Merge branch 'master' into enable_spelling_check

* master: (87 commits) Contourf Antialias Fix (SciTools#4150) minor tidy of cirrus and nox (SciTools#4152) update bug and feature templates (SciTools#4147) 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) ...
tkknight · May 26, 2021 · 9366e71 · 9366e71
2 parents 18c4259 + aee4ce7
commit 9366e71
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diff --git a/.cirrus.yml b/.cirrus.yml
@@ -0,0 +1,243 @@
+# 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://hub.docker.com/_/gcc/
+#   - https://hub.docker.com/_/python/
+
+#
+# Global defaults.
+#
+container:
+  image: gcc:latest
+  cpu: 2
+  memory: 4G
+
+
+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.
+  CARTOPY_CACHE_BUILD: "0"
+  # Increment the build number to force new conda cache upload.
+  CONDA_CACHE_BUILD: "0"
+  # Increment the build number to force new nox cache upload.
+  NOX_CACHE_BUILD: "0"
+  # Increment the build number to force new pip cache upload.
+  PIP_CACHE_BUILD: "0"
+  # 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_VERSION: "2.0.0"
+  # Base directory for the iris-test-data.
+  IRIS_TEST_DATA_DIR: ${HOME}/iris-test-data
+
+
+#
+# YAML alias for common linux test infra-structure.
+#
+linux_task_template: &LINUX_TASK_TEMPLATE
+  auto_cancellation: true
+  env:
+    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} $(sha256sum miniconda.sh)"
+      - echo "${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 ${CONDA_CACHE_PACKAGES}
+  cartopy_cache:
+    folder: ${HOME}/.local/share/cartopy
+    fingerprint_script:
+      - echo "${CIRRUS_OS}"
+      - 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 "${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: ${SKIP_LINT_TASK} == ""
+  << : *CREDITS_TEMPLATE
+  auto_cancellation: true
+  container:
+    image: python:3.8
+    cpu: 2
+    memory: 4G
+  name: "${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${PY_VER} tests (minimal)"
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(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:
+  only_if: ${SKIP_GALLERY_TASK} == "" && ${SKIP_ALL_DOC_TASKS} == ""
+  << : *CREDITS_TEMPLATE
+  env:
+    PY_VER: 3.8
+  name: "${CIRRUS_OS}: py${PY_VER} doc tests (gallery)"
+  << : *IRIS_TEST_DATA_TEMPLATE
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(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
+  env:
+    PY_VER: 3.8
+    MPL_RC_DIR: ${HOME}/.config/matplotlib
+    MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
+  name: "${CIRRUS_OS}: py${PY_VER} doc tests"
+  << : *IRIS_TEST_DATA_TEMPLATE
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(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)
+#
+linkcheck_task:
+  only_if: ${SKIP_LINKCHECK_TASK} == "" && ${SKIP_ALL_DOC_TASKS} == ""
+  << : *CREDITS_TEMPLATE
+  env:
+    PY_VER: 3.8
+    MPL_RC_DIR: ${HOME}/.config/matplotlib
+    MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
+  name: "${CIRRUS_OS}: py${PY_VER} doc link check"
+  << : *LINUX_TASK_TEMPLATE
+  tests_script:
+    - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"
+    - mkdir -p ${MPL_RC_DIR}
+    - echo "backend : agg" > ${MPL_RC_FILE}
+    - echo "image.cmap : viridis" >> ${MPL_RC_FILE}
+    - nox --session linkcheck -- --verbose
diff --git a/.flake8 b/.flake8
@@ -30,7 +30,7 @@ exclude =
     .eggs,
     build,
     compiled_krb,
-    docs/iris/src/sphinxext/*,
+    docs/src/sphinxext/*,
     tools/*,
     #
     # ignore auto-generated files

diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md
@@ -33,8 +33,7 @@ Steps to reproduce the behaviour:
 <summary>Click to expand <b>this section...</b></summary>
 
 ```
-Add additional verbose information in a collapsible section.
+Please add additional verbose information in this section e.g., code, output, tracebacks, screenshots etc
 ```
-See [here](https://gist.github.com/pierrejoubert73/902cc94d79424356a8d20be2b382e1ab) for further details.
 </details>
 
diff --git a/.github/ISSUE_TEMPLATE/feature-request.md b/.github/ISSUE_TEMPLATE/feature-request.md
@@ -20,8 +20,7 @@ assignees: ''
 <summary>Click to expand <b>this section...</b></summary>
 
 ```
-Add additional verbose information in a collapsible section.
+Please add additional verbose information in this section e.g., references, screenshots, listings etc
 ```
-See [here](https://gist.github.com/pierrejoubert73/902cc94d79424356a8d20be2b382e1ab) for further details.
 </details>
 
diff --git a/.github/workflows/refresh-lockfiles.yml b/.github/workflows/refresh-lockfiles.yml
@@ -0,0 +1,77 @@
+# This workflow periodically creates new environment lock files based on the newest
+# available packages and dependencies.
+#
+# Environment specifications are given as conda environment.yml files found in
+# `requirements/ci/py**.yml`.  These state the pacakges required, the conda channels
+# that the packages will be pulled from, and any versions of packages that need to be
+# pinned at specific versions.
+#
+# For environments that have changed, a pull request will be made and submitted
+# to the master branch
+
+name: Refresh Lockfiles
+
+
+on:
+  workflow_dispatch:
+  schedule:
+    # Run once a week on a Saturday night 
+    - cron: 1 0 * * 6
+
+
+jobs:
+
+  gen_lockfiles:
+    # this is a matrix job: it splits to create new lockfiles for each
+    # of the CI test python versions.
+    # this list below should be changed when covering more python versions
+    # TODO: generate this matrix automatically from the list of available py**.yml files
+    #       ref: https://tomasvotruba.com/blog/2020/11/16/how-to-make-dynamic-matrix-in-github-actions/
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python: ['36', '37', '38']
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: install conda-lock
+        run: |
+          source $CONDA/bin/activate base
+          conda install -y -c conda-forge conda-lock
+      - name: generate lockfile
+        run: |
+          $CONDA/bin/conda-lock lock -p linux-64 -f requirements/ci/py${{matrix.python}}.yml
+          mv conda-linux-64.lock py${{matrix.python}}-linux-64.lock
+      - name: output lockfile
+        uses: actions/upload-artifact@v2
+        with:
+          path: py${{matrix.python}}-linux-64.lock
+
+  create_pr:
+    # once the matrix job has completed all the lock files will have been uploaded as artifacts.
+    # Download the artifacts, add them to the repo, and create a PR.
+    runs-on: ubuntu-latest
+    needs: gen_lockfiles
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: get artifacts
+        uses: actions/download-artifact@v2
+        with:
+          path: artifacts
+
+      - name: Update lock files in repo
+        run: | 
+          cp artifacts/artifact/*.lock requirements/ci/nox.lock
+          rm -r artifacts
+        
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@052fc72b4198ba9fbc81b818c6e1859f747d49a8
+        with:
+          commit-message: Updated environment lockfiles
+          delete-branch: true
+          branch: auto-update-lockfiles
+          title: Update CI environment lockfiles
+          body: |
+            Lockfiles updated to the latest resolvable environment.
diff --git a/.gitignore b/.gitignore
@@ -15,6 +15,7 @@ var
 sdist
 develop-eggs
 .installed.cfg
+.nox
 
 # Installer logs
 pip-log.txt
@@ -55,11 +56,11 @@ lib/iris/tests/results/imagerepo.lock
 *.cover
 
 # Auto generated documentation files
-docs/iris/src/_build/*
-docs/iris/src/generated
+docs/src/_build/*
+docs/src/generated
 
 # Example test results
-docs/iris/iris_image_test_output/
+docs/iris_image_test_output/
 
 # Created by editiors
 *~

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v2.4.0'
+    rev: 'v3.4.0'
     hooks:
         # Prevent giant files from being committed.
     -   id: check-added-large-files
@@ -23,8 +23,8 @@ repos:
         # Force black to run on whole repo, using settings from pyproject.toml
         pass_filenames: false
         args: [--config=./pyproject.toml, .]
--   repo: https://gitlab.com/pycqa/flake8
-    rev: '3.8.3'
+-   repo: https://github.com/PyCQA/flake8
+    rev: '3.9.0'
     hooks:
         # Run flake8.
     -   id: flake8