Merge branch 'main' into votable_issues

* main: (94 commits) added support for make html-noapi and html-quick for the docs build (SciTools#4333) Refactor some netcdf save code (SciTools#4301) [pre-commit.ci] pre-commit autoupdate (SciTools#4329) Update to loading docs to cover absence of 'or' for constraints (SciTools#4321) update latest.rst.template (SciTools#4323) stable cartopy feature download (SciTools#4328) Skip TestConstrainedLoad if data missing (SciTools#4319) Add 'Good First Issue' label to reasons an issue doesn't go stale (SciTools#4317) Gallery: simplify quiver example (SciTools#4120) Improve styling in a minor way in docs (SciTools#4314) bump version (SciTools#4310) Made clear we only test on Linux. (SciTools#4309) Updated environment lockfiles (SciTools#4308) Include Discussions in Getting Involved. (SciTools#4307) Fixed text to show as link. (SciTools#4305) [pre-commit.ci] pre-commit autoupdate (SciTools#4299) Updated environment lockfiles (SciTools#4298) cartopy feature download (SciTools#4304) Mesh Loading (AVD-1813) (SciTools#4262) reset whatsnew latest (SciTools#4288) ...
tkknight · Sep 21, 2021 · a0c947b · a0c947b
2 parents 84b1d83 + 63c1220
commit a0c947b
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diff --git a/.cirrus.yml b/.cirrus.yml
@@ -18,30 +18,27 @@ 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_TEST_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"
+  CARTOPY_CACHE_BUILD: "3"
   # 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: "nox pip setuptools wheel"
+  PIP_CACHE_PACKAGES: "nox pip pyyaml setuptools wheel"
   # Conda packages to be installed.
   CONDA_CACHE_PACKAGES: "nox pip"
   # Git commit hash for iris test data.
-  IRIS_TEST_DATA_VERSION: "2.0.0"
+  IRIS_TEST_DATA_VERSION: "2.4"
   # Base directory for the iris-test-data.
   IRIS_TEST_DATA_DIR: ${HOME}/iris-test-data
 
@@ -75,6 +72,14 @@ linux_task_template: &LINUX_TASK_TEMPLATE
     fingerprint_script:
       - echo "${CIRRUS_OS}"
       - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${CARTOPY_CACHE_BUILD}"
+    populate_script:
+      - conda create --quiet --name cartopy-cache cartopy
+      - source ${HOME}/miniconda/etc/profile.d/conda.sh >/dev/null 2>&1
+      - conda activate cartopy-cache >/dev/null 2>&1
+      - cd $(mktemp -d)
+      - wget --quiet https://raw.githubusercontent.com/SciTools/cartopy/v0.20.0/tools/cartopy_feature_download.py
+      - python cartopy_feature_download.py physical --output ${HOME}/.local/share/cartopy --no-warn
+      - conda deactivate >/dev/null 2>&1
   nox_cache:
     folder: ${CIRRUS_WORKING_DIR}/.nox
     reupload_on_changes: true
@@ -108,59 +113,39 @@ iris_test_data_template: &IRIS_TEST_DATA_TEMPLATE
 #
 # Linting
 #
-lint_task:
+task:
   only_if: ${SKIP_LINT_TASK} == ""
   << : *CREDITS_TEMPLATE
   auto_cancellation: true
   container:
     image: python:3.8
     cpu: 2
     memory: 4G
-  name: "${CIRRUS_OS}: linting"
+  name: "${CIRRUS_OS}: pre-commit hooks"
   pip_cache:
     folder: ~/.cache/pip
     fingerprint_script:
       - echo "${CIRRUS_TASK_NAME} py${PYTHON_VERSION}"
       - echo "$(date +%Y).$(expr $(date +%U) / ${CACHE_PERIOD}):${PIP_CACHE_BUILD} ${PIP_CACHE_PACKAGES}"
-  lint_script:
+  precommit_script:
     - pip list
     - python -m pip install --retries 3 --upgrade ${PIP_CACHE_PACKAGES}
     - pip list
-    - nox --session lint
+    - nox --session precommit
 
 
 #
-# Testing Minimal (Linux)
+# Testing (Linux)
 #
-test_minimal_task:
-  only_if: ${SKIP_TEST_MINIMAL_TASK} == "" && ${SKIP_ALL_TEST_TASKS} == ""
+task:
+  only_if: ${SKIP_TEST_TASK} == ""
   << : *CREDITS_TEMPLATE
   matrix:
     env:
       PY_VER: 3.7
     env:
       PY_VER: 3.8
-  name: "${CIRRUS_OS}: py${PY_VER} tests (minimal)"
-  << : *LINUX_TASK_TEMPLATE
-  tests_script:
-    - export CONDA_OVERRIDE_LINUX="$(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} == "" && ${SKIP_ALL_TEST_TASKS} == ""
-  << : *CREDITS_TEMPLATE
-  matrix:
-    env:
-      PY_VER: 3.7
-    env:
-      PY_VER: 3.8
-  name: "${CIRRUS_OS}: py${PY_VER} tests (full)"
+  name: "${CIRRUS_OS}: py${PY_VER} tests"
   container:
     image: gcc:latest
     cpu: 6
@@ -176,35 +161,16 @@ test_full_task:
 
 
 #
-# 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)
+# Documentation Testing and Gallery (Linux)
 #
-doctest_task:
+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${PY_VER} doc tests"
+  name: "${CIRRUS_OS}: py${PY_VER} doctests and gallery"
   << : *IRIS_TEST_DATA_TEMPLATE
   << : *LINUX_TASK_TEMPLATE
   tests_script:
@@ -219,16 +185,16 @@ doctest_task:
 
 
 #
-# Testing Documentation Link Check (Linux)
+# Documentation Link Check (Linux)
 #
-linkcheck_task:
+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${PY_VER} doc link check"
+  name: "${CIRRUS_OS}: py${PY_VER} link check"
   << : *LINUX_TASK_TEMPLATE
   tests_script:
     - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"

diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -0,0 +1,48 @@
+# This is a basic workflow to help you get started with Actions
+
+name: benchmark-check
+
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  pull_request:
+
+jobs:
+  benchmark:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Checkout the branches
+        run: |
+          git fetch --depth=1 origin ${{ github.event.pull_request.base.ref }}
+          git branch _base FETCH_HEAD
+          git fetch --depth=1 origin ${{ github.ref }}
+          git branch _head FETCH_HEAD
+
+      - name: Setup asv
+        run: |
+          pip install asv
+          cd benchmarks
+          asv machine --yes
+
+      - name: Run benchmarks on source and target
+        run: |
+          cd benchmarks
+          asv continuous --factor 1.2 _base _head
+
+      - name: Write a compare file to the output folder
+        if: ${{ always() }}
+        run: |
+          cd benchmarks
+          asv compare -s _base _head > .asv/compare.txt
+
+      - name: Archive asv results
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v2
+        with:
+          name: asv-report
+          path: |
+            benchmarks/.asv/results
+            benchmarks/.asv/compare.txt
diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -0,0 +1,78 @@
+# See https://github.com/actions/stale
+
+name: Stale issues and pull-requests
+on:
+  schedule:
+    - cron: 0 0 * * *
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v4.0.0
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+          # Idle number of days before marking issues/prs stale.
+          days-before-stale: 500
+
+          # Idle number of days before closing stale issues/prs.
+          days-before-close: 28
+
+          # Comment on the staled issues.
+          stale-issue-message: |
+            In order to maintain a backlog of relevant issues, we automatically label them as stale after 500 days of inactivity.
+
+            If this issue is still important to you, then please comment on this issue and the stale label will be removed.
+
+            Otherwise this issue will be automatically closed in 28 days time.
+
+          # Comment on the staled prs.
+          stale-pr-message: | 
+            In order to maintain a backlog of relevant PRs, we automatically label them as stale after 500 days of inactivity.
+
+            If this PR is still important to you, then please comment on this PR and the stale label will be removed.
+
+            Otherwise this PR will be automatically closed in 28 days time.
+
+          # Comment on the staled issues while closed.
+          close-issue-message: |
+            This stale issue has been automatically closed due to a lack of community activity.
+            
+            If you still care about this issue, then please either:
+              * Re-open this issue, if you have sufficient permissions, or
+              * Add a comment pinging `@SciTools/iris-devs` who will re-open on your behalf.
+
+          # Comment on the staled prs while closed.
+          close-pr-message: |
+            This stale PR has been automatically closed due to a lack of community activity.
+            
+            If you still care about this PR, then please either:
+              * Re-open this PR, if you have sufficient permissions, or
+              * Add a comment pinging `@SciTools/iris-devs` who will re-open on your behalf.
+
+          # Label to apply on staled issues. 
+          stale-issue-label: Stale
+
+          # Label to apply on staled prs.
+          stale-pr-label: Stale
+
+          # Labels on issues exempted from stale.
+          exempt-issue-labels: |
+            "Status: Blocked,Status: Decision Required,Peloton 🚴‍♂️,Good First Issue"
+
+          # Labels on prs exempted from stale.
+          exempt-pr-labels: |
+            "Status: Blocked,Status: Decision Required,Peloton 🚴‍♂️,Good First Issue"
+
+          # Max number of operations per run.
+          operations-per-run: 300
+
+          # Remove stale label from issues/prs on updates/comments.
+          remove-stale-when-updated: true
+
+          # Order to get issues/PRs.
+          ascending: true
+
+          # Exempt all issues/prs with milestones from stale.
+          exempt-all-milestones: true
diff --git a/.gitignore b/.gitignore
@@ -35,7 +35,6 @@ pip-cache
 # Created by Iris build
 *.so
 lib/iris/etc/site.cfg
-lib/iris/fileformats/_pyke_rules/compiled_krb/
 lib/iris/std_names.py
 
 # Iris test result files

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,8 +1,18 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+
+files: |
+    (?x)(
+        noxfile\.py|
+        setup\.py|
+        docs\/.+\.py|
+        lib\/.+\.py
+    )
+minimum_pre_commit_version: 1.21.0
+
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v4.0.1"
+    rev: v4.0.1
     hooks:
         # Prevent giant files from being committed.
     -   id: check-added-large-files
@@ -16,27 +26,31 @@ repos:
     -   id: debug-statements
         # Don't commit to main branch.
     -   id: no-commit-to-branch
+
 -   repo: https://github.com/psf/black
-    rev: "21.6b0"
+    rev: 21.9b0
     hooks:
     -   id: black
         pass_filenames: false
-        args: ["--config=./pyproject.toml", "--check", "docs", "lib", "noxfile.py", "setup.py"]
+        args: [--config=./pyproject.toml, .]
+
 -   repo: https://github.com/PyCQA/flake8
-    rev: "3.9.2"
+    rev: 3.9.2
     hooks:
     -   id: flake8
-        args: ["--config=./setup.cfg", "docs", "lib", "noxfile.py", "setup.py"]
+        types: [file, python]
+        args: [--config=./setup.cfg]
+
 -   repo: https://github.com/pycqa/isort
-    rev: "5.9.1"
+    rev: 5.9.3
     hooks:
     -   id: isort
-        # Align CLI usage with other hooks, rather than use isort "src_paths" option
-        # in the pyproject.toml configuration.
-        name: isort
-        args: ["--filter-files", "--check", "docs", "lib", "noxfile.py", "setup.py"]
+        types: [file, python]
+        args: [--filter-files]
+
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.8.0
+    rev: v1.11.0
     hooks:
     -   id: blacken-docs
+        types: [file, rst]
         additional_dependencies: [black==21.6b0]
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -3,9 +3,8 @@ include CHANGES COPYING COPYING.LESSER
 
 # Files from setup.py package_data that are not automatically added to source distributions
 recursive-include lib/iris/tests/results *.cml *.cdl *.txt *.xml *.json
-recursive-exclude lib/iris/fileformats/_pyke_rules/compiled_krb *
 recursive-include lib/iris/etc *
-include lib/iris/fileformats/_pyke_rules/*.krb
+include lib/iris/tests/stock/file_headers/*
 
 recursive-include requirements *