Merge branch 'master' into stringio_input

weiji14 · weiji14 · commit 2909662f0a40 · 2020-09-07T14:11:06.000+12:00
diff --git a/.github/workflows/cache_data.yaml b/.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
diff --git a/.github/workflows/ci_tests.yaml b/.github/workflows/ci_tests.yaml
@@ -65,10 +65,11 @@ jobs:
 
       # Setup Miniconda
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.6.0
+        uses: conda-incubator/setup-miniconda@v1.7.0
         with:
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
+          miniconda-version: "latest"
 
       # Install GMT and other required dependencies from conda-forge
       - name: Install GMT and required dependencies
@@ -77,7 +78,7 @@ 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
diff --git a/.travis.yml b/.travis.yml
@@ -26,7 +26,7 @@ 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
 
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -310,8 +310,38 @@ Leave a comment in the PR and we'll help you out.
 
 ### Testing plots
 
-We use the [pytest-mpl](https://github.com/matplotlib/pytest-mpl) plug-in to test plot
-generating code.
+Writing an image-based test is only slightly more difficult than a simple test.
+The main consideration is that you must specify the "baseline" or reference
+image, and compare it with a "generated" or test image. This is handled using
+the *decorator* functions `@check_figures_equal` and
+`@pytest.mark.mpl_image_compare` whose usage are further described below.
+
+#### Using check_figures_equal
+
+This approach draws the same figure using two different methods (the reference
+method and the tested method), and checks that both of them are the same.
+It takes two `pygmt.Figure` objects ('fig_ref' and 'fig_test'), generates a png
+image, and checks for the Root Mean Square (RMS) error between the two.
+Here's an example:
+
+```python
+@check_figures_equal()
+def test_my_plotting_case(fig_ref, fig_test):
+  "Test that my plotting function works"
+  fig_ref.grdimage("@earth_relief_01d_g", projection="W120/15c", cmap="geo")
+  fig_test.grdimage(grid, projection="W120/15c", cmap="geo")
+```
+
+Note: This is the recommended way to test plots whenever possible, such as when
+we want to compare a reference GMT plot created from NetCDF files with one
+generated by PyGMT that passes through several layers of virtualfile machinery.
+Using this method will help save space in the git repository by not having to
+store baseline images as with the other method below.
+
+#### Using mpl_image_compare
+
+This method uses the [pytest-mpl](https://github.com/matplotlib/pytest-mpl)
+plug-in to test plot generating code.
 Every time the tests are run, `pytest-mpl` compares the generated plots with known
 correct ones stored in `pygmt/tests/baseline`.
 If your test created a `pygmt.Figure` object, you can test it by adding a *decorator* and
diff --git a/Makefile b/Makefile
@@ -29,11 +29,7 @@ test:
 	@echo ""
 	@cd $(TESTDIR); python -c "import $(PROJECT); $(PROJECT).show_versions()"
 	@echo ""
-	# There are two steps to the test here because `test_grdimage_over_dateline`
-	# passes only when it runs before the other tests.
-	# See also https://github.com/GenericMappingTools/pygmt/pull/476
-	cd $(TESTDIR); pytest -m runfirst $(PYTEST_ARGS) $(PROJECT)
-	cd $(TESTDIR); pytest -m 'not runfirst' $(PYTEST_ARGS) $(PROJECT)
+	cd $(TESTDIR); pytest $(PYTEST_ARGS) $(PROJECT)
 	cp $(TESTDIR)/coverage.xml .
 	cp -r $(TESTDIR)/htmlcov .
 	rm -r $(TESTDIR)
diff --git a/doc/install.rst b/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>`__.
 
diff --git a/environment.yml b/environment.yml
@@ -5,7 +5,7 @@ channels:
 dependencies:
     - python=3.7
     - pip
-    - gmt=6.1.0
+    - gmt=6.1.1
     - numpy
     - pandas
     - xarray
diff --git a/examples/gallery/grid/track_sampling.py b/examples/gallery/grid/track_sampling.py
@@ -24,7 +24,7 @@
 
 fig = pygmt.Figure()
 # Plot the earth relief grid on Cylindrical Stereographic projection, masking land areas
-fig.basemap(region="d", frame=True, projection="Cyl_stere/8i")
+fig.basemap(region="g", frame=True, projection="Cyl_stere/150/-20/8i")
 fig.grdimage(grid=grid, cmap="gray")
 fig.coast(land="#666666")
 # Plot using circles (c) of 0.15cm, the sampled bathymetry points
diff --git a/package.json b/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"
   }
diff --git a/pygmt/base_plotting.py b/pygmt/base_plotting.py
@@ -3,8 +3,6 @@
 Does not define any special non-GMT methods (savefig, show, etc).
 """
 import contextlib
-import csv
-
 import numpy as np
 import pandas as pd
 
@@ -993,28 +991,16 @@ def text(
         if position is not None and isinstance(position, str):
             kwargs["F"] += f'+c{position}+t"{text}"'
 
-        with GMTTempFile(suffix=".txt") as tmpfile:
-            with Session() as lib:
-                fname = textfiles if kind == "file" else ""
-                if kind == "vectors":
-                    if position is not None:
-                        fname = ""
-                    else:
-                        pd.DataFrame.from_dict(
-                            {
-                                "x": np.atleast_1d(x),
-                                "y": np.atleast_1d(y),
-                                "text": np.atleast_1d(text),
-                            }
-                        ).to_csv(
-                            tmpfile.name,
-                            sep="\t",
-                            header=False,
-                            index=False,
-                            quoting=csv.QUOTE_NONE,
-                        )
-                    fname = tmpfile.name
-
+        with Session() as lib:
+            file_context = dummy_context(textfiles) if kind == "file" else ""
+            if kind == "vectors":
+                if position is not None:
+                    file_context = dummy_context("")
+                else:
+                    file_context = lib.virtualfile_from_vectors(
+                        np.atleast_1d(x), np.atleast_1d(y), np.atleast_1d(text)
+                    )
+            with file_context as fname:
                 arg_str = " ".join([fname, build_arg_string(kwargs)])
                 lib.call_module("text", arg_str)
 
diff --git a/pygmt/clib/session.py b/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):
diff --git a/pygmt/exceptions.py b/pygmt/exceptions.py
@@ -44,3 +44,9 @@ class GMTVersionError(GMTError):
     """
     Raised when an incompatible version of GMT is being used.
     """
+
+
+class GMTImageComparisonFailure(AssertionError):
+    """
+    Raised when a comparison between two images fails.
+    """
diff --git a/pygmt/figure.py b/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"]
diff --git a/pygmt/helpers/testing.py b/pygmt/helpers/testing.py
@@ -0,0 +1,113 @@
+"""
+Helper functions for testing.
+"""
+
+import inspect
+import os
+
+from matplotlib.testing.compare import compare_images
+
+from ..exceptions import GMTImageComparisonFailure
+from ..figure import Figure
+
+
+def check_figures_equal(*, tol=0.0, result_dir="result_images"):
+    """
+    Decorator for test cases that generate and compare two figures.
+
+    The decorated function must take two arguments, *fig_ref* and *fig_test*,
+    and draw the reference and test images on them. After the function
+    returns, the figures are saved and compared.
+
+    This decorator is practically identical to matplotlib's check_figures_equal
+    function, but adapted for PyGMT figures. See also the original code at
+    https://matplotlib.org/3.3.1/api/testing_api.html#
+    matplotlib.testing.decorators.check_figures_equal
+
+    Parameters
+    ----------
+    tol : float
+        The RMS threshold above which the test is considered failed.
+    result_dir : str
+        The directory where the figures will be stored.
+
+    Examples
+    --------
+
+    >>> import pytest
+    >>> import shutil
+
+    >>> @check_figures_equal(result_dir="tmp_result_images")
+    ... def test_check_figures_equal(fig_ref, fig_test):
+    ...     fig_ref.basemap(projection="X5c", region=[0, 5, 0, 5], frame=True)
+    ...     fig_test.basemap(projection="X5c", region=[0, 5, 0, 5], frame="af")
+    >>> test_check_figures_equal()
+    >>> assert len(os.listdir("tmp_result_images")) == 0
+    >>> shutil.rmtree(path="tmp_result_images")  # cleanup folder if tests pass
+
+    >>> @check_figures_equal(result_dir="tmp_result_images")
+    ... def test_check_figures_unequal(fig_ref, fig_test):
+    ...     fig_ref.basemap(projection="X5c", region=[0, 5, 0, 5], frame=True)
+    ...     fig_test.basemap(projection="X5c", region=[0, 3, 0, 3], frame=True)
+    >>> with pytest.raises(GMTImageComparisonFailure):
+    ...     test_check_figures_unequal()
+    >>> for suffix in ["", "-expected", "-failed-diff"]:
+    ...     assert os.path.exists(
+    ...         os.path.join(
+    ...             "tmp_result_images",
+    ...             f"test_check_figures_unequal{suffix}.png",
+    ...         )
+    ...     )
+    >>> shutil.rmtree(path="tmp_result_images")  # cleanup folder if tests pass
+    """
+
+    def decorator(func):
+
+        os.makedirs(result_dir, exist_ok=True)
+        old_sig = inspect.signature(func)
+
+        def wrapper(*args, **kwargs):
+            try:
+                fig_ref = Figure()
+                fig_test = Figure()
+                func(*args, fig_ref=fig_ref, fig_test=fig_test, **kwargs)
+                ref_image_path = os.path.join(
+                    result_dir, func.__name__ + "-expected.png"
+                )
+                test_image_path = os.path.join(result_dir, func.__name__ + ".png")
+                fig_ref.savefig(ref_image_path)
+                fig_test.savefig(test_image_path)
+
+                # Code below is adapted for PyGMT, and is originally based on
+                # matplotlib.testing.decorators._raise_on_image_difference
+                err = compare_images(
+                    expected=ref_image_path,
+                    actual=test_image_path,
+                    tol=tol,
+                    in_decorator=True,
+                )
+                if err is None:  # Images are the same
+                    os.remove(ref_image_path)
+                    os.remove(test_image_path)
+                else:  # Images are not the same
+                    for key in ["actual", "expected", "diff"]:
+                        err[key] = os.path.relpath(err[key])
+                    raise GMTImageComparisonFailure(
+                        "images not close (RMS %(rms).3f):\n\t%(actual)s\n\t%(expected)s "
+                        % err
+                    )
+            finally:
+                del fig_ref
+                del fig_test
+
+        parameters = [
+            param
+            for param in old_sig.parameters.values()
+            if param.name not in {"fig_test", "fig_ref"}
+        ]
+        new_sig = old_sig.replace(parameters=parameters)
+        wrapper.__signature__ = new_sig
+
+        return wrapper
+
+    return decorator
diff --git a/pygmt/helpers/utils.py b/pygmt/helpers/utils.py
@@ -21,6 +21,7 @@ def data_kind(data, x=None, y=None, z=None):
     Possible types:
 
     * a file name provided as 'data'
+    * an xarray.DataArray provided as 'data'
     * a matrix provided as 'data'
     * 1D arrays x and y (and z, optionally)
 
@@ -29,8 +30,8 @@ def data_kind(data, x=None, y=None, z=None):
 
     Parameters
     ----------
-    data : str, 2d array, or None
-       Data file name or numpy array.
+    data : str, xarray.DataArray, 2d array, or None
+       Data file name, xarray.DataArray or numpy array.
     x/y : 1d arrays or None
         x and y columns as numpy arrays.
     z : 1d array or None
@@ -40,18 +41,21 @@ def data_kind(data, x=None, y=None, z=None):
     Returns
     -------
     kind : str
-        One of: ``'file'``, ``'matrix'``, ``'vectors'``.
+        One of: ``'file'``, ``'grid'``, ``'matrix'``, ``'vectors'``.
 
     Examples
     --------
 
     >>> import numpy as np
+    >>> import xarray as xr
     >>> data_kind(data=None, x=np.array([1, 2, 3]), y=np.array([4, 5, 6]))
     'vectors'
     >>> data_kind(data=np.arange(10).reshape((5, 2)), x=None, y=None)
     'matrix'
     >>> data_kind(data='my-data-file.txt', x=None, y=None)
     'file'
+    >>> data_kind(data=xr.DataArray(np.random.rand(4, 3)))
+    'grid'
 
     """
     if data is None and x is None and y is None:
diff --git a/pygmt/tests/test_clib.py b/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():
diff --git a/pygmt/tests/test_clib_put_matrix.py b/pygmt/tests/test_clib_put_matrix.py
diff --git a/pygmt/tests/test_clib_put_strings.py b/pygmt/tests/test_clib_put_strings.py
diff --git a/pygmt/tests/test_figure.py b/pygmt/tests/test_figure.py
diff --git a/pygmt/tests/test_grdimage.py b/pygmt/tests/test_grdimage.py
diff --git a/setup.cfg b/setup.cfg

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"scripts": {`
`3`	`3`	`"build:miniconda": "curl -o ~/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash ~/miniconda.sh -b -p $HOME/miniconda",`
`4`		`- "build:pygmt": "conda env create -f environment.yml && source activate pygmt && conda install -c conda-forge -y gmt==6.1.0 && make install",`
	`4`	`+ "build:pygmt": "conda env create -f environment.yml && source activate pygmt && conda install -c conda-forge -y gmt==6.1.1 && make install",`
`5`	`5`	`"build:docs": "source activate pygmt && cd doc && make all && mv _build/html ../public",`
`6`	`6`	`"build": "export PATH=$HOME/miniconda/bin:$PATH && npm run build:miniconda && npm run build:pygmt && npm run build:docs"`
`7`	`7`	`}`