Merge pull request #56 from mbakker7/dev

Update master for release v0.6.6
mbakker7 · Feb 14, 2024 · 297343e · 297343e
2 parents 8a05801 + e813936
commit 297343e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,9 +5,11 @@ on:
   push:
     branches:
       - master
+      - dev
   pull_request:
     branches:
       - master
+      - dev
   workflow_dispatch:
 
 jobs:
@@ -41,6 +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/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -14,18 +14,21 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: '3.x'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install wheel twine build
+    
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python3 -m build
+        python3 -m twine upload --repository pypi dist/*
diff --git a/.gitignore b/.gitignore
@@ -109,4 +109,4 @@ Info.plist
 
 # docs
 _build
-/docs/api/generated/
+/docs/05api/generated/
diff --git a/README.md b/README.md
@@ -16,19 +16,21 @@ New analytic elements may be added to the code without making any changes in the
 TTim is coded in Python and uses numba to speed up evaluation of the line elements and inverse laplace transforms.
 
 ## Latest version
-New in version 0.5:
-* FORTRAN extension has been ported to Python and numba (many thanks to Davíd Brakenhoff)
-* Python invlap routine (again with numba) ported from routine by Kris Kuhlman
-* New invlap routine requires fewer terms in inverse Laplace transform (M=10 is usually enough)
-* Calibrate now works on ranges of parameters.
-* Calibrate now adjusts c values between layers when calibrating for hydraulic conductivity in Model3D
+New in version 0.6.6:
+* Many documentation improvements: new look, better organization, tutorials, how-to guides, etc. Check it out [here](https://ttim.readthedocs.io)!
 
 ## Installation
 
 **Python versions and dependencies**
 
-TTim requires **Python** >= 3.6 and can be installed from PyPI.
-Required packages: **NumPy** >=1.12, **Scipy** >=0.19 and **matplotlib** >=2.0, **numba>=0.4**, **lmfit>=1.0**
+TTim requires Python >= 3.8 and can be installed from PyPI.
+
+Required packages: 
+* numpy
+* scipy
+* matplotlib 
+* numba
+* lmfit
 
 **Installation:**
 

diff --git a/docs/00tutorials/index.rst b/docs/00tutorials/index.rst
@@ -0,0 +1,10 @@
+Tutorials
+=========
+
+TTim tutorials.
+
+.. toctree::
+    :maxdepth: 3
+    :glob:
+
+    models.rst
diff --git a/docs/userguide/getting_started/models.rst → docs/00tutorials/models.rst b/docs/userguide/getting_started/models.rst → docs/00tutorials/models.rst
diff --git a/notebooks/data/oudekorendijk_h30.dat → docs/01howto/data/oudekorendijk_h30.dat b/notebooks/data/oudekorendijk_h30.dat → docs/01howto/data/oudekorendijk_h30.dat
diff --git a/notebooks/data/oudekorendijk_h90.dat → docs/01howto/data/oudekorendijk_h90.dat b/notebooks/data/oudekorendijk_h90.dat → docs/01howto/data/oudekorendijk_h90.dat
diff --git a/docs/01howto/howto_pumpingtest.ipynb b/docs/01howto/howto_pumpingtest.ipynb
diff --git a/docs/01howto/index.rst b/docs/01howto/index.rst
@@ -0,0 +1,10 @@
+How To Guides
+=============
+
+This section contains how to guides on building groundwater models with TTim.
+
+
+.. toctree::
+    :maxdepth: 1
+
+    howto_pumpingtest
diff --git a/docs/userguide/elements/areasinks.rst → docs/02concepts/elements/areasinks.rst b/docs/userguide/elements/areasinks.rst → docs/02concepts/elements/areasinks.rst
diff --git a/docs/userguide/elements/index.rst → docs/02concepts/elements/index.rst b/docs/userguide/elements/index.rst → docs/02concepts/elements/index.rst
diff --git a/docs/userguide/elements/linedoublets.rst → docs/02concepts/elements/linedoublets.rst b/docs/userguide/elements/linedoublets.rst → docs/02concepts/elements/linedoublets.rst
diff --git a/docs/userguide/elements/linesinks.rst → docs/02concepts/elements/linesinks.rst b/docs/userguide/elements/linesinks.rst → docs/02concepts/elements/linesinks.rst
diff --git a/docs/userguide/elements/wells.rst → docs/02concepts/elements/wells.rst b/docs/userguide/elements/wells.rst → docs/02concepts/elements/wells.rst
diff --git a/docs/02concepts/index.rst b/docs/02concepts/index.rst
@@ -0,0 +1,11 @@
+Concepts
+========
+
+This section contains explanations of some basic concepts that are used in TTim.
+
+
+.. toctree::
+    :maxdepth: 3
+
+    elements/index.rst
+    pathlines.rst
diff --git a/docs/userguide/getting_started/pathlines.rst → docs/02concepts/pathlines.rst b/docs/userguide/getting_started/pathlines.rst → docs/02concepts/pathlines.rst
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
@@ -157,7 +157,7 @@
     "plt.plot(to, hm[0], \"r\", label=\"modeled\")\n",
     "plt.legend()\n",
     "plt.xlabel(\"time (d)\")\n",
-    "plt.ylabel(\"head (m)\");"
+    "plt.ylabel(\"head (m)\")"
    ]
   },
   {
@@ -339,7 +339,7 @@
     "plt.plot(to, hm[0], \"r\", label=\"modeled\")\n",
     "plt.legend()\n",
     "plt.xlabel(\"time (d)\")\n",
-    "plt.ylabel(\"head (m)\");"
+    "plt.ylabel(\"head (m)\")"
    ]
   },
   {
@@ -503,7 +503,7 @@
     "plt.plot(to, hm[0], \"r\", label=\"modeled\")\n",
     "plt.legend()\n",
     "plt.xlabel(\"time (d)\")\n",
-    "plt.ylabel(\"head (m)\");"
+    "plt.ylabel(\"head (m)\")"
    ]
   }
  ],

diff --git a/notebooks/circareasink_example.ipynb → docs/03examples/circareasink_example.ipynb b/notebooks/circareasink_example.ipynb → docs/03examples/circareasink_example.ipynb
@@ -85,7 +85,7 @@
     "plt.axhline(-qxb, color=\"r\", ls=\"--\")\n",
     "plt.xlabel(\"x (m)\")\n",
     "plt.ylabel(\"Qx (m^2/d)\")\n",
-    "plt.legend(loc=\"best\");"
+    "plt.legend(loc=\"best\")"
    ]
   },
   {
@@ -168,7 +168,7 @@
     "plt.semilogx(t, h[0])\n",
     "plt.xlabel(\"time\")\n",
     "plt.ylabel(\"head\")\n",
-    "plt.title(\"head at center of area-sink\");"
+    "plt.title(\"head at center of area-sink\")"
    ]
   },
   {

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
@@ -101,7 +101,7 @@
     "plt.semilogx(t, h2b[0], \"r--\")\n",
     "plt.xlabel(\"time\")\n",
     "plt.ylabel(\"head\")\n",
-    "plt.legend();"
+    "plt.legend()"
    ]
   },
   {
@@ -146,7 +146,7 @@
    "source": [
     "plt.figure(figsize=(12, 4))\n",
     "ml.contour([-2, 2, -2, 2], [40, 40], t=5)\n",
-    "ml2.contour([-2, 2, -2, 2], [40, 40], t=5);"
+    "ml2.contour([-2, 2, -2, 2], [40, 40], t=5)"
    ]
   },
   {

diff --git a/docs/03examples/data/oudekorendijk_h30.dat b/docs/03examples/data/oudekorendijk_h30.dat
@@ -0,0 +1,34 @@
+0.1 0.04
+0.25 0.08
+0.50 0.13
+0.70 0.18
+1.0 0.23
+1.40 0.28
+1.90 0.33
+2.33 0.36
+2.80 0.39
+3.36 0.42
+4.00 0.45
+5.35 0.50
+6.80 0.54
+8.3 0.57
+8.7 0.58
+10.0 0.60
+13.1 0.64
+ 18 0.680 
+ 27 0.742 
+ 33 0.753 
+ 41 0.779 
+ 48 0.793 
+ 59 0.819 
+ 80 0.855 
+ 95 0.873 
+139 0.915 
+181 0.935 
+245 0.966 
+300 0.990 
+360 1.007 
+480 1.050 
+600 1.053 
+728 1.072 
+830 1.088 
diff --git a/docs/03examples/data/oudekorendijk_h90.dat b/docs/03examples/data/oudekorendijk_h90.dat
@@ -0,0 +1,35 @@
+1.5  0.015 
+2.0  0.021 
+2.16 0.023 
+2.66 0.044 
+3    0.054 
+3.5  0.075 
+4    0.090 
+4.33 0.104 
+5.5  0.133 
+6    0.153 
+7.5  0.178 
+9    0.206 
+13   0.250 
+15   0.275 
+18   0.305 
+25   0.348 
+30   0.364
+40 0.404 
+53 0.429 
+60 0.444 
+75 0.467 
+90 0.494 
+105 0.507
+120 0.528
+150 0.550
+180 0.569
+248 0.593
+301 0.614
+363 0.636
+422 0.657
+542 0.679
+602 0.688
+680 0.701
+785 0.718
+845 0.716
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 +1,91 @@
+Examples
+========
+
+TTim example notebooks.
+
+.. toctree::
+    :maxdepth: 4
+    :hidden:
+
+    well_example
+    well_near_wall
+    well_near_river_or_wall
+    line_sink_well_sol
+    wells_in_different_systems
+    ttim_exercise1_sol
+    meandering_river
+    circareasink_example
+    pathline_trace
+    aem_ttim_sol
+    pumpingtest_hypothetical
+    pumpingtest
+    ttim_pumptest_neuman
+    ttim_slugtest
+    theis_storage
+    ttim_neuman_comparison
+    compare_wells_linesink
+    line-sink-ditch
+
+Modeling wells
+--------------
+
+* `well_example`_
+* `well_near_wall`_
+* `well_near_river_or_wall`_
+* `line_sink_well_sol`_
+* `wells_in_different_systems`_
+* `ttim_exercise1_sol`_
+
+Modeling rivers
+---------------
+
+* `meandering_river`_
+
+Recharge
+--------
+
+* `circareasink_example`_
+
+Pathlines
+---------
+
+* `pathline_trace`_
+
+
+Pumping tests
+-------------
+
+* `aem_ttim_sol`_
+* `pumpingtest_hypothetical`_
+* `pumpingtest`_
+* `ttim_pumptest_neuman`_
+* `ttim_slugtest`_
+
+Benchmarks
+----------
+
+* `theis_storage`_
+* `ttim_neuman_comparison`_
+* `Comparing linesink with row of wells`_
+* `line-sink-ditch`_
+
+
+.. _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_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
@@ -111,7 +111,7 @@
     "Q = ls1.discharge(t)\n",
     "plt.semilogx(t, Q[0])\n",
     "plt.ylabel(\"Q [m$^3$/d]\")\n",
-    "plt.xlabel(\"time [days]\");"
+    "plt.xlabel(\"time [days]\")"
    ]
   },
   {
@@ -234,7 +234,7 @@
     "Q = ls1.discharge(t)\n",
     "plt.plot(t, Q[0])\n",
     "plt.ylabel(\"Q [m$^3$/d]\")\n",
-    "plt.xlabel(\"time [days]\");"
+    "plt.xlabel(\"time [days]\")"
    ]
   }
  ],

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,
-Original file line number
+Diff line change
@@ Expand Up / @@ -109,4 +109,4 @@ Info.plist @@
     # docs
     _build
-    /docs/api/generated/
+    /docs/05api/generated/