pastastore 1.5.0__tar.gz → 1.6.1__tar.gz

{pastastore-1.5.0 → pastastore-1.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pastastore
-Version: 1.5.0
+Version: 1.6.1
 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>
@@ -54,14 +54,16 @@ Requires-Dist: tqdm>=4.36
 Requires-Dist: pyyaml
 Provides-Extra: full
 Requires-Dist: pastastore[arcticdb,optional]; extra == "full"
-Provides-Extra: lint
-Requires-Dist: black; extra == "lint"
-Requires-Dist: flake8; extra == "lint"
-Requires-Dist: isort; extra == "lint"
+Provides-Extra: extensions
+Requires-Dist: hydropandas; extra == "extensions"
 Provides-Extra: optional
 Requires-Dist: contextily; extra == "optional"
 Requires-Dist: pyproj; extra == "optional"
 Requires-Dist: adjustText; extra == "optional"
+Provides-Extra: arcticdb
+Requires-Dist: arcticdb; extra == "arcticdb"
+Provides-Extra: lint
+Requires-Dist: ruff; extra == "lint"
 Provides-Extra: test
 Requires-Dist: pastastore[arcticdb,lint,optional]; extra == "test"
 Requires-Dist: hydropandas[full]; extra == "test"
@@ -82,8 +84,6 @@ 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"
-Provides-Extra: arcticdb
-Requires-Dist: arcticdb; extra == "arcticdb"
 Provides-Extra: docs
 Requires-Dist: pastastore[optional]; extra == "docs"
 Requires-Dist: sphinx_rtd_theme; extra == "docs"

{pastastore-1.5.0 → pastastore-1.6.1}/pastastore/base.py

@@ -1471,6 +1471,7 @@ class ConnectorUtil:
                         else:
                             msg = "stress '{}' not present in library".format(name)
                             raise KeyError(msg)
+
         # hack for pcov w dtype object (when filled with NaNs on store?)
         if "fit" in mdict:
             if "pcov" in mdict["fit"]:
@@ -1534,7 +1535,7 @@ class ConnectorUtil:
         if isinstance(series, pd.Series):
             series.name = name
             # empty string on index name causes trouble when reading
-            # data from Arctic VersionStores
+            # data from ArcticDB: TODO: check if still an issue?
             if series.index.name == "":
                 series.index.name = None
 

{pastastore-1.5.0 → pastastore-1.6.1}/pastastore/connectors.py

@@ -4,7 +4,6 @@ import json
 import os
 import warnings
 from copy import deepcopy
-from importlib import import_module
 from typing import Dict, Optional, Union
 
 import pandas as pd
@@ -17,195 +16,6 @@ FrameorSeriesUnion = Union[pd.DataFrame, pd.Series]
 warnings.showwarning = _custom_warning
 
 
-class ArcticConnector(BaseConnector, ConnectorUtil):  # pragma: no cover
-    """ArcticConnector object that connects to a running MongoDB database via Arctic."""
-
-    conn_type = "arctic"
-
-    def __init__(self, name: str, connstr: str):
-        """Create an ArcticConnector object that connects to a MongoDB database.
-
-        Parameters
-        ----------
-        name : str
-            name of the database
-        connstr : str
-            connection string (e.g. 'mongodb://localhost:27017/')
-        """
-        warnings.warn(
-            "ArcticConnector is deprecated. Please use a different "
-            "connector, e.g. `pst.ArcticDBConnector`.",
-            DeprecationWarning,
-            stacklevel=1,
-        )
-        try:
-            import arctic
-        except ModuleNotFoundError as e:
-            print(
-                "Please install arctic (also requires "
-                "a MongoDB instance running somewhere, e.g. "
-                "MongoDB Community: \n"
-                "https://docs.mongodb.com/manual/administration"
-                "/install-community/)!"
-            )
-            raise e
-        self.connstr = connstr
-        self.name = name
-
-        self.libs: dict = {}
-        self.arc = arctic.Arctic(connstr)
-        self._initialize()
-        self.models = ModelAccessor(self)
-        # for older versions of PastaStore, if oseries_models library is empty
-        # populate oseries - models database
-        self._update_all_oseries_model_links()
-
-    def _initialize(self) -> None:
-        """Initialize the libraries (internal method)."""
-        for libname in self._default_library_names:
-            if self._library_name(libname) not in self.arc.list_libraries():
-                self.arc.initialize_library(self._library_name(libname))
-            else:
-                print(
-                    f"ArcticConnector: library "
-                    f"'{self._library_name(libname)}'"
-                    " already exists. Linking to existing library."
-                )
-            self.libs[libname] = self._get_library(libname)
-
-    def _library_name(self, libname: str) -> str:
-        """Get full library name according to Arctic (internal method)."""
-        return ".".join([self.name, libname])
-
-    def _get_library(self, libname: str):
-        """Get Arctic library handle.
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-
-        Returns
-        -------
-        lib : arctic.Library handle
-            handle to the library
-        """
-        # get library handle
-        lib = self.arc.get_library(self._library_name(libname))
-        return lib
-
-    def _add_item(
-        self,
-        libname: str,
-        item: Union[FrameorSeriesUnion, Dict],
-        name: str,
-        metadata: Optional[Dict] = None,
-        **_,
-    ) -> None:
-        """Add item to library (time series or model) (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-        item : Union[FrameorSeriesUnion, Dict]
-            item to add, either time series or pastas.Model as dictionary
-        name : str
-            name of the item
-        metadata : Optional[Dict], optional
-            dictionary containing metadata, by default None
-        """
-        lib = self._get_library(libname)
-        lib.write(name, item, metadata=metadata)
-
-    def _get_item(self, libname: str, name: str) -> Union[FrameorSeriesUnion, Dict]:
-        """Retrieve item from library (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-        name : str
-            name of the item
-
-        Returns
-        -------
-        item : Union[FrameorSeriesUnion, Dict]
-            time series or model dictionary
-        """
-        lib = self._get_library(libname)
-        return lib.read(name).data
-
-    def _del_item(self, libname: str, name: str) -> None:
-        """Delete items (series or models) (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of library to delete item from
-        name : str
-            name of item to delete
-        """
-        lib = self._get_library(libname)
-        lib.delete(name)
-
-    def _get_metadata(self, libname: str, name: str) -> dict:
-        """Retrieve metadata for an item (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-        name : str
-            name of the item
-
-        Returns
-        -------
-        dict
-            dictionary containing metadata
-        """
-        lib = self._get_library(libname)
-        return lib.read_metadata(name).metadata
-
-    @property
-    def oseries_names(self):
-        """List of oseries names.
-
-        Returns
-        -------
-        list
-            list of oseries in library
-        """
-        return self._get_library("oseries").list_symbols()
-
-    @property
-    def stresses_names(self):
-        """List of stresses names.
-
-        Returns
-        -------
-        list
-            list of stresses in library
-        """
-        return self._get_library("stresses").list_symbols()
-
-    @property
-    def model_names(self):
-        """List of model names.
-
-        Returns
-        -------
-        list
-            list of models in library
-        """
-        return self._get_library("models").list_symbols()
-
-    @property
-    def oseries_with_models(self):
-        """List of oseries with models."""
-        return self._get_library("oseries_models").list_symbols()
-
-
 class ArcticDBConnector(BaseConnector, ConnectorUtil):
     """ArcticDBConnector object using ArcticDB to store data."""
 
@@ -388,234 +198,6 @@ class ArcticDBConnector(BaseConnector, ConnectorUtil):
         return self._get_library("oseries_models").list_symbols()
 
 
-class PystoreConnector(BaseConnector, ConnectorUtil):  # pragma: no cover
-    """PystoreConnector object using pystore as database backend."""
-
-    conn_type = "pystore"
-
-    def __init__(self, name: str, path: str):
-        """Create a PystoreConnector object that points to a Pystore.
-
-        Parameters
-        ----------
-        name : str
-            name of the store
-        path : str
-            path to the pystore directory
-        """
-        warnings.warn(
-            "PystoreConnector is deprecated. Please use a different "
-            "connector, e.g. `pst.PasConnector`.",
-            DeprecationWarning,
-            stacklevel=1,
-        )
-        try:
-            import pystore
-        except ModuleNotFoundError as e:
-            print(
-                "Install pystore, follow instructions at "
-                "https://github.com/ranaroussi/pystore#dependencies"
-            )
-            raise e
-        self.name = name
-        self.path = path
-        pystore.set_path(self.path)
-        self.store = pystore.store(self.name)
-        self.libs: dict = {}
-        self._initialize()
-        self.models = ModelAccessor(self)
-        # for older versions of PastaStore, if oseries_models library is empty
-        # populate oseries - models database
-        self._update_all_oseries_model_links()
-
-    def _initialize(self) -> None:
-        """Initialize the libraries (stores) (internal method)."""
-        for libname in self._default_library_names:
-            if libname in self.store.list_collections():
-                print(
-                    f"PystoreConnector: library '{self.path}/{libname}' "
-                    "already exists. Linking to existing library."
-                )
-            lib = self.store.collection(libname)
-            self.libs[libname] = lib
-
-    def _get_library(self, libname: str):
-        """Get Pystore library handle.
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-
-        Returns
-        -------
-        Pystore.Collection handle
-            handle to the library
-        """
-        # get library handle
-        lib = self.store.collection(libname)
-        return lib
-
-    def _add_item(
-        self,
-        libname: str,
-        item: Union[FrameorSeriesUnion, Dict],
-        name: str,
-        metadata: Optional[Dict] = None,
-        overwrite: bool = False,
-    ) -> None:
-        """Add item to library (time series or model) (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-        item : Union[FrameorSeriesUnion, Dict]
-            item to add, either time series or pastas.Model as dictionary
-        name : str
-            name of the item
-        metadata : Optional[Dict], optional
-            dictionary containing metadata, by default None
-        overwrite : bool, optional
-            overwrite item if it already exists, by default False.
-        """
-        # convert to DataFrame because pystore doesn't accept pandas.Series
-        # (maybe has an easy fix, but converting w to_frame for now)
-        if isinstance(item, pd.Series):
-            s = item.to_frame(name=name)
-            is_type = "series"
-        elif isinstance(item, dict):
-            s = pd.DataFrame()  # empty DataFrame as placeholder
-            jsondict = json.loads(json.dumps(item, cls=PastasEncoder, indent=4))
-            metadata = jsondict  # model dict is stored in metadata
-            is_type = "series"
-        elif isinstance(item, list):
-            s = pd.Series(item).to_frame(name="modelnames")
-            is_type = "list"
-        elif isinstance(item, pd.DataFrame):
-            s = item
-            is_type = "dataframe"
-
-        # store info about input type to ensure same type is returned
-        if metadata is None:
-            metadata = {"_is_type": is_type}
-        else:
-            metadata["_is_type"] = is_type
-
-        lib = self._get_library(libname)
-        lib.write(name, s, metadata=metadata, overwrite=overwrite)
-
-    def _get_item(self, libname: str, name: str) -> Union[FrameorSeriesUnion, Dict]:
-        """Retrieve item from pystore library (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-        name : str
-            name of the item
-
-        Returns
-        -------
-        item : Union[FrameorSeriesUnion, Dict]
-            time series or model dictionary
-        """
-        load_mod = import_module("pastas.io.pas")  # type: ignore
-        lib = self._get_library(libname)
-        # hack for storing models, stored as metadata
-        if libname == "models":
-            jsonpath = lib._item_path(name).joinpath("metadata.json")
-            s = load_mod.load(jsonpath)  # type: ignore
-        else:
-            # read series and convert to pandas
-            item = lib.item(name)
-            s = item.to_pandas()
-            # remove _is_type key and return correct type
-            is_type = item.metadata.pop("_is_type")
-            if is_type == "series":
-                s = s.squeeze()
-            elif is_type == "list":
-                s = s["modelnames"].tolist()
-        return s
-
-    def _del_item(self, libname: str, name: str) -> None:
-        """Delete data from the store (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library
-        name : str
-            name of the item to delete
-        """
-        lib = self._get_library(libname)
-        lib.delete_item(name)
-        self._clear_cache(libname)
-
-    def _get_metadata(self, libname: str, name: str) -> dict:
-        """Read metadata from pystore (internal method).
-
-        Parameters
-        ----------
-        libname : str
-            name of the library the series are in ("oseries" or "stresses")
-        name : str
-            name of item to load metadata for
-
-        Returns
-        -------
-        imeta : dict
-            dictionary containing metadata
-        """
-        from pystore.utils import read_metadata
-
-        lib = self._get_library(libname)
-        imeta = read_metadata(lib._item_path(name))
-        if "name" not in imeta.keys():
-            imeta["name"] = name
-        if "_is_type" in imeta.keys():
-            imeta.pop("_is_type")
-        return imeta
-
-    @property
-    def oseries_names(self):
-        """List of oseries names.
-
-        Returns
-        -------
-        list
-            list of oseries in library
-        """
-        return list(self._get_library("oseries").list_items())
-
-    @property
-    def stresses_names(self):
-        """List of stresses names.
-
-        Returns
-        -------
-        list
-            list of stresses in library
-        """
-        return list(self._get_library("stresses").list_items())
-
-    @property
-    def model_names(self):
-        """List of model names.
-
-        Returns
-        -------
-        list
-            list of models in library
-        """
-        return list(self._get_library("models").list_items())
-
-    @property
-    def oseries_with_models(self):
-        """List of oseries with models."""
-        return list(self._get_library("oseries_models").list_items())
-
-
 class DictConnector(BaseConnector, ConnectorUtil):
     """DictConnector object that stores timeseries and models in dictionaries."""
 

{pastastore-1.5.0 → pastastore-1.6.1}/pastastore/datasets.py

@@ -176,8 +176,7 @@ def _default_connector(conntype: str):
     Parameters
     ----------
     conntype : str
-        name of connector (DictConnector, PasConnector,
-        ArcticConnector, ArcticDBConnector or PystoreConnector)
+        name of connector (DictConnector, PasConnector, ArcticDBConnector)
 
     Returns
     -------
@@ -185,14 +184,9 @@ def _default_connector(conntype: str):
         default Connector based on type.
     """
     Conn = getattr(pst, conntype)
-    if Conn.conn_type == "arctic":
-        connstr = "mongodb://localhost:27017/"
-        conn = Conn("my_db", connstr)
-    elif Conn.conn_type == "arcticdb":
+    if Conn.conn_type == "arcticdb":
         uri = "lmdb://./arctic_db"
         conn = Conn("my_db", uri)
-    elif Conn.conn_type == "pystore":
-        conn = Conn("my_db", "./pystore_db")
     elif Conn.conn_type == "dict":
         conn = Conn("my_db")
     elif Conn.conn_type == "pas":