Add integral model solutions

.github/workflows/main.yml

@@ -12,34 +12,33 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-env:
-  # needed by coveralls
-  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
 jobs:
   source_check:
     name: source check
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --editable .[check]
+          pip install --editable .[check,test]
+          pip install "coveralls>=3.0.0"
 
       - name: black check
         run: |
           python -m black --check --diff --color .
 
+      - name: black preview
+        run: |
+          python -m black --preview --diff --color .
+
       - name: isort check
         run: |
           python -m isort --check --diff --color .
@@ -48,53 +47,60 @@ jobs:
         run: |
           python -m pylint src/anaflow/
 
+      - name: coveralls check
+        run: |
+          python -m pytest --cov anaflow --cov-report term-missing -v tests/
+          python -m coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
   build_sdist:
     name: sdist on ${{ matrix.os }} with py ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        os: [ubuntu-latest, windows-latest, macos-13]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build coveralls>=3.0.0
+          pip install build
           pip install --editable .[test]
 
       - name: Run tests
         run: |
           python -m pytest --cov anaflow --cov-report term-missing -v tests/
-          python -m coveralls --service=github
 
       - name: Build sdist
         run: |
           python -m build
 
-      - uses: actions/upload-artifact@v2
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
+      - uses: actions/upload-artifact@v4
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
         with:
-          path: dist
+          name: dist
+          path: dist/*
 
   upload_to_pypi:
     needs: [build_sdist]
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          name: dist
           path: dist
 
       - name: Publish to Test PyPI

.gitignore

@@ -63,6 +63,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/source/sg_execution_times.rst
 
 # PyBuilder
 target/

.readthedocs.yml

@@ -1,12 +1,16 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
 sphinx:
   configuration: docs/source/conf.py
 
-formats: all
+formats: [pdf]
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .

CHANGELOG.md

@@ -2,6 +2,24 @@
 
 All notable changes to **AnaFlow** will be documented in this file.
 
+## [1.2.0] - 2025-05
+
+See [#12](https://github.com/GeoStat-Framework/AnaFlow/pull/12)
+
+### Enhancements
+- added solutions based on the effective transmissivity for the ["Integral" variogram model](https://geostat-framework.readthedocs.io/projects/gstools/en/v1.7.0/api/gstools.covmodel.Integral.html):
+  - `ext_thiem_int`: steady state solution
+  - `ext_thiem_int_3d`: steady state solution incorporating vertical anisotropy
+  - `ext_theis_int`: transient solution
+  - `ext_theis_int_3d`: transient solution incorporating vertical anisotropy
+- added `fix_T_well` and `fix_K_well` bool flag to transient heterogeneous solutions to be able to set if the well value for the effective transmissivity/conductivity should be determined from the limit (`True`) or from the upscaled value in the first ring segment (`False`, default)
+  - **breaking**: the previous behavior was effectively this set to `True`, which for steep effective curves resulted in an increasing error in the effective head near the well
+
+### Changes
+- updated docs (use myst parser for markdown files, only generate html and pdf)
+- updated CI (fixed artifacts up-/download action, see #14)
+- use hatchling as build backend
+
 
 ## [1.1.0] - 2023-04
 
@@ -88,6 +106,7 @@ Containing:
 - lap_transgwflow_cyl - Solution for a diskmodel in laplace inversion
 
 
+[1.2.0]: https://github.com/GeoStat-Framework/AnaFlow/compare/v1.1.0...v1.2.0
 [1.1.0]: https://github.com/GeoStat-Framework/AnaFlow/compare/v1.0.1...v1.1.0
 [1.0.1]: https://github.com/GeoStat-Framework/AnaFlow/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/GeoStat-Framework/AnaFlow/compare/v0.4.0...v1.0.0

docs/source/changelog.rst

@@ -1 +1,2 @@
-.. mdinclude:: ../../CHANGELOG.md
+.. include:: ../../CHANGELOG.md
+   :parser: myst_parser.docutils_

docs/source/conf.py

@@ -55,7 +55,7 @@ def setup(app):
     "sphinx.ext.napoleon",  # parameters look better than with numpydoc only
     "numpydoc",
     "sphinx_gallery.gen_gallery",
-    "m2r2",
+    "myst_parser",
 ]
 
 # autosummaries from source-files
@@ -87,8 +87,12 @@ def setup(app):
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
 # source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+# source_suffix = ".rst"
 
 # The master toctree document.
 # --> this is the sitemap (or content-list in latex -> needs a heading)
@@ -141,7 +145,7 @@ def setup(app):
     #    'canonical_url': '',
     #    'analytics_id': '',
     "logo_only": False,
-    "display_version": True,
+    "version_selector": True,
     "prev_next_buttons_location": "top",
     #    'style_external_links': False,
     #    'vcs_pageview_mode': '',
@@ -267,7 +271,7 @@ def setup(app):
     # Remove the "Download all examples" button from the top level gallery
     "download_all_examples": False,
     # Sort gallery example by file name instead of number of lines (default)
-    "within_subsection_order": FileNameSortKey,
+    "within_subsection_order": "FileNameSortKey",
     # directory where function granular galleries are stored
     "backreferences_dir": None,
     # Modules for which function level galleries are created.  In

examples/01_call_theis.py

@@ -7,6 +7,7 @@
 
 Reference: `Theis 1935 <https://doi.org/10.1029/TR016i002p00519>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 

examples/02_call_ext_theis2d.py

@@ -12,6 +12,7 @@
 
 Reference: `Zech et. al. 2016 <http://dx.doi.org/10.1002/2015WR018509>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -51,12 +52,8 @@
     label_TG = "Theis($T_G$)" if i == 0 else None
     label_TH = "Theis($T_H$)" if i == 0 else None
     label_ef = "extended Theis" if i == 0 else None
-    plt.plot(
-        rad, head_TG[i], label=label_TG, color="C" + str(i), linestyle="--"
-    )
-    plt.plot(
-        rad, head_TH[i], label=label_TH, color="C" + str(i), linestyle=":"
-    )
+    plt.plot(rad, head_TG[i], label=label_TG, color="C" + str(i), linestyle="--")
+    plt.plot(rad, head_TH[i], label=label_TH, color="C" + str(i), linestyle=":")
     plt.plot(rad, head_ef[i], label=label_ef, color="C" + str(i))
     time_ticks.append(head_ef[i][-1])
 

examples/03_call_ext_theis3d.py

@@ -14,6 +14,7 @@
 
 Reference: `Müller 2015 <http://dx.doi.org/10.13140/RG.2.2.34074.24002>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -59,12 +60,8 @@
     label_TG = "Theis($K_{efu}$)" if i == 0 else None
     label_TH = "Theis($K_H$)" if i == 0 else None
     label_ef = "extended Theis 3D" if i == 0 else None
-    plt.plot(
-        rad, head_Kefu[i], label=label_TG, color="C" + str(i), linestyle="--"
-    )
-    plt.plot(
-        rad, head_KH[i], label=label_TH, color="C" + str(i), linestyle=":"
-    )
+    plt.plot(rad, head_Kefu[i], label=label_TG, color="C" + str(i), linestyle="--")
+    plt.plot(rad, head_KH[i], label=label_TH, color="C" + str(i), linestyle=":")
     plt.plot(rad, head_ef[i], label=label_ef, color="C" + str(i))
     time_ticks.append(head_ef[i][-1])
 

examples/04_call_ext_theis_tpl.py

@@ -13,6 +13,7 @@
 
 Reference: (not yet published)
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -62,12 +63,8 @@
     label_TG = "Theis($K_G$)" if i == 0 else None
     label_TH = "Theis($K_H$)" if i == 0 else None
     label_ef = "extended Theis TPL 2D" if i == 0 else None
-    plt.plot(
-        rad, head_KG[i], label=label_TG, color="C" + str(i), linestyle="--"
-    )
-    plt.plot(
-        rad, head_KH[i], label=label_TH, color="C" + str(i), linestyle=":"
-    )
+    plt.plot(rad, head_KG[i], label=label_TG, color="C" + str(i), linestyle="--")
+    plt.plot(rad, head_KH[i], label=label_TH, color="C" + str(i), linestyle=":")
     plt.plot(rad, head_ef[i], label=label_ef, color="C" + str(i))
     time_ticks.append(head_ef[i][-1])
 

examples/05_call_neuman2004.py

@@ -14,6 +14,7 @@
 
 Reference: `Neuman 2004 <https://doi.org/10.1029/2003WR002405>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -61,12 +62,8 @@
     label_TG = "Theis($T_G$)" if i == 0 else None
     label_TH = "Theis($T_H$)" if i == 0 else None
     label_ef = "transient Neuman [2004]" if i == 0 else None
-    plt.plot(
-        rad, head_TG[i], label=label_TG, color="C" + str(i), linestyle="--"
-    )
-    plt.plot(
-        rad, head_TH[i], label=label_TH, color="C" + str(i), linestyle=":"
-    )
+    plt.plot(rad, head_TG[i], label=label_TG, color="C" + str(i), linestyle="--")
+    plt.plot(rad, head_TH[i], label=label_TH, color="C" + str(i), linestyle=":")
     plt.plot(rad, head_ef[i], label=label_ef, color="C" + str(i))
     time_ticks.append(head_ef[i][-1])
 

examples/06_compare_extthiem2d_grfsteady.py

@@ -11,6 +11,7 @@
 - `Schneider & Attinger 2008 <https://doi.org/10.1029/2007WR005898>`__
 - `Zech & Attinger 2016 <https://doi.org/10.5194/hess-20-1655-2016>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 

examples/07_compare_extthiem3d_grfsteady.py

@@ -8,6 +8,7 @@
 
 Reference: `Zech et. al. 2012 <https://doi.org/10.1029/2012WR011852>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 

examples/08_compare_extthiem2d_neuman.py

@@ -13,6 +13,7 @@
 - `Neuman 2004 <https://doi.org/10.1029/2003WR002405>`__
 - `Zech & Attinger 2016 <https://doi.org/10.5194/hess-20-1655-2016>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 

examples/09_compare_exttheis2d_neuman.py

@@ -13,6 +13,7 @@
 - `Neuman 2004 <https://doi.org/10.1029/2003WR002405>`__
 - `Zech et. al. 2016 <http://dx.doi.org/10.1002/2015WR018509>`__
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -40,9 +41,7 @@
     plt.plot(rad, head2[i], label=label2, color="C" + str(i), linestyle="--")
     time_ticks.append(head1[i][-1])
 
-plt.title(
-    "$T_G={}$, $\sigma^2={}$, $\ell={}$, $S={}$".format(TG, var, len_scale, S)
-)
+plt.title(r"$T_G={}$, $\sigma^2={}$, $\ell={}$, $S={}$".format(TG, var, len_scale, S))
 plt.xlabel("r in [m]")
 plt.ylabel("h in [m]")
 plt.legend()

examples/10_convergence_ext_theis_tpl.py

@@ -7,6 +7,7 @@
 
 Reference: (not yet published)
 """
+
 import numpy as np
 from matplotlib import pyplot as plt
 
@@ -25,9 +26,7 @@
 S = 1e-4  # storativity
 rate = -1e-4  # pumping rate
 
-head1 = ext_thiem_tpl(
-    rad, r_ref, KG, len_scale, hurst, var, dim=dim, rate=rate
-)
+head1 = ext_thiem_tpl(rad, r_ref, KG, len_scale, hurst, var, dim=dim, rate=rate)
 head2 = ext_theis_tpl(
     time, rad, S, KG, len_scale, hurst, var, dim=dim, rate=rate, r_bound=r_ref
 )