Merge pull request #43 from pastas/dev

Dev

.github/workflows/ci.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.7, 3.8]
     services:
       mongodb:
         image: mongo:latest

docs/connectors.rst

@@ -46,7 +46,7 @@ Arctic
 The :ref:`ArcticConnector` is an object that creates a
 connection with a MongoDB database. This can be an existing or a new database.
 For each of the datasets a collection or library is created. These are named
-using the following convention: `<database name>.<collection name>`.
+using the following convention: `<database name>.<library name>`.
 
 The Arctic implementation uses the following structure:
 
@@ -61,14 +61,12 @@ are stored as pandas.DataFrames. Models are stored in JSON (actually binary
 JSON) and *do not* contain the timeseries themselves. These are picked up from
 the other libraries when the model is loaded from the database.
 
-The `ArcticConnector` object allows the user to add different versions for
-datasets, which can be used to keep a history of older models for example.
-
 Pystore
 -------
 The :ref:`PystoreConnector` is an object that links
 to a location on disk. This can either be an existing or a new Pystore. A new
-store is created with collections that hold the different datasets:
+store is created with collections (or libraries) that hold the different 
+datasets:
 
 * observation timeseries
 * stresses timeseries
@@ -79,7 +77,7 @@ The Pystores have the following structure:
 .. code-block:: bash
 
    +-- store
-   |   +-- collections... (i.e. oseries, stresses, models)
+   |   +-- collections or libraries... (i.e. oseries, stresses, models)
    |   |   +-- items... (i.e. individual timeseries or models)
 
 
@@ -91,28 +89,27 @@ design allows the models to be saved in a PyStore. The timeseries are picked
 up from their respective stores when the model is loaded from disk.
 
 PyStore supports so-called snapshots (which store the current state of the
-store) but this has not been actively implemented in this module. Pystore does
-not have the same versioning capabilities as Arctic.
+store) but this has not been actively implemented in this module.
 
 Custom Connectors
 -----------------
 It should be relatively straightforward to write your own custom connector
 object. The :ref:`Base` submodule contains the
 `BaseConnector` class that defines which methods and properties *must*
 be defined. The `ConnectorUtil` mix-in class contains some general methods that
-are used by each connector. Each Connector object should inherit from these
+are used by each connector. Each Connector object should inherit from these two
 classes.
 
 The `BaseConnector` class also shows the expected call signature for each
 method. Following the same call signature should ensure that your new connector
-works directly with `PastaStore`. Though extra keyword arguments can be
+works directly with `PastaStore`. Extra keyword arguments can be
 added in the custom class.
 
 Below is a small snippet showing a custom Connector class::
 
    class MyCustomConnector(BaseConnector, ConnectorUtil):
       """Must override each method and property in BaseConnector, e.g."""
 
-      def get_oseries(self, name, progressbar=False):
-         # your code to get oseries from database here
+      def _get_item(self, name, progressbar=False):
+         # your code here for getting an item from your database
          pass

docs/examples/003_pastastore_plots_and_maps.nblink

@@ -0,0 +1,3 @@
+{
+    "path": "../../examples/notebooks/ex03_pastastore_plots_and_maps.ipynb"
+}

docs/modules.rst

@@ -21,13 +21,15 @@ DictConnector
 
 .. autoclass:: pastastore.DictConnector
    :members:
+   :private-members:
    :show-inheritance:
 
 PasConnector
 ^^^^^^^^^^^^
 
 .. autoclass:: pastastore.PasConnector
    :members:
+   :private-members:
    :show-inheritance:
 
 ArcticConnector
@@ -36,6 +38,7 @@ ArcticConnector
 .. autoclass:: pastastore.ArcticConnector
    :members:
    :undoc-members:
+   :private-members:
    :show-inheritance:
 
 PystoreConnector
@@ -44,6 +47,7 @@ PystoreConnector
 .. autoclass:: pastastore.PystoreConnector
    :members:
    :undoc-members:
+   :private-members:
    :show-inheritance:
 
 .. _Pastastore_API:
@@ -54,6 +58,24 @@ PastaStore
 .. automodule:: pastastore.store
     :members:
 
+
+Plots
+-----
+
+.. autoclass:: pastastore.plotting.Plots
+   :members:
+   :undoc-members:
+   :private-members:
+
+Maps
+----
+
+.. autoclass:: pastastore.plotting.Maps
+   :members:
+   :undoc-members:
+   :private-members:
+
+
 Util
 ----
 

docs/pstore.rst

@@ -3,7 +3,7 @@ PastaStore object
 =================
 
 The `PastaStore` object is essentially a class for working with timeseries and
-pastas Models. A connector has to be passed to the object which manages the
+pastas Models. A Connector has to be passed to the object which manages the
 retrieval and storage of data.
 
 Methods are available for the following tasks:

docs/utils.rst

@@ -3,16 +3,16 @@ Utilities
 =========
 
 The `pastastore.util` submodule contains useful functions, i.e. for deleting
-databases, connector objects, and PastaStore objects or emptying a library of
-all its contents:
+databases, connector objects, and PastaStore objects, emptying a library of
+all its contents or copying all data to a new database:
 
 
 * :meth:`pastastore.util.delete_pastastore`
 * :meth:`pastastore.util.delete_dict_connector`
 * :meth:`pastastore.util.delete_pas_connector`
 * :meth:`pastastore.util.delete_pystore_connector`
 * :meth:`pastastore.util.delete_arctic_connector`
-* :meth:`pastastore.util.empty_library`
+* :meth:`pastastore.util.copy_database`
 
 
 It also contains a method for making a detailed comparison between two 

examples/notebooks/ex01_intro+guide_for_pastas-Project_users.ipynb

@@ -49,14 +49,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import pastastore as pst\n",
     "import os\n",
     "import pandas as pd\n",
     "import pastas as ps\n",
     "\n",
     "import sys\n",
-    "sys.path.insert(1, \"../..\")\n",
-    "\n",
-    "import pastastore as pst"
+    "sys.path.insert(1, \"../..\")"
    ]
   },
   {
@@ -221,7 +220,8 @@
    ],
    "source": [
     "datadir = \"../../tests/data/\"  # relative path to data directory\n",
-    "oseries1 = pd.read_csv(os.path.join(datadir, \"head_nb1.csv\"), index_col=0, parse_dates=True)\n",
+    "oseries1 = pd.read_csv(os.path.join(\n",
+    "    datadir, \"head_nb1.csv\"), index_col=0, parse_dates=True)\n",
     "ometa = {\"x\": 100300, \"y\": 400400}\n",
     "oseries1.head()"
    ]
@@ -275,13 +275,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# prec \n",
-    "p = pd.read_csv(os.path.join(datadir, \"rain_nb1.csv\"), index_col=0, parse_dates=True)\n",
+    "# prec\n",
+    "p = pd.read_csv(os.path.join(datadir, \"rain_nb1.csv\"),\n",
+    "                index_col=0, parse_dates=True)\n",
     "p.columns = ['value']\n",
     "pmeta = {\"x\": 100300, \"y\": 400400}\n",
     "\n",
-    "# evap \n",
-    "e = pd.read_csv(os.path.join(datadir, \"evap_nb1.csv\"), index_col=0, parse_dates=True)\n",
+    "# evap\n",
+    "e = pd.read_csv(os.path.join(datadir, \"evap_nb1.csv\"),\n",
+    "                index_col=0, parse_dates=True)\n",
     "e.columns = [\"value\"]\n",
     "emeta = {\"x\": 100300, \"y\": 400400}"
    ]
@@ -1006,16 +1008,19 @@
    "outputs": [],
    "source": [
     "# oseries 2\n",
-    "o2 = pd.read_csv(os.path.join(datadir, \"obs.csv\"), index_col=0, parse_dates=True)\n",
+    "o2 = pd.read_csv(os.path.join(datadir, \"obs.csv\"),\n",
+    "                 index_col=0, parse_dates=True)\n",
     "o2.index.name = \"oseries2\"\n",
     "ometa2 = {\"x\": 100000, \"y\": 400000}\n",
     "\n",
     "# prec 2\n",
-    "p2 = pd.read_csv(os.path.join(datadir, \"rain.csv\"), index_col=0, parse_dates=True)\n",
+    "p2 = pd.read_csv(os.path.join(datadir, \"rain.csv\"),\n",
+    "                 index_col=0, parse_dates=True)\n",
     "pmeta2 = {\"x\": 100000, \"y\": 400000}\n",
     "\n",
     "# evap 2\n",
-    "e2 = pd.read_csv(os.path.join(datadir, \"evap.csv\"), index_col=0, parse_dates=True)\n",
+    "e2 = pd.read_csv(os.path.join(datadir, \"evap.csv\"),\n",
+    "                 index_col=0, parse_dates=True)\n",
     "emeta2 = {\"x\": 100000, \"y\": 400000}"
    ]
   },
@@ -1353,7 +1358,8 @@
    ],
    "source": [
     "# pastas.Project\n",
-    "prj.get_parameters([\"recharge_A\", \"recharge_a\", \"recharge_n\", \"recharge_f\", \"constant_d\", \"noise_alpha\"])"
+    "prj.get_parameters([\"recharge_A\", \"recharge_a\", \"recharge_n\",\n",
+    "                   \"recharge_f\", \"constant_d\", \"noise_alpha\"])"
    ]
   },
   {