Merge pull request #1593 from lisphilar/issue1592

Drop Python 3.8 and add Python 3.12 support

.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

.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

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)

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

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):

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))

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.

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}")