ['3.8', '3.9', '3.10', '3.11']
-  #       os: [ubuntu-20.04, macos-latest]
+  #       python-version: ['3.9']
+  #       os: [ubuntu-latest, macos-latest, windows-latest]
   #   steps:
-  #   - uses: actions/checkout@v1
+  #   - uses: actions/checkout@v4
   #   - name: Set up Python ${{ matrix.python-version }}
-  #     uses: actions/setup-python@v2
+  #     uses: actions/setup-python@v5
   #     with:
   #       python-version: ${{ matrix.python-version }}
   #   - name: Install package and dependencies
-  #     run: pip install invoke .[test]
-  #   - name: invoke minimum
+  #     run: |
+  #         python -m pip install --upgrade pip
+  #         python -m pip install invoke .[test]
+  #   - name: Run unit tests on 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:
-  #       python-version: ${{ matrix.python-version }}
-  #   - name: Install package and dependencies
-  #     run: pip install invoke jupyter matplotlib .
-  #   - name: invoke tutorials
-  #     run: invoke tutorials

MANIFEST.in

@@ -44,11 +44,9 @@ 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 '>' '=')
-
 .PHONY: install-minimum
-install-minimum: ## install the minimum supported versions of the package dependencies
-	pip install $(MINIMUM)
+install-minimum: clean-build clean-pyc ## install the package with depencencies in minimum versions
+	invoke install-minimum
 
 .PHONY: check-dependencies
 check-dependencies: ## test if there are any broken dependencies
@@ -63,14 +61,17 @@ lint: ## check style with flake8 and isort
 
 .PHONY: lint-sigllm
 lint-sigllm: ## check style with flake8 and isort
-	flake8 sigllm tests
-	isort -c --recursive sigllm tests
+	ruff check sigllm/
+	ruff format --check --diff sigllm/
+
+.PHONY: lint-tests
+lint-tests: ## 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 sigllm tests -name '*.py' | xargs autoflake --in-place --remove-all-unused-imports --remove-unused-variables
-	autopep8 --in-place --recursive --aggressive sigllm tests
-	isort --apply --atomic --recursive sigllm tests
+	invoke fix-lint
 
 
 # TEST TARGETS
@@ -93,10 +94,6 @@ test: test-unit test-readme test-tutorials ## test everything that needs test de
 .PHONY: test-minimum
 test-minimum: install-minimum check-dependencies test ## run tests using the minimum supported dependencies
 
-.PHONY: test-sigllm
-test: ## run tests quickly with the default Python
-	python -m pytest --basetemp=${ENVTMPDIR} --cov=sigllm --cov-report xml
-
 .PHONY: test-all
 test-all: ## run tests on every Python version with tox
 	tox -r -p auto
@@ -152,34 +149,34 @@ 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

Makefile

@@ -38,6 +38,8 @@
     'sphinx.ext.githubpages',
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
+    'IPython.sphinxext.ipython_console_highlighting',
+    'IPython.sphinxext.ipython_directive',
 ]
 
 ipython_execlines = [
@@ -77,7 +79,7 @@
 title = project + ' Documentation',
 copyright = '2023, MIT Data To AI Lab'
 author = 'MIT Data To AI Lab'
-description = 'Signals plus LLMs'
+description = 'LLMs for unsupervised time series anomaly detection.'
 user = 'sintel-dev'
 
 # The version info for the project you're documenting, acts as replacement