Merge remote-tracking branch 'upstream/main' into all_benchmarks

.cirrus.yml

@@ -60,7 +60,6 @@ linux_task_template: &LINUX_TASK_TEMPLATE
       - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${CONDA_CACHE_BUILD}"
       - uname -r
     populate_script:
-      - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
       - bash miniconda.sh -b -p ${HOME}/miniconda
       - conda config --set always_yes yes --set changeps1 no
       - conda config --set show_channel_urls True
@@ -141,8 +140,6 @@ task:
   only_if: ${SKIP_TEST_TASK} == ""
   << : *CREDITS_TEMPLATE
   matrix:
-    env:
-      PY_VER: 3.7
     env:
       PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} tests"
@@ -153,7 +150,6 @@ task:
   << : *IRIS_TEST_DATA_TEMPLATE
   << : *LINUX_TASK_TEMPLATE
   tests_script:
-    - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
     - echo "[Resources]" > ${SITE_CFG}
     - echo "test_data_dir = ${IRIS_TEST_DATA_DIR}/test_data" >> ${SITE_CFG}
     - echo "doc_dir = ${CIRRUS_WORKING_DIR}/docs" >> ${SITE_CFG}
@@ -174,7 +170,6 @@ task:
   << : *IRIS_TEST_DATA_TEMPLATE
   << : *LINUX_TASK_TEMPLATE
   tests_script:
-    - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
     - echo "[Resources]" > ${SITE_CFG}
     - echo "test_data_dir = ${IRIS_TEST_DATA_DIR}/test_data" >> ${SITE_CFG}
     - echo "doc_dir = ${CIRRUS_WORKING_DIR}/docs" >> ${SITE_CFG}
@@ -197,7 +192,6 @@ task:
   name: "${CIRRUS_OS}: py${PY_VER} link check"
   << : *LINUX_TASK_TEMPLATE
   tests_script:
-    - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
     - mkdir -p ${MPL_RC_DIR}
     - echo "backend : agg" > ${MPL_RC_FILE}
     - echo "image.cmap : viridis" >> ${MPL_RC_FILE}

.github/workflows/refresh-lockfiles.yml

@@ -71,7 +71,7 @@ jobs:
 
     strategy:
       matrix:
-        python: ['37', '38']
+        python: ['38']
 
     steps:
       - uses: actions/checkout@v2

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ minimum_pre_commit_version: 1.21.0
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.1.0
     hooks:
         # Prevent giant files from being committed.
     -   id: check-added-large-files
@@ -29,7 +29,7 @@ repos:
     -   id: no-commit-to-branch
 
 -   repo: https://github.com/psf/black
-    rev: 21.11b1
+    rev: 22.1.0
     hooks:
     -   id: black
         pass_filenames: false
@@ -50,7 +50,7 @@ repos:
         args: [--filter-files]
 
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.12.0
+    rev: v1.12.1
     hooks:
     -   id: blacken-docs
         types: [file, rst]

.readthedocs.yml

@@ -1,20 +1,20 @@
 version: 2
 
 build:
-    image: latest
+  os: ubuntu-20.04
+  tools:
+    python: mambaforge-4.10
 
 conda:
-    environment: requirements/ci/readthedocs.yml
+  environment: requirements/ci/readthedocs.yml
 
 sphinx:
-    configuration: docs/src/conf.py
-    fail_on_warning: false
+  configuration: docs/src/conf.py
+  fail_on_warning: false
 
 python:
-    install: 
-        - method: setuptools
-          path: .
-
-formats:
-    - htmlzip
-    - pdf
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

benchmarks/benchmarks/plot.py

@@ -22,7 +22,7 @@ def setup(self):
         # Should generate 10 distinct contours, regardless of dim size.
         dim_size = int(ARTIFICIAL_DIM_SIZE / 5)
         repeat_number = int(dim_size / 10)
-        repeat_range = range(int((dim_size ** 2) / repeat_number))
+        repeat_range = range(int((dim_size**2) / repeat_number))
         data = np.repeat(repeat_range, repeat_number)
         data = data.reshape((dim_size,) * 2)
 

docs/gallery_code/README.rst

@@ -23,4 +23,4 @@ you may start the jupyter notebook via::
 
 If you wish to contribute to the gallery see the 
 :ref:`contributing.documentation.gallery` section of the 
-:ref:`contributing.documentation`.
+:ref:`contributing.documentation_full`.

docs/gallery_code/meteorology/plot_wind_barbs.py

@@ -30,7 +30,7 @@ def main():
 
     # To illustrate the full range of barbs, scale the wind speed up to pretend
     # that a storm is passing over
-    magnitude = (uwind ** 2 + vwind ** 2) ** 0.5
+    magnitude = (uwind**2 + vwind**2) ** 0.5
     magnitude.convert_units("knot")
     max_speed = magnitude.collapsed(
         ("latitude", "longitude"), iris.analysis.MAX
@@ -41,7 +41,7 @@ def main():
     vwind = vwind / max_speed * max_desired
 
     # Create a cube containing the wind speed
-    windspeed = (uwind ** 2 + vwind ** 2) ** 0.5
+    windspeed = (uwind**2 + vwind**2) ** 0.5
     windspeed.rename("windspeed")
     windspeed.convert_units("knot")
 

docs/gallery_code/meteorology/plot_wind_speed.py

@@ -27,7 +27,7 @@ def main():
     vwind = iris.load_cube(infile, "y_wind")
 
     # Create a cube containing the wind speed.
-    windspeed = (uwind ** 2 + vwind ** 2) ** 0.5
+    windspeed = (uwind**2 + vwind**2) ** 0.5
     windspeed.rename("windspeed")
 
     # Plot the wind speed as a contour plot.

docs/src/_templates/imagehash.html

@@ -0,0 +1,15 @@
+{% extends "!layout.html" %}
+
+{% block body %}
+
+<h1>Test: {{ test }}</h1>
+
+
+{% for hash, file in hashfiles %}
+<div>
+    <h3>{{hash}}</h3>
+    <img src="{{file}}" />
+</div>
+{% endfor %}
+
+{% endblock %}

docs/src/common_links.inc

@@ -37,6 +37,7 @@
 .. _test-iris-imagehash: https://github.com/SciTools/test-iris-imagehash
 .. _using git: https://docs.github.com/en/github/using-git
 .. _requirements/ci/: https://github.com/SciTools/iris/tree/main/requirements/ci
+.. _CF-UGRID: https://ugrid-conventions.github.io/ugrid-conventions/
 
 
 .. comment

docs/src/conf.py

@@ -158,6 +158,7 @@ def _dotv(version):
     "sphinx_gallery.gen_gallery",
     "matplotlib.sphinxext.mathmpl",
     "matplotlib.sphinxext.plot_directive",
+    "image_test_output",
 ]
 
 if skip_api == "1":
@@ -199,7 +200,9 @@ def _dotv(version):
 
 # -- copybutton extension -----------------------------------------------------
 # See https://sphinx-copybutton.readthedocs.io/en/latest/
-copybutton_prompt_text = ">>> "
+copybutton_prompt_text = r">>> |\.\.\. "
+copybutton_prompt_is_regexp = True
+copybutton_line_continuation_character = "\\"
 
 # sphinx.ext.todo configuration -----------------------------------------------
 # See https://www.sphinx-doc.org/en/master/usage/extensions/todo.html
@@ -208,6 +211,7 @@ def _dotv(version):
 # api generation configuration
 autodoc_member_order = "groupwise"
 autodoc_default_flags = ["show-inheritance"]
+autodoc_typehints = "none"
 autosummary_generate = True
 autosummary_imported_members = True
 autopackage_name = ["iris"]
@@ -327,8 +331,10 @@ def _dotv(version):
     "gallery_dirs": ["generated/gallery"],
     # filename pattern for the files in the gallery
     "filename_pattern": "/plot_",
-    # filename patternt to ignore in the gallery
+    # filename pattern to ignore in the gallery
     "ignore_pattern": r"__init__\.py",
+    # force gallery building, unless overridden (see src/Makefile)
+    "plot_gallery": "'True'",
 }
 
 # -----------------------------------------------------------------------------