From 0112822616c90d7efccd28211edf8eb439e9423f Mon Sep 17 00:00:00 2001 From: Venaturum Date: Mon, 24 Jun 2024 16:10:16 +1000 Subject: [PATCH 1/2] Py312 (#177) * Python 3.12 dependencies * fixes for deprecations * GH action update * remove support for Python 3.7 --- .github/workflows/ci.yml | 18 +- .github/workflows/pre-commit.yml | 4 +- docs/release_notes/changelog.rst | 3 + poetry.lock | 3870 +++++++++++++----------- pyproject.toml | 16 +- setup.cfg | 2 +- staircase/core/layering.py | 2 +- staircase/core/ops/masking.py | 8 +- staircase/core/stairs.py | 12 +- staircase/util/_decorators.py | 1 - tests/test_dates/__init__.py | 0 tests/test_dates/test_dates_slicing.py | 2 +- tests/test_dates/test_dates_stats.py | 4 +- tests/test_exceptions.py | 8 +- tests/test_floats/__init__.py | 0 tests/test_masking/__init__.py | 0 tox.ini | 29 +- 17 files changed, 2214 insertions(+), 1765 deletions(-) create mode 100644 tests/test_dates/__init__.py create mode 100644 tests/test_floats/__init__.py create mode 100644 tests/test_masking/__init__.py diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dbda4c4..bd72100 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,14 +10,14 @@ jobs: strategy: matrix: platform: [ubuntu-latest, macos-latest, windows-latest] - python-version: ['3.7', '3.8', '3.10', '3.11'] + python-version: ['3.8', '3.10', '3.11', '3.12'] defaults: run: shell: bash steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Upgrade pip @@ -43,19 +43,19 @@ jobs: run: poetry run flake8 ./staircase - name: Test with pytest run: | - poetry run pytest ./tests --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov=staircase --cov-report=xml + poetry run pytest ./tests --junitxml=junit/test-results-${{ matrix.platform }}-${{ matrix.python-version }}.xml --cov=staircase --cov-report=xml codecov - name: Upload pytest test results - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: - name: pytest-results-${{ matrix.python-version }} - path: junit/test-results-${{ matrix.python-version }}.xml + name: pytest-results-${{ matrix.platform }}-${{ matrix.python-version }} + path: junit/test-results-${{ matrix.platform }}-${{ matrix.python-version }}.xml # Use always() to always run this step to publish test results when there are test failures if: ${{ always() }} - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 with: token: ${{ secrets.CODECOV_TOKEN }} - fail_ci_if_error: true + fail_ci_if_error: false diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 5f27942..b40d34b 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -11,6 +11,6 @@ jobs: group: ${{ github.ref }}-pre-commit cancel-in-progress: ${{github.event_name == 'pull_request'}} steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v3 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 - uses: pre-commit/action@v3.0.0 diff --git a/docs/release_notes/changelog.rst b/docs/release_notes/changelog.rst index ce786bc..2c31cf9 100644 --- a/docs/release_notes/changelog.rst +++ b/docs/release_notes/changelog.rst @@ -7,6 +7,9 @@ Changelog UNRELEASED +- support for Python 3.12 added +- support for Python 3.7 removed + Please list new changes above this comment **v2.5.2 2023-07-04** diff --git a/poetry.lock b/poetry.lock index d82bf65..14f4cb0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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(>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [extras] codecov = [] [metadata] lock-version = "2.0" -python-versions = "^3.7" -content-hash = "989998c79b1e66bccca118c8f6e1142414d6a70209c2c18508e27a4e1d156b94" +python-versions = "^3.8" +content-hash = "23bb853c2f9b64720e4590dbacfc1f7c018590a41d1417e2495e6b1168d655cc" diff --git a/pyproject.toml b/pyproject.toml index 74e5ee5..ffe5ef8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,8 @@ # Poetry pyproject.toml: https://python-poetry.org/docs/pyproject/ [build-system] -requires = ["poetry>=1.0"] -build-backend = "poetry.masonry.api" +requires = ["poetry-core>=1.0.0"] +build-backend = "poetry.core.masonry.api" [tool.poetry] name = "staircase" @@ -30,11 +30,11 @@ keywords=[ classifiers=[ 'Operating System :: OS Independent', 'Intended Audience :: Science/Research', - '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', + 'Programming Language :: Python :: 3.12', 'Topic :: Scientific/Engineering', ] @@ -43,12 +43,12 @@ classifiers=[ [tool.poetry.dependencies] -python = "^3.7" +python = "^3.8" pytz = "*" typing-extensions = "^4.4.0" [[tool.poetry.dependencies.pandas]] -python = ">=3.7,<3.10" +python = ">=3.8,<3.10" version = "^1" [[tool.poetry.dependencies.pandas]] @@ -56,15 +56,15 @@ python = "^3.10" version = ">=1.3.4,<3" [[tool.poetry.dependencies.numpy]] -python = ">=3.7,<3.10" -version = "^1.15" +python = ">=3.8,<3.10" +version = "^1.16" [[tool.poetry.dependencies.numpy]] python = "^3.10" version = "^1.21.2" [[tool.poetry.dependencies.matplotlib]] -python = ">=3.7,<3.11" +python = ">=3.8,<3.11" version = ">=2" [[tool.poetry.dependencies.matplotlib]] diff --git a/setup.cfg b/setup.cfg index 874d264..29585f9 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,4 +1,4 @@ [flake8] max-line-length = 88 -ignore = E203, E231, E402, E501, F401, W503 +ignore = E203, E231, E402, E501, F401, W503, W604 exclude = docs \ No newline at end of file diff --git a/staircase/core/layering.py b/staircase/core/layering.py index 3220bc1..82c0505 100644 --- a/staircase/core/layering.py +++ b/staircase/core/layering.py @@ -115,7 +115,7 @@ def _layer_scalar(self, start, end, value): if start in deltas.index: deltas.loc[start] += value else: - deltas.loc[start] = value + deltas.loc[start] = float(value) if deltas.loc[start] == 0: deltas.drop(start, inplace=True) diff --git a/staircase/core/ops/masking.py b/staircase/core/ops/masking.py index dadeafe..9c9186f 100644 --- a/staircase/core/ops/masking.py +++ b/staircase/core/ops/masking.py @@ -173,9 +173,15 @@ def _make_data_fillna_method(self, value): data = None else: values = self._get_values().copy() + fillmethod = { + "pad": pd.Series.ffill, + "ffill": pd.Series.ffill, + "backfill": pd.Series.bfill, + "bfill": pd.Series.bfill, + }[value] if value in ("pad", "ffill") and np.isnan(values.iloc[0]): values.iloc[0] = self.initial_value - values = values.fillna(method=value) + values = fillmethod(values) if value in ("backfill", "bfill") and np.isnan(self.initial_value): initial_value = values.iloc[0] data = pd.DataFrame({"value": values}) diff --git a/staircase/core/stairs.py b/staircase/core/stairs.py index c6c19be..934ae06 100644 --- a/staircase/core/stairs.py +++ b/staircase/core/stairs.py @@ -6,6 +6,7 @@ staircase is a MIT licensed library, written in pure-Python, for modelling step functions. See :ref:`Getting Started ` for more information. """ + from __future__ import annotations import warnings @@ -33,9 +34,11 @@ def _make_deltas_from_vals(init_val, vals: pd.DataFrame) -> pd.Series: if not np.isnan(vals).any(): - result = pd.Series(np.diff((np.append([init_val], vals.values)))) + result = pd.Series( + np.diff((np.append([init_val], vals.values))), dtype="float64" + ) else: - temp = pd.Series(np.append([init_val], vals.values)) + temp = pd.Series(np.append([init_val], vals.values), dtype="float64") result = pd.Series.add( temp[pd.notnull(temp)].diff(), temp[pd.isnull(temp)], fill_value=0 )[1:] @@ -570,7 +573,10 @@ def __bool__(self) -> bool: def describe( self, where: tuple[float | int, float | int] - | list[float | int, float | int] = (-inf, inf), + | list[float | int, float | int] = ( + -inf, + inf, + ), percentiles: list[float | int] | tuple[float | int] = (25, 50, 75), ) -> pd.Series: """ diff --git a/staircase/util/_decorators.py b/staircase/util/_decorators.py index b95be1c..59d8193 100644 --- a/staircase/util/_decorators.py +++ b/staircase/util/_decorators.py @@ -6,7 +6,6 @@ class Appender: - """ A function decorator that will append an addendum to the docstring of the target function. diff --git a/tests/test_dates/__init__.py b/tests/test_dates/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_dates/test_dates_slicing.py b/tests/test_dates/test_dates_slicing.py index 6f3d2e7..b808084 100644 --- a/tests/test_dates/test_dates_slicing.py +++ b/tests/test_dates/test_dates_slicing.py @@ -5,7 +5,7 @@ # Not testing "W", it's a pain for period index -@pytest.mark.parametrize("freq_str", ["N", "U", "L", "S", "T", "H", "D", "M"]) +@pytest.mark.parametrize("freq_str", ["ns", "us", "ms", "s", "min", "h", "D", "M"]) def test_slice_month_period_range(freq_str): # GH108 date_freq = "MS" if freq_str == "M" else freq_str diff --git a/tests/test_dates/test_dates_stats.py b/tests/test_dates/test_dates_stats.py index c7079ff..10f7b73 100644 --- a/tests/test_dates/test_dates_stats.py +++ b/tests/test_dates/test_dates_stats.py @@ -397,7 +397,7 @@ def test_integral_dates_3(date_func): s1(date_func).agg( "integral", (timestamp(2020, 1, 4, date_func=date_func), None) ) - / pd.Timedelta("1 H") + / pd.Timedelta("1 h") == 108 ), "Expected integral to be 108 hours" @@ -411,7 +411,7 @@ def test_integral_dates_4(date_func): timestamp(2020, 1, 8, date_func=date_func), ), ) - / pd.Timedelta("1 H") + / pd.Timedelta("1 h") == 132 ), "Expected integral to be 132 hours" diff --git a/tests/test_exceptions.py b/tests/test_exceptions.py index 36fbc31..20dfe03 100644 --- a/tests/test_exceptions.py +++ b/tests/test_exceptions.py @@ -86,8 +86,8 @@ def test_layering_args_warning(start, end): [(1, None), (None, 1), (1, sc.inf), (-sc.inf, 1)], ) def test_layering_args_no_warning(start, end): - with pytest.warns(None) as warnings: - Stairs(start=start, end=end) + import warnings - if len(warnings) > 0: - raise AssertionError("Warnings were raised, but not expected") + with warnings.catch_warnings(): + warnings.simplefilter("error") + Stairs(start=start, end=end) diff --git a/tests/test_floats/__init__.py b/tests/test_floats/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_masking/__init__.py b/tests/test_masking/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tox.ini b/tox.ini index 2c2fa1e..895c83e 100644 --- a/tox.ini +++ b/tox.ini @@ -1,28 +1,33 @@ [tox] isolated_build=true -envlist = py{36,37,38,39,310,311}-numpy{114,115,116,117,118,119,120,121}-pandas{024,025,10,11,12,13} +envlist = + py{38}-pandas11 + py{38,39}-pandas12 + py{38,39}-pandas13 + py{38,39,310}-pandas14 + py{38,39,310}-pandas15 + py{38,39,310,311}-pandas20 + py{39,310,311}-pandas21 + py{310,311,312}-pandas22 skipdist = true [testenv] deps = matplotlib pytz + typing-extensions pytest pytest-cov - pandas024: pandas>=0.24,<0.25 - pandas025: pandas>=0.25,<1 pandas10: pandas>=1.0,<1.1 pandas11: pandas>=1.1,<1.2 pandas12: pandas>=1.2,<1.3 pandas13: pandas>=1.3,<1.4 - numpy114: numpy>=1.14,<1.15 - numpy115: numpy>=1.15,<1.16 - numpy116: numpy>=1.16,<1.17 - numpy117: numpy>=1.17,<1.18 - numpy118: numpy>=1.18,<1.19 - numpy119: numpy>=1.19,<1.20 - numpy120: numpy>=1.20,<1.21 - numpy121: numpy>=1.21,<1.22 + pandas14: pandas>=1.4,<1.5 + pandas15: pandas>=1.5,<1.6 + pandas20: pandas>=2.0,<2.1 + pandas21: pandas>=2.1,<2.2 + pandas22: pandas>=2.2,<2.3 + numpy <2 skip_install = true commands = - pytest tests/ + pytest tests/test_masking/test_masking_ne.py From b12f82d5f0037b61773463c4087a14624e010bdd Mon Sep 17 00:00:00 2001 From: staircase-dev Date: Mon, 24 Jun 2024 16:46:41 +1000 Subject: [PATCH 2/2] v2.6.0 --- docs/release_notes/changelog.rst | 5 ++++- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/release_notes/changelog.rst b/docs/release_notes/changelog.rst index 2c31cf9..aa268c2 100644 --- a/docs/release_notes/changelog.rst +++ b/docs/release_notes/changelog.rst @@ -7,10 +7,13 @@ Changelog UNRELEASED +Please list new changes above this comment + +**v2.6.0 2024-06-24** + - support for Python 3.12 added - support for Python 3.7 removed -Please list new changes above this comment **v2.5.2 2023-07-04** diff --git a/pyproject.toml b/pyproject.toml index ffe5ef8..8935e33 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "staircase" -version = "2.5.2" +version = "2.6.0" description = "A data analysis package based on modelling and manipulation of mathematical step functions. Strongly aligned with pandas." readme = "README.md" authors = ["Riley Clement "]