Merge branch 'main' into fix-inset

Author: seisman

README.rst

@@ -86,6 +86,10 @@ Simple installation using `conda <https://docs.conda.io/projects/conda/en/latest
 
     conda install --channel conda-forge pygmt
 
+If you use `mamba <https://mamba.readthedocs.org/>`__::
+
+    mamba install --channel conda-forge pygmt
+
 For other ways to install ``pygmt``, see `full installation instructions <https://www.pygmt.org/latest/install.html>`__.
 
 

doc/install.rst

@@ -8,14 +8,43 @@ Quickstart
 
 The fastest way to install PyGMT is with the
 `conda <https://docs.conda.io/projects/conda/en/latest/user-guide/index.html>`__
+or `mamba <https://mamba.readthedocs.io/en/latest/>`__
 package manager which takes care of setting up a virtual environment, as well
-as the installation of GMT and all the dependencies PyGMT depends on::
+as the installation of GMT and all the dependencies PyGMT depends on:
 
-    conda create --name pygmt --channel conda-forge pygmt
+.. tab-set::
 
-To activate the virtual environment, you can do::
+    .. tab-item:: conda
+        :sync: conda
 
-    conda activate pygmt
+        ::
+
+            conda create --name pygmt --channel conda-forge pygmt
+
+    .. tab-item:: mamba
+        :sync: mamba
+
+        ::
+
+            mamba create --name pygmt --channel conda-forge pygmt
+
+To activate the virtual environment, you can do:
+
+.. tab-set::
+
+    .. tab-item:: conda
+        :sync: conda
+
+        ::
+
+            conda activate pygmt
+
+    .. tab-item:: mamba
+        :sync: mamba
+
+        ::
+
+            mamba activate pygmt
 
 After this, check that everything works by running the following in a Python
 interpreter (e.g., in a Jupyter notebook)::
@@ -96,13 +125,41 @@ First, we must configure conda to get packages from the
 
 Now we can create a new conda environment with Python and all our dependencies
 installed (we'll call it ``pygmt`` but feel free to change it to whatever you
-want)::
+want):
+
+.. tab-set::
+
+    .. tab-item:: conda
+        :sync: conda
+
+        ::
+
+            conda create --name pygmt python=3.9 numpy pandas xarray netcdf4 packaging gmt
+
+    .. tab-item:: mamba
+        :sync: mamba
+
+        ::
 
-    conda create --name pygmt python=3.9 numpy pandas xarray netcdf4 packaging gmt
+            mamba create --name pygmt python=3.9 numpy pandas xarray netcdf4 packaging gmt
 
-Activate the environment by running the following (**do not forget this step!**)::
+Activate the environment by running the following (**do not forget this step!**):
 
-    conda activate pygmt
+.. tab-set::
+
+    .. tab-item:: conda
+        :sync: conda
+
+        ::
+
+            conda activate pygmt
+
+    .. tab-item:: mamba
+        :sync: mamba
+
+        ::
+
+            mamba activate pygmt
 
 From now on, all commands will take place inside the conda virtual environment
 called ``pygmt`` and won't affect your default ``base`` installation.
@@ -114,17 +171,45 @@ Installing PyGMT
 Now that you have GMT installed and your conda virtual environment activated,
 you can install PyGMT using any of the following methods:
 
-Using conda (recommended)
-~~~~~~~~~~~~~~~~~~~~~~~~~
+Using conda/mamba (recommended)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This installs the latest stable release of PyGMT from
-`conda-forge <https://anaconda.org/conda-forge/pygmt>`__::
+`conda-forge <https://anaconda.org/conda-forge/pygmt>`__:
+
+.. tab-set::
+
+    .. tab-item:: conda
+        :sync: conda
+
+        ::
+
+            conda install pygmt
+
+    .. tab-item:: mamba
+        :sync: mamba
+
+        ::
+
+            mamba install pygmt
+
+This upgrades the installed PyGMT version to be the latest stable release:
+
+.. tab-set::
+
+    .. tab-item:: conda
+        :sync: conda
+
+        ::
+
+            conda update pygmt
 
-    conda install pygmt
+    .. tab-item:: mamba
+        :sync: mamba
 
-This upgrades the installed PyGMT version to be the latest stable release::
+        ::
 
-    conda update pygmt
+            mamba update pygmt
 
 Using pip
 ~~~~~~~~~

pygmt/src/histogram.py

@@ -2,17 +2,10 @@
 Histogram - Create a histogram
 """
 from pygmt.clib import Session
-from pygmt.helpers import (
-    build_arg_string,
-    deprecate_parameter,
-    fmt_docstring,
-    kwargs_to_strings,
-    use_alias,
-)
+from pygmt.helpers import build_arg_string, fmt_docstring, kwargs_to_strings, use_alias
 
 
 @fmt_docstring
-@deprecate_parameter("table", "data", "v0.5.0", remove_version="v0.7.0")
 @use_alias(
     A="horizontal",
     B="frame",

pygmt/src/info.py

@@ -6,15 +6,13 @@
 from pygmt.helpers import (
     GMTTempFile,
     build_arg_string,
-    deprecate_parameter,
     fmt_docstring,
     kwargs_to_strings,
     use_alias,
 )
 
 
 @fmt_docstring
-@deprecate_parameter("table", "data", "v0.5.0", remove_version="v0.7.0")
 @use_alias(
     C="per_column",
     I="spacing",

pygmt/src/surface.py

@@ -7,7 +7,6 @@
     GMTTempFile,
     build_arg_string,
     check_data_input_order,
-    deprecate_parameter,
     fmt_docstring,
     kwargs_to_strings,
     use_alias,
@@ -18,7 +17,6 @@
 
 
 @fmt_docstring
-@deprecate_parameter("outfile", "outgrid", "v0.5.0", remove_version="v0.7.0")
 @check_data_input_order("v0.5.0", remove_version="v0.7.0")
 @use_alias(
     I="spacing",

pygmt/src/wiggle.py

@@ -5,15 +5,13 @@
 from pygmt.helpers import (
     build_arg_string,
     check_data_input_order,
-    deprecate_parameter,
     fmt_docstring,
     kwargs_to_strings,
     use_alias,
 )
 
 
 @fmt_docstring
-@deprecate_parameter("columns", "incols", "v0.5.0", remove_version="v0.7.0")
 @check_data_input_order("v0.5.0", remove_version="v0.7.0")
 @use_alias(
     B="frame",

pygmt/tests/test_info.py

@@ -31,23 +31,6 @@ def test_info():
     assert output == expected_output
 
 
-def test_info_deprecate_table_to_data():
-    """
-    Make sure that the old parameter "table" is supported and it reports a
-    warning.
-    """
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        output = info(table=POINTS_DATA)  # pylint: disable=no-value-for-parameter
-        expected_output = (
-            f"{POINTS_DATA}: N = 20 "
-            "<11.5309/61.7074> "
-            "<-2.9289/7.8648> "
-            "<0.1412/0.9338>\n"
-        )
-        assert output == expected_output
-        assert len(record) == 1  # check that only one warning was raised
-
-
 @pytest.mark.parametrize(
     "table",
     [

pygmt/tests/test_surface.py

@@ -145,25 +145,3 @@ def test_surface_with_outgrid_param(data, region, spacing, expected_grid):
         assert os.path.exists(path=tmpfile.name)  # check that outgrid exists at path
         with xr.open_dataarray(tmpfile.name) as grid:
             check_values(grid, expected_grid)
-
-
-def test_surface_deprecate_outfile_to_outgrid(data, region, spacing, expected_grid):
-    """
-    Make sure that the old parameter "outfile" is supported and it reports a
-    warning.
-    """
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        data = data.values  # convert pandas.DataFrame to numpy.ndarray
-        with GMTTempFile(suffix=".nc") as tmpfile:
-            output = surface(
-                data=data,
-                spacing=spacing,
-                region=region,
-                outfile=tmpfile.name,
-                verbose="e",  # Suppress warnings for IEEE 754 rounding
-            )
-            assert output is None  # check that output is None since outfile is set
-            assert os.path.exists(path=tmpfile.name)  # check that file exists at path
-            with xr.open_dataarray(tmpfile.name) as grid:
-                check_values(grid, expected_grid)
-        assert len(record) == 1  # check that only one warning was raised

pygmt/tests/test_wiggle.py

@@ -32,33 +32,28 @@ def test_wiggle():
 
 
 @pytest.mark.mpl_image_compare(filename="test_wiggle.png")
-def test_wiggle_deprecate_columns_to_incols():
+def test_wiggle_data_incols():
     """
-    Make sure that the old parameter "columns" is supported and it reports a
-    warning.
-
-    Modified from the test_wiggle() test.
+    Make sure that incols parameter works with input data array.
     """
 
     # put data into numpy array and swap x and y columns
-    # as the use of the 'columns' parameter will reverse this action
+    # as the use of the 'incols' parameter will reverse this action
     x = np.arange(-2, 2, 0.02)
     y = np.zeros(x.size)
     z = np.cos(2 * np.pi * x)
     data = np.array([y, x, z]).T
 
     fig = Figure()
-    with pytest.warns(expected_warning=FutureWarning) as record:
-        fig.wiggle(
-            data,
-            region=[-4, 4, -1, 1],
-            projection="X8c",
-            columns=[1, 0, 2],
-            scale="0.5c",
-            color=["red+p", "gray+n"],
-            pen="1.0p",
-            track="0.5p",
-            position="jRM+w2+lnT",
-        )
-        assert len(record) == 1  # check that only one warning was raised
+    fig.wiggle(
+        data,
+        region=[-4, 4, -1, 1],
+        projection="X8c",
+        incols=[1, 0, 2],
+        scale="0.5c",
+        color=["red+p", "gray+n"],
+        pen="1.0p",
+        track="0.5p",
+        position="jRM+w2+lnT",
+    )
     return fig