Release branch prepare for v3.0.2

.cirrus.yml

@@ -1,5 +1,6 @@
 # Reference:
 #   - https://cirrus-ci.org/guide/writing-tasks/
+#   - https://cirrus-ci.org/guide/writing-tasks/#environment-variables
 #   - https://cirrus-ci.org/guide/tips-and-tricks/#sharing-configuration-between-tasks
 #   - https://cirrus-ci.org/guide/linux/
 #   - https://cirrus-ci.org/guide/macOS/
@@ -17,6 +18,16 @@ container:
 
 
 env:
+  # Skip specific tasks by name. Set to a non-empty string to skip.
+  SKIP_LINT_TASK: ""
+  SKIP_TEST_MINIMAL_TASK: ""
+  SKIP_TEST_FULL_TASK: ""
+  SKIP_GALLERY_TASK: ""
+  SKIP_DOCTEST_TASK: ""
+  SKIP_LINKCHECK_TASK: ""
+  # Skip task groups by type. Set to a non-empty string to skip.
+  SKIP_ALL_TEST_TASKS: ""
+  SKIP_ALL_DOC_TASKS: ""
   # Maximum cache period (in weeks) before forcing a new cache upload.
   CACHE_PERIOD: "2"
   # Increment the build number to force new cartopy cache upload.
@@ -35,25 +46,6 @@ env:
   IRIS_TEST_DATA_DIR: ${HOME}/iris-test-data
 
 
-#
-# Linting
-#
-lint_task:
-  auto_cancellation: true
-  name: "${CIRRUS_OS}: flake8 and black"
-  pip_cache:
-    folder: ~/.cache/pip
-    fingerprint_script:
-      - echo "${CIRRUS_TASK_NAME}"
-      - echo "$(date +%Y).$(($(date +%U) / ${CACHE_PERIOD})):${PIP_CACHE_BUILD} ${PIP_CACHE_PACKAGES}"
-  lint_script:
-    - pip list
-    - python -m pip install --retries 3 --upgrade ${PIP_CACHE_PACKAGES}
-    - pip list
-    - nox --session flake8
-    - nox --session black
-
-
 #
 # YAML alias for common linux test infra-structure.
 #
@@ -68,7 +60,7 @@ linux_task_template: &LINUX_TASK_TEMPLATE
     fingerprint_script:
       - wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
       - echo "${CIRRUS_OS} $(sha256sum miniconda.sh)"
-      - echo "$(date +%Y).$(($(date +%U) / ${CACHE_PERIOD})):${CONDA_CACHE_BUILD}"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${CONDA_CACHE_BUILD}"
     populate_script:
       - bash miniconda.sh -b -p ${HOME}/miniconda
       - conda config --set always_yes yes --set changeps1 no
@@ -80,19 +72,49 @@ linux_task_template: &LINUX_TASK_TEMPLATE
     folder: ${HOME}/.local/share/cartopy
     fingerprint_script:
       - echo "${CIRRUS_OS}"
-      - echo "$(date +%Y).$(($(date +%U) / ${CACHE_PERIOD})):${CARTOPY_CACHE_BUILD}"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${CARTOPY_CACHE_BUILD}"
   nox_cache:
     folder: ${CIRRUS_WORKING_DIR}/.nox
     fingerprint_script:
       - echo "${CIRRUS_TASK_NAME}"
-      - echo "$(date +%Y).$(($(date +%U) / ${CACHE_PERIOD})):${NOX_CACHE_BUILD}"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${NOX_CACHE_BUILD}"
       - sha256sum ${CIRRUS_WORKING_DIR}/requirements/ci/py$(echo ${PY_VER} | tr -d ".").yml
 
 
+#
+# YAML alias for compute credits
+#
+compute_credits_template: &CREDITS_TEMPLATE
+  # Only use credits for non-DRAFT pull-requests to SciTools/iris master branch by collaborators
+  use_compute_credits: $CIRRUS_REPO_FULL_NAME == 'SciTools/iris' && $CIRRUS_USER_COLLABORATOR == 'true' && $CIRRUS_PR_DRAFT == 'false' && $CIRRUS_BASE_BRANCH == 'master' && $CIRRUS_PR != ''
+
+#
+# Linting
+#
+lint_task:
+  only_if: $SKIP_LINT_TASK == ""
+  << : *CREDITS_TEMPLATE
+  auto_cancellation: true
+  name: "${CIRRUS_OS}: flake8 and black"
+  pip_cache:
+    folder: ~/.cache/pip
+    fingerprint_script:
+      - echo "${CIRRUS_TASK_NAME}"
+      - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${PIP_CACHE_BUILD} ${PIP_CACHE_PACKAGES}"
+  lint_script:
+    - pip list
+    - python -m pip install --retries 3 --upgrade ${PIP_CACHE_PACKAGES}
+    - pip list
+    - nox --session flake8
+    - nox --session black
+
+
 #
 # Testing Minimal (Linux)
 #
-linux_minimal_task:
+test_minimal_task:
+  only_if: $SKIP_TEST_MINIMAL_TASK == "" && $SKIP_ALL_TEST_TASKS == ""
+  << : *CREDITS_TEMPLATE
   matrix:
     env:
       PY_VER: 3.6
@@ -113,7 +135,9 @@ linux_minimal_task:
 #
 # Testing Full (Linux)
 #
-linux_task:
+test_full_task:
+  only_if: $SKIP_TEST_FULL_TASK == "" && $SKIP_ALL_TEST_TASKS == ""
+  << : *CREDITS_TEMPLATE
   matrix:
     env:
       PY_VER: 3.6
@@ -144,6 +168,8 @@ linux_task:
 # Testing Documentation Gallery (Linux)
 #
 gallery_task:
+  only_if: $SKIP_GALLERY_TASK == "" && $SKIP_ALL_DOC_TASKS == ""
+  << : *CREDITS_TEMPLATE
   matrix:
     env:
       PY_VER: 3.6
@@ -174,6 +200,8 @@ gallery_task:
 # Testing Documentation (Linux)
 #
 doctest_task:
+  only_if: $SKIP_DOCTEST_TASK == "" && $SKIP_ALL_DOC_TASKS == ""
+  << : *CREDITS_TEMPLATE
   matrix:
     env:
       PY_VER: 3.7
@@ -207,7 +235,9 @@ doctest_task:
 #
 # Testing Documentation Link Check (Linux)
 #
-link_task:
+linkcheck_task:
+  only_if: $SKIP_LINKCHECK_TASK == "" && $SKIP_ALL_DOC_TASKS == ""
+  << : *CREDITS_TEMPLATE
   matrix:
     env:
       PY_VER: 3.7

docs/iris/gallery_code/general/plot_anomaly_log_colouring.py

@@ -12,18 +12,15 @@
 "zero band" which is plotted in white.
 
 To do this, we create a custom value mapping function (normalization) using
-the matplotlib Norm class `matplotlib.colours.SymLogNorm
-<https://matplotlib.org/api/_as_gen/matplotlib.colors.SymLogNorm.html#matplotlib.colors.SymLogNorm>`_.
-We use this to make a cell-filled pseudocolour plot with a colorbar.
+the matplotlib Norm class :obj:`matplotlib.colors.SymLogNorm`.
+We use this to make a cell-filled pseudocolor plot with a colorbar.
 
 NOTE: By "pseudocolour", we mean that each data point is drawn as a "cell"
 region on the plot, coloured according to its data value.
 This is provided in Iris by the functions :meth:`iris.plot.pcolor` and
 :meth:`iris.plot.pcolormesh`, which call the underlying matplotlib
-functions of the same names (i.e. `matplotlib.pyplot.pcolor
-<http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.pcolor>`_
-and  `matplotlib.pyplot.pcolormesh
-<http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.pcolormesh>`_).
+functions of the same names (i.e., :obj:`matplotlib.pyplot.pcolor`
+and :obj:`matplotlib.pyplot.pcolormesh`).
 See also: http://en.wikipedia.org/wiki/False_color#Pseudocolor.
 
 """
@@ -65,7 +62,7 @@ def main():
 
     # Use a standard colour map which varies blue-white-red.
     # For suitable options, see the 'Diverging colormaps' section in:
-    # http://matplotlib.org/examples/color/colormaps_reference.html
+    # http://matplotlib.org/stable/gallery/color/colormap_reference.html
     anom_cmap = "bwr"
 
     # Create a 'logarithmic' data normalization.

docs/iris/src/common_links.inc

@@ -1,9 +1,11 @@
 .. _SciTools: https://github.com/SciTools
+.. _black: https://black.readthedocs.io/en/stable/
 .. _Iris: https://github.com/SciTools/iris
 .. _Iris GitHub: https://github.com/SciTools/iris
 .. _iris mailing list: https://groups.google.com/forum/#!forum/scitools-iris
 .. _issue: https://github.com/SciTools/iris/issues
 .. _issues: https://github.com/SciTools/iris/issues
+.. _matplotlib: https://matplotlib.org/stable/
 .. _pull request: https://github.com/SciTools/iris/pulls
 .. _pull requests: https://github.com/SciTools/iris/pulls
 .. _contributor: https://github.com/SciTools/scitools.org.uk/blob/master/contributors.json
@@ -14,14 +16,13 @@
 .. _readthedocs.yml: https://github.com/SciTools/iris/blob/master/requirements/ci/readthedocs.yml
 .. _cirrus-ci: https://cirrus-ci.com/github/SciTools/iris
 .. _.cirrus.yml: https://github.com/SciTools/iris/blob/master/.cirrus.yml
+.. _flake8: https://flake8.pycqa.org/en/stable/
 .. _.flake8.yml: https://github.com/SciTools/iris/blob/master/.flake8
 .. _GitHub Help Documentation: https://docs.github.com/en/github
 .. _using git: https://docs.github.com/en/github/using-git
 .. _generating sss keys for GitHub: https://docs.github.com/en/github/authenticating-to-github/adding-a-new-ssh-key-to-your-github-account
 .. _New Issue: https://github.com/scitools/iris/issues/new/choose
-.. _matplotlib: https://matplotlib.org/
 .. _conda: https://docs.conda.io/en/latest/
 .. _sphinx: https://www.sphinx-doc.org/en/master/
 .. _napolean: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/sphinxcontrib.napoleon.html
 .. _legacy documentation: https://scitools.org.uk/iris/docs/v2.4.0/
-.. _cirrus-ci: https://cirrus-ci.com/github/SciTools/iris

docs/iris/src/conf.py

@@ -179,18 +179,18 @@ def autolog(message):
 # -- intersphinx extension ----------------------------------------------------
 # See https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html
 intersphinx_mapping = {
-    "cartopy": ("http://scitools.org.uk/cartopy/docs/latest/", None),
-    "matplotlib": ("http://matplotlib.org/", None),
-    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
-    "python": ("http://docs.python.org/2.7", None),
-    "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+    "cartopy": ("https://scitools.org.uk/cartopy/docs/latest/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
 }
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = "sphinx"
 
 # -- plot_directive extension -------------------------------------------------
-# See https://matplotlib.org/3.1.3/devel/plot_directive.html#options
+# See https://matplotlib.org/stable/api/sphinxext_plot_directive_api.html#options
 plot_formats = [
     ("png", 100),
 ]

docs/iris/src/developers_guide/contributing_ci_tests.rst

@@ -5,9 +5,9 @@
 Continuous Integration (CI) Testing
 ===================================
 
-The `Iris`_ GitHub repository is configured to run checks on the code
-automatically when a pull request is created, updated or merged against
-Iris **master**.  The checks performed are:
+The `Iris`_ GitHub repository is configured to run checks against all its
+branches automatically whenever a pull request is created, updated or merged.
+The checks performed are:
 
 * :ref:`testing_cla`
 * :ref:`testing_cirrus`
@@ -18,29 +18,65 @@ Iris **master**.  The checks performed are:
 SciTools CLA Checker
 ********************
 
-A bot that checks the user who created the pull request has signed the
-**Contributor's License Agreement (CLA)**.  For more information on this this
-please see https://scitools.org.uk/organisation.html#governance
+A bot which checks that the GitHub author of the pull request has signed the
+**SciTools Contributor's License Agreement (CLA)**.  For more information on
+this please see https://scitools.org.uk/organisation.html#governance.
 
 
 .. _testing_cirrus:
 
 Cirrus-CI
 *********
 
-The unit and integration tests in Iris are an essential mechanism to ensure
+Iris unit and integration tests are an essential mechanism to ensure
 that the Iris code base is working as expected.  :ref:`developer_running_tests`
-may be run manually but to ensure the checks are performed a
-continuous integration testing tool named `cirrus-ci`_ is used.
+may be performed manually by a developer locally. However Iris is configured to
+use the `cirrus-ci`_ service for automated Continuous Integration (CI) testing.
 
-A `cirrus-ci`_ configuration file named `.cirrus.yml`_
-is in the Iris repository which tells Cirrus-CI what commands to run.  The
-commands include retrieving the Iris code base and associated test files using
-conda and then running the tests.  `cirrus-ci`_ allows for a matrix of tests to
-be performed to ensure that all expected variations test successfully.
+The `cirrus-ci`_ configuration file  `.cirrus.yml`_ in the root of the Iris repository
+defines the tasks to be performed by `cirrus-ci`_. For further details
+refer to the `Cirrus-CI Documentation`_. The tasks performed during CI include:
+
+* linting the code base and ensuring it adheres to the `black`_ format
+* running the system, integration and unit tests for Iris
+* ensuring the documentation gallery builds successfully
+* performing all doc-tests within the code base
+* checking all URL references within the code base and documentation are valid
+
+The above `cirrus-ci`_ tasks are run automatically against all `Iris`_ branches
+on GitHub whenever a pull request is submitted, updated or merged. See the
+`Cirrus-CI Dashboard`_ for details of recent past and active Iris jobs.
+
+.. _skipping Cirrus-CI tasks:
+
+Skipping Cirrus-CI Tasks
+------------------------
+
+As a developer you may wish to not run all the CI tasks when you are actively
+developing e.g., you are writing documentation and there is no need for linting,
+or long running compute intensive testing tasks to be executed.
+
+As a convenience, it is possible to easily skip one or more tasks by setting
+the appropriate environment variable within the `.cirrus.yml`_ file to a
+**non-empty** string:
+
+* ``SKIP_LINT_TASK`` to skip `flake8`_ linting and `black`_ formatting
+* ``SKIP_TEST_MINIMAL_TASK`` to skip restricted unit and integration testing
+* ``SKIP_TEST_FULL_TASK`` to skip full unit and integration testing
+* ``SKIP_GALLERY_TASK`` to skip building the documentation gallery
+* ``SKIP_DOCTEST_TASK`` to skip running the documentation doc-tests
+* ``SKIP_LINKCHECK_TASK`` to skip checking for broken documentation URL references
+* ``SKIP_ALL_TEST_TASKS`` which is equivalent to setting ``SKIP_TEST_MINIMAL_TASK`` and ``SKIP_TEST_FULL_TASK``
+* ``SKIP_ALL_DOC_TASKS`` which is equivalent to setting ``SKIP_GALLERY_TASK``, ``SKIP_DOCTEST_TASK``, and ``SKIP_LINKCHECK_TASK``
+
+e.g., to skip the linting task, the following are all equivalent::
+
+   SKIP_LINT_TASK: "1"
+   SKIP_LINT_TASK: "true"
+   SKIP_LINT_TASK: "false"
+   SKIP_LINT_TASK: "skip"
+   SKIP_LINT_TASK: "unicorn"
 
-The `cirrus-ci`_ tests are run automatically against the `Iris`_ master
-repository when a pull request is submitted, updated or merged.
 
 GitHub Checklist
 ****************
@@ -50,6 +86,10 @@ passing:
 
 .. image:: ci_checks.png
 
-If any CI checks fail, then the pull request is unlikely to be merged to the
+If any CI tasks fail, then the pull request is unlikely to be merged to the
 Iris target branch by a core developer.
 
+
+.. _Cirrus-CI Dashboard: https://cirrus-ci.com/github/SciTools/iris
+.. _Cirrus-CI Documentation: https://cirrus-ci.org/guide/writing-tasks/
+

docs/iris/src/developers_guide/contributing_code_formatting.rst

@@ -58,6 +58,4 @@ will look similar to::
           their officially documentation for more information.
 
 
-.. _black: https://black.readthedocs.io/en/stable/
-.. _flake8: https://flake8.pycqa.org/en/stable/
 .. _pre-commit: https://pre-commit.com/