Some doc changes and building pit updates (#99)

* add building pits to docs * add 3D building pit elements - add 3D versions of building pit elements (leaky and impermeable) - allow resistance to be passed as array (LeakyBuildingPit) - update docs * add building pits to docs * start of new docs (#93) (#98) * start of new docs * Create tutorial0_well_single_layer.ipynb first tutorial notebook * add sections following tip by @Hugovdberg - merge nb output streams - improve some toctrees - improve tutorial nb (start w/ H1 heading) * modified tutorial 0 and added tutorial 1 * renamed tutorial 0 --------- Co-authored-by: Mark Bakker <markbak@gmail.com> * update nb * Update index.rst fixed some links * update circular pit nb * return intnormflux per layer and line segment * update nb * Updated documentation of intnormflux * up version * fix parallel builds for coveralls * get rid of extra github icon --------- Co-authored-by: Davíd Brakenhoff <d.brakenhoff@artesia-water.nl>
mbakker7 · Dec 6, 2023 · d980d6a · d980d6a
1 parent 940a847
commit d980d6a
Show file tree

Hide file tree

Showing 12 changed files with 619 additions and 134 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -44,4 +44,14 @@ jobs:
       - name: Publish to coveralls.io
         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/docs/00tutorials/index.rst b/docs/00tutorials/index.rst
@@ -8,9 +8,15 @@ TimML tutorials.
     :hidden:
     :glob:
 
-    tutorial0_well_single_layer
+    tutorial0_well_single_layer_aquifer
+    tutorial1_well_multi_layer_aquifer
 
 
-`Tutorial 1 - Well in a single aquifer`_
+`Tutorial 0 - Well in a single aquifer`_
 
-.. _Tutorial 1 - Well in a single aquifer: tutorial0_well_single_layer.html
+.. _Tutorial 0 - Well in a single aquifer: tutorial0_well_single_layer_aquifer.html
+
+
+`Tutorial 1 - Well in a multi-aquifer system`_
+
+.. _Tutorial 1 - Well in a multi aquifer system: tutorial1_well_multi_layer_aquifer.html
diff --git a/docs/01howto/elements/inhoms.rst b/docs/01howto/elements/inhoms.rst
@@ -1,7 +1,9 @@
 Inhomogeneities
 ===============
 
-Polygonal inhomogeneities can be added in the following ways:
+The following polygonal inhomogeneities are available in TimML. Note that there are 
+inhomogeneities for both multi-aquifer style models (:class:`~timml.model.ModelMaq`)
+and single aquifer models (with multiple layers, :class:`~timml.model.Model3D`).
 
 1. :class:`~timml.inhomogeneity.PolygonInhomMaq`, which is an inhomogeneity consisting
    of a regular sequence of aquifer - leaky layer - aquifer - leaky layer, aquifer, etc.
@@ -12,10 +14,18 @@ Polygonal inhomogeneities can be added in the following ways:
    the resistance from the middle of one layer to the middle of the next layer. Vertical
    anisotropy can be specified. The system may be bounded on top by a leaky layer.
 
-3. :class:`~timml.inhomogeneity.BuildingPit`, which is an inhomogeneity similar to
+3. :class:`~timml.inhomogeneity.BuildingPitMaq`, which is an inhomogeneity similar to
    `PolygonInhomMaq` in which impermeable walls can be placed along the edges of the
    imhomogeneity in specified layers.
 
-4. :class:`~timml.inhomogeneity.LeakyBuildingPit`, which is an inhomogeneity like
-   `BuildingPit` but with leaky walls instead of impermeable walls. The resistance of the
+4. :class:`~timml.inhomogeneity.BuildingPit3D`, which is an inhomogeneity similar to
+   `PolygonInhom3D` in which impermeable walls can be placed along the edges of the
+   imhomogeneity in specified layers.
+
+5. :class:`~timml.inhomogeneity.LeakyBuildingPitMaq`, which is an inhomogeneity like
+   `BuildingPitMaq` but with leaky walls instead of impermeable walls. The resistance of the
+   leaky walls can be specified.
+
+6. :class:`~timml.inhomogeneity.LeakyBuildingPit3D`, which is an inhomogeneity like
+   `BuildingPit3D` but with leaky walls instead of impermeable walls. The resistance of the
    leaky walls can be specified.
diff --git a/docs/conf.py b/docs/conf.py
@@ -49,14 +49,14 @@
     "github_url": "https://github.com/mbakker7/timml",
     "use_edit_page_button": True,
     "header_links_before_dropdown": 6,
-    "icon_links": [
-        {
-            "name": "GitHub",  # Label for this link
-            "url": "https://github.com/mbakker7/timml",  # required
-            "icon": "fab fa-github-square",
-            "type": "fontawesome",  # Default is fontawesome
-        }
-    ],
+    # "icon_links": [
+    #     {
+    #         "name": "GitHub",  # Label for this link
+    #         "url": "https://github.com/mbakker7/timml",  # required
+    #         "icon": "fab fa-github-square",
+    #         "type": "fontawesome",  # Default is fontawesome
+    #     }
+    # ],
 }
 
 html_context = {

diff --git a/notebooks/BuildingPit.ipynb b/notebooks/BuildingPit.ipynb
diff --git a/notebooks/circular_buildingpit.ipynb b/notebooks/circular_buildingpit.ipynb
diff --git a/timml/__init__.py b/timml/__init__.py
@@ -18,8 +18,10 @@
 from .circareasink import CircAreaSink
 from .constant import Constant, ConstantStar
 from .inhomogeneity import (
-    BuildingPit,
-    LeakyBuildingPit,
+    BuildingPit3D,
+    BuildingPitMaq,
+    LeakyBuildingPit3D,
+    LeakyBuildingPitMaq,
     PolygonInhom3D,
     PolygonInhomMaq,
 )

diff --git a/timml/equation.py b/timml/equation.py
@@ -523,9 +523,9 @@ def equation(self):
                         / self.aqout.Tcol[self.layers]
                     )
 
-                    mat[
-                        istart : istart + self.nlayers, ieq : ieq + e.nunknowns
-                    ] = flux - self.resfac * (headin - headout)
+                    mat[istart : istart + self.nlayers, ieq : ieq + e.nunknowns] = (
+                        flux - self.resfac * (headin - headout)
+                    )
                     ieq += e.nunknowns
                 else:
                     flux = self.intflux(
@@ -562,7 +562,7 @@ def equation(self):
                         / self.aqout.T[self.layers]
                     )
 
-                    rhs[istart : istart + self.nlayers] += -flux + self.resfac * (
-                        headin - headout
+                    rhs[istart : istart + self.nlayers] += (
+                        -flux + self.resfac.squeeze() * (headin - headout)
                     )
         return mat, rhs