Merge branch 'master' into spelling3

* master: (49 commits) Update CI environment lockfiles + Cartopy 0.19 changes (SciTools#4125) separate arg types from descriptions (SciTools#4100) Use assertArrayAllClose for sqrt test (SciTools#4118) Removed branch suffix (SciTools#4117) Corrected plot_anomaly_log_colouring for new Matplotlib linscale rules. (SciTools#4115) replace most recent hashes (SciTools#4112) Linkcheck update (SciTools#4104) CI lockfiles (SciTools#4108) Fix bug in gallery_tests runner (SciTools#4111) add logo to conda and pypi badges (SciTools#4088) pre-commit-ci update (SciTools#4092) Fix cirrus ci and mpl (SciTools#4087) Update readme docs stable (SciTools#4089) linux kernel version fix for conda 4.10+ (SciTools#4084) update docs pypi instructions (SciTools#4077) update flake8 pre-commit (SciTools#4067) Add GitHub discussions badge (SciTools#4070) conda requirements add pip (SciTools#4062) add pre-commit.ci badge and doc support (SciTools#4061) cirrus-ci credits for non-master (SciTools#4060) ...
tkknight · May 17, 2021 · c4f8b49 · c4f8b49
2 parents eb742d3 + 83309c3
commit c4f8b49
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Showing 73 changed files with 2,315 additions and 732 deletions.
diff --git a/.cirrus.yml b/.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.
@@ -27,190 +38,212 @@ env:
   NOX_CACHE_BUILD: "0"
   # Increment the build number to force new pip cache upload.
   PIP_CACHE_BUILD: "0"
-  # Pip package to be upgraded/installed.
+  # Pip packages to be upgraded/installed.
   PIP_CACHE_PACKAGES: "pip setuptools wheel nox"
+  # Conda packages to be installed.
+  CONDA_CACHE_PACKAGES: "nox pip"
   # Git commit hash for iris test data.
-  IRIS_TEST_DATA_REF: "fffb9b14b9cb472c5eb2ebb7fd19acb7f6414a30"
+  IRIS_TEST_DATA_VERSION: "2.0.0"
   # Base directory for the iris-test-data.
   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.
 #
 linux_task_template: &LINUX_TASK_TEMPLATE
   auto_cancellation: true
   env:
-    IRIS_REPO_DIR: ${CIRRUS_WORKING_DIR}
     PATH: ${HOME}/miniconda/bin:${PATH}
     SITE_CFG: ${CIRRUS_WORKING_DIR}/lib/iris/etc/site.cfg
   conda_cache:
     folder: ${HOME}/miniconda
     fingerprint_script:
       - wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
       - echo "${CIRRUS_OS} $(sha256sum miniconda.sh)"
-      - echo "$(date +%Y).$(($(date +%U) / ${CACHE_PERIOD})):${CONDA_CACHE_BUILD}"
+      - echo "${CONDA_CACHE_PACKAGES}"
+      - echo "$(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
       - conda config --add channels conda-forge
       - conda update --quiet --name base conda
-      - conda install --quiet --name base nox pip
+      - conda install --quiet --name base ${CONDA_CACHE_PACKAGES}
   cartopy_cache:
     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: ${CIRRUS_WORKING_DIR}/.nox
+    reupload_on_changes: true
     fingerprint_script:
       - echo "${CIRRUS_TASK_NAME}"
-      - echo "$(date +%Y).$(($(date +%U) / ${CACHE_PERIOD})):${NOX_CACHE_BUILD}"
-      - sha256sum ${CIRRUS_WORKING_DIR}/requirements/ci/py$(echo ${PY_VER} | tr -d ".").yml
-
-
-# #
-# # Testing Minimal (Linux)
-# #
-# linux_minimal_task:
-#   matrix:
-#     env:
-#       PY_VER: 3.6
-#     env:
-#       PY_VER: 3.7
-#   name: "${CIRRUS_OS}: py${PY_VER} tests (minimal)"
-#   container:
-#     image: gcc:latest
-#     cpu: 2
-#     memory: 4G
-#   << : *LINUX_TASK_TEMPLATE
-#   tests_script:
-#     - echo "[Resources]" > ${SITE_CFG}
-#     - echo "doc_dir = ${CIRRUS_WORKING_DIR}/docs" >> ${SITE_CFG}
-#     - nox --session tests -- --verbose
-
-
-# #
-# # Testing Full (Linux)
-# #
-# linux_task:
-#   matrix:
-#     env:
-#       PY_VER: 3.6
-#     env:
-#       PY_VER: 3.7
-#   name: "${CIRRUS_OS}: py${PY_VER} tests (full)"
-#   container:
-#     image: gcc:latest
-#     cpu: 6
-#     memory: 8G
-#   data_cache:
-#     folder: ${IRIS_TEST_DATA_DIR}
-#     fingerprint_script:
-#       - echo "${IRIS_TEST_DATA_REF}"
-#     populate_script:
-#       - wget --quiet https://github.com/SciTools/iris-test-data/archive/${IRIS_TEST_DATA_REF}.zip -O iris-test-data.zip
-#       - unzip -q iris-test-data.zip
-#       - mv iris-test-data-$(echo "${IRIS_TEST_DATA_REF}" | sed "s/^v//") ${IRIS_TEST_DATA_DIR}
-#   << : *LINUX_TASK_TEMPLATE
-#   tests_script:
-#     - echo "[Resources]" > ${SITE_CFG}
-#     - echo "test_data_dir = ${IRIS_TEST_DATA_DIR}/test_data" >> ${SITE_CFG}
-#     - echo "doc_dir = ${CIRRUS_WORKING_DIR}/docs" >> ${SITE_CFG}
-#     - nox --session tests -- --verbose
+      - echo "${NOX_CACHE_BUILD}"
+
+#
+# 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_PR} != ""
+
+
+#
+# YAML alias for the iris-test-data cache.
+#
+iris_test_data_template: &IRIS_TEST_DATA_TEMPLATE
+  data_cache:
+    folder: ${IRIS_TEST_DATA_DIR}
+    fingerprint_script:
+      - echo "iris-test-data v${IRIS_TEST_DATA_VERSION}"
+    populate_script:
+      - wget --quiet https://github.com/SciTools/iris-test-data/archive/v${IRIS_TEST_DATA_VERSION}.zip -O iris-test-data.zip
+      - unzip -q iris-test-data.zip
+      - mv iris-test-data-${IRIS_TEST_DATA_VERSION} ${IRIS_TEST_DATA_DIR}
+
+
+#
+# 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 "${CIRRUS_TASK_NAME} py${PYTHON_VERSION}"
+      - 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)
+#
+test_minimal_task:
+  only_if: ${SKIP_TEST_MINIMAL_TASK} == "" && ${SKIP_ALL_TEST_TASKS} == ""
+  << : *CREDITS_TEMPLATE
+  matrix:
+    env:
+      PY_VER: 3.6
+    env:
+      PY_VER: 3.7
+    env:
+      PY_VER: 3.8
+  name: "${CIRRUS_OS}: py${PY_VER} tests (minimal)"
+  container:
+    image: gcc:latest
+    cpu: 2
+    memory: 4G
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
+    - echo "[Resources]" > ${SITE_CFG}
+    - echo "doc_dir = ${CIRRUS_WORKING_DIR}/docs" >> ${SITE_CFG}
+    - nox --session tests -- --verbose
+
+
+#
+# Testing Full (Linux)
+#
+test_full_task:
+  only_if: ${SKIP_TEST_FULL_TASK} == "" && ${SKIP_ALL_TEST_TASKS} == ""
+  << : *CREDITS_TEMPLATE
+  matrix:
+    env:
+      PY_VER: 3.6
+    env:
+      PY_VER: 3.7
+    env:
+      PY_VER: 3.8
+  name: "${CIRRUS_OS}: py${PY_VER} tests (full)"
+  container:
+    image: gcc:latest
+    cpu: 6
+    memory: 8G
+  << : *IRIS_TEST_DATA_TEMPLATE
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(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}
+    - nox --session tests -- --verbose
 
 
 #
 # Testing Documentation Gallery (Linux)
 #
-# gallery_task:
-#   matrix:
-#     env:
-#       PY_VER: 3.6
-#     env:
-#       PY_VER: 3.7
-#   name: "${CIRRUS_OS}: py${PY_VER} doc tests (gallery)"
-#   container:
-#     image: gcc:latest
-#     cpu: 2
-#     memory: 4G
-#   data_cache:
-#     folder: ${IRIS_TEST_DATA_DIR}
-#     fingerprint_script:
-#       - echo "${IRIS_TEST_DATA_REF}"
-#     populate_script:
-#       - wget --quiet https://github.com/SciTools/iris-test-data/archive/${IRIS_TEST_DATA_REF}.zip -O iris-test-data.zip
-#       - unzip -q iris-test-data.zip
-#       - mv iris-test-data-$(echo "${IRIS_TEST_DATA_REF}" | sed "s/^v//") ${IRIS_TEST_DATA_DIR}
-#   << : *LINUX_TASK_TEMPLATE
-#   tests_script:
-#     - echo "[Resources]" > ${SITE_CFG}
-#     - echo "test_data_dir = ${IRIS_TEST_DATA_DIR}/test_data" >> ${SITE_CFG}
-#     - echo "doc_dir = ${CIRRUS_WORKING_DIR}/docs" >> ${SITE_CFG}
-#     - nox --session gallery -- --verbose
-
-
-# #
-# # Testing Documentation (Linux)
-# #
-# doctest_task:
-#   matrix:
-#     env:
-#       PY_VER: 3.7
-#   name: "${CIRRUS_OS}: py${PY_VER} doc tests"
-#   container:
-#     image: gcc:latest
-#     cpu: 2
-#     memory: 4G
-#   env:
-#     MPL_RC_DIR: ${HOME}/.config/matplotlib
-#     MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
-#   data_cache:
-#     folder: ${IRIS_TEST_DATA_DIR}
-#     fingerprint_script:
-#       - echo "${IRIS_TEST_DATA_REF}"
-#     populate_script:
-#       - wget --quiet https://github.com/SciTools/iris-test-data/archive/${IRIS_TEST_DATA_REF}.zip -O iris-test-data.zip
-#       - unzip -q iris-test-data.zip
-#       - mv iris-test-data-$(echo "${IRIS_TEST_DATA_REF}" | sed "s/^v//") ${IRIS_TEST_DATA_DIR}
-#   << : *LINUX_TASK_TEMPLATE
-#   tests_script:
-#     - 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}
-#     - mkdir -p ${MPL_RC_DIR}
-#     - echo "backend : agg" > ${MPL_RC_FILE}
-#     - echo "image.cmap : viridis" >> ${MPL_RC_FILE}
-#     - nox --session doctest -- --verbose
+gallery_task:
+  only_if: ${SKIP_GALLERY_TASK} == "" && ${SKIP_ALL_DOC_TASKS} == ""
+  << : *CREDITS_TEMPLATE
+  matrix:
+    env:
+      PY_VER: 3.8
+  name: "${CIRRUS_OS}: py${PY_VER} doc tests (gallery)"
+  container:
+    image: gcc:latest
+    cpu: 2
+    memory: 4G
+  << : *IRIS_TEST_DATA_TEMPLATE
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(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}
+    - nox --session gallery -- --verbose
+
+
+#
+# Testing Documentation (Linux)
+#
+doctest_task:
+  only_if: ${SKIP_DOCTEST_TASK} == "" && ${SKIP_ALL_DOC_TASKS} == ""
+  << : *CREDITS_TEMPLATE
+  matrix:
+    env:
+      PY_VER: 3.8
+  name: "${CIRRUS_OS}: py${PY_VER} doc tests"
+  container:
+    image: gcc:latest
+    cpu: 2
+    memory: 4G
+  env:
+    MPL_RC_DIR: ${HOME}/.config/matplotlib
+    MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
+  << : *IRIS_TEST_DATA_TEMPLATE
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(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}
+    - mkdir -p ${MPL_RC_DIR}
+    - echo "backend : agg" > ${MPL_RC_FILE}
+    - echo "image.cmap : viridis" >> ${MPL_RC_FILE}
+    - nox --session doctest -- --verbose
 
 
 #
 # Testing Documentation Link Check (Linux)
 #
-link_task:
+linkcheck_task:
+  only_if: ${SKIP_LINKCHECK_TASK} == "" && ${SKIP_ALL_DOC_TASKS} == ""
+  << : *CREDITS_TEMPLATE
   matrix:
     env:
-      PY_VER: 3.7
+      PY_VER: 3.8
   name: "${CIRRUS_OS}: py${PY_VER} doc link check"
   container:
     image: gcc:latest
@@ -221,6 +254,7 @@ link_task:
     MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
   << : *LINUX_TASK_TEMPLATE
   tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
     - mkdir -p ${MPL_RC_DIR}
     - echo "backend : agg" > ${MPL_RC_FILE}
     - echo "image.cmap : viridis" >> ${MPL_RC_FILE}