pastastore 1.3.0__py3-none-any.whl → 1.5.0__py3-none-any.whl

pastastore/util.py

@@ -1,4 +1,7 @@
+"""Useful utilities for pastastore."""
+
 import os
+import warnings
 from typing import Dict, List, Optional, Union
 
 import numpy as np
@@ -16,9 +19,12 @@ def _custom_warning(message, category=UserWarning, filename="", lineno=-1, *args
 
 
 class ItemInLibraryException(Exception):
+    """Exception when item is already in library."""
+
     pass
 
 
+# TODO: remove in future version
 def delete_pystore_connector(
     conn=None,
     path: Optional[str] = None,
@@ -39,6 +45,12 @@ def delete_pystore_connector(
         list of library names to delete, by default None which deletes
         all libraries
     """
+    warnings.warn(
+        "This function is deprecated. We recommend to migrate to a different "
+        "Connector, e.g. `pst.PasConnector`.",
+        DeprecationWarning,
+        stacklevel=1,
+    )
     import pystore
 
     if conn is not None:
@@ -60,6 +72,7 @@ def delete_pystore_connector(
             print(f" - deleted: {lib}")
 
 
+# TODO: remove in future version
 def delete_arctic_connector(
     conn=None,
     connstr: Optional[str] = None,
@@ -80,6 +93,12 @@ def delete_arctic_connector(
         list of library names to delete, by default None which deletes
         all libraries
     """
+    warnings.warn(
+        "This function is deprecated. We recommend to migrate to a different "
+        "Connector, e.g. `pst.ArcticDBConnector`.",
+        DeprecationWarning,
+        stacklevel=1,
+    )
     import arctic
 
     if conn is not None:
@@ -172,6 +191,7 @@ def delete_arcticdb_connector(
 
 
 def delete_dict_connector(conn, libraries: Optional[List[str]] = None) -> None:
+    """Delete DictConnector object."""
     print(f"Deleting DictConnector: '{conn.name}' ... ", end="")
     if libraries is None:
         del conn
@@ -185,6 +205,7 @@ def delete_dict_connector(conn, libraries: Optional[List[str]] = None) -> None:
 
 
 def delete_pas_connector(conn, libraries: Optional[List[str]] = None) -> None:
+    """Delete PasConnector object."""
     import shutil
 
     print(f"Deleting PasConnector database: '{conn.name}' ... ", end="")
@@ -222,10 +243,12 @@ def delete_pastastore(pstore, libraries: Optional[List[str]] = None) -> None:
     TypeError
         when Connector type is not recognized
     """
+    # TODO: remove in future version
     if pstore.conn.conn_type == "pystore":
         delete_pystore_connector(conn=pstore.conn, libraries=libraries)
     elif pstore.conn.conn_type == "dict":
         delete_dict_connector(pstore)
+    # TODO: remove in future version
     elif pstore.conn.conn_type == "arctic":
         delete_arctic_connector(conn=pstore.conn, libraries=libraries)
     elif pstore.conn.conn_type == "arcticdb":
@@ -303,7 +326,6 @@ def compare_models(ml1, ml2, stats=None, detailed_comparison=False):
         returns True if models are equivalent when detailed_comparison=True
         else returns DataFrame containing comparison details.
     """
-
     df = pd.DataFrame(columns=["model 0", "model 1"])
     so1 = []  # for storing series_original
     sv1 = []  # for storing series_validated
@@ -335,9 +357,11 @@ def compare_models(ml1, ml2, stats=None, detailed_comparison=False):
             try:
                 assert_series_equal(
                     oso,
-                    ml.oseries.series_original
-                    if PASTAS_LEQ_022
-                    else ml.oseries._series_original,
+                    (
+                        ml.oseries.series_original
+                        if PASTAS_LEQ_022
+                        else ml.oseries._series_original
+                    ),
                 )
                 compare_oso = True
             except (ValueError, AssertionError):
@@ -378,9 +402,9 @@ def compare_models(ml1, ml2, stats=None, detailed_comparison=False):
             for ts in stresses:
                 df.loc[f"- time series: '{ts.name}'"] = ts.name
                 for tsk in ts.settings.keys():
-                    df.loc[
-                        f"  - {ts.name} settings: {tsk}", f"model {i}"
-                    ] = ts.settings[tsk]
+                    df.loc[f"  - {ts.name} settings: {tsk}", f"model {i}"] = (
+                        ts.settings[tsk]
+                    )
 
                 if i == 0:
                     if PASTAS_LEQ_022:
@@ -403,9 +427,11 @@ def compare_models(ml1, ml2, stats=None, detailed_comparison=False):
                     try:
                         assert_series_equal(
                             so1[counter],
-                            ts.series_original
-                            if PASTAS_LEQ_022
-                            else ts._series_original,
+                            (
+                                ts.series_original
+                                if PASTAS_LEQ_022
+                                else ts._series_original
+                            ),
                         )
                         compare_so1 = True
                     except (ValueError, AssertionError):
@@ -548,6 +574,7 @@ def frontiers_checks(
     check4_gain: bool = True,
     check5_parambounds: bool = False,
     csv_dir: Optional[str] = None,
+    progressbar: bool = False,
 ) -> pd.DataFrame:  # pragma: no cover
     """Check models in a PastaStore to see if they pass reliability criteria.
 
@@ -593,6 +620,8 @@ def frontiers_checks(
     csv_dir : string, optional
         directory to store CSV file with overview of checks for every
         model, by default None which will not store results
+    progressbar : bool, optional
+        show progressbar, by default False
 
     Returns
     -------
@@ -608,7 +637,6 @@ def frontiers_checks(
     Application of Time Series Analysis to Estimate Drawdown From Multiple Well
     Fields. Front. Earth Sci., 14 June 2022 doi:10.3389/feart.2022.907609
     """
-
     df = pd.DataFrame(columns=["all_checks_passed"])
 
     if modelnames is not None:
@@ -625,7 +653,9 @@ def frontiers_checks(
     else:
         models = pstore.model_names
 
-    for mlnam in tqdm(models, desc="Running model diagnostics"):
+    for mlnam in (
+        tqdm(models, desc="Running model diagnostics") if progressbar else models
+    ):
         ml = pstore.get_models(mlnam)
 
         if ml.parameters["optimal"].hasnans:
@@ -703,7 +733,7 @@ def frontiers_checks(
                             check_tmem_passed,
                         )
                 else:
-                    tmem = ml.get_response_tmax(sm_name)
+                    tmem = ml.get_response_tmax(sm_name, cutoff=check3_cutoff)
                     if tmem is None:  # no rfunc in stressmodel
                         tmem = 0
                     check_tmem_passed = tmem < len_oseries_calib / 2
@@ -730,7 +760,10 @@ def frontiers_checks(
                         else:
                             check_gain_passed = np.abs(gain) > 2 * gain_std
                         checks.loc[
-                            f"gain > 2*std: {sm_name}-{iw:02g} ({sm.distances.index[iw]})",
+                            (
+                                f"gain > 2*std: {sm_name}-{iw:02g}"
+                                f" ({sm.distances.index[iw]})"
+                            ),
                             :,
                         ] = (
                             gain,
@@ -825,7 +858,6 @@ def frontiers_aic_select(
     Multiple Well Fields. Front. Earth Sci., 14 June 2022
     doi:10.3389/feart.2022.907609
     """
-
     if modelnames is None and oseries is None:
         modelnames = pstore.model_names
     elif modelnames is None and oseries is not None:
@@ -849,7 +881,7 @@ def frontiers_aic_select(
         # with lowest AIC per location
         collect = []
         gr = df.join(aic).groupby("oseries")
-        for o, idf in gr:
+        for _, idf in gr:
             idf.index.name = "modelname"
             idf = (
                 idf.sort_values("aic").reset_index().set_index(["oseries", "modelname"])

pastastore/version.py

@@ -1,7 +1,38 @@
+# ruff: noqa: D100
+from importlib import import_module, metadata
+from platform import python_version
+
 import pastas as ps
 from packaging.version import parse as parse_version
 
 PASTAS_VERSION = parse_version(ps.__version__)
 PASTAS_LEQ_022 = PASTAS_VERSION <= parse_version("0.22.0")
+PASTAS_GEQ_150 = PASTAS_VERSION >= parse_version("1.5.0")
+
+__version__ = "1.5.0"
+
+
+def show_versions(optional=False) -> None:
+    """Print the version of dependencies.
+
+    Parameters
+    ----------
+    optional : bool, optional
+        Print the version of optional dependencies, by default False
+    """
+    msg = (
+        f"Python version     : {python_version()}\n"
+        f"Pandas version     : {metadata.version('pandas')}\n"
+        f"Matplotlib version : {metadata.version('matplotlib')}\n"
+        f"Pastas version     : {metadata.version('pastas')}\n"
+        f"PyYAML version     : {metadata.version('pyyaml')}\n"
+    )
+    if optional:
+        msg += "\nArcticDB version   : "
+        try:
+            import_module("arcticdb")
+            msg += f"{metadata.version('arctidb')}"
+        except ImportError:
+            msg += "Not Installed"
 
-__version__ = "1.3.0"
+    print(msg)

pastastore/yaml_interface.py

@@ -1,3 +1,5 @@
+"""Module containing YAML interface for Pastas models using PastaStore."""
+
 import datetime
 import logging
 import os
@@ -11,14 +13,11 @@ import yaml
 
 from pastastore.version import PASTAS_LEQ_022
 
-ps.logger.setLevel("ERROR")
-
-logging.basicConfig(level="INFO")
 logger = logging.getLogger(__name__)
 
 
 def _convert_dict_dtypes_for_yaml(d: Dict[str, Any]):
-    """Internal method to convert dictionary values for storing in YAML format.
+    """Convert dictionary values for storing in YAML format (internal function).
 
     Parameters
     ----------
@@ -95,7 +94,6 @@ def reduce_to_minimal_dict(d, keys=None):
         ["name", "oseries", "settings", "tmin", "tmax", "noise",
         "stressmodels", "rfunc", "stress", "prec", "evap", "stressmodel"]
     """
-
     if keys is None:
         keys = [
             "name",
@@ -170,7 +168,7 @@ class PastastoreYAML:
     """
 
     def __init__(self, pstore):
-        """Constructor for PastasstoreYAML class.
+        """Create for PastasstoreYAML class.
 
         Parameters
         ----------
@@ -181,7 +179,7 @@ class PastastoreYAML:
         self.pstore = pstore
 
     def _parse_rechargemodel_dict(self, d: Dict, onam: Optional[str] = None) -> Dict:
-        """Internal method to parse RechargeModel dictionary.
+        """Parse RechargeModel dictionary (internal method).
 
         Note: supports 'nearest' as input to 'prec' and 'evap',
         which will automatically select nearest stress with kind="prec" or
@@ -208,7 +206,7 @@ class PastastoreYAML:
         if isinstance(prec_val, dict):
             pnam = prec_val["name"]
             p = self.pstore.get_stresses(pnam)
-            prec_val["series"] = p
+            prec_val["series"] = p.squeeze()
             prec = prec_val
         elif prec_val.startswith("nearest"):
             if onam is None:
@@ -224,7 +222,7 @@ class PastastoreYAML:
                 "name": pnam,
                 "settings": "prec",
                 "metadata": pmeta,
-                "series": p,
+                "series": p.squeeze(),
             }
         elif isinstance(prec_val, str):
             pnam = d["prec"]
@@ -233,7 +231,7 @@ class PastastoreYAML:
                 "name": pnam,
                 "settings": "prec",
                 "metadata": pmeta,
-                "series": p,
+                "series": p.squeeze(),
             }
         else:
             raise NotImplementedError(f"Could not parse prec value: '{prec_val}'")
@@ -244,7 +242,7 @@ class PastastoreYAML:
         if isinstance(evap_val, dict):
             enam = evap_val["name"]
             e = self.pstore.get_stresses(enam)
-            evap_val["series"] = e
+            evap_val["series"] = e.squeeze()
             evap = evap_val
         elif evap_val.startswith("nearest"):
             if onam is None:
@@ -260,7 +258,7 @@ class PastastoreYAML:
                 "name": enam,
                 "settings": "evap",
                 "metadata": emeta,
-                "series": e,
+                "series": e.squeeze(),
             }
         elif isinstance(evap_val, str):
             enam = d["evap"]
@@ -269,7 +267,7 @@ class PastastoreYAML:
                 "name": enam,
                 "settings": "evap",
                 "metadata": emeta,
-                "series": e,
+                "series": e.squeeze(),
             }
         else:
             raise NotImplementedError(f"Could not parse evap value: '{evap_val}'")
@@ -310,12 +308,12 @@ class PastastoreYAML:
             onam = d["oseries"]
             if isinstance(onam, str):
                 o = self.pstore.get_oseries(onam)
-                d["oseries"] = o
+                d["oseries"] = o.squeeze()
 
         return d
 
     def _parse_stressmodel_dict(self, d: Dict, onam: Optional[str] = None) -> Dict:
-        """Internal method to parse StressModel dictionary.
+        """Parse StressModel dictionary (internal method).
 
         Note: supports 'nearest' or 'nearest <kind>' as input to 'stress',
         which will automatically select nearest stress with kind=<kind>.
@@ -337,7 +335,6 @@ class PastastoreYAML:
             containing stresses obtained from PastaStore, and setting
             defaults if they were not already provided.
         """
-
         # get stress
         snam = d.pop("stress")
 
@@ -361,7 +358,7 @@ class PastastoreYAML:
             "name": snam,
             "settings": d.pop("settings", None),
             "metadata": smeta,
-            "series": s,
+            "series": s.squeeze(),
         }
         d["stress"] = [s] if PASTAS_LEQ_022 else s
 
@@ -380,7 +377,7 @@ class PastastoreYAML:
         return d
 
     def _parse_wellmodel_dict(self, d: Dict, onam: Optional[str] = None) -> Dict:
-        """Internal method to parse WellModel dictionary.
+        """Parse WellModel dictionary (internal method).
 
         Note: supports 'nearest' or 'nearest <number> <kind>' as input to
         'stress', which will automatically select nearest or <number> of
@@ -402,7 +399,6 @@ class PastastoreYAML:
             containing stresses obtained from PastaStore, and setting
             defaults if they were not already provided.
         """
-
         # parse stress
         snames = d.pop("stress")
 
@@ -415,12 +411,12 @@ class PastastoreYAML:
                 elif len(snames.split()) == 2:
                     try:
                         n = int(snames.split()[1])
-                    except ValueError:
+                    except ValueError as e:
                         raise ValueError(
                             f"Could not parse: '{snames}'! "
                             "When using option 'nearest' for WellModel,  "
                             "use 'nearest <n>' or 'nearest <n> <kind>'!"
-                        )
+                        ) from e
                     kind = "well"
                 elif len(snames.split()) == 1:
                     n = 1
@@ -444,7 +440,7 @@ class PastastoreYAML:
                 "name": snam,
                 "settings": "well",
                 "metadata": smeta,
-                "series": s,
+                "series": s.squeeze(),
             }
             slist.append(sdict)
         d["stress"] = slist
@@ -479,6 +475,20 @@ class PastastoreYAML:
         return d
 
     def construct_mldict(self, mlyml: dict, mlnam: str) -> dict:
+        """Create Pastas.Model dictionary from YAML dictionary.
+
+        Parameters
+        ----------
+        mlyml : dict
+            YAML dictionary
+        mlnam : str
+            model name
+
+        Returns
+        -------
+        dict
+            dictionary of pastas.Model that can be read by Pastas
+        """
         # get oseries + metadata
         if isinstance(mlyml["oseries"], dict):
             onam = str(mlyml["oseries"]["name"])
@@ -490,7 +500,7 @@ class PastastoreYAML:
         o, ometa = self.pstore.get_oseries(onam, return_metadata=True)
 
         # create model to obtain default model settings
-        ml = ps.Model(o, name=mlnam, metadata=ometa)
+        ml = ps.Model(o.squeeze(), name=mlnam, metadata=ometa)
         mldict = ml.to_dict(series=True)
 
         # update with stored model settings
@@ -608,7 +618,6 @@ class PastastoreYAML:
         NotImplementedError
             if unsupported stressmodel is encountered
         """
-
         with open(fyaml, "r") as f:
             yml = yaml.load(f, Loader=yaml.CFullLoader)
 
@@ -654,7 +663,6 @@ class PastastoreYAML:
             the time series are actually the nearest ones! Only used
             when minimal_yaml=True. Default is False.
         """
-
         onames = self.pstore.conn._parse_names(oseries, "oseries")
 
         for onam in onames:

{pastastore-1.3.0.dist-info → pastastore-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pastastore
-Version: 1.3.0
+Version: 1.5.0
 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>
@@ -40,11 +40,10 @@ Classifier: Operating System :: Unix
 Classifier: Operating System :: MacOS
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Topic :: Scientific/Engineering :: Hydrology
 Requires-Python: >=3.7
@@ -53,8 +52,6 @@ License-File: LICENSE
 Requires-Dist: pastas >=0.13
 Requires-Dist: tqdm >=4.36
 Requires-Dist: pyyaml
-Provides-Extra: arctic
-Requires-Dist: arctic ; extra == 'arctic'
 Provides-Extra: arcticdb
 Requires-Dist: arcticdb ; extra == 'arcticdb'
 Provides-Extra: docs
@@ -74,10 +71,6 @@ Provides-Extra: optional
 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: python-snappy ; extra == 'pystore'
-Requires-Dist: dask[dataframe] ; extra == 'pystore'
 Provides-Extra: test
 Requires-Dist: pastastore[arcticdb,lint,optional] ; extra == 'test'
 Requires-Dist: hydropandas[full] ; extra == 'test'
@@ -88,7 +81,16 @@ Requires-Dist: pytest-cov ; extra == 'test'
 Requires-Dist: pytest-dependency ; extra == 'test'
 Requires-Dist: pytest-benchmark ; extra == 'test'
 Requires-Dist: codacy-coverage ; extra == 'test'
-Requires-Dist: lxml ; extra == 'test'
+Provides-Extra: test_py312
+Requires-Dist: pastastore[lint,optional] ; extra == 'test_py312'
+Requires-Dist: hydropandas[full] ; extra == 'test_py312'
+Requires-Dist: coverage ; extra == 'test_py312'
+Requires-Dist: codecov ; extra == 'test_py312'
+Requires-Dist: pytest ; extra == 'test_py312'
+Requires-Dist: pytest-cov ; extra == 'test_py312'
+Requires-Dist: pytest-dependency ; extra == 'test_py312'
+Requires-Dist: pytest-benchmark ; extra == 'test_py312'
+Requires-Dist: codacy-coverage ; extra == 'test_py312'
 
 ![pastastore](https://github.com/pastas/pastastore/workflows/pastastore/badge.svg)
 [![Documentation Status](https://readthedocs.org/projects/pastastore/badge/?version=latest)](https://pastastore.readthedocs.io/en/latest/?badge=latest)

pastastore-1.5.0.dist-info/RECORD

@@ -0,0 +1,15 @@
+pastastore/__init__.py,sha256=l6zRpDO0j6MIrfdljCTbkF70bt-GFlPseBd4IlmaC-o,269
+pastastore/base.py,sha256=tUWIenFjiIeQHkA2CYBxmwMy7KXXq5JZ5jZCphRjuj8,67145
+pastastore/connectors.py,sha256=-Rsw8Uf7wcos9XsQMDPgysU2acT-kqt25WFeNnpf5K0,29588
+pastastore/datasets.py,sha256=VTjlekM3UryGpslSdMLAaT-QIAVJfaZql0dka2AbMyc,6665
+pastastore/plotting.py,sha256=t6gEeHVGzrwvM6q1l8V3OkklpU75O2Y4h6nKEHRWdjo,46416
+pastastore/store.py,sha256=1HEkr84vmCiB07Yj8iOMybFRY_l93C4J1e2suGd92SU,44171
+pastastore/styling.py,sha256=ioaH10ELV8CFvJA-xAKFbnBklTd6FB1TZV8sqvZrEcw,1518
+pastastore/util.py,sha256=4P1cQ_euEo3-YopKGReQ18EznTxBVfDpXFiEczpn_Bw,31811
+pastastore/version.py,sha256=xF0vR3dPK9WQScTFt_osbszvZt9GKJQTBvrT8nRgswc,1155
+pastastore/yaml_interface.py,sha256=MddELxWe8_aqJRMUydOCbjoU1-ZodzxFKYnAaqJ5SqA,29947
+pastastore-1.5.0.dist-info/LICENSE,sha256=DtHftfUEm99KzgwLr3rQUTg8H3kAS0Z-p5WWJgLf_OY,1082
+pastastore-1.5.0.dist-info/METADATA,sha256=_JrozH-4rPhQdxsVuzzHhmW3rWd_T_9oC8H-b68B_7s,8023
+pastastore-1.5.0.dist-info/WHEEL,sha256=R0nc6qTxuoLk7ShA2_Y-UWkN8ZdfDBG2B6Eqpz2WXbs,91
+pastastore-1.5.0.dist-info/top_level.txt,sha256=QKfonr1KJZN46MFsj8eGRBw9Mg-jO-HFvgE2orVX7Sk,11
+pastastore-1.5.0.dist-info/RECORD,,

{pastastore-1.3.0.dist-info → pastastore-1.5.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (72.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pastastore-1.3.0.dist-info/RECORD

@@ -1,14 +0,0 @@
-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,,