Fix unclosed file warnings

.github/workflows/run_tests.yml

@@ -41,7 +41,7 @@ jobs:
       - uses: "actions/setup-python@v2"
         with:
           python-version: "${{ matrix.python }}"
-      - uses: "actions/cache@v2"
+      - uses: "actions/cache@v3"
         id: "cache"
         with:
           path: "${{ env.pythonLocation }}"

README.md

@@ -23,8 +23,14 @@ conda install -c conda-forge xarray_selafin
 
 ```python
 import xarray as xr
-ds = xr.open_dataset("tests/data/r3d_tidal_flats.slf", engine="selafin")
+
+with xr.open_dataset("tests/data/r3d_tidal_flats.slf", engine="selafin") as ds:
+    print(ds)  # do something with `ds`...
+    # `ds.close()` not necessary
+
 ds = xr.open_dataset("tests/data/r3d_tidal_flats.slf", lang="fr", engine="selafin")  # if variables are in French
+print(ds)  # do something with `ds`...
+ds.close()  # avoid a ResourceWarning (unclosed file)
 ```
 
 ```

tests/io_test.py

@@ -34,54 +34,61 @@ def write_netcdf(ds, nc_out):
     ds.to_netcdf(nc_out)
 
 
-@TIDAL_FLATS
-def test_open_dataset(slf_in):
-    ds = xr.open_dataset(slf_in, engine="selafin")
-    assert isinstance(ds, xr.Dataset)
-    repr(ds)
-
-    # Dimensions
-    assert ds.sizes["time"] == 17
-    assert ds.sizes["node"] == 648
-    if "r3d" in slf_in:
-        assert ds.sizes["plan"] == 21
+def equals_dataset_vs_netcdf_export(ds, nc_out):
+    write_netcdf(ds, nc_out)
+    ds_nc = xr.open_dataset(nc_out)
+    return ds_nc.equals(ds)
 
-    # Coordinates
-    assert "x" in ds.coords
-    assert "y" in ds.coords
-    assert "time" in ds.coords
 
-    # Attributes
-    assert ds.attrs["endian"] == ">"
-    assert ds.attrs["date_start"] == (1900, 1, 1, 0, 0, 0)
-    assert "ipobo" in ds.attrs
-    assert "ikle2" in ds.attrs
-    if "r3d_" in slf_in:
-        assert "ikle3" in ds.attrs
-    else:
-        assert "ikle3" not in ds.attrs
+@TIDAL_FLATS
+def test_open_dataset(slf_in):
+    with xr.open_dataset(slf_in, engine="selafin") as ds:
+        assert isinstance(ds, xr.Dataset)
+        repr(ds)
+
+        # Dimensions
+        assert ds.sizes["time"] == 17
+        assert ds.sizes["node"] == 648
+        if "r3d" in slf_in:
+            assert ds.sizes["plan"] == 21
+
+        # Coordinates
+        assert "x" in ds.coords
+        assert "y" in ds.coords
+        assert "time" in ds.coords
+
+        # Attributes
+        assert ds.attrs["endian"] == ">"
+        assert ds.attrs["date_start"] == (1900, 1, 1, 0, 0, 0)
+        assert "ipobo" in ds.attrs
+        assert "ikle2" in ds.attrs
+        if "r3d_" in slf_in:
+            assert "ikle3" in ds.attrs
+        else:
+            assert "ikle3" not in ds.attrs
 
 
 @TIDAL_FLATS
 def test_to_netcdf(tmp_path, slf_in):
-    ds_slf = xr.open_dataset(slf_in, engine="selafin")
-    nc_out = tmp_path / "test.nc"
-    write_netcdf(ds_slf, nc_out)
-    ds_nc = xr.open_dataset(nc_out)
-    assert ds_nc.equals(ds_slf)
+    with xr.open_dataset(slf_in, engine="selafin") as ds_slf:
+        nc_out = tmp_path / "test.nc"
+        write_netcdf(ds_slf, nc_out)
+        ds_nc = xr.open_dataset(nc_out)
+        assert ds_nc.equals(ds_slf)
 
 
 @TIDAL_FLATS
 def test_to_selafin(tmp_path, slf_in):
-    ds_slf = xr.open_dataset(slf_in, engine="selafin")
+    with xr.open_dataset(slf_in, engine="selafin") as ds_slf:
 
-    # Remove some data which is rebuilt
-    del ds_slf.attrs["date_start"]
+        # Remove some data which is rebuilt
+        del ds_slf.attrs["date_start"]
 
-    slf_out = tmp_path / "test.slf"
-    ds_slf.selafin.write(slf_out)
-    ds_slf2 = xr.open_dataset(slf_out, engine="selafin")
-    assert ds_slf2.equals(ds_slf)
+        slf_out = tmp_path / "test.slf"
+        ds_slf.selafin.write(slf_out)
+
+        with xr.open_dataset(slf_out, engine="selafin") as ds_slf2:
+            assert ds_slf2.equals(ds_slf)
 
     # Compare binary files
     with open(slf_in, "rb") as in_slf1, open(slf_out, "rb") as in_slf2:
@@ -90,15 +97,16 @@ def test_to_selafin(tmp_path, slf_in):
 
 @TIDAL_FLATS
 def test_to_selafin_eager_mode(tmp_path, slf_in):
-    ds_slf = xr.open_dataset(slf_in, lazy_loading=False, engine="selafin")
+    with xr.open_dataset(slf_in, lazy_loading=False, engine="selafin") as ds_slf:
 
-    # Remove some data which is rebuilt
-    del ds_slf.attrs["date_start"]
+        # Remove some data which is rebuilt
+        del ds_slf.attrs["date_start"]
 
-    slf_out = tmp_path / "test.slf"
-    ds_slf.selafin.write(slf_out)
-    ds_slf2 = xr.open_dataset(slf_out, engine="selafin")
-    assert ds_slf2.equals(ds_slf)
+        slf_out = tmp_path / "test.slf"
+        ds_slf.selafin.write(slf_out)
+
+        with xr.open_dataset(slf_out, engine="selafin") as ds_slf2:
+            assert ds_slf2.equals(ds_slf)
 
     # Compare binary files
     with open(slf_in, "rb") as in_slf1, open(slf_out, "rb") as in_slf2:
@@ -108,34 +116,26 @@ def test_to_selafin_eager_mode(tmp_path, slf_in):
 @TIDAL_FLATS
 def test_slice(tmp_path, slf_in):
     # simple selection
-    ds_slf = xr.open_dataset(slf_in, engine="selafin")
-    nc_out = tmp_path / "test1.nc"
-    ds_slice = ds_slf.isel(time=0)
-    write_netcdf(ds_slice, nc_out)
-    ds_nc = xr.open_dataset(nc_out)
-    assert ds_nc.equals(ds_slice)
+    with xr.open_dataset(slf_in, engine="selafin") as ds_slf:
+        nc_out = tmp_path / "test1.nc"
+        ds_slice = ds_slf.isel(time=0)
+        assert equals_dataset_vs_netcdf_export(ds_slice, nc_out)
     # simple range
-    ds_slf = xr.open_dataset(slf_in, engine="selafin")
-    nc_out = tmp_path / "test2.nc"
-    ds_slice = ds_slf.isel(time=slice(0, 10))
-    write_netcdf(ds_slice, nc_out)
-    ds_nc = xr.open_dataset(nc_out)
-    assert ds_nc.equals(ds_slice)
+    with xr.open_dataset(slf_in, engine="selafin") as ds_slf:
+        nc_out = tmp_path / "test2.nc"
+        ds_slice = ds_slf.isel(time=slice(0, 10))
+        assert equals_dataset_vs_netcdf_export(ds_slice, nc_out)
     if "r3d" in slf_in:
         # multiple slices
-        ds_slf = xr.open_dataset(slf_in, engine="selafin")
-        nc_out = tmp_path / "test3.nc"
-        ds_slice = ds_slf.isel(time=slice(0, 10), plan=0)
-        write_netcdf(ds_slice, nc_out)
-        ds_nc = xr.open_dataset(nc_out)
-        assert ds_nc.equals(ds_slice)
+        with xr.open_dataset(slf_in, engine="selafin") as ds_slf:
+            nc_out = tmp_path / "test3.nc"
+            ds_slice = ds_slf.isel(time=slice(0, 10), plan=0)
+            assert equals_dataset_vs_netcdf_export(ds_slice, nc_out)
         # multiple range slices
-        ds_slf = xr.open_dataset(slf_in, engine="selafin")
-        nc_out = tmp_path / "test4.nc"
-        ds_slice = ds_slf.isel(time=slice(0, 10), plan=slice(5, 10))
-        write_netcdf(ds_slice, nc_out)
-        ds_nc = xr.open_dataset(nc_out)
-        assert ds_nc.equals(ds_slice)
+        with xr.open_dataset(slf_in, engine="selafin") as ds_slf:
+            nc_out = tmp_path / "test4.nc"
+            ds_slice = ds_slf.isel(time=slice(0, 10), plan=slice(5, 10))
+            assert equals_dataset_vs_netcdf_export(ds_slice, nc_out)
 
 
 def test_from_scratch(tmp_path):
@@ -165,5 +165,5 @@ def test_from_scratch(tmp_path):
 
 @DIMS
 def test_dim(slf_in):
-    ds = xr.open_dataset(slf_in, engine="selafin")
-    repr(ds)
+    with xr.open_dataset(slf_in, engine="selafin") as ds:
+        repr(ds)

xarray_selafin/Serafin.py

@@ -987,7 +987,7 @@ def __enter__(self):
         self.file = open(self.filename, self.mode)
         return self
 
-    def __exit__(self, exc_type, exc_val, exc_tb):
+    def __exit__(self, *args, **kwargs):
         self.file.close()
         return False
 

xarray_selafin/xarray_backend.py

@@ -146,32 +146,31 @@ def write_serafin(fout, ds):
     except KeyError:
         slf_header.build_params()
 
-    resout = Serafin.Write(fout, slf_header.language, overwrite=True)
-    resout.__enter__()
-    resout.write_header(slf_header)
+    with Serafin.Write(fout, slf_header.language, overwrite=True) as resout:
+        resout.write_header(slf_header)
 
-    t0 = np.datetime64(datetime(*slf_header.date))
+        t0 = np.datetime64(datetime(*slf_header.date))
 
-    try:
-        time_serie = compute_duration_between_datetime(t0, ds.time.values)
-    except AttributeError:
-        return  # no time (header only is written)
-    if isinstance(time_serie, float):
-        time_serie = [time_serie]
-    for it, t_ in enumerate(time_serie):
-        temp = np.empty(shape, dtype=slf_header.np_float_type)
-        for iv, var in enumerate(slf_header.var_IDs):
-            if slf_header.nb_frames == 1:
-                temp[iv] = ds[var]
-            else:
-                temp[iv] = ds.isel(time=it)[var]
-            if slf_header.nb_planes > 1:
-                temp[iv] = np.reshape(np.ravel(temp[iv]), (slf_header.nb_planes, slf_header.nb_nodes_2d))
-        resout.write_entire_frame(
-            slf_header,
-            t_,
-            np.reshape(temp, (slf_header.nb_var, slf_header.nb_nodes)),
-        )
+        try:
+            time_serie = compute_duration_between_datetime(t0, ds.time.values)
+        except AttributeError:
+            return  # no time (header only is written)
+        if isinstance(time_serie, float):
+            time_serie = [time_serie]
+        for it, t_ in enumerate(time_serie):
+            temp = np.empty(shape, dtype=slf_header.np_float_type)
+            for iv, var in enumerate(slf_header.var_IDs):
+                if slf_header.nb_frames == 1:
+                    temp[iv] = ds[var]
+                else:
+                    temp[iv] = ds.isel(time=it)[var]
+                if slf_header.nb_planes > 1:
+                    temp[iv] = np.reshape(np.ravel(temp[iv]), (slf_header.nb_planes, slf_header.nb_nodes_2d))
+            resout.write_entire_frame(
+                slf_header,
+                t_,
+                np.reshape(temp, (slf_header.nb_var, slf_header.nb_nodes)),
+            )
 
 
 class SelafinLazyArray(BackendArray):
@@ -319,6 +318,11 @@ def open_dataset(
 
         ds = xr.Dataset(data_vars=data_vars, coords=coords)
 
+        # Avoid a ResourceWarning (unclosed file)
+        def close():
+            slf.__exit__()
+        ds.set_close(close)
+
         ds.attrs["title"] = slf.header.title.decode(Serafin.SLF_EIT).strip()
         ds.attrs["language"] = slf.header.language
         ds.attrs["float_size"] = slf.header.float_size