Update configurations (#51)

- updated GitHub Actions workflow: skip publishing existing versions - included ruff pre commit hook - updated dependency lock - included tests for python 3.12
jannikmi · Apr 8, 2024 · 6aa182c · 6aa182c
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "pyproject.toml"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml
@@ -22,14 +22,19 @@ jobs:
           - "3.9"
           - "3.10"
           - "3.11"
+          - "3.12"
     env:
       TOXENV: ${{ matrix.tox-env }}
       TOX_SKIP_MISSING_INTERPRETERS: False
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - name: Run pre-commit hook
+        uses: pre-commit/action@v3.0.1
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -42,16 +47,18 @@ jobs:
       - name: Run tox
         run: tox
 
-  tag_release:
-    name: tag current release
-    if: endsWith(github.ref, '/master')
-    needs: test
+  deploy:
     runs-on: ubuntu-latest
+    needs: test
+    if: endsWith(github.ref, '/master')
+    permissions:
+      id-token: write
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -61,26 +68,33 @@ jobs:
 
       - name: Fetch version
         id: fetch_version
-        run: echo "::set-output name=version_nr::$(poetry version -s)"
+        run: echo "version_nr=$(poetry version -s)" >> $GITHUB_OUTPUT
 
       - name: Build a binary wheel and a source tarball
         run: |
-          poetry build
+          poetry build --no-interaction
+
+      - name: Test PyPI Publishing
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.TEST_PYPI_DEPLOYMENT_API_KEY }}
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
 
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
+      - name: Create GitHub Release
+        id: create_gh_release
+        uses: ncipollo/release-action@v1
         env:
-          # use token provided by Actions
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           VERSION: ${{ steps.fetch_version.outputs.version_nr }}
         with:
-          tag_name: ${{env.VERSION}}
-          release_name: Release ${{env.VERSION}}
+          tag: ${{env.VERSION}}
+          name: Release ${{env.VERSION}}
           draft: false
           prerelease: false
+          skipIfReleaseExists: true
 
       - name: PyPI Publishing
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_DEPLOYMENT_API_KEY }}
+          skip-existing: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,82 +1,74 @@
 repos:
-    -   repo: https://github.com/pre-commit/pre-commit-hooks
-        rev: v4.4.0
-        hooks:
-            -   id: check-ast  # Is it valid Python?
-            -   id: debug-statements # no debugging statements used
-            -   id: trailing-whitespace
-            -   id: end-of-file-fixer
-            -   id: check-yaml
-            -   id: check-added-large-files
-            -   id: check-case-conflict
-            -   id: check-merge-conflict
-            #      - id: name-tests-test
-            -   id: check-docstring-first
-            -   id: requirements-txt-fixer
-            -   id: detect-private-key
-    #      - id: check-executables-have-shebangs
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-ast  # Is it valid Python?
+      - id: debug-statements # no debugging statements used
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      #      - id: name-tests-test
+      - id: check-docstring-first
+      - id: requirements-txt-fixer
+      - id: detect-private-key
+  #      - id: check-executables-have-shebangs
 
-    -   repo: https://github.com/pycqa/isort
-        rev: 5.12.0
-        hooks:
-            -   id: isort
-                args:
-                    - --profile=black
-                    - --filter-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5
+    hooks:
+      # linter.
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
 
-    -   repo: https://github.com/psf/black
-        rev: 23.1.0
-        hooks:
-            -   id: black
-                language_version: python3
-                args:
-                    - --line-length=120
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [ black==22.1 ]
 
-    -   repo: https://github.com/asottile/blacken-docs
-        rev: 1.13.0
-        hooks:
-            -   id: blacken-docs
-                additional_dependencies: [ black==22.1 ]
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+        exclude: (docs|tests)
+        args:
+          - --max-line-length=120
+          - --ignore=E501,W503
+        additional_dependencies:
+          - flake8-bugbear
+          - flake8-comprehensions
+          - flake8-tidy-imports
 
-    -   repo: https://github.com/pycqa/flake8
-        rev: 6.0.0
-        hooks:
-            -   id: flake8
-                exclude: (docs|tests)
-                args:
-                    - --max-line-length=120
-                    - --ignore=E501,W503
-                additional_dependencies:
-                    - flake8-bugbear
-                    - flake8-comprehensions
-                    - flake8-tidy-imports
+  #    -   repo: https://github.com/mgedmin/check-manifest
+  #        rev: "0.49"
+  #        hooks:
+  #            -   id: check-manifest
+  #                args: [ "--no-build-isolation", "--ignore",  "*.png,docs/*,paper/*,scripts/*,setup.py,publish.py,readthedocs.yml,poetry.lock" ]
+  #                additional_dependencies: [ numpy, poetry==1.3.2]
 
-#    -   repo: https://github.com/mgedmin/check-manifest
-#        rev: "0.49"
-#        hooks:
-#            -   id: check-manifest
-#                args: [ "--no-build-isolation", "--ignore",  "*.png,docs/*,paper/*,scripts/*,setup.py,publish.py,readthedocs.yml,poetry.lock" ]
-#                additional_dependencies: [ numpy, poetry==1.3.2]
+  # TODO sphinx check
+  #    -   repo: https://github.com/myint/rstcheck
+  #        rev: 'v3.3.1'
+  #        hooks:
+  #        -   id: rstcheck
 
-    # TODO sphinx check
-    #    -   repo: https://github.com/myint/rstcheck
-    #        rev: 'v3.3.1'
-    #        hooks:
-    #        -   id: rstcheck
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.2
+    hooks:
+      - id: pyupgrade
 
-    -   repo: https://github.com/asottile/pyupgrade
-        rev: v3.3.1
-        hooks:
-            -   id: pyupgrade
+  #    # very detailed linting:
+  #    -   repo: https://github.com/pycqa/pylint
+  #        rev: pylint-2.6.0
+  #        hooks:
+  #            -   id: pylint
 
-    #    # very detailed linting:
-    #    -   repo: https://github.com/pycqa/pylint
-    #        rev: pylint-2.6.0
-    #        hooks:
-    #            -   id: pylint
-
-    -   repo: https://github.com/pre-commit/mirrors-mypy
-        rev: v1.0.0
-        hooks:
-            -   id: mypy
-                exclude: ^((tests|scripts)/)
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.9.0
+    hooks:
+      - id: mypy
+        exclude: ^((tests|scripts)/)
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -54,6 +54,18 @@ idea:
 - the evaluation of subtrees is independent and could theoretically be done in parallel
     probably not worth the effort. more reasonable to just evaluate multiple polynomials in parallel
 
+3.x.x (TBA)
+__________________
+
+
+internal:
+
+- updated GitHub Actions workflow: skip publishing existing versions
+- included ruff pre commit hook
+- updated dependency lock
+- included tests for python 3.12
+
+
 3.1.0 (2023-02-15)
 __________________
 

diff --git a/Makefile b/Makefile
@@ -6,7 +6,7 @@ update:
 	poetry update
 
 install:
-	poetry install --all-extras
+	poetry install --with docs,dev --all-extras --sync
 
 VENV_NAME=multivar_horner
 venv:
@@ -17,9 +17,16 @@ hook:
 	pre-commit install
 	pre-commit run --all-files
 
-hook2:
+hookup:
 	pre-commit autoupdate
 
+test:
+	poetry run pytest
+
+tox:
+	tox
+
+
 clean:
 	rm -rf .pytest_cache .coverage coverage.xml tests/__pycache__ src/__pycache__ mlruns/ .mypyp_cache/
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -25,15 +25,15 @@
 sys.path.insert(0, os.path.join(project_root))
 
 # needed for auto document, ATTENTION: must then be installed during online build!
-import multivar_horner
+import multivar_horner  # noqa: E402 Module level import not at top of file
 
 print(multivar_horner)
 
 # -- Project information -----------------------------------------------------
 
 project = "multivar_horner"
-copyright = "2018, Jannik Michelfeit"
-author = "Jannik Michelfeit"
+copyright = "2018, Jannik Kissinger"
+author = "Jannik Kissinger"
 
 # The full version, including alpha/beta/rc tags.
 release = subprocess.getoutput("poetry version -s")

diff --git a/multivar_horner/__init__.py b/multivar_horner/__init__.py
@@ -1,5 +1,13 @@
 from multivar_horner.classes.abstract_poly import load_pickle
-from multivar_horner.classes.horner_poly import HornerMultivarPolynomial, HornerMultivarPolynomialOpt
+from multivar_horner.classes.horner_poly import (
+    HornerMultivarPolynomial,
+    HornerMultivarPolynomialOpt,
+)
 from multivar_horner.classes.regular_poly import MultivarPolynomial
 
-__all__ = ["HornerMultivarPolynomial", "MultivarPolynomial", "HornerMultivarPolynomialOpt", "load_pickle"]
+__all__ = [
+    "HornerMultivarPolynomial",
+    "MultivarPolynomial",
+    "HornerMultivarPolynomialOpt",
+    "load_pickle",
+]
diff --git a/multivar_horner/_numba_replacements.py b/multivar_horner/_numba_replacements.py
@@ -1,4 +1,4 @@
-""" 'transparent' numba functionality replacements
+"""'transparent' numba functionality replacements
 
 njit decorator
 data types

diff --git a/multivar_horner/c_evaluation.py b/multivar_horner/c_evaluation.py
@@ -36,7 +36,9 @@ def write_c_file(
     instr = "#include <math.h>\n"
     # NOTE: the coefficient array will be used to store intermediary results
     # -> copy to use independent instance of array (NO pointer to external array!)
-    func_def = f"{DOUBLE} {EVAL_FCT}({DOUBLE} x[{nr_dims}], {DOUBLE} {COEFFS}[{nr_coeffs}])"
+    func_def = (
+        f"{DOUBLE} {EVAL_FCT}({DOUBLE} x[{nr_dims}], {DOUBLE} {COEFFS}[{nr_coeffs}])"
+    )
     # declare function ("header")
     instr += f"{func_def};\n"
     # function definition

diff --git a/multivar_horner/classes/abstract_poly.py b/multivar_horner/classes/abstract_poly.py
@@ -58,16 +58,22 @@ def __init__(
         self.compute_representation: bool = compute_representation
 
         if rectify_input:
-            coefficients, exponents = rectify_construction_parameters(coefficients, exponents)
+            coefficients, exponents = rectify_construction_parameters(
+                coefficients, exponents
+            )
         validate_construction_parameters(coefficients, exponents)
         self.coefficients: np.ndarray = coefficients
         self.exponents: np.ndarray = exponents
 
         self.num_monomials: int = self.exponents.shape[0]
         self.dim: int = self.exponents.shape[1]
-        self.unused_variables = np.where(~np.any(self.exponents.astype(BOOL_DTYPE), axis=1))[0]
+        self.unused_variables = np.where(
+            ~np.any(self.exponents.astype(BOOL_DTYPE), axis=1)
+        )[0]
         self.total_degree: int = np.max(np.sum(self.exponents, axis=0))
-        self.euclidean_degree: float = np.max(np.linalg.norm(self.exponents, ord=2, axis=0))
+        self.euclidean_degree: float = np.max(
+            np.linalg.norm(self.exponents, ord=2, axis=0)
+        )
         self.maximal_degree: int = np.max(self.exponents)
         self.num_ops: int = 0
         self.representation: str
@@ -158,7 +164,9 @@ def get_partial_derivative(self, i: int, *args, **kwargs) -> "AbstractPolynomial
         # multiply the coefficients with the exponent of the i-th coordinate
         # f(x) = a x^b
         # f'(x) = ab x^(b-1)
-        new_coefficients = np.multiply(new_coefficients.flatten(), new_exponents[:, coord_index])
+        new_coefficients = np.multiply(
+            new_coefficients.flatten(), new_exponents[:, coord_index]
+        )
         new_coefficients = new_coefficients.reshape(-1, 1)
 
         # reduce the the exponent of the i-th coordinate by 1
@@ -175,7 +183,10 @@ def get_gradient(self, *args, **kwargs) -> List["AbstractPolynomial"]:
         Returns:
              the list of all partial derivatives
         """
-        return [self.get_partial_derivative(i, *args, **kwargs) for i in range(1, self.dim + 1)]
+        return [
+            self.get_partial_derivative(i, *args, **kwargs)
+            for i in range(1, self.dim + 1)
+        ]
 
     def change_coefficients(
         self,