Merge branch 'master' into move-plotting-functions

Author: willschlitzer

.github/workflows/ci_tests.yaml

@@ -21,38 +21,6 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  style_check:
-    name: Style Checks
-    runs-on: ubuntu-latest
-
-    steps:
-      # Checkout current git repository
-      - name: Checkout
-        uses: actions/checkout@v2.3.1
-
-      # Setup Miniconda
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-
-      - name: Install packages
-        run: |
-          pip install black blackdoc docformatter flake8 pylint isort
-          sudo apt-get install dos2unix
-
-      - name: Formatting check (black, blackdoc, docformatter, flake8 and isort)
-        run: make check
-
-      - name: Linting (pylint)
-        run: make lint
-
-      - name: Ensure files use UNIX line breaks and have 644 permission
-        run: |
-          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec dos2unix --quiet {} \;
-          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec chmod 644 {} \;
-          if [[ $(git ls-files -m) ]]; then git --no-pager diff HEAD; exit 1; fi
-
   test:
     name: ${{ matrix.os }} - Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}

.github/workflows/style_checks.yaml

@@ -0,0 +1,42 @@
+name: Style Checks
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+  # Schedule daily tests
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  style_check:
+    name: Style Checks
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checkout current git repository
+      - name: Checkout
+        uses: actions/checkout@v2.3.4
+
+      # Setup Miniconda
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Install packages
+        run: |
+          pip install black blackdoc docformatter flake8 pylint isort
+          sudo apt-get install dos2unix
+
+      - name: Formatting check (black, blackdoc, docformatter, flake8 and isort)
+        run: make check
+
+      - name: Linting (pylint)
+        run: make lint
+
+      - name: Ensure files use UNIX line breaks and have 644 permission
+        run: |
+          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec dos2unix --quiet {} \;
+          find . -type f -not -path '*/\.git/*' -exec grep -Iq . {} \; -exec chmod 644 {} \;
+          if [[ $(git ls-files -m) ]]; then git --no-pager diff HEAD; exit 1; fi

CONTRIBUTING.md

@@ -39,6 +39,7 @@ read it carefully.
 * [Editing the Documentation](#editing-the-documentation)
   - [Gallery plots](#gallery-plots)
   - [Tutorials](#tutorials)
+  - [Example code standards](#example-code-standards)
 * [Contributing Code](#contributing-code)
   - [General guidelines](#general-guidelines)
   - [Setting up your environment](#setting-up-your-environment)
@@ -267,7 +268,7 @@ directory).
 
 We use some tools:
 
-- [Black](https://github.com/ambv/black)
+- [Black](https://github.com/psf/black)
 - [blackdoc](https://github.com/keewis/blackdoc)
 - [docformatter](https://github.com/myint/docformatter)
 - [isort](https://pycqa.github.io/isort/)

MAINTENANCE.md

@@ -47,11 +47,16 @@ conda and the `Makefile` to run the tests and checks.
 
 ### GitHub Actions
 
-There are 4 configuration files located in `.github/workflows`:
+There are 5 configuration files located in `.github/workflows`:
 
-1. `ci_tests.yaml` (Style Checks, Tests on Linux/macOS/Windows)
+1. `style_checks.yaml` (Code lint and style checks)
 
-This is ran on every commit on the *master* and Pull Request branches.
+This is ran on every commit to the *master* and Pull Request branches.
+It is also scheduled to run daily on the *master* branch.
+
+2. `ci_tests.yaml` (Tests on Linux/macOS/Windows)
+
+This is ran on every commit to the *master* and Pull Request branches.
 It is also scheduled to run daily on the *master* branch.
 
 On the *master* branch, the workflow also handles the documentation deployment:
@@ -60,18 +65,18 @@ On the *master* branch, the workflow also handles the documentation deployment:
   *master* branch onto the `dev` folder of the *gh-pages* branch.
 * Updated the `latest` documentation link to the new release.
 
-2. `ci_tests_dev.yaml` (GMT Dev Tests on Linux/macOS/Windows).
+3. `ci_tests_dev.yaml` (GMT Dev Tests on Linux/macOS/Windows).
 
 This is triggered when a PR is marked as "ready for review", or using the slash
 command `/test-gmt-dev`. It is also scheduled to run daily on the *master* branch.
 
-3. `cache_data.yaml` (Caches GMT remote data files needed for GitHub Actions CI)
+4. `cache_data.yaml` (Caches GMT remote data files needed for GitHub Actions CI)
 
 This is scheduled to run every Sunday at 12 noon.
 If new remote files are needed urgently, maintainers can manually uncomment
 the 'pull_request:' line in that `cache_data.yaml` file to refresh the cache.
 
-4. `publish-to-pypi.yml` (Publish wheels to PyPI and TestPyPI)
+5. `publish-to-pypi.yml` (Publish wheels to PyPI and TestPyPI)
 
 This workflow is ran to publish wheels to PyPI and TestPyPI (for testing only).
 Archives will be pushed to TestPyPI on every commit to the *master* branch and

doc/conf.py

@@ -48,9 +48,9 @@
 # intersphinx configuration
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
-    "pandas": ("http://pandas.pydata.org/pandas-docs/stable/", None),
-    "xarray": ("http://xarray.pydata.org/en/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "xarray": ("https://xarray.pydata.org/en/stable/", None),
 }
 
 # options for sphinx-copybutton

pygmt/clib/session.py

@@ -1179,7 +1179,7 @@ def virtualfile_from_vectors(self, *vectors):
                 strings = np.apply_along_axis(
                     func1d=" ".join, axis=0, arr=string_arrays
                 )
-            strings = np.asanyarray(a=strings, dtype=np.str)
+            strings = np.asanyarray(a=strings, dtype=str)
             self.put_strings(
                 dataset, family="GMT_IS_VECTOR|GMT_IS_DUPLICATE", strings=strings
             )

pygmt/tests/test_clib.py

@@ -432,7 +432,7 @@ def test_virtualfile_from_vectors():
             assert output == expected
 
 
-@pytest.mark.parametrize("dtype", [np.str, np.object])
+@pytest.mark.parametrize("dtype", [str, object])
 def test_virtualfile_from_vectors_one_string_or_object_column(dtype):
     """
     Test passing in one column with string or object dtype into virtual file
@@ -451,7 +451,7 @@ def test_virtualfile_from_vectors_one_string_or_object_column(dtype):
         assert output == expected
 
 
-@pytest.mark.parametrize("dtype", [np.str, np.object])
+@pytest.mark.parametrize("dtype", [str, object])
 def test_virtualfile_from_vectors_two_string_or_object_columns(dtype):
     """
     Test passing in two columns of string or object dtype into virtual file

pygmt/tests/test_clib_put_strings.py

@@ -26,7 +26,7 @@ def test_put_strings():
         )
         x = np.array([1, 2, 3, 4, 5], dtype=np.int32)
         y = np.array([6, 7, 8, 9, 10], dtype=np.int32)
-        strings = np.array(["a", "bc", "defg", "hijklmn", "opqrst"], dtype=np.str)
+        strings = np.array(["a", "bc", "defg", "hijklmn", "opqrst"], dtype=str)
         lib.put_vector(dataset, column=lib["GMT_X"], vector=x)
         lib.put_vector(dataset, column=lib["GMT_Y"], vector=y)
         lib.put_strings(
@@ -62,5 +62,5 @@ def test_put_strings_fails():
             lib.put_strings(
                 dataset=None,
                 family="GMT_IS_VECTOR|GMT_IS_DUPLICATE",
-                strings=np.empty(shape=(3,), dtype=np.str),
+                strings=np.empty(shape=(3,), dtype=str),
             )