Update Master to Pastas 1.2 (#619)

pastas · Aug 17, 2023 · f0df7e1 · f0df7e1
2 parents 5424a28 + 1906713
commit f0df7e1
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diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -18,6 +18,7 @@ left-hand menu you will find the different categories of the API documentation.
     rfunc
     recharge
     solver
+    objective_functions
     modelplots.Plotting
     modelcompare.CompareModels
     timeseries.TimeSeries

diff --git a/doc/benchmarks/noisemodel.ipynb b/doc/benchmarks/noisemodel.ipynb
diff --git a/doc/conf.py b/doc/conf.py
@@ -35,8 +35,8 @@
     "sphinx.ext.ifconfig",
     "sphinx.ext.viewcode",
     "IPython.sphinxext.ipython_console_highlighting",  # lowercase didn't work
-    "nbsphinx",
     "numpydoc",
+    "myst_nb",
     "sphinxcontrib.bibtex",
     "sphinx_design",
     "sphinx.ext.autosectionlabel",
@@ -52,7 +52,7 @@
 
 # General information about the project.
 project = "Pastas"
-copyright = "{}, R.A. Collenteur, M. Bakker, R. Calje, F. Schaars".format(year)
+copyright = "{}, The Pastas Team".format(year)
 author = "R.A. Collenteur, M. Bakker, R. Calje, F. Schaars"
 
 # The version.
@@ -170,7 +170,7 @@
     "matplotlib": ("https://matplotlib.org/stable", None),
 }
 
-# -- nbsphinx options---------- -------------------------------------------------------
+# -- myst_nb options ------------------------------------------------------------------
 
-nbsphinx_allow_errors = True  # Allow errors in notebooks, to see the error online
-nbsphinx_execute = "auto"
+nb_execution_allow_errors = True  # Allow errors in notebooks, to see the error online
+nb_execution_mode = "auto"
diff --git a/doc/examples/index.rst b/doc/examples/index.rst
@@ -45,11 +45,11 @@ Basics
 
 `Modeling with different timesteps`_
 
-.. _Preprocessing user-provided time series: prepare_timeseries.ipynb
-.. _A basic model: basic_model.ipynb
-.. _Fixating parameters while fitting: fix_parameters.ipynb
-.. _Calibration: calibration_options.ipynb
-.. _Modeling with different timesteps: modeling_timestep.ipynb
+.. _Preprocessing user-provided time series: prepare_timeseries.html
+.. _A basic model: basic_model.html
+.. _Fixating parameters while fitting: fix_parameters.html
+.. _Calibration: calibration_options.html
+.. _Modeling with different timesteps: modeling_timestep.html
 
 Stressmodels
 ------------
@@ -64,11 +64,11 @@ Stressmodels
 
 `Changing response functions`_
 
-.. _Adding surface water levels: adding_rivers.ipynb
-.. _Adding pumping wells: adding_wells.ipynb
-.. _Adding multiple wells: multiple_wells.ipynb
-.. _Adding trends: adding_trends.ipynb
-.. _Changing response functions: changing_responses.ipynb
+.. _Adding surface water levels: adding_rivers.html
+.. _Adding pumping wells: adding_wells.html
+.. _Adding multiple wells: multiple_wells.html
+.. _Adding trends: adding_trends.html
+.. _Changing response functions: changing_responses.html
 
 Non-linear (Recharge) Models
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -81,10 +81,10 @@ Non-linear (Recharge) Models
 
 `Modeling snow`_
 
-.. _Threshold non-linearities: threshold_non_linear.ipynb
-.. _Non-linear recharge models: non_linear_recharge.ipynb
-.. _Estimating recharge: recharge_estimation.ipynb
-.. _Modeling snow: snowmodel.ipynb
+.. _Threshold non-linearities: threshold_non_linear.html
+.. _Non-linear recharge models: non_linear_recharge.html
+.. _Estimating recharge: recharge_estimation.html
+.. _Modeling snow: snowmodel.html
 
 
 Model Evaluation
@@ -100,11 +100,11 @@ Model Evaluation
 
 `MCMC uncertainty`_
 
-.. _Comparing models visually: comparing_models.ipynb
-.. _Diagnostic checking: diagnostic_checking.ipynb
-.. _`Reducing autocorrelation`: timestep_analysis.ipynb
-.. _Uncertainty quantification: uncertainty.ipynb
-.. _MCMC uncertainty: uncertainty_emcee.ipynb
+.. _Comparing models visually: comparing_models.html
+.. _Diagnostic checking: diagnostic_checking.html
+.. _`Reducing autocorrelation`: timestep_analysis.html
+.. _Uncertainty quantification: uncertainty.html
+.. _MCMC uncertainty: uncertainty_emcee.html
 
 
 Applications
@@ -114,8 +114,8 @@ Applications
 
 `Groundwater signatures`_
 
-.. _Standardized Groundwater Index: standardized_groundwater_index.ipynb
-.. _Groundwater signatures: signatures.ipynb
+.. _Standardized Groundwater Index: standardized_groundwater_index.html
+.. _Groundwater signatures: signatures.html
 
 
 STOWA Manual (Dutch only)

diff --git a/doc/examples/multiple_wells.ipynb b/doc/examples/multiple_wells.ipynb
@@ -28,6 +28,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -68,6 +69,7 @@
    ]
   },
   {
+   "attachments": {},
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    "metadata": {},
    "source": [
@@ -95,6 +97,7 @@
    ]
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   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -119,6 +122,7 @@
    ]
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   {
+   "attachments": {},
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    "metadata": {},
    "source": [
@@ -138,6 +142,7 @@
    ]
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+   "attachments": {},
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    "metadata": {},
    "source": [
@@ -159,6 +164,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -176,6 +182,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -208,6 +215,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -226,6 +234,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -242,6 +251,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -252,15 +262,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "tags": []
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "ml.plots.decomposition();"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -282,6 +291,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -303,6 +313,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -321,11 +332,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "w = ps.WellModel(list(extraction_ts.values()), \"Wells\", distances)\n",
+    "w = ps.WellModel(list(extraction_ts.values()), \"WellModel\", distances)\n",
     "ml_wm.add_stressmodel(w)"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -344,6 +356,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -361,6 +374,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -373,10 +387,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ml_wm.plots.stacked_results(figsize=(10, 8));"
+    "ml_wm.plots.stacked_results(figsize=(10, 8), stacklegend=True);"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -391,9 +406,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "wm = ml_wm.stressmodels[\"Wells\"]\n",
+    "wm = ml_wm.stressmodels[\"WellModel\"]\n",
     "for i, name in enumerate(relevant_extractions.keys()):\n",
-    "    # get parameters\n",
+    "    # get parameters (note use of stressmodel for this)\n",
     "    p = wm.get_parameters(model=ml_wm, istress=i)\n",
     "    # calculate gain\n",
     "    gain = wm.rfunc.gain(p) * 1e6 / 365.25\n",
@@ -403,6 +418,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -449,13 +465,15 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Compare individual StressModels and WellModel"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -472,6 +490,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -489,7 +508,7 @@
     "ml_wm.name = \"WellModel\"\n",
     "\n",
     "# plot well stresses together on same plot:\n",
-    "smdict = {0: [\"Recharge\"], 1: [\"Extraction_2\", \"Extraction_3\", \"Wells\"]}\n",
+    "smdict = {0: [\"Recharge\"], 1: [\"Extraction_2\", \"Extraction_3\", \"WellModel\"]}\n",
     "\n",
     "# comparison plot\n",
     "mc = ps.CompareModels([ml, ml_wm])\n",
@@ -503,30 +522,18 @@
     ")\n",
     "mc.axes[\"con1\"].legend(loc=(0, 1), frameon=False, ncol=4);"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.9.7"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "dace5e1b41a98a8e52d2a8eebc3b981caf2c12e7a76736ebfb89a489e3b62e79"
-   }
+   "name": "python"
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  "nbformat": 4,