Merge branch 'master' of https://github.com/Deltares/Fm2Prof

FM2PROF_WINDOWS.spec

@@ -42,5 +42,5 @@ exe = EXE(
     target_arch=None,
     codesign_identity=None,
     entitlements_file=None,
-    icon='docs/source/_static/favicon.ico'
+    icon='docs/figures/favicon.ico'
 )

docs/markdown/contributing.md

@@ -17,4 +17,31 @@ To check coverage:
 `poetry run pytest --cov=fm2prof`
 
 
+## Deploying
+
+### Locally build executable
+
+To build a local version of an FM2PROF executable, run:
+
+`poetry run pyinstaller FM2PROF_WINDOWS.spec`
+
+### Making a new release
+
+After merging a PR, make a new tag. Using version `v2.3.0` as an example;
+
+`git tag v2.3.0`
+
+Use Github interface to draft a new release. Attach the executable. Then, update the documentation:
+
+`poetry run mike deploy v2.3.0 latest -u`
+
+Checkout the documentation branch
+
+`git checkout gh-pages`
+
+and push changes to github
+
+`git push`
+
+
 

docs/markdown/quickstart.md

@@ -24,14 +24,27 @@ This case is a simple 2D compound channel model.
 
 To start a new project:
 
-``` shell
-FM2PROF create MyProject
-```
+=== "Python"
+
+    ``` python
+    from fm2prof.IniFile import IniFile
+
+    inifile = IniFile().print_configuration()
+    ini_path = f"MyProject.ini"
+
+    with open(ini_path, "w") as f:
+        f.write(inifile)
+
+    ```
+
+=== "CLI"
+
+    ``` bash
+    FM2PROF create MyProject
+    ```
 
-This will create a new directory \"MyProject\". In this directory you
-will find [MyProject.ini]{.title-ref}. This is a valid configuration
-file with all parameters set to their default values. You will also find
-an [input]{.title-ref} and [output]{.title-ref} directory.
+
+This will create a valid configuration file with all parameters set to their default values. 
 
 ## Modify the input
 
@@ -50,9 +63,23 @@ CrossSectionLocationFile      =           # .csv or .txt file (, as delimiter) t
 
 To be sure you used the correct data, run:
 
-``` shell
-FM2PROF check MyProject
-```
+
+=== "Python"
+
+    ``` python
+    from fm2prof import Project
+
+    project = Project("MyProject.ini")
+
+    ```
+
+=== "CLI"
+
+    ``` bash
+    FM2PROF check MyProject
+    ```
+
+
 
 Study the output. Errors indicate that something is wrong with your
 input. In that case, you will need to correct the configurationfile.
@@ -64,18 +91,43 @@ settings that will be used and can be altered using a config file. The
 configuration file does not need all parameters to be specified. If a
 parameter is not in the configuration file, default values will be used.
 
-To generate output, use:
+The following examples run FM2PROF, overwrite any existing results and
+produce figures of the generated cross-sections. 
 
-``` shell
-FM2PROF run MyProject
-```
+=== "Python"
+
+    ``` python
+    from fm2prof import Project
+    from fm2prof.utils import VisualiseOutput
+
+    # load project
+    project = Project("MyProject.ini")
+
+    # overwrite = True overwrites any existing output
+    project.run(overwrite=True)
+
+    # to visualize cross-sectino putput:
+    vis = VisualiseOutput(
+                project.get_output_directory(), 
+                logger=project.get_logger()
+            )
 
-All `outputFiles`{.interpreted-text role="ref"} are written to the
-[output]{.title-ref} directory.
+    for css in vis.cross_sections:
+        vis.figure_cross_section(css)
+
+    ```
 
-## Inspect the results
+=== "CLI"
+
+    ``` bash
+    FM2PROF run MyProject -o -p
+    ```
+
+
+
+All `outputFiles` are written to the `output` directory specified in the FM2PROF configuration file. 
 
 After generating output it is important to check whether everything went
-well. provides various tools and output files to do this. Go to
-`diagnosis`{.interpreted-text role="ref"} and try to generate figures
-with [fm2prof.utils]{.title-ref}.
+well. See the following links to learn more about available tools:
+
+- [Inspection cross-sections using a notebook](../../notebooks/cross_section_data)

fm2prof/utils.py

@@ -1238,8 +1238,8 @@ class ModelOutputReader(FM2ProfBase):
 
     def __init__(self, 
                  logger=None, 
-                 start_time: datetime = None,
-                 stop_time: datetime = None):
+                 start_time: datetime | None = None,
+                 stop_time: datetime | None = None):
         super().__init__(logger=logger)
 
         self._path_out: Path = Path(".")
@@ -1249,8 +1249,8 @@ def __init__(self,
         self._data_1D_Q: pd.DataFrame = None
         self._time_offset_1d: int = 0
 
-        self._start_time: Union[datetime, type(None)] = start_time
-        self._stop_time: Union[datetime, type(None)] = stop_time
+        self._start_time: datetime | None = start_time
+        self._stop_time: datetime | None = stop_time
 
     @property
     def start_time(self) -> Union[datetime, None]:
@@ -1307,13 +1307,13 @@ def load_flow1d_data(self):
                 self.file_1D_Q,
                 index_col=0,
                 parse_dates=True,
-                date_parser=self._dateparser,
+                date_format=self._time_fmt,
             )
             self._data_1D_H = pd.read_csv(
                 self.file_1D_H,
                 index_col=0,
                 parse_dates=True,
-                date_parser=self._dateparser,
+                date_format=self._time_fmt,
             )
             self.set_logger_message("Using existing flow1d csv files")
         else:
@@ -1338,13 +1338,13 @@ def load_flow2d_data(self):
                 self.file_2D_Q,
                 index_col=0,
                 parse_dates=True,
-                date_parser=self._dateparser,
+                date_format=self._time_fmt,
             )
             self._data_2D_H = pd.read_csv(
                 self.file_2D_H,
                 index_col=0,
                 parse_dates=True,
-                date_parser=self._dateparser,
+                date_format=self._time_fmt,
             )
             self.set_logger_message("Using existing flow2d csv files")
         else:
@@ -1356,13 +1356,13 @@ def load_flow2d_data(self):
                 self.file_2D_Q,
                 index_col=0,
                 parse_dates=True,
-                date_parser=self._dateparser,
+                date_format=self._time_fmt,
             )
             self._data_2D_H = pd.read_csv(
                 self.file_2D_H,
                 index_col=0,
                 parse_dates=True,
-                date_parser=self._dateparser,
+                date_format=self._time_fmt,
             )
 
     def get_1d2d_map(self):
@@ -1380,6 +1380,7 @@ def read_all_data(self) -> None:
         self.load_flow2d_data()
 
     def _dateparser(self, t):
+        #DEPRECATED
         return datetime.strptime(t, self._time_fmt)
 
     @property
@@ -1439,7 +1440,14 @@ def time_offset_1d(self, seconds: int = 0):
         self._time_offset_1d = seconds
 
     def _apply_startstop_time(self, data: pd.DataFrame) -> pd.DataFrame:
-        """ Applies stop/start time to data """
+        """ 
+        Applies stop/start time to data 
+        """
+        if self.stop_time is None:
+            self.stop_time = data.index[-1]
+        if self.start_time is None:
+            self.start_time = data.index[0]
+
         if self.start_time >= self.stop_time:
             self.set_logger_message("Stop time ({self.stop_time}) should be later than start time ({self.start_time})", "error")
             raise ValueError
@@ -1604,8 +1612,8 @@ class Compare1D2D(ModelOutputReader):
     def __init__(
         self,
         project: Project,
-        path_1d: Union[Path, str],
-        path_2d: Union[Path, str],
+        path_1d: Union[Path, str] | None,
+        path_2d: Union[Path, str] | None,
         routes: List[List[str]],
         start_time: Union[None, datetime] = None,
         stop_time: Union[None, datetime] = None,
@@ -1616,11 +1624,11 @@ def __init__(
         else:
             super().__init__()
 
-        if isinstance(path_1d, (Path, str)) & Path(path_1d).is_file():
+        if isinstance(path_1d, (Path, str)) and Path(path_1d).is_file():
             self.path_flow1d = path_1d
         else:
             self.set_logger_message(f'1D netCDF file does not exist or is not provided. Input provided: {path_1d}.', 'debug')
-        if isinstance(path_1d, (Path, str)) & Path(path_2d).is_file():
+        if isinstance(path_1d, (Path, str)) and Path(path_2d).is_file():
             self.path_flow2d = path_2d
         else:
             self.set_logger_message(f'2D netCDF file does not exist or is not provided. Input provided: {path_2d}.', 'debug')
@@ -1911,7 +1919,16 @@ def _style_error_axes(self, ax, ylim: List[float] = [-0.5, 0.5]):
         ax.tick_params(axis="y", colors=self._color_error)
         ax.grid(False)
 
-    def _compute_statistics(self):
+    def _compute_statistics(self) -> pd.DataFrame:
+        """
+        Computes statistics for the difference between 1D and 2D water levels
+
+        Returns DataFrame with 
+            columns: rkm, branch, is_lmw, bias, std, mae
+            rows: observation stations
+    
+        """
+
         diff = self.data_1D_H - self.data_2D_H
         station_names = diff.columns
         rkms = self._names_to_rkms(station_names)