Merge branch 'master' into double-yaxis

Author: core-man

.github/workflows/check-links.yml

@@ -31,7 +31,9 @@ jobs:
         # 429: Too many requests
         args: >
           --accept 429
+          --exclude "^https://doi.org/10.5281/zenodo$"
           --exclude "^https://zenodo.org/badge/DOI/$"
+          --exclude "^https://zenodo.org/badge/DOI/10.5281/zenodo$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/pull/[0-9]*$"
           --exclude "^https://github.com/GenericMappingTools/pygmt/issues/[0-9]*$"
           --exclude "^https://www.generic-mapping-tools.org/_static/gmt-logo.png/$"
@@ -40,6 +42,7 @@ jobs:
           --exclude "^git"
           --exclude "^file://"
           --exclude "^https://docs.generic-mapping-tools.org/latest/%s$"
+          --exclude "https://hackmd.io/@pygmt"
           --verbose
           "repository/**/*.rst"
           "repository/**/*.md"

.github/workflows/ci_tests.yaml

@@ -86,7 +86,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.11.1
+        uses: dawidd6/action-download-artifact@v2.12.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

.github/workflows/ci_tests_dev.yaml

@@ -97,7 +97,7 @@ jobs:
 
       # Download cached remote files (artifacts) from GitHub
       - name: Download remote data from GitHub
-        uses: dawidd6/action-download-artifact@v2.11.1
+        uses: dawidd6/action-download-artifact@v2.12.0
         with:
           workflow: cache_data.yaml
           workflow_conclusion: success

doc/Makefile

@@ -1,35 +1,31 @@
 # Makefile for Sphinx documentation
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -j auto
 SPHINXBUILD   = sphinx-build
 SPHINXAUTOGEN = sphinx-autogen
 BUILDDIR      = _build
 
 # Internal variables.
-ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees  $(SPHINXOPTS) .
+ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees  $(SPHINXOPTS) .
 
-.PHONY: help clean html linkcheck doctest api
-
-all: html
+.PHONY: help all api html server clean
 
 help:
-	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  all        generate the complete webpage"
-	@echo "  html       make only the HTML files from the existing rst sources"
-	@echo "  linkcheck  check all external links for integrity"
-	@echo "  doctest    run all doctests embedded in the documentation (if enabled)"
+	@echo "Please use 'make <target>' where <target> is one of"
+	@echo "  all        build the HTML files from the existing rst sources"
+	@echo "  api        generate rst source files of API documentation"
+	@echo "  html       build the HTML files from the existing rst sources"
+	@echo "  server     make a local HTTP server for previewing the built documentation"
+	@echo "  clean      clean up built and generated files"
 
-clean:
-	rm -rf $(BUILDDIR)/html
-	rm -rf $(BUILDDIR)/doctrees
-	rm -rf $(BUILDDIR)/linkcheck
-	rm -rf modules
-	rm -rf api/generated
-	rm -rf gallery
-	rm -rf tutorials
-	rm -rf projections
-	rm -rf .ipynb_checkpoints
+all: html
+
+api:
+	@echo
+	@echo "Generating rst source files of API documentation."
+	@echo
+	$(SPHINXAUTOGEN) -i -t _templates -o api/generated api/*.rst
 
 html: api
 	@echo
@@ -39,23 +35,16 @@ html: api
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
-api:
+server:
 	@echo
-	@echo "Building API docs."
+	@echo "Running a server on port 8009."
+	@echo "Open http://localhost:8009 in a web browser to preview the documentation."
 	@echo
-	$(SPHINXAUTOGEN) -i -t _templates -o api/generated api/*.rst
-
-
-linkcheck:
-	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
-	@echo
-	@echo "Link check complete; look for any errors in the above output " \
-	      "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
-	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
-	@echo "Testing of doctests in the sources finished, look at the " \
-	      "results in $(BUILDDIR)/doctest/output.txt."
-
-serve:
 	cd $(BUILDDIR)/html && python -m http.server 8009
+
+clean:
+	rm -rf $(BUILDDIR)
+	rm -rf api/generated
+	rm -rf gallery
+	rm -rf tutorials
+	rm -rf projections

pygmt/clib/session.py

@@ -1360,7 +1360,9 @@ def virtualfile_from_grid(self, grid):
         with self.open_virtual_file(*args) as vfile:
             yield vfile
 
-    def virtualfile_from_data(self, check_kind=None, data=None, x=None, y=None, z=None):
+    def virtualfile_from_data(
+        self, check_kind=None, data=None, x=None, y=None, z=None, extra_arrays=None
+    ):
         """
         Store any data inside a virtual file.
 
@@ -1378,6 +1380,9 @@ def virtualfile_from_data(self, check_kind=None, data=None, x=None, y=None, z=No
             raster grid, a vector matrix/arrays, or other supported data input.
         x/y/z : 1d arrays or None
             x, y and z columns as numpy arrays.
+        extra_arrays : list of 1d arrays
+            Optional. A list of numpy arrays in addition to x, y and z. All
+            of these arrays must be of the same size as the x/y/z arrays.
 
         Returns
         -------
@@ -1430,14 +1435,26 @@ def virtualfile_from_data(self, check_kind=None, data=None, x=None, y=None, z=No
         if kind in ("file", "grid"):
             _data = (data,)
         elif kind == "vectors":
-            _data = (x, y, z)
+            _data = [np.atleast_1d(x), np.atleast_1d(y)]
+            if z is not None:
+                _data.append(np.atleast_1d(z))
+            if extra_arrays:
+                _data.extend(extra_arrays)
         elif kind == "matrix":  # turn 2D arrays into list of vectors
             try:
                 # pandas.DataFrame and xarray.Dataset types
                 _data = [array for _, array in data.items()]
             except AttributeError:
-                # Python lists, tuples, and numpy ndarray types
-                _data = np.atleast_2d(np.asanyarray(data).T)
+                try:
+                    # Just use virtualfile_from_matrix for 2D numpy.ndarray
+                    # which are signed integer (i), unsigned integer (u) or
+                    # floating point (f) types
+                    assert data.ndim == 2 and data.dtype.kind in "iuf"
+                    _virtualfile_from = self.virtualfile_from_matrix
+                    _data = (data,)
+                except (AssertionError, AttributeError):
+                    # Python lists, tuples, and numpy ndarray types
+                    _data = np.atleast_2d(np.asanyarray(data).T)
 
         # Finally create the virtualfile from the data, to be passed into GMT
         file_context = _virtualfile_from(*_data)

pygmt/src/plot.py

@@ -1,13 +1,11 @@
 """
 plot - Plot in two dimensions.
 """
-import numpy as np
 from pygmt.clib import Session
 from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import (
     build_arg_string,
     data_kind,
-    dummy_context,
     fmt_docstring,
     is_nonstr_iter,
     kwargs_to_strings,
@@ -226,14 +224,9 @@ def plot(self, x=None, y=None, data=None, sizes=None, direction=None, **kwargs):
 
     with Session() as lib:
         # Choose how data will be passed in to the module
-        if kind == "file":
-            file_context = dummy_context(data)
-        elif kind == "matrix":
-            file_context = lib.virtualfile_from_matrix(data)
-        elif kind == "vectors":
-            file_context = lib.virtualfile_from_vectors(
-                np.atleast_1d(x), np.atleast_1d(y), *extra_arrays
-            )
+        file_context = lib.virtualfile_from_data(
+            check_kind="vector", data=data, x=x, y=y, extra_arrays=extra_arrays
+        )
 
         with file_context as fname:
             arg_str = " ".join([fname, build_arg_string(kwargs)])

pygmt/src/plot3d.py

@@ -1,13 +1,11 @@
 """
 plot3d - Plot in three dimensions.
 """
-import numpy as np
 from pygmt.clib import Session
 from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import (
     build_arg_string,
     data_kind,
-    dummy_context,
     fmt_docstring,
     is_nonstr_iter,
     kwargs_to_strings,
@@ -189,14 +187,9 @@ def plot3d(
 
     with Session() as lib:
         # Choose how data will be passed in to the module
-        if kind == "file":
-            file_context = dummy_context(data)
-        elif kind == "matrix":
-            file_context = lib.virtualfile_from_matrix(data)
-        elif kind == "vectors":
-            file_context = lib.virtualfile_from_vectors(
-                np.atleast_1d(x), np.atleast_1d(y), np.atleast_1d(z), *extra_arrays
-            )
+        file_context = lib.virtualfile_from_data(
+            check_kind="vector", data=data, x=x, y=y, z=z, extra_arrays=extra_arrays
+        )
 
         with file_context as fname:
             arg_str = " ".join([fname, build_arg_string(kwargs)])

pygmt/tests/test_grdinfo.py

@@ -10,7 +10,7 @@
 
 def test_grdinfo():
     """
-    Make sure grd info works as expected.
+    Make sure grdinfo works as expected.
     """
     grid = load_earth_relief(registration="gridline")
     result = grdinfo(grid=grid, force_scan=0, per_column="n")

pygmt/tests/test_info.py

@@ -29,6 +29,15 @@ def test_info():
     assert output == expected_output
 
 
+def test_info_2d_list():
+    """
+    Make sure info works on a 2d list.
+    """
+    output = info(table=[[0, 8], [3, 5], [6, 2]])
+    expected_output = "<vector memory>: N = 3 <0/6> <2/8>\n"
+    assert output == expected_output
+
+
 def test_info_dataframe():
     """
     Make sure info works on pandas.DataFrame inputs.
@@ -105,7 +114,7 @@ def test_info_2d_array():
     table = np.loadtxt(POINTS_DATA)
     output = info(table=table)
     expected_output = (
-        "<vector memory>: N = 20 <11.5309/61.7074> <-2.9289/7.8648> <0.1412/0.9338>\n"
+        "<matrix memory>: N = 20 <11.5309/61.7074> <-2.9289/7.8648> <0.1412/0.9338>\n"
     )
     assert output == expected_output