Merge pull request #133 from pastas/dev

Release v1.6.0

.github/workflows/ci.yml

@@ -86,18 +86,19 @@ jobs:
         if: ${{ matrix.python-version == '3.12'}}  
         run: |
           pip install --upgrade pip
-          pip install numpy
+          # TODO: remove numpy pin when numba or ? doesn't crash on NaN being deprecated
+          pip install "numpy<2.0"  
           pip install ${{ matrix.pastas-version }}
           pip install -e .[test_py312]
 
       - name: Run pytest
         run: |
-          pytest -m "not bgmap"
+          pytest -m "not (bgmap or pastas150)"
 
-      - name: Test backgroundmap once
+      - name: Run all tests once
         if: ${{ matrix.python-version == '3.11' && matrix.pastas-version == 'git+https://github.com/pastas/pastas.git@dev' }}
         run: |
-          pytest -m "bgmap"
+          pytest -m ""
 
       - name: Run codacy-coverage-reporter
         if: ${{ github.repository == 'pastas/pastastore' && success() }}

.gitignore

@@ -115,6 +115,5 @@ venv.bak/
 .idea/workspace.xml
 
 */_old
-examples/notebooks/pystore
 cov.xml
 *.bat

docs/connectors.rst

@@ -43,7 +43,7 @@ the other directories when the model is loaded from the database.
 
 ArcticDB
 --------
-Note: this Connector uses ArcticDB the next-generation version of Arctic. Requires arcticdb Python package.
+Note: this Connector uses ArcticDB. Requires arcticdb Python package.
 
 The :ref:`ArcticDBConnector` is an object that creates a
 local database. This can be an existing or a new database.

docs/examples.rst

@@ -19,7 +19,7 @@ is stored in-memory (in dictionaries)::
    import pastastore as pst
 
    # define dict connector
-   conn = pst.DictConnect("my_db")
+   conn = pst.DictConnector("my_db")
 
    # create project for managing Pastas data and models
    store = pst.PastaStore(conn)
@@ -50,7 +50,7 @@ a `PastaStore` object::
 
    import pastastore as pst
 
-   # define arctic connector
+   # define ArcticDB connector
    uri = "lmdb://./my_path_here/"
    conn = pst.ArcticDBConnector("my_db", uri)
 

examples/notebooks/ex01_introduction_to_pastastore_databases.ipynb

@@ -59,6 +59,13 @@
       "PyYAML version     : 6.0\n",
       "\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DeprecationWarning: As of Pastas 1.5, no noisemodel is added to the pastas Model class by default anymore. To solve your model using a noisemodel, you have to explicitly add a noisemodel to your model before solving. For more information, and how to adapt your code, please see this issue on GitHub: https://github.com/pastas/pastas/issues/735"
+     ]
     }
    ],
    "source": [
@@ -1190,7 +1197,7 @@
     "- `solve_models`: solve all or selection of models in database\n",
     "- `model_results`: get results for all or selection of models in database. Requires the `art_tools` module!\n",
     "\n",
-    "Let's add some more data to the pystore to show how the bulk operations work."
+    "Let's add some more data to the pastastore to show how the bulk operations work."
    ]
   },
   {
@@ -1202,6 +1209,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
+      "The Time Series 'oseries2' has nan-values. Pastas will use the fill_nan settings to fill up the nan-values.\n",
       "The Time Series 'oseries2' has nan-values. Pastas will use the fill_nan settings to fill up the nan-values.\n"
      ]
     }
@@ -1285,7 +1293,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "15ac33d49a044a7a8367b8145287cc55",
+       "model_id": "3a1f6710cd1942a78adc916d56280bb4",
        "version_major": 2,
        "version_minor": 0
       },
@@ -1342,7 +1350,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a694566aa81a4df69a55e4c0d28397c8",
+       "model_id": "577068d685134722a0208d807122da7b",
        "version_major": 2,
        "version_minor": 0
       },

examples/notebooks/ex03_pastastore_yaml_interface.ipynb

@@ -33,7 +33,15 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DeprecationWarning: As of Pastas 1.5, no noisemodel is added to the pastas Model class by default anymore. To solve your model using a noisemodel, you have to explicitly add a noisemodel to your model before solving. For more information, and how to adapt your code, please see this issue on GitHub: https://github.com/pastas/pastas/issues/735"
+     ]
+    }
+   ],
    "source": [
     "import logging\n",
     "import os\n",

pastastore/base.py

@@ -1471,6 +1471,7 @@ def _parse_model_dict(self, mdict: dict, update_ts_settings: bool = False):
                         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 @@ def _set_series_name(series, name):
         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