Merge pull request #62 from wpreimes/fix-append-mode

Fix append mode

.github/workflows/ubuntu.yml

@@ -12,19 +12,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
         os: ["ubuntu-latest"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
-          submodules: false # does not work with self-hosted testdata
+          submodules: false
       - name: Checkout Testdata
         shell: bash -l {0}
         run : |
           git submodule init
           git submodule update
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           auto-update-conda: true
@@ -43,18 +43,18 @@ jobs:
       - name: Export Environment
         shell: bash -l {0}
         run: |
-          mkdir -p .artifacts
+          mkdir -p artifacts
           filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
-          conda env export --no-builds | grep -v "prefix" > .artifacts/$filename
+          conda env export --no-builds | grep -v "prefix" > artifacts/$filename
       - name: Upload Artifacts
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
-          name: os_py_environments
-          path: .artifacts/*
+          name: Artifacts-py${{ matrix.python-version }}-${{ matrix.os }}
+          path: artifacts/*
       - name: Install package and test
         shell: bash -l {0}
         run: |
-          pip install -e .
+          pip install -e .[testing]
           pytest --cache-clear
       - name: Upload Coverage
         shell: bash -l {0}

.github/workflows/windows.yml

@@ -12,19 +12,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.12']
         os: ['windows-latest']
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
-          submodules: false # does not work with self-hosted testdata
+          submodules: false
       - name: Checkout Testdata
         shell: bash -l {0}
         run : |
           git submodule init
           git submodule update
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: "latest"
           auto-update-conda: true
@@ -43,5 +43,5 @@ jobs:
       - name: Install package and test
         shell: bash -l {0}
         run: |
-          pip install -e .
+          pip install -e .[testing]
           pytest --cache-clear

CHANGELOG.rst

@@ -2,6 +2,12 @@
 Changelog
 =========
 
+Version 0.5.1
+=============
+
+- Fixed a bug where global attrs were not updated when appending data
+- Fixed some numpy warnings
+
 Version 0.5.0
 =============
 

environment.yml

@@ -12,5 +12,3 @@ dependencies:
 - pip:
   - pygeobase
   - pygeogrids
-  - pytest
-  - pytest-cov

setup.cfg

@@ -61,7 +61,6 @@ exclude =
 
 # Add here test requirements (semicolon/line-separated)
 testing =
-    setuptools
     pytest
     pytest-cov
 

src/pynetcf/base.py

@@ -286,7 +286,7 @@ def read_var(self, name):
             name of the variable
         """
 
-        if self.mode in ["r", "r+"]:
+        if self.mode in ["r", "r+", "a"]:
             if name in self.dataset.variables.keys():
                 return self.dataset.variables[name][:]
 
@@ -308,7 +308,7 @@ def flush(self):
         Flush data to disk.
         """
         if self.dataset is not None:
-            if self.mode in ["w", "r+"]:
+            if self.mode in ["w", "r+", "a"]:
                 self._set_global_attr()
                 self.dataset.sync()
 

src/pynetcf/point_data.py

@@ -342,7 +342,7 @@ def write(self,
                 # convert dict to recarray
                 metadata = {"dims": md_dict}
                 dtype = np.dtype(dtype_list, metadata=metadata)
-                data = np.core.records.fromarrays(data.values(), dtype=dtype)
+                data = np.rec.fromarrays(data.values(), dtype=dtype)
 
             for var_data in data.dtype.names:
                 if var_data not in self.nc.variables:

src/pynetcf/time_series.py

@@ -309,7 +309,7 @@ def _get_loc_id_index(self, loc_id):
         loc_id = np.atleast_1d(loc_id)
         # check if the location ids are all actually in the location id
         # variable
-        in1d = np.in1d(loc_id, self.loc_ids_var.data, assume_unique=True)
+        in1d = np.isin(loc_id, self.loc_ids_var.data, assume_unique=True)
         if loc_id[in1d].size != loc_id.size:
             raise IOError("Location not yet defined")
         loc_ids_sorted = np.argsort(self.loc_ids_var.data)
@@ -380,7 +380,7 @@ def _add_location(self, loc_id, lon, lat, alt=None, loc_descr=None):
 
         loc_count = len(locations)
         if loc_count > 0:
-            loc_ids_new = np.invert(np.in1d(loc_id, locations))
+            loc_ids_new = np.invert(np.isin(loc_id, locations))
             if len(np.nonzero(loc_ids_new)[0]) == 0:
                 # no new locations to add
                 return None