diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml index f57a4c368..913c8005f 100644 --- a/.github/workflows/deploy.yml +++ b/.github/workflows/deploy.yml @@ -32,7 +32,7 @@ jobs: - name: set up Python uses: actions/setup-python@v4 with: - python-version: "3.11" + python-version: "3.12" - name: install Poetry uses: snok/install-poetry@v1 diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index f2cbfa8b6..5847a8086 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -21,11 +21,13 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - poetry-test: - name: quality check and pytest with Poetry + poetry--quality-check: + name: quality check runs-on: ubuntu-latest strategy: matrix: + # Use 3.11 because pyproject-flake8 does not support Python 3.12 + # https://github.com/csachs/pyproject-flake8/issues/30 python-version: ["3.11"] steps: @@ -56,8 +58,46 @@ jobs: if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' run: poetry install --no-interaction --no-root --with test - - name: run quality check with "make test" command - run: make test + - name: run quality check with "make check" command + run: make check + + poetry-test: + name: Pytest with Poetry + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.12"] + + steps: + - name: check out repository + uses: actions/checkout@v3 + + - name: set up Python + id: setup-python + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + + - name: load cached venv if available + id: cached-poetry-dependencies + uses: actions/cache@v2 + with: + path: .venv + key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }} + + - name: install dependencies and test tools if cache does not exist + if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true' + run: poetry install --no-interaction --no-root --with test + + - name: run tests + run: poetry run pytest tests - name: upload test coverage to Codecov uses: codecov/codecov-action@v3 @@ -67,7 +107,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] steps: - name: Checkout @@ -91,7 +131,7 @@ jobs: strategy: matrix: os: ["windows-latest"] - python-version: ["3.11"] + python-version: ["3.12"] steps: - uses: actions/checkout@v3 diff --git a/covsirphy/downloading/downloader.py b/covsirphy/downloading/downloader.py index 976d8c258..6804ee645 100644 --- a/covsirphy/downloading/downloader.py +++ b/covsirphy/downloading/downloader.py @@ -23,7 +23,7 @@ class DataDownloader(Term): """ LAYERS: list[str] = [Term.ISO3, Term.PROVINCE, Term.CITY] - def __init__(self, directory: str or Path = "input", update_interval: int = 12, **kwargs) -> None: + def __init__(self, directory: str | Path = "input", update_interval: int = 12, **kwargs) -> None: self._directory = directory self._update_interval = Validator(update_interval, "update_interval").int(value_range=(0, None)) self._gis = GIS(layers=self.LAYERS, country=self.ISO3, date=self.DATE) diff --git a/covsirphy/dynamics/dynamics.py b/covsirphy/dynamics/dynamics.py index 16c0649f2..470522026 100644 --- a/covsirphy/dynamics/dynamics.py +++ b/covsirphy/dynamics/dynamics.py @@ -175,8 +175,15 @@ def register(self, data: pd.DataFrame | None = None) -> pd.DataFrame: if data is not None: new_df = Validator(data, "data").dataframe(time_index=True) new_df.index = pd.to_datetime(new_df.index).round("D") - all_df = pd.DataFrame(np.nan, index=self._df.index, columns=self._df.columns) + all_df = pd.DataFrame( + np.nan, + index=self._df.index, + columns=self._df.columns, + ) all_df[self._PH] = 0 + for col in new_df: + new_df[col] = new_df[col].astype(pd.Float64Dtype()) + all_df[col] = all_df[col].astype(pd.Float64Dtype()) all_df.update(new_df, overwrite=True) if all_df.loc[self._first, self._SIRF].isna().any(): raise EmptyError( @@ -333,7 +340,7 @@ def track(self) -> pd.DataFrame: """ df = self.summary() df[self.DATE] = df[[self.START, self.END]].apply( - lambda x: pd.date_range(start=x[0], end=x[1], freq="D"), axis=1) + lambda x: pd.date_range(start=x[self.START], end=x[self.END], freq="D"), axis=1) return df.explode(self.DATE).set_index(self.DATE).drop([self.START, self.END], axis=1) def simulate(self, model_specific: bool = False) -> pd.DataFrame: @@ -473,13 +480,16 @@ def estimate_params(self, metric: str = "RMSLE", digits: int | None = None, n_jo config.info(f"\n<{self._model._NAME}: parameter estimation>") config.info(f"Running optimization with {n_jobs_validated} CPUs...") stopwatch = StopWatch() + # p-tqdm with Python 3.12: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. + warnings.filterwarnings("ignore", category=DeprecationWarning) results = p_umap(est_f, phase_dataframes, num_cpus=n_jobs_validated) config.info(f"Completed optimization. Total: {stopwatch.stop_show()}\n") est_df = pd.concat(results, sort=True, axis=0) est_df = est_df.loc[:, [*self._parameters, metric, self.TRIALS, self.RUNTIME]].ffill().convert_dtypes() # Update registered parameter values r_df = self.register() - warnings.filterwarnings("ignore", category=FutureWarning) + for col in self._parameters: + r_df[col] = r_df[col].astype(pd.Float64Dtype()) r_df.update(est_df, overwrite=True) self.register(data=r_df) return est_df diff --git a/covsirphy/engineering/_cleaner.py b/covsirphy/engineering/_cleaner.py index 179540d0a..3fef70b37 100644 --- a/covsirphy/engineering/_cleaner.py +++ b/covsirphy/engineering/_cleaner.py @@ -63,7 +63,7 @@ def resample(self, date_range=None): end_date, name="the second date of @date_range").date(default=df[self._date].max(), value_range=(start, None)) df = df[df[self._date].between(start, end, inclusive="both")] grouped = df.set_index(self._date).groupby(self._layers, as_index=False, observed=True) - df = grouped.resample("D").ffill() + df = grouped[list(set(df.columns) - set([self._date]))].resample("D").ffill() self._df = df.reset_index().drop("level_0", errors="ignore", axis=1) def fillna(self): diff --git a/covsirphy/science/_autots.py b/covsirphy/science/_autots.py index d5a50505a..b341e9171 100644 --- a/covsirphy/science/_autots.py +++ b/covsirphy/science/_autots.py @@ -22,6 +22,7 @@ class _AutoTSHandler(Term): """ def __init__(self, Y, days, seed, **kwargs): + warnings.simplefilter("ignore", SyntaxWarning) from autots import AutoTS # https://github.com/lisphilar/covid19-sir/issues/1265 self._Y = Validator(Y, "Y").dataframe(time_index=True, empty_ok=False) self._days = Validator(days, name="days").int(value_range=(1, None)) diff --git a/covsirphy/visualization/vbase.py b/covsirphy/visualization/vbase.py index b90777394..a20a05a9a 100644 --- a/covsirphy/visualization/vbase.py +++ b/covsirphy/visualization/vbase.py @@ -2,6 +2,7 @@ from inspect import signature import sys import matplotlib +from matplotlib.axes import Axes if not hasattr(sys, "ps1"): matplotlib.use("Agg") from matplotlib import pyplot as plt @@ -91,7 +92,7 @@ def ax(self): @ax.setter def ax(self, ax): - self._ax = Validator(ax, "ax").instance(matplotlib.axes.Axes) + self._ax = Validator(ax, "ax").instance(Axes) def plot(self): """Method for plotting. This will be defined in child classes. diff --git a/example/demo.py b/example/demo.py index c1c150076..3a475e36c 100644 --- a/example/demo.py +++ b/example/demo.py @@ -16,7 +16,7 @@ def main(geo="Japan", file_prefix="jpn"): geo (str): location identifier file_prefix (str): prefix of the filenames """ - print("This script works with version >= 2.26.0-eta") + print("This script works with version >= 3.0.0") print(cs.get_version()) code_path = Path(__file__) output_dir = code_path.with_name("output").joinpath(f"{code_path.stem}_{file_prefix}") diff --git a/example/output/demo_jpn/01_actual.png b/example/output/demo_jpn/01_actual.png index f1d04ad6b..e9215b581 100644 Binary files a/example/output/demo_jpn/01_actual.png and b/example/output/demo_jpn/01_actual.png differ diff --git a/example/output/demo_jpn/02_segmentation.png b/example/output/demo_jpn/02_segmentation.png index f7f858e01..7f0076a57 100644 Binary files a/example/output/demo_jpn/02_segmentation.png and b/example/output/demo_jpn/02_segmentation.png differ diff --git a/example/output/demo_jpn/03_simulate.png b/example/output/demo_jpn/03_simulate.png index 79b1ccc96..0013c73e1 100644 Binary files a/example/output/demo_jpn/03_simulate.png and b/example/output/demo_jpn/03_simulate.png differ diff --git a/example/output/demo_jpn/04_predicted.png b/example/output/demo_jpn/04_predicted.png index 2762c5e40..cec5a2f50 100644 Binary files a/example/output/demo_jpn/04_predicted.png and b/example/output/demo_jpn/04_predicted.png differ diff --git a/example/output/demo_jpn/05_Rt.png b/example/output/demo_jpn/05_Rt.png index cfe43dd6f..d3c80f37b 100644 Binary files a/example/output/demo_jpn/05_Rt.png and b/example/output/demo_jpn/05_Rt.png differ diff --git a/example/output/demo_jpn/06_confirmed.png b/example/output/demo_jpn/06_confirmed.png index d902e2a97..4180e45ca 100644 Binary files a/example/output/demo_jpn/06_confirmed.png and b/example/output/demo_jpn/06_confirmed.png differ diff --git a/poetry.lock b/poetry.lock index 2b76f49ba..937607945 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,71 +2,71 @@ [[package]] name = "adjusttext" -version = "0.8" +version = "1.0.4" description = "Iteratively adjust text position in matplotlib plots to minimize overlaps" optional = false python-versions = "*" files = [ - {file = "adjustText-0.8-py3-none-any.whl", hash = "sha256:6da99f9d739c496f79346753a3fcadb6354d8d09699cde112fed46cfb837d271"}, - {file = "adjustText-0.8.tar.gz", hash = "sha256:bb0682bb53abb626d6afc9c1db108ccb67f2c35ddc8d20ac6a802c756c07ee17"}, + {file = "adjustText-1.0.4-py3-none-any.whl", hash = "sha256:7bb022044c1de9c1e41c3f713a857be85f1e0fc4c1d1743af9c62a827de22588"}, + {file = "adjustText-1.0.4.tar.gz", hash = "sha256:b8611b2b3660307165aabdadbdc6f9a85d02f2912989fe209379f7e699e10b83"}, ] [package.dependencies] matplotlib = "*" numpy = "*" +scipy = "*" [[package]] name = "alabaster" -version = "0.7.13" -description = "A configurable sidebar-enabled Sphinx theme" +version = "0.7.16" +description = "A light, configurable Sphinx theme" optional = false -python-versions = ">=3.6" +python-versions = ">=3.9" files = [ - {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, - {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, + {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, + {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, ] [[package]] name = "alembic" -version = "1.12.0" +version = "1.13.1" description = "A database migration tool for SQLAlchemy." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "alembic-1.12.0-py3-none-any.whl", hash = "sha256:03226222f1cf943deee6c85d9464261a6c710cd19b4fe867a3ad1f25afda610f"}, - {file = "alembic-1.12.0.tar.gz", hash = "sha256:8e7645c32e4f200675e69f0745415335eb59a3663f5feb487abfa0b30c45888b"}, + {file = "alembic-1.13.1-py3-none-any.whl", hash = "sha256:2edcc97bed0bd3272611ce3a98d98279e9c209e7186e43e75bbb1b2bdfdbcc43"}, + {file = "alembic-1.13.1.tar.gz", hash = "sha256:4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595"}, ] [package.dependencies] -importlib-metadata = {version = "*", markers = "python_version < \"3.9\""} -importlib-resources = {version = "*", markers = "python_version < \"3.9\""} Mako = "*" SQLAlchemy = ">=1.3.0" typing-extensions = ">=4" [package.extras] -tz = ["python-dateutil"] +tz = ["backports.zoneinfo"] [[package]] name = "anyio" -version = "4.0.0" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, - {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, + {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, + {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.22)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "appnope" @@ -138,34 +138,40 @@ tests = ["pytest"] [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, ] [package.dependencies] python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "asttokens" -version = "2.4.0" +version = "2.4.1" description = "Annotate AST trees with source code positions" optional = false python-versions = "*" files = [ - {file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"}, - {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"}, + {file = "asttokens-2.4.1-py2.py3-none-any.whl", hash = "sha256:051ed49c3dcae8913ea7cd08e46a606dba30b79993209636c4875bc1d637bc24"}, + {file = "asttokens-2.4.1.tar.gz", hash = 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options" optional = false python-versions = ">=3.8" files = [ - {file = "websocket-client-1.6.2.tar.gz", hash = "sha256:53e95c826bf800c4c465f50093a8c4ff091c7327023b10bfaff40cf1ef170eaa"}, - {file = "websocket_client-1.6.2-py3-none-any.whl", hash = "sha256:ce54f419dfae71f4bdba69ebe65bf7f0a93fe71bc009ad3a010aacc3eebad537"}, + {file = "websocket-client-1.7.0.tar.gz", hash = "sha256:10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6"}, + {file = "websocket_client-1.7.0-py3-none-any.whl", hash = "sha256:f4c3d22fec12a2461427a29957ff07d35098ee2d976d3ba244e688b8b4057588"}, ] [package.extras] @@ -4555,20 +4564,20 @@ dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"] [[package]] name = "zipp" -version = "3.16.2" +version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"}, - 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"d901e725aafbeca2b3100c630192da6311729a0fad3e10cd631151f9e68a518d" +python-versions = "^3.9,<3.13" +content-hash = "f981279b4454a90adc03782debaa8847f8843809723bce94f919a1e51bd921d2" diff --git a/pyproject.toml b/pyproject.toml index 1ec97023c..2bc0ced16 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,37 +21,37 @@ classifiers = [ [tool.poetry.dependencies] # `poetry install` installs all dependencies, including optional ones # `poetry install --only main` install only main dependencies -python = "^3.8,<3.12" -numpy = "^1.23.3" -optuna = "^3.0.1" -pandas = "^2.0.0" -pyarrow = ">=9,<15" +python = "^3.9,<3.13" +numpy = "^1.26.3" +optuna = "^3.5.0" +pandas = "^2.2.0" +pyarrow = "^15.0.0" tabulate = "^0.9.0" -scipy = "^1.9.3" -ruptures = "^1.1.7" -matplotlib = "^3.6.1" -country-converter = ">=0.7.7,<1.3.0" -geopandas = ">=0.11.1,<0.14.0" -Unidecode = "^1.3.4" -AutoTS = ">=0.5,<0.7" +scipy = "^1.12.0" +ruptures = "^1.1.9" +matplotlib = "^3.8.2" +country-converter = "^1.2.0" +geopandas = "^0.14.3" +Unidecode = "^1.3.8" +AutoTS = "^0.6.10" p-tqdm = "^1.4.0" -pca = ">=1.8.3,<3.0.0" -loguru = ">=0.6,<0.8" -requests = "^2.28.1" -typing-extensions = "^4.4.0" +pca = "^2.0.5" +loguru = "^0.7.2" +requests = "^2.31.0" +typing-extensions = "^4.9.0" [tool.poetry.group.test] # poetry install --with test optional = true [tool.poetry.group.test.dependencies] -autopep8 = ">=1.7,<3.0" -flake8 = "^5.0.4" -pyproject-flake8 = "^5.0.4.post1" -deptry = "0.12.0" -pyright = "^1.1.275" -pytest = "^7.2.0" +autopep8 = "^2.0.4" +flake8 = "^6.1.0" +pyproject-flake8 = "^6.1.0" +deptry = "^0.12.0" +pyright = "^1.1.349" +pytest = "^8.0.0" pytest-profiling = "^1.7.0" -pytest-cov = ">=3,<5" +pytest-cov = "^4.1.0" tuna = "^0.5.11" [tool.poetry.group.docs] @@ -59,23 +59,22 @@ tuna = "^0.5.11" optional = true [tool.poetry.group.docs.dependencies] jupyter = "^1.0.0" -ipykernel = "^6.15.3" -ipywidgets = "^8.0.2" -docutils = "0.19" -Sphinx = "^5.2.3" -sphinx-rtd-theme = ">=1,<3" +ipykernel = "^6.29.0" +ipywidgets = "^8.1.1" +docutils = "^0.20.1" +Sphinx = "^7.2.6" +sphinx-rtd-theme = "^2.0.0" sphinxcontrib-seqdiag = "^3.0.0" -sphinx-copybutton = "^0.5.0" -nbsphinx = ">=0.8.9,<0.10.0" -Pillow = ">=9.2,<11.0" -myst-parser = ">=0.18,<1.1" -sympy = "^1.11.1" -sphinx = "^5.2.3" -sphinx-autodoc-typehints = "^1.19.4" - +sphinx-copybutton = "^0.5.2" +nbsphinx = "^0.9.3" +Pillow = "^10.2.0" +myst-parser = "^2.0.0" +sympy = "^1.12.0" +sphinx = "^7.2.6" +sphinx-autodoc-typehints = "^1.25.3" [tool.poetry.group.data.dependencies] -openpyxl = "^3.1.1" +openpyxl = "^3.1.2" [build-system] requires = ["poetry-core>=1.0.0"] @@ -94,12 +93,21 @@ filterwarnings = ["error", "ignore::pytest.PytestDeprecationWarning"] addopts = "--cov=covsirphy --cov-report=xml --cov-report=term-missing -vv --no-cov-on-fail -p no:cacheprovider --durations=1 --maxfail=1" [tool.deptry] -ignore_transitive = ['urllib3'] -ignore_unused = ['pyarrow', 'tabulate', 'requests'] -exclude = ['tests', '.venv', 'example', 'docs'] +exclude = ["tests", ".venv", "example", "docs"] + +[tool.deptry.per_rule_ignores] +DEP003 = ["urllib3"] +DEP002 = ["pyarrow", "tabulate", "requests"] + [tool.pyright] include = ["covsirphy"] +reportArgumentType = false +reportAttributeAccessIssue = false +reportCallIssue = false +reportGeneralTypeIssues = false +reportIncompatibleMethodOverride = false +reportOperatorIssue = false reportOptionalMemberAccess = false +reportReturnType = false reportUnboundVariable = false -reportGeneralTypeIssues = false diff --git a/tests/conftest.py b/tests/conftest.py index f9a8c5774..4f79560d5 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,4 +1,7 @@ from pathlib import Path +import warnings + +warnings.simplefilter("ignore", DeprecationWarning) import pandas as pd import pytest