pastastore 1.2.2__py3-none-any.whl → 1.3.0__py3-none-any.whl

pastastore/__init__.py

@@ -1,10 +1,11 @@
-from . import connectors, util
-from .connectors import (
+# ruff: noqa: F401
+from pastastore import connectors, util
+from pastastore.connectors import (
     ArcticConnector,
     ArcticDBConnector,
     DictConnector,
     PasConnector,
     PystoreConnector,
 )
-from .store import PastaStore
-from .version import __version__
+from pastastore.store import PastaStore
+from pastastore.version import __version__

pastastore/base.py

@@ -11,10 +11,10 @@ import pastas as ps
 from numpy import isin
 from packaging.version import parse as parse_version
 from pastas.io.pas import PastasEncoder
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
-from .util import ItemInLibraryException, _custom_warning, validate_names
-from .version import PASTAS_LEQ_022
+from pastastore.util import ItemInLibraryException, _custom_warning, validate_names
+from pastastore.version import PASTAS_LEQ_022
 
 FrameorSeriesUnion = Union[pd.DataFrame, pd.Series]
 warnings.showwarning = _custom_warning
@@ -934,13 +934,24 @@ class BaseConnector(ABC):
             )
             if ui.lower() != "y":
                 return
-        names = self._parse_names(None, libname)
-        for name in (
-            tqdm(names, desc=f"Deleting items from {libname}") if progressbar else names
-        ):
-            self._del_item(libname, name)
-        self._clear_cache(libname)
-        print(f"Emptied library {libname} in {self.name}: " f"{self.__class__}")
+
+        if libname == "models":
+            # also delete linked modelnames linked to oseries
+            libs = ["models", "oseries_models"]
+        else:
+            libs = [libname]
+
+        # delete items and clear caches
+        for libname in libs:
+            names = self._parse_names(None, libname)
+            for name in (
+                tqdm(names, desc=f"Deleting items from {libname}")
+                if progressbar
+                else names
+            ):
+                self._del_item(libname, name)
+            self._clear_cache(libname)
+            print(f"Emptied library {libname} in {self.name}: " f"{self.__class__}")
 
     def _iter_series(self, libname: str, names: Optional[List[str]] = None):
         """Internal method iterate over time series in library.

pastastore/connectors.py

@@ -8,8 +8,8 @@ from typing import Dict, Optional, Union
 import pandas as pd
 from pastas.io.pas import PastasEncoder, pastas_hook
 
-from .base import BaseConnector, ConnectorUtil, ModelAccessor
-from .util import _custom_warning
+from pastastore.base import BaseConnector, ConnectorUtil, ModelAccessor
+from pastastore.util import _custom_warning
 
 FrameorSeriesUnion = Union[pd.DataFrame, pd.Series]
 warnings.showwarning = _custom_warning

pastastore/plotting.py

@@ -14,9 +14,6 @@ follows::
     ax = pstore.maps.oseries()
     pstore.maps.add_background_map(ax)  # for adding a background map
 """
-
-from collections.abc import Iterable
-
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -96,15 +93,11 @@ class Plots:
 
         if ax is None:
             if split:
-                fig, axes = plt.subplots(len(names), 1, sharex=True, figsize=figsize)
+                _, axes = plt.subplots(len(names), 1, sharex=True, figsize=figsize)
             else:
-                fig, axes = plt.subplots(1, 1, figsize=figsize)
+                _, axes = plt.subplots(1, 1, figsize=figsize)
         else:
             axes = ax
-            if isinstance(axes, Iterable):
-                fig = axes[0].figure
-            else:
-                fig = axes.figure
 
         tsdict = self.pstore.conn._get_series(
             libname, names, progressbar=progressbar, squeeze=False
@@ -397,20 +390,31 @@ class Plots:
                     linewidth=0,
                     rasterized=True,
                 )
+
         # make a colorbar in an ax on the
         # right side, then set the current axes to ax again
         cb = fig.colorbar(pc, ax=ax, cax=cax, extend="both")
         cb.set_ticks(bounds)
         cb.ax.set_yticklabels(labels)
         cb.ax.minorticks_off()
+
         if set_yticks:
-            ax.set_yticks(np.arange(0.5, len(series) + 0.5))
+            ax.set_yticks(np.arange(0.5, len(series) + 0.5), minor=False)
+            ax.set_yticks(np.arange(0, len(series) + 1), minor=True)
             if names is None:
                 names = [s.name for s in series]
             ax.set_yticklabels(names)
+
+            for tick in ax.yaxis.get_major_ticks():  # don't show major ytick marker
+                tick.tick1line.set_visible(False)
+
+            ax.grid(True, which="minor", axis="y")
+            ax.grid(True, which="major", axis="x")
+
         else:
             ax.set_ylabel("Timeseries (-)")
-        ax.grid(True)
+            ax.grid(True, which="both")
+            ax.grid(True, which="both")
 
         return ax
 
@@ -712,6 +716,7 @@ class Maps:
     def modelstat(
         self,
         statistic,
+        modelnames=None,
         label=True,
         adjust=False,
         cmap="viridis",
@@ -728,6 +733,8 @@ class Maps:
         ----------
         statistic: str
             name of the statistic, e.g. "evp" or "aic"
+        modelnames : list of str, optional
+            list of modelnames to include
         label: bool, optional
             label points, by default True
         adjust: bool, optional
@@ -757,7 +764,9 @@ class Maps:
         --------
         self.add_background_map
         """
-        statsdf = self.pstore.get_statistics([statistic], progressbar=False).to_frame()
+        statsdf = self.pstore.get_statistics(
+            [statistic], modelnames=modelnames, progressbar=False
+        ).to_frame()
 
         statsdf["oseries"] = [
             self.pstore.get_models(m, return_dict=True)["oseries"]["name"]

pastastore/store.py

@@ -8,11 +8,13 @@ import pandas as pd
 import pastas as ps
 from packaging.version import parse as parse_version
 from pastas.io.pas import pastas_hook
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
-from .plotting import Maps, Plots
-from .util import _custom_warning
-from .yaml_interface import PastastoreYAML
+from pastastore.base import BaseConnector
+from pastastore.connectors import DictConnector
+from pastastore.plotting import Maps, Plots
+from pastastore.util import _custom_warning
+from pastastore.yaml_interface import PastastoreYAML
 
 FrameorSeriesUnion = Union[pd.DataFrame, pd.Series]
 warnings.showwarning = _custom_warning
@@ -38,14 +40,19 @@ class PastaStore:
         name of the PastaStore, by default takes the name of the Connector object
     """
 
-    def __init__(self, connector, name: str = None):
+    def __init__(
+        self,
+        connector: Optional[BaseConnector] = None,
+        name: Optional[str] = None,
+    ):
         """Initialize PastaStore for managing pastas time series and models.
 
         Parameters
         ----------
-        connector : Connector object
-            object that provides the interface to the
-            database
+        connector : Connector object, optional
+            object that provides the connection to the database. Default is None, which
+            will create a DictConnector. This default Connector does not store data on
+            disk.
         name : str, optional
             name of the PastaStore, if not provided uses the Connector name
         """
@@ -53,6 +60,8 @@ class PastaStore:
             raise DeprecationWarning(
                 "PastaStore expects the connector as the first argument since v1.1!"
             )
+        if connector is None:
+            connector = DictConnector("pastas_db")
         self.conn = connector
         self.name = name if name is not None else self.conn.name
         self._register_connector_methods()
@@ -300,6 +309,81 @@ class PastaStore:
             data = pd.concat([data, series], axis=0)
         return data
 
+    def get_signatures(
+        self,
+        signatures=None,
+        names=None,
+        libname="oseries",
+        progressbar=False,
+        ignore_errors=False,
+    ):
+        """Get groundwater signatures. NaN-values are returned when the
+        signature could not be computed.
+
+        Parameters
+        ----------
+        signatures : list of str, optional
+            list of groundwater signatures to compute, if None all groundwater
+            signatures in ps.stats.signatures.__all__ are used, by default None
+        names : str, list of str, or None, optional
+            names of the time series, by default None which
+            uses all the time series in the library
+        libname : str
+            name of the library containing the time series
+            ('oseries' or 'stresses'), by default "oseries"
+        progressbar : bool, optional
+            show progressbar, by default False
+        ignore_errors : bool, optional
+            ignore errors when True, i.e. when non-existent timeseries is
+            encountered in names, by default False
+
+        Returns
+        -------
+        signatures_df : pandas.DataFrame
+            DataFrame containing the signatures (columns) per time series (rows)
+        """
+        names = self.conn._parse_names(names, libname=libname)
+
+        if signatures is None:
+            signatures = ps.stats.signatures.__all__.copy()
+
+        # create dataframe for results
+        signatures_df = pd.DataFrame(index=names, columns=signatures, data=np.nan)
+
+        # loop through oseries names
+        desc = "Get groundwater signatures"
+        for name in tqdm(names, desc=desc) if progressbar else names:
+            try:
+                if libname == "oseries":
+                    s = self.conn.get_oseries(name)
+                else:
+                    s = self.conn.get_stresses(name)
+            except Exception as e:
+                if ignore_errors:
+                    signatures_df.loc[name, :] = np.nan
+                    continue
+                else:
+                    raise e
+
+            try:
+                i_signatures = ps.stats.signatures.summary(s.squeeze(), signatures)
+            except Exception as e:
+                if ignore_errors:
+                    i_signatures = []
+                    for signature in signatures:
+                        try:
+                            sign_val = getattr(ps.stats.signatures, signature)(
+                                s.squeeze()
+                            )
+                        except Exception as _:
+                            sign_val = np.nan
+                        i_signatures.append(sign_val)
+                else:
+                    raise e
+            signatures_df.loc[name, signatures] = i_signatures
+
+        return signatures_df
+
     def get_tmin_tmax(self, libname, names=None, progressbar=False):
         """Get tmin and tmax for time series.
 
@@ -334,6 +418,23 @@ class PastaStore:
             tmintmax.loc[n, "tmax"] = s.last_valid_index()
         return tmintmax
 
+    def get_extent(self, libname, names=None, buffer=0.0):
+        names = self.conn._parse_names(names, libname=libname)
+        if libname in ["oseries", "stresses"]:
+            df = getattr(self, libname)
+        elif libname == "models":
+            df = self.oseries
+        else:
+            raise ValueError(f"Cannot get extent for library '{libname}'.")
+
+        extent = [
+            df.loc[names, "x"].min() - buffer,
+            df.loc[names, "x"].max() + buffer,
+            df.loc[names, "y"].min() - buffer,
+            df.loc[names, "y"].max() + buffer,
+        ]
+        return extent
+
     def get_parameters(
         self,
         parameters: Optional[List[str]] = None,
@@ -428,13 +529,13 @@ class PastaStore:
 
         modelnames = self.conn._parse_names(modelnames, libname="models")
 
-        # create dataframe for results
-        s = pd.DataFrame(index=modelnames, columns=statistics, data=np.nan)
-
         # if statistics is str
         if isinstance(statistics, str):
             statistics = [statistics]
 
+        # create dataframe for results
+        s = pd.DataFrame(index=modelnames, columns=statistics, data=np.nan)
+
         # loop through model names
         desc = "Get model statistics"
         for mlname in tqdm(modelnames, desc=desc) if progressbar else modelnames:
@@ -836,7 +937,7 @@ class PastaStore:
     def from_zip(
         cls,
         fname: str,
-        conn,
+        conn: Optional[BaseConnector] = None,
         storename: Optional[str] = None,
         progressbar: bool = True,
     ):
@@ -846,8 +947,9 @@ class PastaStore:
         ----------
         fname : str
             pathname of zipfile
-        conn : Connector object
-            connector for storing loaded data
+        conn : Connector object, optional
+            connector for storing loaded data, default is None which creates a
+            DictConnector. This Connector does not store data on disk.
         storename : str, optional
             name of the PastaStore, by default None, which
             defaults to the name of the Connector.
@@ -861,6 +963,9 @@ class PastaStore:
         """
         from zipfile import ZipFile
 
+        if conn is None:
+            conn = DictConnector("pastas_db")
+
         with ZipFile(fname, "r") as archive:
             namelist = [
                 fi for fi in archive.namelist() if not fi.endswith("_meta.json")
@@ -868,7 +973,7 @@ class PastaStore:
             for f in tqdm(namelist, desc="Reading zip") if progressbar else namelist:
                 libname, fjson = os.path.split(f)
                 if libname in ["stresses", "oseries"]:
-                    s = pd.read_json(archive.open(f), orient="columns")
+                    s = pd.read_json(archive.open(f), dtype=float, orient="columns")
                     if not isinstance(s.index, pd.DatetimeIndex):
                         s.index = pd.to_datetime(s.index, unit="ms")
                     s = s.sort_index()
@@ -983,9 +1088,45 @@ class PastaStore:
                     structure.loc[mlnam, pnam] = 1
                     structure.loc[mlnam, enam] = 1
                 elif "stress" in sm:
-                    for s in sm["stress"]:
+                    smstress = sm["stress"]
+                    if isinstance(smstress, dict):
+                        smstress = [smstress]
+                    for s in smstress:
                         structure.loc[mlnam, s["name"]] = 1
         if dropna:
             return structure.dropna(how="all", axis=1)
         else:
             return structure
+
+    def apply(self, libname, func, names=None, progressbar=True):
+        """Apply function to items in library.
+
+        Supported libraries are oseries, stresses, and models.
+
+        Parameters
+        ----------
+        libname : str
+            library name, supports "oseries", "stresses" and "models"
+        func : callable
+            function that accepts items from one of the supported libraries as input
+        names : str, list of str, optional
+            apply function to these names, by default None which loops over all stored
+            items in library
+        progressbar : bool, optional
+            show progressbar, by default True
+
+        Returns
+        -------
+        dict
+            dict of results of func, with names as keys and results as values
+        """
+        names = self.conn._parse_names(names, libname)
+        result = {}
+        if libname not in ("oseries", "stresses", "models"):
+            raise ValueError(
+                "'libname' must be one of ['oseries', 'stresses', 'models']!"
+            )
+        getter = getattr(self.conn, f"get_{libname}")
+        for n in tqdm(names) if progressbar else names:
+            result[n] = func(getter(n))
+        return result

pastastore/util.py

@@ -6,9 +6,9 @@ import pandas as pd
 from numpy.lib._iotools import NameValidator
 from pandas.testing import assert_series_equal
 from pastas.stats.tests import runs_test, stoffer_toloi
-from tqdm import tqdm
+from tqdm.auto import tqdm
 
-from .version import PASTAS_LEQ_022
+from pastastore.version import PASTAS_LEQ_022
 
 
 def _custom_warning(message, category=UserWarning, filename="", lineno=-1, *args):
@@ -704,6 +704,8 @@ def frontiers_checks(
                         )
                 else:
                     tmem = ml.get_response_tmax(sm_name)
+                    if tmem is None:  # no rfunc in stressmodel
+                        tmem = 0
                     check_tmem_passed = tmem < len_oseries_calib / 2
                     checks.loc[f"calib_period > 2*t_mem_95%: {sm_name}", :] = (
                         tmem,
@@ -736,23 +738,30 @@ def frontiers_checks(
                             "(unit head)/(unit well stress)",
                             check_gain_passed,
                         )
+                    continue
+                elif sm._name == "LinearTrend":
+                    gain = ml.parameters.loc[f"{sm_name}_a", "optimal"]
+                    gain_std = ml.parameters.loc[f"{sm_name}_a", "stderr"]
+                elif sm._name == "StepModel":
+                    gain = ml.parameters.loc[f"{sm_name}_d", "optimal"]
+                    gain_std = ml.parameters.loc[f"{sm_name}_d", "stderr"]
                 else:
                     gain = ml.parameters.loc[f"{sm_name}_A", "optimal"]
                     gain_std = ml.parameters.loc[f"{sm_name}_A", "stderr"]
-                    if gain_std is None:
-                        gain_std = np.nan
-                        check_gain_passed = pd.NA
-                    elif np.isnan(gain_std):
-                        check_gain_passed = pd.NA
-                    else:
-                        check_gain_passed = np.abs(gain) > 2 * gain_std
+
+                if gain_std is None:
+                    gain_std = np.nan
+                    check_gain_passed = pd.NA
+                elif np.isnan(gain_std):
+                    check_gain_passed = pd.NA
+                else:
                     check_gain_passed = np.abs(gain) > 2 * gain_std
-                    checks.loc[f"gain > 2*std: {sm_name}", :] = (
-                        gain,
-                        2 * gain_std,
-                        "(unit head)/(unit well stress)",
-                        check_gain_passed,
-                    )
+                checks.loc[f"gain > 2*std: {sm_name}", :] = (
+                    gain,
+                    2 * gain_std,
+                    "(unit head)/(unit well stress)",
+                    check_gain_passed,
+                )
 
         # Check 5 - Parameter Bounds
         if check5_parambounds:

pastastore/version.py

@@ -4,4 +4,4 @@ from packaging.version import parse as parse_version
 PASTAS_VERSION = parse_version(ps.__version__)
 PASTAS_LEQ_022 = PASTAS_VERSION <= parse_version("0.22.0")
 
-__version__ = "1.2.2"
+__version__ = "1.3.0"

pastastore/yaml_interface.py

@@ -2,14 +2,14 @@ import datetime
 import logging
 import os
 from copy import deepcopy
-from typing import Dict, List, Optional, Union
+from typing import Any, Dict, List, Optional, Union
 
 import numpy as np
 import pandas as pd
 import pastas as ps
 import yaml
 
-from .version import PASTAS_LEQ_022
+from pastastore.version import PASTAS_LEQ_022
 
 ps.logger.setLevel("ERROR")
 
@@ -17,7 +17,7 @@ logging.basicConfig(level="INFO")
 logger = logging.getLogger(__name__)
 
 
-def _convert_dict_dtypes_for_yaml(d: Dict):
+def _convert_dict_dtypes_for_yaml(d: Dict[str, Any]):
     """Internal method to convert dictionary values for storing in YAML format.
 
     Parameters

{pastastore-1.2.2.dist-info → pastastore-1.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pastastore
-Version: 1.2.2
+Version: 1.3.0
 Summary: Tools for managing Pastas time series models.
 Author: D.A. Brakenhoff
 Maintainer-email: "D.A. Brakenhoff" <d.brakenhoff@artesia-water.nl>, "R. Calje" <r.calje@artesia-water.nl>, "M.A. Vonk" <m.vonk@artesia-water.nl>
@@ -50,8 +50,8 @@ Classifier: Topic :: Scientific/Engineering :: Hydrology
 Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pastas (>=0.13)
-Requires-Dist: tqdm (>=4.36)
+Requires-Dist: pastas >=0.13
+Requires-Dist: tqdm >=4.36
 Requires-Dist: pyyaml
 Provides-Extra: arctic
 Requires-Dist: arctic ; extra == 'arctic'
@@ -75,7 +75,7 @@ Requires-Dist: contextily ; extra == 'optional'
 Requires-Dist: pyproj ; extra == 'optional'
 Requires-Dist: adjustText ; extra == 'optional'
 Provides-Extra: pystore
-Requires-Dist: fsspec (>=0.3.3) ; extra == 'pystore'
+Requires-Dist: fsspec >=0.3.3 ; extra == 'pystore'
 Requires-Dist: python-snappy ; extra == 'pystore'
 Requires-Dist: dask[dataframe] ; extra == 'pystore'
 Provides-Extra: test

pastastore-1.3.0.dist-info/RECORD

@@ -0,0 +1,14 @@
+pastastore/__init__.py,sha256=GZvAtp_p3y2bOlcuLG2-jSHrYd72bIMDdBA5Wcy-diU,283
+pastastore/base.py,sha256=nPIIiDHJMDUlvPaE2dftjPRxAM2kFtC8kHXvmB9Ayw0,62631
+pastastore/connectors.py,sha256=QH6jvnhIIivn1Is9ThBeMAEcJBVnfcK46pJClGMdiBA,28747
+pastastore/datasets.py,sha256=f-92WOh2ROCxOVvKGHXjnzd66Q7hO_-BtXRfMKwg1KU,6640
+pastastore/plotting.py,sha256=3WTnnOfFZlt4PEsqDzNLFzFOJBtDb0vmwx4ZzdZI_xo,42120
+pastastore/store.py,sha256=vIPnq-XYU-HstweWa4RSuNHotYLTBNVQjljt6SH9fWY,39529
+pastastore/util.py,sha256=aVIrAtfJPatH7BfASChzwHsoug1KDthcgHlEbxl1-uk,30678
+pastastore/version.py,sha256=JXttE_aGZnNgRq0bbXfNL4jCLuHlFt9gD0xf0G99owU,203
+pastastore/yaml_interface.py,sha256=yNpyEHtIapx44Thv2PCm7Sc_W-reXDHjT3uRC2gDAzw,29515
+pastastore-1.3.0.dist-info/LICENSE,sha256=DtHftfUEm99KzgwLr3rQUTg8H3kAS0Z-p5WWJgLf_OY,1082
+pastastore-1.3.0.dist-info/METADATA,sha256=gXxIFp2Ge_pHkDPc0qfuI2wiNQGUZUSOSMWavKWQ8Fo,7844
+pastastore-1.3.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+pastastore-1.3.0.dist-info/top_level.txt,sha256=QKfonr1KJZN46MFsj8eGRBw9Mg-jO-HFvgE2orVX7Sk,11
+pastastore-1.3.0.dist-info/RECORD,,

{pastastore-1.2.2.dist-info → pastastore-1.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.40.0)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pastastore-1.2.2.dist-info/RECORD

@@ -1,14 +0,0 @@
-pastastore/__init__.py,sha256=1janwX-BqYJobFi0dvVNW-zTnCUba_jxkBcT2pRj4fg,225
-pastastore/base.py,sha256=CHg7mKkdaQGTvQdVnbaPK6WslKZjkYhMMs84nrmMxvs,62290
-pastastore/connectors.py,sha256=riiSPX_N6Tcmn-_jQgDbw32hkq1iGLLHcH0U9wueMG8,28727
-pastastore/datasets.py,sha256=f-92WOh2ROCxOVvKGHXjnzd66Q7hO_-BtXRfMKwg1KU,6640
-pastastore/plotting.py,sha256=IZuri_U0b4hgvCgXCTNJv00bPK_KvD8DOPZvI-ZZNMI,41758
-pastastore/store.py,sha256=gqr1qi9sdUlmSQfkn3CC-ZKmqOro7bUw0-E-VlZRads,34126
-pastastore/util.py,sha256=lYlKrToHYh4rZHCMmVL2fp28GGAVPt7goEOb0HrmSfM,30268
-pastastore/version.py,sha256=kBMPTkZdkocSOnb2tjCjb04Zpe_3zTlbqK7OODZQYfA,203
-pastastore/yaml_interface.py,sha256=9nep4ALV9IomAeVuaafsPzlGDcmi6gL0rNHAjHiPbMc,29490
-pastastore-1.2.2.dist-info/LICENSE,sha256=DtHftfUEm99KzgwLr3rQUTg8H3kAS0Z-p5WWJgLf_OY,1082
-pastastore-1.2.2.dist-info/METADATA,sha256=kKIoYj0Nx8OD4wl9oaN8vofVWc96yJltsFnCkVETO90,7850
-pastastore-1.2.2.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
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