Sync dev branch

CONTRIBUTING.md

@@ -2,8 +2,6 @@
 
 First of all, thanks to take time to contribute to Itzï.
 This is much appreciated.
-This file is a work in progress.
-It will be updated as time goes.
 
 ## Code of Conduct
 
@@ -14,7 +12,7 @@ Please report unacceptable behaviour to [contact@itzi.org](mailto:contact@itzi.o
 ## How Can I Contribute?
 
 ### Reporting Bugs
-If a developer don't know about a bug, he/she cannot fix it!
+If a developer does not know about a bug, they cannot fix it!
 Therefore, it is very valuable to thoroughly describe the problem you encounter on the bug-tracker.
 
 ### Write documentation
@@ -25,12 +23,11 @@ But writing good documentation is time consuming.
 The documentation of Itzï is hosted on [Readthedocs](https://itzi.readthedocs.io).
 It is written in [reStructuredText](http://docutils.sourceforge.net/rst.html)
 and generated with [Sphinx](http://www.sphinx-doc.org/en/stable/).
-The source code of the documentation lies on its own git [repository](https://bitbucket.org/itzi-model/itzi_docs).
+The source code of the documentation is in `the docs/` directory of the main repository.
 
 Please use one sentence per line and try to keep line length under 90 characters.
 If above that threshold, break the line.
 
-
 ### Code
 
 Please have a look at the [programer's manual](http://itzi.readthedocs.io/en/latest/prog_manual.html).

src/itzi/bmi_itzi.py

@@ -61,7 +61,7 @@ def __init__(self):
 
     # Model control functions #
 
-    def initialize(self, filename=None):
+    def initialize(self, filename=None) -> None:
         """Initialize the Itzï model.
 
         Parameters

src/itzi/grass_session.py

@@ -17,7 +17,7 @@
 import sys
 import os
 import subprocess
-import importlib
+import importlib.util
 
 import itzi.messenger as msgr
 

src/itzi/itzi.py

@@ -41,7 +41,7 @@
 import itzi.itzi_error as itzi_error
 import itzi.messenger as msgr
 from itzi.const import VerbosityLevel
-from itzi.parser import build_parser
+from itzi.cli_parser import build_parser
 from itzi.profiler import profile_context
 from itzi.simulation_builder import SimulationBuilder
 from itzi.grass_session import GrassSessionManager

src/itzi/messenger.py

@@ -12,10 +12,10 @@
 GNU General Public License for more details.
 """
 
+from typing import Callable, NoReturn
 import sys
 import logging
 import os
-from typing import NoReturn
 from datetime import timedelta, datetime
 
 from itzi.itzi_error import ItziFatal
@@ -40,7 +40,7 @@ class ItziLogger:
 
     def __init__(self):
         self.logger = logging.getLogger("itzi")
-        self.raise_on_error = True
+        self.raise_on_error: bool = True
         self._setup_handlers()
 
     def _setup_handlers(self):
@@ -66,7 +66,7 @@ def add_file_handler(self, filepath, level=logging.DEBUG):
         file_handler.setFormatter(logging.Formatter("%(asctime)s - %(levelname)s - %(message)s"))
         self.logger.addHandler(file_handler)
 
-    def set_verbosity(self, verbosity_level):
+    def set_verbosity(self, verbosity_level: int):
         """Map verbosity to logging level"""
         mapping = {
             VerbosityLevel.SUPER_QUIET: logging.ERROR,
@@ -83,37 +83,37 @@ def set_verbosity(self, verbosity_level):
             ):
                 handler.setLevel(level)
 
-    def fatal(self, msg) -> NoReturn:
+    def fatal(self, msg: str) -> NoReturn:
         """Log fatal error and raise or exit"""
         self.logger.error(f"ERROR: {msg}")
         if raise_on_error:
             raise ItziFatal(msg)
         else:
             sys.exit(f"ERROR: {msg}")
 
-    def warning(self, msg) -> None:
+    def warning(self, msg: str) -> None:
         self.logger.warning(f"WARNING: {msg}")
 
-    def message(self, msg) -> None:
+    def message(self, msg: str) -> None:
         self.logger.info(msg)
 
-    def verbose(self, msg) -> None:
+    def verbose(self, msg: str) -> None:
         self.logger.log(self.VERBOSE_LEVEL, msg)
 
-    def debug(self, msg) -> None:
+    def debug(self, msg: str) -> None:
         self.logger.debug(msg)
 
 
 # Global instance
 _itzi_logger = ItziLogger()
 
 # Backward-compatible module-level interface
-raise_on_error = _itzi_logger.raise_on_error
-fatal = _itzi_logger.fatal
-warning = _itzi_logger.warning
-message = _itzi_logger.message
-verbose = _itzi_logger.verbose
-debug = _itzi_logger.debug
+raise_on_error: bool = _itzi_logger.raise_on_error
+fatal: Callable[[str], NoReturn] = _itzi_logger.fatal
+warning: Callable[[str], None] = _itzi_logger.warning
+message: Callable[[str], None] = _itzi_logger.message
+verbose: Callable[[str], None] = _itzi_logger.verbose
+debug: Callable[[str], None] = _itzi_logger.debug
 
 
 def percent(start_time, end_time, sim_time, sim_start_time):

src/itzi/providers/base.py

@@ -45,7 +45,7 @@ def get_domain_data(self) -> DomainData:
     @abstractmethod
     def get_array(
         self, map_key: str, current_time: datetime
-    ) -> tuple[np.ndarray, datetime, datetime]:
+    ) -> tuple[np.ndarray | None, datetime, datetime]:
         """Take a given map key and current time
         return a numpy array associated with its half-open validity window `[start, end)`.
 

src/itzi/providers/grass_input.py

@@ -31,7 +31,7 @@
 class GrassRasterInputConfig(TypedDict):
     grass_interface: GrassInterface
     # A dict of key: input names
-    input_map_names: Mapping[str, str]
+    input_map_names: Mapping[str, str | None]
     default_start_time: datetime
     default_end_time: datetime
 
@@ -56,8 +56,8 @@ def get_domain_data(self) -> DomainData:
         )
 
     def get_map_lists(
-        self, map_names: Mapping[str, str]
-    ) -> Mapping[str, list[GrassInterface.MapData]]:
+        self, map_names: Mapping[str, str | None]
+    ) -> Mapping[str, list[GrassInterface.MapData] | None]:
         """Read maps names from GIS.
         input map_names is a dictionary of maps/STDS names
         for each entry in map_names:
@@ -69,7 +69,7 @@ def get_map_lists(
         each map is stored as a MapData namedtuple
         store result in instance's dictionary
         """
-        map_lists: dict[str, None] = {
+        map_lists: dict[str, list[GrassInterface.MapData] | None] = {
             arr_def.key: None
             for arr_def in ARRAY_DEFINITIONS
             if ArrayCategory.INPUT in arr_def.category

src/itzi/providers/grass_interface.py

@@ -264,7 +264,8 @@ def to_datetime(self, unit: str, time: int) -> datetime:
         """
         return self.start_time + timedelta(seconds=self.to_s(unit, time))
 
-    def has_mask(self) -> bool:
+    @staticmethod
+    def has_mask() -> bool:
         """Return True if the mapset has a mask, False otherwise."""
         return bool(gscript.read_command("g.list", type="raster", pattern="MASK"))
 
@@ -330,6 +331,10 @@ def format_id(name: str) -> str:
         else:
             return "@".join((name, gutils.getenv("MAPSET")))
 
+    @staticmethod
+    def get_current_mapset() -> str:
+        return gutils.getenv("MAPSET")
+
     @staticmethod
     def name_is_stds(name: str) -> bool:
         """return True if the name given as input is a registered strds
@@ -355,7 +360,7 @@ def set_null(map_id: str, threshold: float) -> None:
         """Set null values under a given threshold"""
         gscript.run_command("r.null", flags="f", map=map_id, setnull=f"0.0-{threshold}")
 
-    def get_sim_extend_in_stds_unit(self, strds) -> tuple[int, int]:
+    def get_sim_extend_in_stds_unit(self, strds) -> tuple[int | datetime, int | datetime]:
         """Take a strds object as input
         Return the simulation start_time and end_time, expressed in
         the unit of the input strds

src/itzi/providers/grass_output.py

@@ -14,7 +14,7 @@
 
 from __future__ import annotations
 
-from typing import Dict, TypedDict, Union, TYPE_CHECKING
+from typing import TypedDict, TYPE_CHECKING
 
 import numpy as np
 
@@ -29,7 +29,7 @@
 
 class GrassRasterOutputConfig(TypedDict):
     grass_interface: "GrassInterface"
-    out_map_names: Dict[str, str]
+    out_map_names: dict[str, str | None]
     hmin: float
     temporal_type: TemporalType
 
@@ -60,7 +60,7 @@ def __init__(self, config: GrassRasterOutputConfig) -> None:
         self.output_maplist = {k: [] for k in self.out_map_names.keys()}
 
     def _write_array(
-        self, array: np.ndarray, map_key: str, sim_time: Union[datetime, timedelta]
+        self, array: np.ndarray, map_key: str, sim_time: datetime | timedelta
     ) -> None:
         """Write simulation data for current time step."""
         suffix = str(self.record_counter[map_key]).zfill(4)
@@ -75,7 +75,7 @@ def _write_array(
         self.record_counter[map_key] += 1
 
     def write_arrays(
-        self, array_dict: Dict[str, np.ndarray], sim_time: Union[datetime, timedelta]
+        self, array_dict: dict[str, np.ndarray], sim_time: datetime | timedelta
     ) -> None:
         for arr_key, arr in array_dict.items():
             if isinstance(arr, np.ndarray):
@@ -123,7 +123,7 @@ def __init__(self, config: GrassVectorOutputConfig) -> None:
         self.vector_drainage_maplist = []
 
     def write_vector(
-        self, drainage_data: DrainageNetworkData | None, sim_time: Union[datetime, timedelta]
+        self, drainage_data: DrainageNetworkData | None, sim_time: datetime | timedelta
     ) -> None:
         """Write drainage simulation data for current time step."""
         if self.drainage_map_name and drainage_data:

src/itzi/surfaceflow.py

@@ -12,6 +12,7 @@
 GNU General Public License for more details.
 """
 
+from __future__ import annotations
 import math
 from datetime import timedelta
 from typing import TYPE_CHECKING
@@ -24,6 +25,7 @@
 
 if TYPE_CHECKING:
     from itzi.data_containers import SurfaceFlowParameters
+    from itzi.rasterdomain import RasterDomain
 
 
 class SurfaceFlowSimulation:
@@ -36,8 +38,8 @@ class SurfaceFlowSimulation:
 
     def __init__(
         self,
-        domain,
-        flow_params: "SurfaceFlowParameters",
+        domain: RasterDomain,
+        flow_params: SurfaceFlowParameters,
     ):
         self.dom = domain
         self.dtmax = flow_params.dtmax
@@ -77,23 +79,27 @@ def solve_dt(self):
         accommodate non-square cells
         The time-step is limited by the maximum time-step dtmax.
         """
-        maxh = np.amax(self.dom.get_array("water_depth"))  # max depth in domain
+        maxh = float(np.amax(self.dom.get_array("water_depth")))  # max depth in domain
         min_dim = min(self.dx, self.dy)
         if maxh > 0:
-            dt = self.cfl * (min_dim / (math.sqrt(self.g * maxh)))
-            self._dt = min(self.dtmax, dt)
+            dt = self.dt_s(self.cfl, min_dim, self.g, maxh)
+            self._dt = float(min(self.dtmax, dt))
         else:
-            self._dt = self.dtmax
+            self._dt = float(self.dtmax)
         if self._dt <= self._dt_fudge:
             raise DtError(f"Tiny computed dt ({self._dt}s)")
         return self
 
+    @staticmethod
+    def dt_s(cfl, min_dim, g, maxh):
+        return cfl * (min_dim / (math.sqrt(g * maxh)))
+
     @property
     def dt(self):
         return timedelta(seconds=self._dt)
 
     @dt.setter
-    def dt(self, newdt):
+    def dt(self, newdt: timedelta):
         """return an error if new dt is higher than current one or negative"""
         newdt_s = newdt.total_seconds()
         if self._dt is None:

tests/cli/test_cli.py

@@ -8,7 +8,7 @@
 from itzi.const import VerbosityLevel
 from itzi.itzi import main, itzi_run, reconcile_hotstart_commands
 from itzi.itzi_error import ItziFatal
-from itzi.parser import build_parser
+from itzi.cli_parser import build_parser
 
 
 def test_run_parser_accepts_multiple_config_files():