Merge pull request #127 from timflow-org/dev

Release v0.3.0

Author: dbrakenhoff

.readthedocs.yaml

@@ -20,7 +20,6 @@ sphinx:
 
 python:
   install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+    - method: uv
+      command: sync
+      extras: ["docs"]

docs/Makefile

@@ -3,7 +3,7 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
+SPHINXOPTS    ?= -j auto
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build

docs/_templates/autoapi/index.rst

@@ -2,7 +2,7 @@ API Reference
 =============
 
 This section contains the Documentation of the Application Programming Interface (API)
-of Pastas. The information in this section is automatically created from the
+of timflow. The information in this section is automatically created from the
 documentation strings in original Python code. In the left-hand menu you will find the
 different categories of the API documentation.
 

docs/_templates/autoapi/python/class.rst

@@ -0,0 +1,104 @@
+{% if obj.display %}
+   {% if is_own_page %}
+{{ obj.short_name }}
+{{ "=" * obj.short_name | length }}
+
+   {% endif %}
+   {% set visible_children = obj.children|selectattr("display")|list %}
+   {% set own_page_children = visible_children|selectattr("type", "in", own_page_types)|list %}
+   {% if is_own_page and own_page_children %}
+.. toctree::
+   :hidden:
+
+      {% for child in own_page_children %}
+   {{ child.include_path }}
+      {% endfor %}
+
+   {% endif %}
+.. py:{{ obj.type }}:: {% if is_own_page %}{{ obj.id }}{% else %}{{ obj.short_name }}{% endif %}{% if obj.type_params %}[{{ obj.type_params }}]{% endif %}{% if obj.args %}({{ obj.args }}){% endif %}
+
+   {% for (args, return_annotation) in obj.overloads %}
+      {{ " " * (obj.type | length) }}   {{ obj.short_name }}{% if args %}({{ args }}){% endif %}
+
+   {% endfor %}
+   {% if obj.bases %}
+      {% if "show-inheritance" in autoapi_options %}
+
+   Bases: {% for base in obj.bases %}{{ base|link_objs }}{% if not loop.last %}, {% endif %}{% endfor %}
+      {% endif %}
+
+
+      {% if "show-inheritance-diagram" in autoapi_options and obj.bases != ["object"] %}
+   .. autoapi-inheritance-diagram:: {{ obj.obj["full_name"] }}
+      :parts: 1
+         {% if "private-members" in autoapi_options %}
+      :private-bases:
+         {% endif %}
+
+      {% endif %}
+   {% endif %}
+   {% if obj.docstring %}
+
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+   {% for obj_item in visible_children %}
+      {% if obj_item.type not in own_page_types %}
+
+   {{ obj_item.render()|indent(3) }}
+      {% endif %}
+   {% endfor %}
+   {% if is_own_page and own_page_children %}
+      {% set visible_attributes = own_page_children|selectattr("type", "equalto", "attribute")|list %}
+      {% if visible_attributes %}
+Attributes
+----------
+
+.. autoapisummary::
+
+         {% for attribute in visible_attributes %}
+   {{ attribute.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_exceptions = own_page_children|selectattr("type", "equalto", "exception")|list %}
+      {% if visible_exceptions %}
+Exceptions
+----------
+
+.. autoapisummary::
+
+         {% for exception in visible_exceptions %}
+   {{ exception.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_classes = own_page_children|selectattr("type", "equalto", "class")|list %}
+      {% if visible_classes %}
+Classes
+-------
+
+.. autoapisummary::
+
+         {% for klass in visible_classes %}
+   {{ klass.id }}
+         {% endfor %}
+
+
+      {% endif %}
+      {% set visible_methods = own_page_children|selectattr("type", "equalto", "method")|list %}
+      {% if visible_methods %}
+Methods
+-------
+
+.. autoapisummary::
+
+            {% for method in visible_methods %}
+   {{ method.id }}
+            {% endfor %}
+
+
+      {% endif %}
+   {% endif %}
+{% endif %}

docs/conf.py

@@ -31,7 +31,7 @@
 ]
 
 # templates_path = ["_templates"]
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ["_build", "_templates", "Thumbs.db", ".DS_Store"]
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
@@ -79,8 +79,16 @@
     "inherited-members",
     "show-inheritance",
 ]
-autoapi_own_page_level = "method"
+autoapi_own_page_level = "class"
 autoapi_template_dir = "_templates/autoapi"
+suppress_warnings = ["autoapi"]
+
+# Keep API signatures and section navigation compact by omitting module prefixes
+# (e.g., show `River` instead of `timflow.steady.linesink.River`).
+add_module_names = False
+
+# Keep local object TOC entries compact in the right sidebar.
+toc_object_entries_show_parents = "hide"
 
 # -- Numpydoc settings ----------------------------------------------------------------
 
@@ -99,31 +107,22 @@
 
 # -- myst_nb options ------------------------------------------------------------------
 
+nb_execution_mode = "cache"
+
 nb_execution_allow_errors = True  # Allow errors in notebooks, to see the error online
-nb_execution_mode = "auto"
-nb_merge_streams = True
+nb_execution_show_tb = True
+nb_execution_timeout = 100
 nb_execution_excludepatterns = [
     "besselnumba_timing.ipynb",
     "vertical_anisotropy.ipynb",
+    "transient/04pumpingtests/*.ipynb",
 ]
 
 myst_enable_extensions = ["dollarmath", "amsmath", "html_image"]
 myst_dmath_double_inline = True
-nb_render_markdown_format = "myst"  # Enable MyST markdown parsing in notebooks
-nb_render_text_lexer = "myst-ansi"  # Better rendering of ANSI output
-# nb_mime_priority_overrides = {
-#     "html": (
-#         "application/vnd.jupyter.widget-view+json",
-#         "application/javascript",
-#         "text/html",
-#         "image/svg+xml",
-#         "image/png",
-#         "image/jpeg",
-#         "text/markdown",
-#         "text/latex",
-#         "text/plain",
-#     )
-# }
+
+nb_merge_streams = True
+
 
 # -- bibtex options ------------------------------------------------------------------
 

docs/index.rst

@@ -54,5 +54,7 @@ view the code documentation.
 
    Steady <steady/index>
    Transient <transient/index>
+   Utilities <utils/index>
    Code Reference <api/index>
+   Timings <timings>
    Cite <about/index>

docs/steady/00userguide/tutorials/tutorial1_well_multi_layer_aquifer.ipynb

@@ -250,13 +250,6 @@
     "    ax=axes,\n",
     ")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

docs/steady/02examples/01_well_in_uniform_flow.ipynb

@@ -222,6 +222,13 @@
     "print(\"The discharge at the abandoned well is:\")\n",
     "print(wabandoned.discharge())"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

docs/steady/03xsections/cross_section_models.ipynb

@@ -124,7 +124,9 @@
    "outputs": [],
    "source": [
     "fig, ax = plt.subplots(1, 1, figsize=(10, 3))\n",
-    "ml.plots.xsection(xy=[(-150, 0), (150, 0)], ax=ax, params=True);"
+    "ml.plots.xsection(\n",
+    "    xy=[(-150, 0), (150, 0)], ax=ax, params=True, units={\"kaq\": \"m/d\", \"c\": \"d\"}\n",
+    ")"
    ]
   },
   {
@@ -149,7 +151,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ml.plots.vcontoursf1D(x1=-200, x2=200, nx=100, levels=20, color=\"C0\", figsize=(10, 3));"
+    "ml.plots.vcontour_stream_function(\n",
+    "    x1=-200, x2=200, nx=100, levels=20, color=\"C0\", figsize=(10, 3)\n",
+    ");"
    ]
   },
   {
@@ -238,7 +242,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ml.plots.vcontoursf1D(x1=-200, x2=200, nx=100, levels=20, color=\"C0\", figsize=(10, 3));"
+    "ml.plots.vcontour_stream_function(\n",
+    "    x1=-200, x2=200, nx=100, levels=20, color=\"C0\", figsize=(10, 3)\n",
+    ");"
    ]
   },
   {
@@ -302,7 +308,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ax = ml.plots.vcontoursf1D(\n",
+    "ax = ml.plots.vcontour_stream_function(\n",
     "    x1=-200, x2=200, nx=100, levels=20, color=\"C0\", figsize=(10, 3), horizontal_axis=\"x\"\n",
     ")\n",
     "ld1.plot(ax);  # plot wall"
@@ -359,7 +365,9 @@
     "tfs.Constant(ml, 100, 0, 10)\n",
     "ml.solve()\n",
     "\n",
-    "ml.plots.vcontoursf1D(x1=-100, x2=100, nx=100, levels=20, color=\"C0\", figsize=(10, 3));"
+    "ml.plots.vcontour_stream_function(\n",
+    "    x1=-100, x2=100, nx=100, levels=20, color=\"C0\", figsize=(10, 3)\n",
+    ");"
    ]
   },
   {
@@ -372,7 +380,7 @@
     "tfs.XsectionAreaSink(ml2, -50, 50, 0.001)\n",
     "tfs.Constant(ml2, -100, 0, 10)\n",
     "ml2.solve()\n",
-    "ml2.plots.vcontoursf1D(\n",
+    "ml2.plots.vcontour_stream_function(\n",
     "    x1=-100, x2=100, nx=100, levels=20, color=\"C0\", figsize=(10, 3), horizontal_axis=\"x\"\n",
     ");"
    ]
@@ -419,7 +427,9 @@
     "\n",
     "ml.solve()\n",
     "\n",
-    "ml.plots.vcontoursf1D(x1=-20, x2=20, nx=100, levels=20, color=\"C0\", figsize=(10, 3));"
+    "ml.plots.vcontour_stream_function(\n",
+    "    x1=-20, x2=20, nx=100, levels=20, color=\"C0\", figsize=(10, 3)\n",
+    ");"
    ]
   },
   {
@@ -448,7 +458,9 @@
     "\n",
     "ml.solve()\n",
     "\n",
-    "ml.plots.vcontoursf1D(x1=-20, x2=20, nx=100, levels=20, color=\"C0\", figsize=(10, 3));"
+    "ml.plots.vcontour_stream_function(\n",
+    "    x1=-20, x2=20, nx=100, levels=20, color=\"C0\", figsize=(10, 3)\n",
+    ");"
    ]
   },
   {
@@ -499,9 +511,7 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": [
-    "from timflow.steady.linesink1d import FluxDiffLineSink1D, HeadDiffLineSink1D"
-   ]
+   "source": []
   },
   {
    "cell_type": "code",
@@ -512,8 +522,8 @@
     "ml = tfs.ModelMaq(kaq=[10], z=[0, -10], topboundary=\"conf\")\n",
     "ls = tfs.River1D(ml, xls=0, hls=1, wh=\"H\", layers=0)\n",
     "ls = tfs.River1D(ml, xls=200, hls=0, wh=\"H\", layers=0)\n",
-    "hd = HeadDiffLineSink1D(ml, xls=100)\n",
-    "fd = FluxDiffLineSink1D(ml, xls=100)\n",
+    "hd = tfs.linesink1d.HeadDiffLineSink1D(ml, xls=100)\n",
+    "fd = tfs.linesink1d.FluxDiffLineSink1D(ml, xls=100)\n",
     "ml.solve()\n",
     "\n",
     "x = np.linspace(0, 200, 101)\n",
@@ -526,9 +536,21 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "timflow (3.13.11)",
    "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": "3.13.11"
   }
  },
  "nbformat": 4,

docs/steady/04benchmarks/test_linesink_discharge.ipynb

@@ -36,7 +36,7 @@
    "source": [
     "ml1 = tfs.ModelMaq(kaq=20)\n",
     "rf1 = tfs.Constant(ml1, xr=0, yr=20, hr=30)\n",
-    "ls1 = tfs.LineSinkBase(ml1, x1=-10, y1=-10, x2=10, y2=10, Qls=1000)\n",
+    "ls1 = tfs.linesink.LineSinkBase(ml1, x1=-10, y1=-10, x2=10, y2=10, Qls=1000)\n",
     "ml1.solve()"
    ]
   },