Improve docs (#54)

* improve docs - add new sections (like TimML) - run docformatter - fix some linting issues * fix coveralls parallel build issue * update gitignore * add sphinx-bibtex to docs deps * move pumptests notebooks to docs * rename api folder * add about section with bibliography * update main docs page layout update conf.py * add all examples * add newline * delete moved notebooks from notebook dir - update tests accordingly * update nbdirs * no more notebooks remaining in notebooks dir * fix nb tests * hopefully final fix
mbakker7 · Dec 20, 2023 · 4d60993 · 4d60993
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -43,6 +43,16 @@ jobs:
           py.test ./tests
 
       - name: Publish to coveralls.io
-        run: coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel: true
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+  finish:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Close parallel build
+        uses: coverallsapp/github-action@v2
+        with:
+          parallel-finished: true
diff --git a/.gitignore b/.gitignore
@@ -109,4 +109,4 @@ Info.plist
 
 # docs
 _build
-/docs/api/generated/
+/docs/05api/generated/
diff --git a/docs/00tutorials/index.rst b/docs/00tutorials/index.rst
@@ -0,0 +1,9 @@
+Tutorials
+=========
+
+TTim tutorials.
+
+.. toctree::
+    :maxdepth: 3
+    :hidden:
+    :glob:
diff --git a/docs/userguide/elements/areasinks.rst → docs/01howto/elements/areasinks.rst b/docs/userguide/elements/areasinks.rst → docs/01howto/elements/areasinks.rst
diff --git a/docs/userguide/elements/index.rst → docs/01howto/elements/index.rst b/docs/userguide/elements/index.rst → docs/01howto/elements/index.rst
diff --git a/docs/userguide/elements/linedoublets.rst → docs/01howto/elements/linedoublets.rst b/docs/userguide/elements/linedoublets.rst → docs/01howto/elements/linedoublets.rst
diff --git a/docs/userguide/elements/linesinks.rst → docs/01howto/elements/linesinks.rst b/docs/userguide/elements/linesinks.rst → docs/01howto/elements/linesinks.rst
diff --git a/docs/userguide/elements/wells.rst → docs/01howto/elements/wells.rst b/docs/userguide/elements/wells.rst → docs/01howto/elements/wells.rst
diff --git a/docs/userguide/getting_started/index.rst → docs/01howto/getting_started/index.rst b/docs/userguide/getting_started/index.rst → docs/01howto/getting_started/index.rst
diff --git a/docs/userguide/getting_started/models.rst → docs/01howto/getting_started/models.rst b/docs/userguide/getting_started/models.rst → docs/01howto/getting_started/models.rst
diff --git a/docs/userguide/getting_started/pathlines.rst → docs/01howto/getting_started/pathlines.rst b/docs/userguide/getting_started/pathlines.rst → docs/01howto/getting_started/pathlines.rst
diff --git a/docs/userguide/index.rst → docs/01howto/index.rst b/docs/userguide/index.rst → docs/01howto/index.rst
diff --git a/docs/02concepts/index.rst b/docs/02concepts/index.rst
@@ -0,0 +1,10 @@
+Concepts
+========
+
+This section contains explanations of some basic concepts that are used in TTim.
+
+
+.. toctree::
+    :maxdepth: 3
+
+
diff --git a/notebooks/aem_ttim_sol.ipynb → docs/03examples/aem_ttim_sol.ipynb b/notebooks/aem_ttim_sol.ipynb → docs/03examples/aem_ttim_sol.ipynb
diff --git a/notebooks/circareasink_example.ipynb → docs/03examples/circareasink_example.ipynb b/notebooks/circareasink_example.ipynb → docs/03examples/circareasink_example.ipynb
diff --git a/docs/examples/compare_wells_linesink.ipynb → docs/03examples/compare_wells_linesink.ipynb b/docs/examples/compare_wells_linesink.ipynb → docs/03examples/compare_wells_linesink.ipynb
diff --git a/notebooks/data/oudekorendijk_h30.dat → docs/03examples/data/oudekorendijk_h30.dat b/notebooks/data/oudekorendijk_h30.dat → docs/03examples/data/oudekorendijk_h30.dat
diff --git a/notebooks/data/oudekorendijk_h90.dat → docs/03examples/data/oudekorendijk_h90.dat b/notebooks/data/oudekorendijk_h90.dat → docs/03examples/data/oudekorendijk_h90.dat
diff --git a/notebooks/data/pumptest_neuman.txt → docs/03examples/data/pumptest_neuman.txt b/notebooks/data/pumptest_neuman.txt → docs/03examples/data/pumptest_neuman.txt
diff --git a/notebooks/data/slugtest.txt → docs/03examples/data/slugtest.txt b/notebooks/data/slugtest.txt → docs/03examples/data/slugtest.txt
diff --git a/notebooks/figs/neuman.png → docs/03examples/figs/neuman.png b/notebooks/figs/neuman.png → docs/03examples/figs/neuman.png
diff --git a/docs/03examples/index.rst b/docs/03examples/index.rst
@@ -0,0 +1,72 @@
+Examples
+========
+
+TTim example notebooks.
+
+.. toctree::
+    :maxdepth: 4
+    :hidden:
+    :glob:
+
+    compare_wells_linesink
+    aem_ttim_sol
+    circareasink_example
+    line_sink_well_sol
+    line-sink-ditch
+    meandering_river
+    pathline_trace
+    pumpingtest_hypothetical
+    pumpingtest
+    theis_storage
+    ttim_exercise1_sol
+    ttim_figures
+    ttim_neuman_comparison
+    ttim_pumptest_neuman
+    ttim_slugtest
+    well_example
+    well_near_river_or_wall
+    well_near_wall
+    wells_in_different_systems
+
+
+* `Comparing linesink with row of wells`_
+* `aem_ttim_sol`_
+* `circareasink_example`_
+* `line_sink_well_sol`_
+* `line-sink-ditch`_
+* `meandering_river`_
+* `pathline_trace`_
+* `pumpingtest_hypothetical`_
+* `pumpingtest`_
+* `theis_storage`_
+* `ttim_exercise1_sol`_
+* `ttim_figures`_
+* `ttim_neuman_comparison`_
+* `ttim_pumptest_neuman`_
+* `ttim_slugtest`_
+* `well_example`_
+* `well_near_river_or_wall`_
+* `well_near_wall`_
+* `wells_in_different_systems`_
+
+
+.. _Comparing linesink with row of wells: compare_wells_linesink.html
+.. _aem_ttim_sol: aem_ttim_sol.html
+.. _circareasink_example: circareasink_example.html
+.. _compare_wells_linesink: compare_wells_linesink.html
+.. _line_sink_well_sol: line_sink_well_sol.html
+.. _line-sink-ditch: line-sink-ditch.html
+.. _meandering_river: meandering_river.html
+.. _pathline_trace: pathline_trace.html
+.. _pumpingtest_hypothetical: pumpingtest_hypothetical.html
+.. _pumpingtest: pumpingtest.html
+.. _theis_storage: theis_storage.html
+.. _ttim_exercise1_sol: ttim_exercise1_sol.html
+.. _ttim_figures: ttim_figures.html
+.. _ttim_neuman_comparison: ttim_neuman_comparison.html
+.. _ttim_pumptest_neuman: ttim_pumptest_neuman.html
+.. _ttim_slugtest: ttim_slugtest.html
+.. _well_example: well_example.html
+.. _well_near_river_or_wall: well_near_river_or_wall.html
+.. _well_near_wall: well_near_wall.html
+.. _wells_in_different_systems: wells_in_different_systems.html
diff --git a/notebooks/line-sink-ditch.ipynb → docs/03examples/line-sink-ditch.ipynb b/notebooks/line-sink-ditch.ipynb → docs/03examples/line-sink-ditch.ipynb
diff --git a/notebooks/line_sink_well_sol.ipynb → docs/03examples/line_sink_well_sol.ipynb b/notebooks/line_sink_well_sol.ipynb → docs/03examples/line_sink_well_sol.ipynb
diff --git a/notebooks/meandering_river.ipynb → docs/03examples/meandering_river.ipynb b/notebooks/meandering_river.ipynb → docs/03examples/meandering_river.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Meandering river"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/notebooks/pathline_trace.ipynb → docs/03examples/pathline_trace.ipynb b/notebooks/pathline_trace.ipynb → docs/03examples/pathline_trace.ipynb
diff --git a/notebooks/pumpingtest.ipynb → docs/03examples/pumpingtest.ipynb b/notebooks/pumpingtest.ipynb → docs/03examples/pumpingtest.ipynb
diff --git a/notebooks/pumpingtest_hypothetical.ipynb → ...03examples/pumpingtest_hypothetical.ipynb b/notebooks/pumpingtest_hypothetical.ipynb → ...03examples/pumpingtest_hypothetical.ipynb
diff --git a/notebooks/theis_storage.ipynb → docs/03examples/theis_storage.ipynb b/notebooks/theis_storage.ipynb → docs/03examples/theis_storage.ipynb
diff --git a/notebooks/ttim_exercise1_sol.ipynb → docs/03examples/ttim_exercise1_sol.ipynb b/notebooks/ttim_exercise1_sol.ipynb → docs/03examples/ttim_exercise1_sol.ipynb
diff --git a/notebooks/ttim_figures.ipynb → docs/03examples/ttim_figures.ipynb b/notebooks/ttim_figures.ipynb → docs/03examples/ttim_figures.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# TTim aquifer figures"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/notebooks/ttim_neuman_comparison.ipynb → docs/03examples/ttim_neuman_comparison.ipynb b/notebooks/ttim_neuman_comparison.ipynb → docs/03examples/ttim_neuman_comparison.ipynb
diff --git a/notebooks/ttim_pumptest_neuman.ipynb → docs/03examples/ttim_pumptest_neuman.ipynb b/notebooks/ttim_pumptest_neuman.ipynb → docs/03examples/ttim_pumptest_neuman.ipynb
diff --git a/notebooks/ttim_slugtest.ipynb → docs/03examples/ttim_slugtest.ipynb b/notebooks/ttim_slugtest.ipynb → docs/03examples/ttim_slugtest.ipynb
diff --git a/notebooks/well_example.ipynb → docs/03examples/well_example.ipynb b/notebooks/well_example.ipynb → docs/03examples/well_example.ipynb
diff --git a/notebooks/well_near_river_or_wall.ipynb → .../03examples/well_near_river_or_wall.ipynb b/notebooks/well_near_river_or_wall.ipynb → .../03examples/well_near_river_or_wall.ipynb
diff --git a/notebooks/well_near_wall.ipynb → docs/03examples/well_near_wall.ipynb b/notebooks/well_near_wall.ipynb → docs/03examples/well_near_wall.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Well near impermeable wall"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

diff --git a/notebooks/wells_in_different_systems.ipynb → ...examples/wells_in_different_systems.ipynb b/notebooks/wells_in_different_systems.ipynb → ...examples/wells_in_different_systems.ipynb
diff --git a/...ingtest_benchmarks/0_synthetic_data.ipynb → docs/04pumpingtests/0_synthetic_data.ipynb b/...ingtest_benchmarks/0_synthetic_data.ipynb → docs/04pumpingtests/0_synthetic_data.ipynb
diff --git a/pumpingtest_benchmarks/10_moench_test.ipynb → docs/04pumpingtests/10_moench_test.ipynb b/pumpingtest_benchmarks/10_moench_test.ipynb → docs/04pumpingtests/10_moench_test.ipynb
diff --git a/...enchmarks/11_slug_test_pratt_county.ipynb → ...pingtests/11_slug_test_pratt_county.ipynb b/...enchmarks/11_slug_test_pratt_county.ipynb → ...pingtests/11_slug_test_pratt_county.ipynb
diff --git a/...enchmarks/12_falling-head_slug_test.ipynb → ...pingtests/12_falling-head_slug_test.ipynb b/...enchmarks/12_falling-head_slug_test.ipynb → ...pingtests/12_falling-head_slug_test.ipynb
diff --git a/..._benchmarks/13_multiwell_slug_test-.ipynb → ...umpingtests/13_multiwell_slug_test-.ipynb b/..._benchmarks/13_multiwell_slug_test-.ipynb → ...umpingtests/13_multiwell_slug_test-.ipynb
diff --git a/...benchmarks/14_dawsonville_slug_test.ipynb → ...mpingtests/14_dawsonville_slug_test.ipynb b/...benchmarks/14_dawsonville_slug_test.ipynb → ...mpingtests/14_dawsonville_slug_test.ipynb
diff --git a/...benchmarks/1_test_of_oude_korendijk.ipynb → ...mpingtests/1_test_of_oude_korendijk.ipynb b/...benchmarks/1_test_of_oude_korendijk.ipynb → ...mpingtests/1_test_of_oude_korendijk.ipynb
diff --git a/pumpingtest_benchmarks/2_test_of_dalem.ipynb → docs/04pumpingtests/2_test_of_dalem.ipynb b/pumpingtest_benchmarks/2_test_of_dalem.ipynb → docs/04pumpingtests/2_test_of_dalem.ipynb
diff --git a/...st_benchmarks/3_test_of_vennebulten.ipynb → ...4pumpingtests/3_test_of_vennebulten.ipynb b/...st_benchmarks/3_test_of_vennebulten.ipynb → ...4pumpingtests/3_test_of_vennebulten.ipynb
diff --git a/...ngtest_benchmarks/4_test_of_gridley.ipynb → docs/04pumpingtests/4_test_of_gridley.ipynb b/...ngtest_benchmarks/4_test_of_gridley.ipynb → docs/04pumpingtests/4_test_of_gridley.ipynb
diff --git a/pumpingtest_benchmarks/5_test_of_sioux.ipynb → docs/04pumpingtests/5_test_of_sioux.ipynb b/pumpingtest_benchmarks/5_test_of_sioux.ipynb → docs/04pumpingtests/5_test_of_sioux.ipynb
diff --git a/...ngtest_benchmarks/6_test_of_schroth.ipynb → docs/04pumpingtests/6_test_of_schroth.ipynb b/...ngtest_benchmarks/6_test_of_schroth.ipynb → docs/04pumpingtests/6_test_of_schroth.ipynb
diff --git a/...ks/7_test_of_neveda_double-porosity.ipynb → ...ts/7_test_of_neveda_double-porosity.ipynb b/...ks/7_test_of_neveda_double-porosity.ipynb → ...ts/7_test_of_neveda_double-porosity.ipynb
diff --git a/...arks/8_test_of_hardinxveld_recovery.ipynb → ...ests/8_test_of_hardinxveld_recovery.ipynb b/...arks/8_test_of_hardinxveld_recovery.ipynb → ...ests/8_test_of_hardinxveld_recovery.ipynb
diff --git a/...est_benchmarks/9_test_of_texas_hill.ipynb → ...04pumpingtests/9_test_of_texas_hill.ipynb b/...est_benchmarks/9_test_of_texas_hill.ipynb → ...04pumpingtests/9_test_of_texas_hill.ipynb
diff --git a/...gtests_new/confined1_oude_korendijk.ipynb → ...mpingtests/confined1_oude_korendijk.ipynb b/...gtests_new/confined1_oude_korendijk.ipynb → ...mpingtests/confined1_oude_korendijk.ipynb
@@ -5,6 +5,7 @@
    "metadata": {},
    "source": [
     "# 1. Confined Aquifer Test - Oude Korendijk\n",
+    "\n",
     "**This example is taken from Kruseman and de Ridder (1970)**"
    ]
   },
@@ -68,7 +69,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a id='step_3'></a>\n",
     "## Step 3: Creating a TTim conceptual model\n",
     "\n",
     "In this example, we are using the ModelMaq model to conceptualize our aquifer. ModelMaq defines the aquifer system as a stacked vertical sequence of aquifers and leaky layers (aquifer-leaky layer, aquifer-leaky layer, etc). Aquifers are conceptualized as having no vertical resistance (Dupuit approximation), with constant hydraulic conductivity and storage. Aquitard layers are approximated as having only vertical flow. They are characterized by the parameter resistance to vertical flow and by having no storage.\n",
@@ -195,7 +195,6 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a id='step_5_1'></a>\n",
     "### Step 5.1: Calibration with Observation from Piezometer 1 (30 m from well)\n",
     "\n",
     "We begin calibrating using only the data from observation 1:"
@@ -408,7 +407,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Plotting the model Results"
+    "#### Plotting the model Results"
    ]
   },
   {
@@ -444,15 +443,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 5.2. Calibrate model Parameters with Observation Well 2 (90 m distance)"
+    "### Step 5.2. Calibrate model Parameters with Observation Well 2 (90 m distance)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     " We proceed to calibrate using only the data from observation well 2.\n",
-    " This time we will rush foward through the calibration steps. If the user feels confused, one can go back and check the inputs in [***step 5.1***](#step_5_1)"
+    " This time we will rush foward through the calibration steps. If the user feels confused, one can go back and check the inputs in [***step 5.1***](#step-51-calibration-with-observation-from-piezometer-1-30-m-from-well)"
    ]
   },
   {
@@ -602,7 +601,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Step 5.3. Calibrate model with two datasets simultaneously"
+    "### Step 5.3. Calibrate model with two datasets simultaneously"
    ]
   },
   {
@@ -798,7 +797,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now, besides the parameters explained in [Step 3](#step_3), we have to add the radius of the caisson (```rc```)"
+    "Now, besides the parameters explained in [Step 3](#step-3-creating-a-ttim-conceptual-model), we have to add the radius of the caisson (```rc```)"
    ]
   },
   {
@@ -1574,13 +1573,6 @@
     "* Kruseman, G.P., De Ridder, N.A., Verweij, J.M., 1970. Analysis and evaluationof pumping test data. volume 11. International institute for land reclamation and improvement The Netherlands.\n",
     "* Yang, Xinzhu (2020) Application and comparison of different methodsfor aquifer test analysis using TTim. Master Thesis, Delft University of Technology (TUDelft), Delft, The Netherlands."
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "#### Next Notebook: 2. reference "
-   ]
   }
  ],
  "metadata": {

diff --git a/pumpingtest_benchmarks/data/dalem_p120.txt → docs/04pumpingtests/data/dalem_p120.txt b/pumpingtest_benchmarks/data/dalem_p120.txt → docs/04pumpingtests/data/dalem_p120.txt
diff --git a/pumpingtest_benchmarks/data/dalem_p30.txt → docs/04pumpingtests/data/dalem_p30.txt b/pumpingtest_benchmarks/data/dalem_p30.txt → docs/04pumpingtests/data/dalem_p30.txt
diff --git a/pumpingtest_benchmarks/data/dalem_p60.txt → docs/04pumpingtests/data/dalem_p60.txt b/pumpingtest_benchmarks/data/dalem_p60.txt → docs/04pumpingtests/data/dalem_p60.txt
diff --git a/pumpingtest_benchmarks/data/dalem_p90.txt → docs/04pumpingtests/data/dalem_p90.txt b/pumpingtest_benchmarks/data/dalem_p90.txt → docs/04pumpingtests/data/dalem_p90.txt
diff --git a/...test_benchmarks/data/dawsonville_slug.txt → .../04pumpingtests/data/dawsonville_slug.txt b/...test_benchmarks/data/dawsonville_slug.txt → .../04pumpingtests/data/dawsonville_slug.txt
diff --git a/..._benchmarks/data/double-porosity-110m.txt → ...umpingtests/data/double-porosity-110m.txt b/..._benchmarks/data/double-porosity-110m.txt → ...umpingtests/data/double-porosity-110m.txt
diff --git a/...arks/data/double-porosity-pumpingwell.txt → ...ests/data/double-porosity-pumpingwell.txt b/...arks/data/double-porosity-pumpingwell.txt → ...ests/data/double-porosity-pumpingwell.txt
diff --git a/pumpingtest_benchmarks/data/falling_head.txt → docs/04pumpingtests/data/falling_head.txt b/pumpingtest_benchmarks/data/falling_head.txt → docs/04pumpingtests/data/falling_head.txt
diff --git a/...ngtest_benchmarks/data/gridley_well_1.txt → docs/04pumpingtests/data/gridley_well_1.txt b/...ngtest_benchmarks/data/gridley_well_1.txt → docs/04pumpingtests/data/gridley_well_1.txt
diff --git a/...ngtest_benchmarks/data/gridley_well_3.txt → docs/04pumpingtests/data/gridley_well_3.txt b/...ngtest_benchmarks/data/gridley_well_3.txt → docs/04pumpingtests/data/gridley_well_3.txt
diff --git a/pumpingtest_benchmarks/data/ln-2.txt → docs/04pumpingtests/data/ln-2.txt b/pumpingtest_benchmarks/data/ln-2.txt → docs/04pumpingtests/data/ln-2.txt
diff --git a/pumpingtest_benchmarks/data/ln-3.txt → docs/04pumpingtests/data/ln-3.txt b/pumpingtest_benchmarks/data/ln-3.txt → docs/04pumpingtests/data/ln-3.txt
diff --git a/pumpingtest_benchmarks/data/moench_pd1.txt → docs/04pumpingtests/data/moench_pd1.txt b/pumpingtest_benchmarks/data/moench_pd1.txt → docs/04pumpingtests/data/moench_pd1.txt
diff --git a/pumpingtest_benchmarks/data/moench_pd2.txt → docs/04pumpingtests/data/moench_pd2.txt b/pumpingtest_benchmarks/data/moench_pd2.txt → docs/04pumpingtests/data/moench_pd2.txt
diff --git a/pumpingtest_benchmarks/data/moench_ps1.txt → docs/04pumpingtests/data/moench_ps1.txt b/pumpingtest_benchmarks/data/moench_ps1.txt → docs/04pumpingtests/data/moench_ps1.txt
diff --git a/pumpingtest_benchmarks/data/moench_ps2.txt → docs/04pumpingtests/data/moench_ps2.txt b/pumpingtest_benchmarks/data/moench_ps2.txt → docs/04pumpingtests/data/moench_ps2.txt
diff --git a/...ingtest_benchmarks/data/moench_pumped.txt → docs/04pumpingtests/data/moench_pumped.txt b/...ingtest_benchmarks/data/moench_pumped.txt → docs/04pumpingtests/data/moench_pumped.txt
diff --git a/...ngtest_benchmarks/data/piezometer_h30.txt → docs/04pumpingtests/data/piezometer_h30.txt b/...ngtest_benchmarks/data/piezometer_h30.txt → docs/04pumpingtests/data/piezometer_h30.txt
diff --git a/...ngtest_benchmarks/data/piezometer_h90.txt → docs/04pumpingtests/data/piezometer_h90.txt b/...ngtest_benchmarks/data/piezometer_h90.txt → docs/04pumpingtests/data/piezometer_h90.txt
diff --git a/pumpingtest_benchmarks/data/recovery.txt → docs/04pumpingtests/data/recovery.txt b/pumpingtest_benchmarks/data/recovery.txt → docs/04pumpingtests/data/recovery.txt
diff --git a/pumpingtest_benchmarks/data/schroth_obs1.txt → docs/04pumpingtests/data/schroth_obs1.txt b/pumpingtest_benchmarks/data/schroth_obs1.txt → docs/04pumpingtests/data/schroth_obs1.txt
diff --git a/pumpingtest_benchmarks/data/schroth_obs2.txt → docs/04pumpingtests/data/schroth_obs2.txt b/pumpingtest_benchmarks/data/schroth_obs2.txt → docs/04pumpingtests/data/schroth_obs2.txt
diff --git a/pumpingtest_benchmarks/data/sioux100.txt → docs/04pumpingtests/data/sioux100.txt b/pumpingtest_benchmarks/data/sioux100.txt → docs/04pumpingtests/data/sioux100.txt
diff --git a/pumpingtest_benchmarks/data/sioux200.txt → docs/04pumpingtests/data/sioux200.txt b/pumpingtest_benchmarks/data/sioux200.txt → docs/04pumpingtests/data/sioux200.txt
diff --git a/pumpingtest_benchmarks/data/sioux400.txt → docs/04pumpingtests/data/sioux400.txt b/pumpingtest_benchmarks/data/sioux400.txt → docs/04pumpingtests/data/sioux400.txt
diff --git a/pumpingtest_benchmarks/data/slug.txt → docs/04pumpingtests/data/slug.txt b/pumpingtest_benchmarks/data/slug.txt → docs/04pumpingtests/data/slug.txt
diff --git a/pumpingtest_benchmarks/data/syn_30_0.0.txt → docs/04pumpingtests/data/syn_30_0.0.txt b/pumpingtest_benchmarks/data/syn_30_0.0.txt → docs/04pumpingtests/data/syn_30_0.0.txt
diff --git a/pumpingtest_benchmarks/data/syn_90_0.0.txt → docs/04pumpingtests/data/syn_90_0.0.txt b/pumpingtest_benchmarks/data/syn_90_0.0.txt → docs/04pumpingtests/data/syn_90_0.0.txt
diff --git a/pumpingtest_benchmarks/data/syn_p30_0.02.txt → docs/04pumpingtests/data/syn_p30_0.02.txt b/pumpingtest_benchmarks/data/syn_p30_0.02.txt → docs/04pumpingtests/data/syn_p30_0.02.txt
diff --git a/pumpingtest_benchmarks/data/syn_p30_0.05.txt → docs/04pumpingtests/data/syn_p30_0.05.txt b/pumpingtest_benchmarks/data/syn_p30_0.05.txt → docs/04pumpingtests/data/syn_p30_0.05.txt
diff --git a/pumpingtest_benchmarks/data/syn_p90_0.02.txt → docs/04pumpingtests/data/syn_p90_0.02.txt b/pumpingtest_benchmarks/data/syn_p90_0.02.txt → docs/04pumpingtests/data/syn_p90_0.02.txt
diff --git a/pumpingtest_benchmarks/data/syn_p90_0.05.txt → docs/04pumpingtests/data/syn_p90_0.05.txt b/pumpingtest_benchmarks/data/syn_p90_0.05.txt → docs/04pumpingtests/data/syn_p90_0.05.txt
diff --git a/pumpingtest_benchmarks/data/texas160.txt → docs/04pumpingtests/data/texas160.txt b/pumpingtest_benchmarks/data/texas160.txt → docs/04pumpingtests/data/texas160.txt
diff --git a/pumpingtest_benchmarks/data/texas40.txt → docs/04pumpingtests/data/texas40.txt b/pumpingtest_benchmarks/data/texas40.txt → docs/04pumpingtests/data/texas40.txt
diff --git a/pumpingtest_benchmarks/data/texas80.txt → docs/04pumpingtests/data/texas80.txt b/pumpingtest_benchmarks/data/texas80.txt → docs/04pumpingtests/data/texas80.txt
diff --git a/pumpingtest_benchmarks/data/venne_deep.txt → docs/04pumpingtests/data/venne_deep.txt b/pumpingtest_benchmarks/data/venne_deep.txt → docs/04pumpingtests/data/venne_deep.txt
diff --git a/...ingtest_benchmarks/data/venne_shallow.txt → docs/04pumpingtests/data/venne_shallow.txt b/...ingtest_benchmarks/data/venne_shallow.txt → docs/04pumpingtests/data/venne_shallow.txt
diff --git a/docs/04pumpingtests/index.rst b/docs/04pumpingtests/index.rst
@@ -0,0 +1,24 @@
+Pumping tests
+=============
+
+TTim pumping test benchmark notebooks.
+
+.. toctree::
+    :maxdepth: 1
+
+    0_synthetic_data
+    1_test_of_oude_korendijk
+    2_test_of_dalem
+    3_test_of_vennebulten
+    4_test_of_gridley
+    5_test_of_sioux
+    6_test_of_schroth
+    7_test_of_neveda_double-porosity
+    8_test_of_hardinxveld_recovery
+    9_test_of_texas_hill
+    10_moench_test
+    11_slug_test_pratt_county
+    12_falling-head_slug_test
+    13_multiwell_slug_test-
+    14_dawsonville_slug_test
+    confined1_oude_korendijk
diff --git a/docs/api/index.rst → docs/05api/index.rst b/docs/api/index.rst → docs/05api/index.rst
@@ -30,5 +30,5 @@ Python code.
 
 .. toctree::
     :hidden:
-    :maxdepth: 4
+    :maxdepth: 2
     :glob:
diff --git a/docs/06about/index.rst b/docs/06about/index.rst
@@ -0,0 +1,11 @@
+Cite
+====
+
+Publications
+------------
+
+.. bibliography:: publications.bib
+    :list: bullet
+
+    bakker_semi-analytic_2013
+    bakker_analytic_2013
diff --git a/docs/06about/publications.bib b/docs/06about/publications.bib
@@ -0,0 +1,38 @@
+
+@article{bakker_semi-analytic_2013,
+	title = {Semi-analytic modeling of transient multi-layer flow with {TTim}},
+	volume = {21},
+	issn = {1435-0157},
+	url = {https://doi.org/10.1007/s10040-013-0975-2},
+	doi = {10.1007/s10040-013-0975-2},
+	abstract = {TTim is a free code for the semi-analytic simulation of transient flow in multi-layer systems consisting of an arbitrary number of layers. No grid or time-stepping is required, nor does a closed model boundary need to be specified in any of the layers. Currently, TTim includes multi-layer wells and line-sinks, which may be used to simulate transient flow to a variety of hydrogeologic features, including wells with a skin and wellbore storage, incompletely sealed abandoned wells, streams with leaky beds, vertical faults, and horizontal wells; transient forcing needs to be represented by a step function. Other features that may be simulated include vertical anisotropy and the delayed response of the water table. Behind the scenes of TTim, the Laplace-transform analytic element method is applied. TTim is written in Python, with Python scripts used as input files. TTim has many practical applications, including the design of riverbank filtration systems, analysis of aquifer tests near surface-water bodies, design and evaluation of recirculation wells, and modeling of the transient pressure response of proposed carbon geologic sequestration projects. In addition, the short and simple input files and the one-to-one link between analytic elements and hydrogeologic features make TTim well suited for education.},
+	language = {en},
+	number = {4},
+	urldate = {2023-03-17},
+	journal = {Hydrogeology Journal},
+	author = {Bakker, Mark},
+	month = jun,
+	year = {2013},
+	keywords = {analytic, analytic element, Analytic element method, and is implemented in, bakker 2012, code ttim, computer, groundwater modeling, Groundwater modeling, method, multi-layer, Multi-layer, pronounced, tee-tim, the free and open-source, transient fl ow, Transient flow},
+	pages = {935--943},
+	file = {Full Text:/home/david/Zotero/storage/SDZGNFL7/Bakker - 2013 - Semi-analytic modeling of transient multi-layer fl.pdf:application/pdf},
+}
+
+@incollection{bakker_analytic_2013,
+	address = {New York, NY},
+	title = {Analytic {Modeling} of {Transient} {Multilayer} {Flow}},
+	isbn = {978-1-4614-6479-2},
+	url = {https://doi.org/10.1007/978-1-4614-6479-2_5},
+	abstract = {An approach is presented for the semi-analytic simulation of transient flow in systems consisting of an arbitrary number of layers. Storage in both aquifer layers and leaky layers is taken into account. Flow in the system is generated by wells and line-sinks. Wells and line-sinks may be open to an arbitrary number of layers, which allows for the simulation of multi-aquifer wells, abandoned wells, partially penetrating streams, and linear fractures that provide a hydraulic connection between aquifer layers.},
+	language = {en},
+	urldate = {2023-03-17},
+	booktitle = {Advances in {Hydrogeology}},
+	publisher = {Springer},
+	author = {Bakker, Mark},
+	editor = {Mishra, Phoolendra K. and Kuhlman, Kristopher L.},
+	year = {2013},
+	doi = {10.1007/978-1-4614-6479-2_5},
+	keywords = {Aquifer Layer, Multilayer System, Stream Segment, Transient Flow, Unconfined Aquifer},
+	pages = {95--114},
+	file = {Full Text:/home/david/Zotero/storage/83T646QS/Bakker - 2013 - Analytic Modeling of Transient Multilayer Flow.pdf:application/pdf},
+}
diff --git a/docs/conf.py b/docs/conf.py
@@ -27,6 +27,7 @@
     "myst_nb",
     "sphinx_design",
     "sphinx.ext.autosectionlabel",
+    "sphinxcontrib.bibtex",
 ]
 
 templates_path = ["_templates"]
@@ -48,15 +49,15 @@
 html_theme_options = {
     "github_url": "https://github.com/mbakker7/ttim",
     "use_edit_page_button": True,
-    "header_links_before_dropdown": 6,
-    "icon_links": [
-        {
-            "name": "GitHub",  # Label for this link
-            "url": "https://github.com/mbakker7/ttim",  # required
-            "icon": "fab fa-github-square",
-            "type": "fontawesome",  # Default is fontawesome
-        }
-    ],
+    "header_links_before_dropdown": 7,
+    # "icon_links": [
+    #     {
+    #         "name": "GitHub",  # Label for this link
+    #         "url": "https://github.com/mbakker7/ttim",  # required
+    #         "icon": "fab fa-github-square",
+    #         "type": "fontawesome",  # Default is fontawesome
+    #     }
+    # ],
 }
 
 html_context = {
@@ -100,3 +101,9 @@
 
 nb_execution_allow_errors = True  # Allow errors in notebooks, to see the error online
 nb_execution_mode = "auto"
+
+# -- bibtex options ------------------------------------------------------------------
+
+# Add some settings for bibtex
+bibtex_bibfiles = ["06about/publications.bib"]
+bibtex_reference_style = "author_year"
diff --git a/docs/examples/index.rst b/docs/examples/index.rst
-Original file line number
+Diff line change
@@ Expand Up / @@ -109,4 +109,4 @@ Info.plist @@
     # docs
     _build
-    /docs/api/generated/
+    /docs/05api/generated/