ci: CLI fix and simplify obs & restart

pyposeidon/telemac.py

@@ -366,22 +366,23 @@ def write_meteo_selafin(outpath, input_atm_zarr):
     remove(input_atm_zarr)
 
 
-def get_boundary_settings(boundary_type, glo_node, bnd_node):
-    settings = {
-        "lihbor": 5 if boundary_type == "open" else 2,
-        "liubor": 6 if boundary_type == "open" else 2,
-        "livbor": 6 if boundary_type == "open" else 2,
-        "hbor": 0.0,
-        "ubor": 0.0,
-        "vbor": 0.0,
-        "aubor": 0.0,
-        "litbor": 5 if boundary_type == "open" else 2,
-        "tbor": 0.0,
-        "atbor": 0.0,
-        "btbor": 0.0,
-        "nbor": glo_node + 1,
-        "k": bnd_node + 1,
-    }
+def get_boundary_settings(boundary_type, glo_node, bnd_node, module):
+    if module in ["telemac2d", "telemac3d", "tomawac"]:
+        settings = {
+            "lihbor": 5 if boundary_type == "open" else 2,
+            "liubor": 6 if boundary_type == "open" else 2,
+            "livbor": 6 if boundary_type == "open" else 2,
+            "hbor": 0.0,
+            "ubor": 0.0,
+            "vbor": 0.0,
+            "aubor": 0.0,
+            "litbor": 5 if boundary_type == "open" else 2,
+            "tbor": 0.0,
+            "atbor": 0.0,
+            "btbor": 0.0,
+            "nbor": glo_node + 1,
+            "k": bnd_node + 1,
+        }
     return settings
 
 
@@ -456,7 +457,6 @@ def export_cli(ds: xr.Dataset, tel_path: str, outCli: str, tel_module: str = "te
     lines = []
     bnd_node = 0
     contours, contours_idx = extract_contour(ds, tel_path)
-    print(contours_idx)
     for bnd in contours_idx:
         poly_bnd = []
         coord_bnd = []
@@ -475,7 +475,7 @@ def export_cli(ds: xr.Dataset, tel_path: str, outCli: str, tel_module: str = "te
                 # If both adjacent nodes are not 'open', then bnd is closed
                 if prev_boundary_type != "open" and next_boundary_type != "open":
                     boundary_type = "Unknown"
-            boundary_settings = get_boundary_settings(boundary_type, glo_node, bnd_node)
+            boundary_settings = get_boundary_settings(boundary_type, glo_node, bnd_node, tel_module)
 
             keys_order = [
                 "lihbor",
@@ -492,9 +492,8 @@ def export_cli(ds: xr.Dataset, tel_path: str, outCli: str, tel_module: str = "te
                 "nbor",
                 "k",
             ]
-            if tel_module == "telemac2d":
-                line = " ".join(str(boundary_settings[key]) for key in keys_order)
-                lines.append(line)
+            line = " ".join(str(boundary_settings[key]) for key in keys_order)
+            lines.append(line)
             bnd_node += 1
         poly_bnd.append((coord_bnd, bnd))
     domains_bnd.append(poly_bnd)
@@ -1441,6 +1440,8 @@ def set_obs(self, **kwargs):
         df.index += 1
         df["ind"] = df.index
         df["unique_id"] = tgn[id_str].values
+        if id_str != "unique_id":
+            df[id_str] = tgn[id_str].values
         df["depth"] = self.mesh.Dataset.depth[df.mesh_index.values]
 
         # convert to MERCATOR coordinates
@@ -1462,6 +1463,7 @@ def set_obs(self, **kwargs):
             timestep=self.params["tstep"],
             offset=offset,
         )
+        self.stations = os.path.join(path, "stations.csv")
 
     def get_output_data(self, **kwargs):
         dic = self.__dict__
@@ -1471,7 +1473,7 @@ def get_output_data(self, **kwargs):
         self.data = data.get_output(**dic)
 
     def get_station_obs_data(self, **kwargs):
-        self.station_obs_data = get_obs_data(self.obs, self.start_date, self.end_date)
+        self.station_obs_data = pd.read_csv(self.stations)
 
     def open_thalassa(self, **kwargs):
         # open a Thalassa instance to visualize the output

pyposeidon/utils/data.py

@@ -220,7 +220,7 @@ def __init__(self, **kwargs):
         res_type = kwargs.get("result_type", "2D")
         convert = kwargs.get("convert_results", True)
         extract_TS = kwargs.get("extract_TS", False)
-        station_id_str = kwargs.get("id_str", "ioc_code")
+        id_str = kwargs.get("id_str", "ioc_code")
         max_dist = kwargs.get("max_dist", 1000)
 
         if res_type not in ["1D", "2D"]:
@@ -307,28 +307,23 @@ def __init__(self, **kwargs):
 
         # export parquet time series
         if extract_TS:
-            if "stations_mesh_id" in p.__dict__:
-                if isinstance(p.stations_mesh_id, dict):
-                    stations = pd.DataFrame(p.stations_mesh_id)
-                elif isinstance(p.stations_mesh_id, pd.DataFrame):
-                    stations = p.stations_mesh_id
-                else:
-                    raise ValueError("stations_mesh_id format not supported")
+            if "stations" in p.__dict__:
+               file = p.stations
             elif "stations.csv" in os.listdir(rpath):
-                stations = pd.read_csv(os.path.join(rpath, "stations.csv"))
+                file = os.path.join(rpath, "stations.csv")
             elif "obs" in self.__dict__:
                 p.set_obs()
-                stations = p.stations_mesh_id
+                file = p.stations
             else:
                 raise ValueError("no stations file info found")
-
+            stations = pd.read_csv(file)
             logger.info("extracting parquet files from TELEMAC Selafin output \n")
-            for i_s, id_ in enumerate(stations[station_id_str]):
-                s = stations[stations[station_id_str] == id_]
+            for i_s, id_ in enumerate(stations[id_str]):
+                s = stations[stations[id_str] == id_]
                 mod, mlon, mlat = extract_t_elev_2D(
                     self.Dataset,
-                    s.longitude.values[0],
-                    s.latitude.values[0],
+                    s.lon.values[0],
+                    s.lat.values[0],
                     var,
                     model_xstr,
                     model_ystr,