Merge branch 'master' into testing

Author: weiji14

.github/workflows/cache_data.yaml

@@ -23,7 +23,7 @@ jobs:
       # Install GMT
       - name: Install GMT
         shell: bash -l {0}
-        run: conda install -c conda-forge gmt=6.1.0
+        run: conda install -c conda-forge gmt=6.1.1
 
       # Download remote files
       - name: Download remote data

.github/workflows/ci_tests.yaml

@@ -77,7 +77,7 @@ jobs:
           requirements_file=full-conda-requirements.txt
           cat requirements.txt requirements-dev.txt > $requirements_file
           cat << EOF >> $requirements_file
-          gmt=6.1.0
+          gmt=6.1.1
           make
           codecov
           EOF

.travis.yml

@@ -26,21 +26,13 @@ env:
         # The file with the listed requirements to be installed by conda
         - CONDA_REQUIREMENTS=requirements.txt
         - CONDA_REQUIREMENTS_DEV=requirements-dev.txt
-        - CONDA_INSTALL_EXTRA="codecov twine gmt=6.1.0"
+        - CONDA_INSTALL_EXTRA="codecov twine gmt=6.1.1"
         # These variables control which actions are performed in a build
         - DEPLOY=false
 
 jobs:
     # Build under the following configurations
     include:
-        - name: "Linux - Python 3.8"
-          os: linux
-          env:
-              - PYTHON=3.8
-        - name: "Linux - Python 3.7"
-          os: linux
-          env:
-              - PYTHON=3.7
         - name: "Linux - Python 3.6 (deploy)"
           os: linux
           env:
@@ -67,11 +59,6 @@ script:
     # Build the documentation
     - make -C doc all
 
-# Things to do if the build is successful
-after_success:
-    # Upload coverage information
-    - codecov -e PYTHON
-
 deploy:
     # Make a release on PyPI
     - provider: script

doc/install.rst

@@ -31,7 +31,7 @@ Which GMT?
 PyGMT requires Generic Mapping Tools (GMT) version 6 as a minimum, which is the latest
 released version that can be found at
 the `GMT official site <https://www.generic-mapping-tools.org>`__.
-We need the latest GMT (>=6.1.0) since there are many changes being made to GMT itself in
+We need the latest GMT (>=6.1.1) since there are many changes being made to GMT itself in
 response to the development of PyGMT, mainly the new
 `modern execution mode <https://docs.generic-mapping-tools.org/latest/cookbook/introduction.html#modern-and-classic-mode>`__.
 

environment.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
     - python=3.7
     - pip
-    - gmt=6.1.0
+    - gmt=6.1.1
     - numpy
     - pandas
     - xarray

package.json

@@ -1,7 +1,7 @@
 {
   "scripts": {
     "build:miniconda": "curl -o ~/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash ~/miniconda.sh -b -p $HOME/miniconda",
-    "build:pygmt": "conda env create -f environment.yml && source activate pygmt && conda install -c conda-forge -y gmt==6.1.0 && make install",
+    "build:pygmt": "conda env create -f environment.yml && source activate pygmt && conda install -c conda-forge -y gmt==6.1.1 && make install",
     "build:docs": "source activate pygmt && cd doc && make all && mv _build/html ../public",
     "build": "export PATH=$HOME/miniconda/bin:$PATH && npm run build:miniconda && npm run build:pygmt && npm run build:docs"
   }

pygmt/base_plotting.py

@@ -226,6 +226,7 @@ def colorbar(self, **kwargs):
         S="resample",
         U="timestamp",
         W="pen",
+        l="label",
     )
     @kwargs_to_strings(R="sequence", L="sequence", A="sequence_plus")
     def grdcontour(self, grid, **kwargs):
@@ -275,6 +276,13 @@ def grdcontour(self, grid, **kwargs):
         {G}
         {U}
         {W}
+        label : str
+            Add a legend entry for the contour being plotted. Normally, the
+            annotated contour is selected for the legend. You can select the
+            regular contour instead, or both of them, by considering the label
+            to be of the format [*annotcontlabel*][/*contlabel*]. If either
+            label contains a slash (/) character then use ``|`` as the
+            separator for the two labels instead.
         """
         kwargs = self._preprocess(**kwargs)
         kind = data_kind(grid, None, None)
@@ -568,6 +576,7 @@ def plot(self, x=None, y=None, data=None, sizes=None, direction=None, **kwargs):
         W="pen",
         L="triangular_mesh_pen",
         i="columns",
+        l="label",
         C="levels",
     )
     @kwargs_to_strings(R="sequence", i="sequence_comma")
@@ -619,6 +628,13 @@ def contour(self, x=None, y=None, z=None, data=None, **kwargs):
         skip : bool or str
             Skip input points outside region ``'[p|t]'``
         {W}
+        label : str
+            Add a legend entry for the contour being plotted. Normally, the
+            annotated contour is selected for the legend. You can select the
+            regular contour instead, or both of them, by considering the label
+            to be of the format [*annotcontlabel*][/*contlabel*]. If either
+            label contains a slash (/) character then use ``|`` as the
+            separator for the two labels instead.
 
         """
         kwargs = self._preprocess(**kwargs)
@@ -997,7 +1013,7 @@ def text(
 
     @fmt_docstring
     @use_alias(R="region", J="projection", B="frame", C="offset")
-    @kwargs_to_strings(R="sequence",)
+    @kwargs_to_strings(R="sequence")
     def meca(
         self,
         spec,

pygmt/clib/session.py

@@ -119,7 +119,7 @@ class Session:
     """
 
     # The minimum version of GMT required
-    required_version = "6.1.0"
+    required_version = "6.1.1"
 
     @property
     def session_pointer(self):
@@ -725,10 +725,10 @@ def _check_dtype_and_dim(self, array, ndim):
             try:
                 # Try to convert any unknown numpy data types to np.datetime64
                 array = np.asarray(array, dtype=np.datetime64)
-            except ValueError:
+            except ValueError as e:
                 raise GMTInvalidInput(
-                    "Unsupported numpy data type '{}'.".format(array.dtype.type)
-                )
+                    f"Unsupported numpy data type '{array.dtype.type}'."
+                ) from e
         return self[DTYPES[array.dtype.type]]
 
     def put_vector(self, dataset, column, vector):
@@ -1065,7 +1065,7 @@ def open_virtual_file(self, family, geometry, direction, data):
         family_int = self._parse_constant(family, valid=FAMILIES, valid_modifiers=VIAS)
         geometry_int = self._parse_constant(geometry, valid=GEOMETRIES)
         direction_int = self._parse_constant(
-            direction, valid=["GMT_IN", "GMT_OUT"], valid_modifiers=METHODS,
+            direction, valid=["GMT_IN", "GMT_OUT"], valid_modifiers=METHODS
         )
 
         buff = ctp.create_string_buffer(self["GMT_VF_LEN"])

pygmt/figure.py

@@ -316,14 +316,6 @@ def shift_origin(self, xshift=None, yshift=None):
             Shift plot origin in x direction.
         yshift : str
             Shift plot origin in y direction.
-
-        Notes
-        -----
-        For GMT 6.1.0, this function can't be used as the first plotting
-        function of :meth:`pygmt.Figure`, since it relies the *region* and
-        *projection* settings from previous commands.
-
-        .. TODO: Remove the notes when PyGMT bumps to GMT>=6.1.1.
         """
         self._preprocess()
         args = ["-T"]

pygmt/tests/test_clib.py

@@ -402,10 +402,6 @@ def test_virtualfile_from_vectors():
             assert output == expected
 
 
-@pytest.mark.xfail(
-    condition=gmt_version < Version("6.1.1"),
-    reason="GMT_Put_Strings only works for GMT 6.1.1 and above",
-)
 def test_virtualfile_from_vectors_one_string_column():
     "Test passing in one column with string dtype into virtual file dataset"
     size = 5
@@ -421,10 +417,6 @@ def test_virtualfile_from_vectors_one_string_column():
         assert output == expected
 
 
-@pytest.mark.xfail(
-    condition=gmt_version < Version("6.1.1"),
-    reason="GMT_Put_Strings only works for GMT 6.1.1 and above",
-)
 def test_virtualfile_from_vectors_two_string_columns():
     "Test passing in two columns of string dtype into virtual file dataset"
     size = 5
@@ -688,7 +680,7 @@ def test_get_default():
     with clib.Session() as lib:
         assert lib.get_default("API_GRID_LAYOUT") in ["rows", "columns"]
         assert int(lib.get_default("API_CORES")) >= 1
-        assert Version(lib.get_default("API_VERSION")) >= Version("6.1.0")
+        assert Version(lib.get_default("API_VERSION")) >= Version("6.1.1")
 
 
 def test_get_default_fails():

pygmt/tests/test_clib_put_strings.py

@@ -14,10 +14,6 @@
     gmt_version = Version(_lib.info["version"])
 
 
-@pytest.mark.xfail(
-    condition=gmt_version < Version("6.1.1"),
-    reason="GMT_Put_Strings only works for GMT 6.1.1 and above",
-)
 def test_put_strings():
     "Check that assigning a numpy array of dtype str to a dataset works"
     with clib.Session() as lib:

pygmt/tests/test_grdtrack.py

@@ -25,7 +25,7 @@ def fixture_dataarray():
     )
 
 
-@pytest.mark.xfail(reason="The reason why it fails is unclear now",)
+@pytest.mark.xfail(reason="The reason why it fails is unclear now")
 def test_grdtrack_input_dataframe_and_dataarray(dataarray):
     """
     Run grdtrack by passing in a pandas.DataFrame and xarray.DataArray as
@@ -41,7 +41,7 @@ def test_grdtrack_input_dataframe_and_dataarray(dataarray):
     return output
 
 
-@pytest.mark.xfail(reason="The reason why it fails is unclear now",)
+@pytest.mark.xfail(reason="The reason why it fails is unclear now")
 def test_grdtrack_input_csvfile_and_dataarray(dataarray):
     """
     Run grdtrack by passing in a csvfile and xarray.DataArray as inputs

pygmt/tests/test_session_management.py

@@ -8,7 +8,7 @@
 
 
 def test_begin_end():
-    """"
+    """
     Run a command inside a begin-end modern mode block.
     First, end the global session. When finished, restart it.
     """