CI(Ubuntu): Install latest version of Python for full config

.github/workflows/python-code-quality.yml

@@ -32,7 +32,7 @@ jobs:
       # renovate: datasource=pypi depName=flake8
       FLAKE8_VERSION: "7.3.0"
       # renovate: datasource=pypi depName=pylint
-      PYLINT_VERSION: "4.0.6"
+      PYLINT_VERSION: "4.1.2"
       # renovate: datasource=pypi depName=bandit
       BANDIT_VERSION: "1.9.4"
       # renovate: datasource=pypi depName=ruff

.github/workflows/ubuntu.yml

@@ -107,6 +107,14 @@ jobs:
         env:
           STEPS_GET_EXCLUDE_OUTPUTS_EXTRA_EXCLUDE: ${{ steps.get-exclude.outputs.extra-exclude }}
 
+      - name: Set up Python
+        if: ${{ matrix.config == 'ubuntu-24.04' }}
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
+        with:
+          python-version: 3.13
+          cache: pip # zizmor: ignore[cache-poisoning] This workflow is not used for release artifacts
+          allow-prereleases: true
+
       - name: Get dependencies
         run: |
           sudo apt-get update -y
@@ -116,6 +124,13 @@ jobs:
           xargs -a <(awk '! /^ *(#|$)/' ".github/workflows/apt.txt") -r -- \
               sudo apt-get install -y --no-install-recommends --no-install-suggests
 
+      - name: Install Python dependencies
+        if: ${{ matrix.config == 'ubuntu-24.04' }}
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r .github/workflows/python_requirements.txt
+          pip install -r .github/workflows/optional_requirements.txt
+
       - name: Create installation directory
         run: |
           mkdir "${HOME}/install"

Dockerfile

@@ -4,7 +4,7 @@
 #       Changes to this file must be copied over to the other file.
 ARG GUI=without
 
-FROM ubuntu:26.04@sha256:61ebaa5cc23ca45450db85eac015435199ec569e28ec222ea13f2aed2110b8a6 AS common_start
+FROM ubuntu:26.04@sha256:88a381d5b5eeb2b35d3ad70925a362c37ce569daf43ede89ff818ec20e4d3794 AS common_start
 
 ARG BASE_NAME="ubuntu:26.04"
 ARG PYTHON_VERSION=3.14

docker/ubuntu/Dockerfile

@@ -4,7 +4,7 @@
 #       Changes to this file must be copied over to the other file.
 ARG GUI=without
 
-FROM ubuntu:26.04@sha256:61ebaa5cc23ca45450db85eac015435199ec569e28ec222ea13f2aed2110b8a6 AS common_start
+FROM ubuntu:26.04@sha256:88a381d5b5eeb2b35d3ad70925a362c37ce569daf43ede89ff818ec20e4d3794 AS common_start
 
 ARG BASE_NAME="ubuntu:26.04"
 ARG PYTHON_VERSION=3.14

gui/wxpython/core/utils.py

@@ -230,11 +230,7 @@ def GetValidLayerName(name):
         cIdx += 1
     retName = "".join(retNameList)
 
-    if (
-        retName
-        and not (retName[0] >= "A" and retName[0] <= "Z")
-        and not (retName[0] >= "a" and retName[0] <= "z")
-    ):
+    if retName and not ("A" <= retName[0] <= "Z") and not ("a" <= retName[0] <= "z"):
         retName = "x" + retName[1:]
 
     if mapset:

gui/wxpython/gui_core/forms.py

@@ -3115,7 +3115,7 @@ def OnVerbosity(self, event):
     def OnPageChange(self, event):
         sel = self.notebook.GetSelection() if not event else event.GetSelection()
         idx = self.notebook.GetPageIndexByName("manual")
-        if idx > -1 and sel == idx:
+        if -1 < idx == sel:
             # calling LoadPage() is strangely time-consuming (only first call)
             # FIXME: move to helpPage.__init__()
             if not self.manualTab.IsLoaded():

gui/wxpython/history/browser.py

@@ -16,6 +16,7 @@
 @author Tomas Zigo
 """
 
+import math
 from datetime import datetime
 
 import wx
@@ -25,7 +26,7 @@
 from history.tree import HistoryBrowserTree
 from icons.icon import MetaIcon
 
-import grass.script as gs
+from grass.tools import Tools
 
 from grass.grassdb import history
 
@@ -40,10 +41,10 @@
     "status": _("Status:"),
     "mask2d": _("Mask 2D:"),
     "mask3d": _("Mask 3D:"),
-    "n": _("North:"),
-    "s": _("South:"),
-    "w": _("West:"),
-    "e": _("East:"),
+    "north": _("North:"),
+    "south": _("South:"),
+    "west": _("West:"),
+    "east": _("East:"),
     "nsres": _("North-south resolution:"),
     "ewres": _("East-west resolution:"),
     "rows": _("Number of rows:"),
@@ -69,13 +70,26 @@ def make_label(key):
     return TRANSLATION_KEYS.get(key, "")
 
 
+# Region keys in the shell format of g.region, which are also the names of the g.region parameters
+REGION_KEYS = {"n": "north", "s": "south", "w": "west", "e": "east"}
+
+
+def normalize_region(region):
+    """Return region settings with the keys used by g.region format=json.
+
+    History entries recorded by older versions use the keys of the shell format.
+    """
+    return {REGION_KEYS.get(key, key): value for key, value in region.items()}
+
+
 class HistoryInfoPanel(SP.ScrolledPanel):
     def __init__(self, parent, giface, title=("Command Info"), style=wx.TAB_TRAVERSAL):
         super().__init__(parent=parent, id=wx.ID_ANY, style=style)
 
         self.parent = parent
         self.giface = giface
         self.title = title
+        self.tools = Tools()
 
         self.region_settings = None
 
@@ -166,7 +180,7 @@ def _general_info_filter(self, key, value):
         return key in filter_keys or ((key in {"mask2d", "mask3d"}) and value is True)
 
     def _region_settings_filter(self, key):
-        return key not in {"projection", "zone", "cells"}
+        return key not in {"crs", "projection", "zone", "cells"}
 
     def _updateGeneralInfoBox(self, command_info):
         """Update a static box for displaying general info about the command.
@@ -213,7 +227,7 @@ def _updateRegionSettingsGrid(self, command_info):
         """
         self.sizer_region_settings_grid.Clear(True)
 
-        self.region_settings = command_info["region"]
+        self.region_settings = normalize_region(command_info["region"])
         idx = 0
         for key, value in self.region_settings.items():
             if self._region_settings_filter(key):
@@ -248,9 +262,12 @@ def _updateRegionSettingsMatch(self):
         self.sizer_region_settings_match.Clear(True)
 
         # Region condition
-        history_region = self.region_settings
+        history_region = self._get_history_region()
         current_region = self._get_current_region()
-        region_matches = history_region == current_region
+        region_matches = all(
+            math.isclose(value, current_region[key], rel_tol=0, abs_tol=1e-8)
+            for key, value in history_region.items()
+        )
 
         # Icon and button according to the condition
         if region_matches:
@@ -320,7 +337,7 @@ def hideCommandInfo(self):
 
     def _get_current_region(self):
         """Get current computational region settings."""
-        return gs.region()
+        return self.tools.g_region(flags="p", format="json").json
 
     def _get_history_region(self):
         """Get computational region settings of executed command."""
@@ -332,8 +349,11 @@ def _get_history_region(self):
 
     def OnUpdateRegion(self, event):
         """Set current region to the region of executed command."""
+        parameters = {value: key for key, value in REGION_KEYS.items()}
         history_region = self._get_history_region()
-        gs.run_command("g.region", **history_region)
+        self.tools.g_region(
+            **{parameters.get(key, key): value for key, value in history_region.items()}
+        )
         self.giface.updateMap.emit(render=False, renderVector=False)
         self._updateRegionSettingsMatch()
         self.Layout()

gui/wxpython/tplot/frame.py

@@ -493,7 +493,7 @@ def _getSTRDdata(self, timeseries):
                 r.open()
                 val = r.get_value(self.poi)
                 r.close()
-                if val == -2147483648 and val < minmin:
+                if -2147483648 == val < minmin:
                     self.timeDataR[name][row[0]]["value"] = None
                 else:
                     self.timeDataR[name][row[0]]["value"] = val

python/grass/grassdb/history.py

@@ -264,7 +264,9 @@ def get_initial_command_info(env_run):
     mask3d_name = f"RASTER3D_MASK@{env['MAPSET']}"
 
     # Computational region settings
-    region_settings = gs.region(env=env_run)
+    region_settings = gs.parse_command(
+        "g.region", flags="p", format="json", env=env_run
+    )
 
     # Finalize the command info dictionary
     return {

python/grass/pygrass/raster/segment.py

@@ -33,7 +33,7 @@ def nseg(self):
         )
 
     def segments_in_mem(self):
-        if self.maxmem > 0 and self.maxmem < 100:
+        if 0 < self.maxmem < 100:
             seg_in_mem = (self.maxmem * self.nseg()) / 100
         else:
             seg_in_mem = 4 * (self.rows() / self.srows + self.cols() / self.scols + 2)

python/grass/temporal/c_libraries_interface.py

@@ -11,6 +11,7 @@
 from __future__ import annotations
 
 import logging
+import math
 import sys
 from ctypes import CFUNCTYPE, POINTER, byref, c_int, c_void_p, cast
 from datetime import datetime
@@ -825,11 +826,11 @@ def _read_raster3d_info(name, mapset):
         return None
     libraster3d.Rast3d_range_min_max(g3map, byref(min), byref(max))
 
-    if min.value != min.value:
+    if math.isnan(min.value):
         kvp["min"] = None
     else:
         kvp["min"] = float(min.value)
-    if max.value != max.value:
+    if math.isnan(max.value):
         kvp["max"] = None
     else:
         kvp["max"] = float(max.value)

python/grass/temporal/temporal_extent.py

@@ -737,8 +737,7 @@ def during(self, extent) -> bool:
         # Check single point of time in interval
         if self.D["end_time"] is None:
             return bool(
-                self.D["start_time"] >= extent.D["start_time"]
-                and self.D["start_time"] < extent.D["end_time"]
+                extent.D["start_time"] <= self.D["start_time"] < extent.D["end_time"]
             )
 
         return bool(
@@ -776,8 +775,7 @@ def contains(self, extent) -> bool:
         # Check single point of time in interval
         if extent.D["end_time"] is None:
             return bool(
-                self.D["start_time"] <= extent.D["start_time"]
-                and self.D["end_time"] > extent.D["start_time"]
+                self.D["start_time"] <= extent.D["start_time"] < self.D["end_time"]
             )
 
         return bool(
@@ -853,9 +851,10 @@ def overlaps(self, extent) -> bool:
         return bool(
             self.D["end_time"] is not None
             and extent.D["end_time"] is not None
-            and self.D["start_time"] < extent.D["start_time"]
-            and self.D["end_time"] < extent.D["end_time"]
-            and self.D["end_time"] > extent.D["start_time"]
+            and self.D["start_time"]
+            < extent.D["start_time"]
+            < self.D["end_time"]
+            < extent.D["end_time"]
         )
 
     def overlapped(self, extent) -> bool:
@@ -893,9 +892,10 @@ def overlapped(self, extent) -> bool:
         return bool(
             self.D["end_time"] is not None
             and extent.D["end_time"] is not None
-            and self.D["start_time"] > extent.D["start_time"]
-            and self.D["end_time"] > extent.D["end_time"]
-            and self.D["start_time"] < extent.D["end_time"]
+            and extent.D["start_time"]
+            < self.D["start_time"]
+            < extent.D["end_time"]
+            < self.D["end_time"]
         )
 
     def temporal_relation(self, extent):

raster/r.sim/r.sim.water/r.sim.water.html

@@ -90,7 +90,15 @@ <h2>DESCRIPTION</h2>
 the time series flag <b>-t</b> and <b>output_step</b> parameter
 defining the time step in minutes for writing output files.
 Files are saved with a suffix representing time since the start of simulation in minutes
-(e.g. wdepth.05, wdepth.10).
+(e.g. wdepth.05, wdepth.10) and are timestamped with that time.
+The simulation advances in time steps which usually do not fall exactly on the output times.
+A map holds the state at the time step closest to the time in its name,
+so at most half a time step earlier or later.
+When the time step is longer than <b>output_step</b>, there are fewer time steps than
+output times, and a time step writes only the maps for the output time closest to it.
+The series always ends with maps named by the <b>duration</b> which hold the state
+at the end of the run, also when the duration is not a multiple of <b>output_step</b>
+or when the simulation stopped early.
 <!-- TODO add example of registering outputs into temporal framework when  #2146 is fixed -->
 Monitoring of water depth at specific points is supported. A vector map with observation points and
 a path to a logfile must be provided. For each point in the vector map which is located in
@@ -209,12 +217,12 @@ <h3>Run summary</h3>
  <tr><td><code>mean_source_rate</code></td><td>Mean rainfall excess</td><td>m/s</td></tr>
  <tr><td><code>mean_infiltration</code></td><td>Mean infiltration rate, 0 without infiltration input</td><td>m/s</td></tr>
  <tr><td><code>threads</code></td><td>Threads used for the computation</td><td>count</td></tr>
- <tr><td><code>outputs</code></td><td>One entry per set of written maps: one per <b>output_step</b> with <b>-t</b>, otherwise a single entry</td><td></td></tr>
+ <tr><td><code>outputs</code></td><td>One entry per set of written maps: with <b>-t</b>, one per written output step, the last one named by <b>duration</b>, otherwise a single entry</td><td></td></tr>
 </table>
 
 <p>
-Each entry of <code>outputs</code> contains the <code>simulated_time</code> (s) and <code>timestamp</code>
-of the written maps, the number of <code>walkers_remaining</code> at that time, and
+Each entry of <code>outputs</code> contains the <code>simulated_time</code> (s) when the maps
+were written, their <code>timestamp</code>, the number of <code>walkers_remaining</code> at that time, and
 the names of the <code>depth</code>, <code>discharge</code>, <code>error</code> and <code>walkers</code> maps, or
 <code>null</code> for maps which were not requested.
 

raster/r.sim/r.sim.water/r.sim.water.md

@@ -80,7 +80,17 @@ water depth and discharge maps can be saved during simulation using the
 time series flag **-t** and **output_step** parameter defining the time
 step in minutes for writing output files. Files are saved with a suffix
 representing time since the start of simulation in minutes (e.g.
-wdepth.05, wdepth.10). Monitoring of water depth at specific points is
+wdepth.05, wdepth.10) and are timestamped with that time. The
+simulation advances in time steps which usually do not fall exactly on
+the output times. A map holds the state at the time step closest to the
+time in its name, so at most half a time step earlier or later. When the
+time step is longer than **output_step**, there are fewer time steps
+than output times, and a time step writes only the maps for the output
+time closest to it. The series always ends with maps named by the
+**duration** which hold the state at the end of the run, also when the
+duration is not a multiple of **output_step** or when the simulation
+stopped early.
+Monitoring of water depth at specific points is
 supported. A vector map with observation points and a path to a logfile
 must be provided. For each point in the vector map which is located in
 the computational region the water depth is logged each time step in the
@@ -197,12 +207,12 @@ stored in the history of the output raster maps under the same keys (see
 | `mean_source_rate` | Mean rainfall excess | m/s |
 | `mean_infiltration` | Mean infiltration rate, 0 without infiltration input | m/s |
 | `threads` | Threads used for the computation | count |
-| `outputs` | One entry per set of written maps: one per **output_step** with **-t**, otherwise a single entry | |
+| `outputs` | One entry per set of written maps: with **-t**, one per written output step, the last one named by **duration**, otherwise a single entry | |
 
-Each entry of `outputs` contains the `simulated_time` (s) and `timestamp`
-of the written maps, the number of `walkers_remaining` at that time, and
-the names of the `depth`, `discharge`, `error` and `walkers` maps, or
-`null` for maps which were not requested.
+Each entry of `outputs` contains the `simulated_time` (s) when the maps
+were written, their `timestamp`, the number of `walkers_remaining` at
+that time, and the names of the `depth`, `discharge`, `error` and
+`walkers` maps, or `null` for maps which were not requested.
 
 Summary of a time series run with two output steps in JSON:
 

raster/r.sim/r.sim.water/tests/r_sim_water_nprocs_test.py

@@ -18,6 +18,8 @@
 RAIN = np.where(
     (abs(row - SIZE // 2) <= SIZE // 4) & (abs(col - SIZE // 2) <= SIZE // 4), 50, 0
 )
+# Infiltration only where it rains, at a lower rate than the rain
+INFILTRATION = np.where(RAIN > 0, 20, 0)
 
 
 @pytest.fixture(scope="module")
@@ -76,3 +78,22 @@ def test_all_walkers_move_with_nprocs(session):
     single = total_water(depth(session, nprocs=1, **options))
     multiple = total_water(depth(session, nprocs=4, **options))
     assert multiple == pytest.approx(single, rel=1e-6)
+
+
+def test_infiltration_takes_exactly_the_capacity(session):
+    """Infiltration removes exactly the capacity of the cells, also in parallel.
+
+    The walkers created in a cell outweigh its infiltration capacity, so the
+    capacity is used up in the first step, before any walker moves, and it
+    is not restored. The water left for the rest of the simulation is then
+    the rain minus the infiltration, so the total is that fraction of the
+    total without infiltration.
+    """
+    expected = total_water(
+        depth(session, nprocs=1, infil_value=0, diffusion_coeff=0)
+    ) * (1 - INFILTRATION.sum() / RAIN.sum())
+    for nprocs in (1, 4):
+        actual = total_water(
+            depth(session, nprocs=nprocs, infil=INFILTRATION, diffusion_coeff=0)
+        )
+        assert actual == pytest.approx(expected, rel=1e-6)