From 825372c0a2a5e42d1afc7da9467c18c11dc747a7 Mon Sep 17 00:00:00 2001
From: George Breyiannis <gbreyiannis@gmail.com>
Date: Sat, 23 Sep 2023 12:11:32 +0200
Subject: [PATCH] schism: do output merging only if files are present

If we define nc_out = 0 in the param.nml there is no map output. This way we avoid waiting for the geometry reindexing.
---
 pyposeidon/schism.py | 47 ++++++++++++++++++++++++++------------------
 tests/test_schism.py | 28 +++++++++++++++++++++++++-
 2 files changed, 55 insertions(+), 20 deletions(-)

diff --git a/pyposeidon/schism.py b/pyposeidon/schism.py
index 9d1f44b7..427da1a3 100644
--- a/pyposeidon/schism.py
+++ b/pyposeidon/schism.py
@@ -1312,10 +1312,16 @@ def results(self, **kwargs):
         path = get_value(self, kwargs, "rpath", "./schism/")
 
         logger.info("get combined 2D netcdf files \n")
+        # check for new IO output
         hfiles = glob.glob(os.path.join(path, "outputs/out2d_*.nc"))
         hfiles.sort()
+        # check for old IO output
+        ofiles = glob.glob(os.path.join(path, "outputs/schout_*_*.nc"))
 
-        if hfiles:
+        if not (ofiles or hfiles):
+            logger.warning("no output netcdf files, moving on")
+
+        elif hfiles:
             x2d = xr.open_mfdataset(hfiles, data_vars="minimal")
 
             # set timestamp
@@ -1350,7 +1356,7 @@ def results(self, **kwargs):
             # save 2D variables to file
             x2d.to_netcdf(os.path.join(path, "outputs/schout_1.nc"))
 
-        else:
+        elif ofiles:
             if len(self.misc) == 0:
                 logger.info("retrieving index references ... \n")
                 self.global2local(**kwargs)
@@ -1719,6 +1725,9 @@ def results(self, **kwargs):
 
                 xc.to_netcdf(os.path.join(path, f"outputs/schout_{val}.nc"))
 
+        else:
+            raise Exception("This should never happen")
+
         logger.info("done with output netCDF files \n")
 
     def set_obs(self, **kwargs):
@@ -1871,25 +1880,25 @@ def get_station_sim_data(self, **kwargs):
         try:
             # get the station flags
             flags = pd.read_csv(os.path.join(path, "station.in"), header=None, nrows=1, delim_whitespace=True).T
-            flags.columns = ["flag"]
-            flags["variable"] = [
-                "elev",
-                "air_pressure",
-                "windx",
-                "windy",
-                "T",
-                "S",
-                "u",
-                "v",
-                "w",
-            ]
-
-            vals = flags[flags.values == 1]  # get the active ones
-        except OSError as e:
-            if e.errno == errno.EEXIST:
-                logger.error("no station.in file present")
+        except FileNotFoundError:
+            logger.error("no station.in file present")
             return
 
+        flags.columns = ["flag"]
+        flags["variable"] = [
+            "elev",
+            "air_pressure",
+            "windx",
+            "windy",
+            "T",
+            "S",
+            "u",
+            "v",
+            "w",
+        ]
+
+        vals = flags[flags.values == 1]  # get the active ones
+
         dstamp = kwargs.get("dstamp", self.rdate)
 
         dfs = []
diff --git a/tests/test_schism.py b/tests/test_schism.py
index c55ebd9f..20d154a1 100644
--- a/tests/test_schism.py
+++ b/tests/test_schism.py
@@ -84,6 +84,32 @@
 }
 
 
+case4 = {
+    "solver_name": "schism",
+    "mesh_file": MESH_FILE,
+    "manning": 0.12,
+    "windrot": 0.00001,
+    "tag": "test",
+    "start_date": "2011-1-1 0:0:0",
+    "time_frame": "12H",
+    "meteo_source": [(DATA_DIR / "era5.grib").as_posix()],  # meteo file
+    "dem_source": DEM_FILE,
+    "monitor": True,
+    "update": ["all"],  # update only meteo, keep dem
+    "parameters": {
+        "dt": 400,
+        "rnday": 0.3,
+        "nhot": 0,
+        "ihot": 0,
+        "nspool": 9,
+        "ihfskip": 36,
+        "nhot_write": 108,
+        "nc_out": 0,
+    },
+    "scribes": 2,
+}
+
+
 def schism(tmpdir, dic):
     # initialize a model
     rpath = str(tmpdir) + "/"
@@ -105,7 +131,7 @@ def schism(tmpdir, dic):
 
 
 @pytest.mark.schism
-@pytest.mark.parametrize("case", [case1, case2, case3])
+@pytest.mark.parametrize("case", [case1, case2, case3, case4])
 def test_answer(tmpdir, case):
     assert schism(tmpdir, case) == True