Merge branch 'main' into theme_play

* main: (43 commits) [pre-commit.ci] pre-commit autoupdate (SciTools#4244) Updated environment lockfiles (SciTools#4242) [pre-commit.ci] pre-commit autoupdate (SciTools#4239) Documented the --force option on conda env create (SciTools#4240) Updated environment lockfiles (SciTools#4237) pre-commit isort and black --check only for cirrus-ci (SciTools#4235) Only run docs-building sessions with Python 3.8. (SciTools#4210) consolidate cirrus-ci documentation tasks (SciTools#4219) Updated environment lockfiles (SciTools#4223) Replace pyke nopyke (SciTools#4198) drop cirrus-ci minimal tests (SciTools#4218) remove change management tech paper (SciTools#4217) [pre-commit.ci] pre-commit autoupdate (SciTools#4213) Updated environment lockfiles (SciTools#4212) Widen cube printout for long ancil or cell-measure names. (SciTools#4124) convert docs print statements (SciTools#4209) optimise pre-commit (SciTools#4208) drop black and flake8 dependencies (SciTools#4181) pre-commit blacked docs (SciTools#4205) pre-commit update (SciTools#4204) ...
tkknight · Jul 21, 2021 · 2155913 · 2155913
2 parents b7b8539 + a6cd220
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diff --git a/.cirrus.yml b/.cirrus.yml
@@ -3,30 +3,25 @@
 #   - 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/
-#   - https://cirrus-ci.org/guide/windows/
 #   - https://hub.docker.com/_/gcc/
 #   - https://hub.docker.com/_/python/
 
 #
 # Global defaults.
 #
 container:
-  image: python:3.8
+  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_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"
@@ -39,7 +34,7 @@ env:
   # 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"
+  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.
@@ -84,11 +79,12 @@ linux_task_template: &LINUX_TASK_TEMPLATE
       - 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
+  # Restrict where compute credits are used.
   use_compute_credits: ${CIRRUS_REPO_FULL_NAME} == "SciTools/iris" && ${CIRRUS_USER_COLLABORATOR} == "true" && ${CIRRUS_PR_DRAFT} == "false" && ${CIRRUS_PR} != ""
 
 
@@ -109,64 +105,39 @@ iris_test_data_template: &IRIS_TEST_DATA_TEMPLATE
 #
 # Linting
 #
-lint_task:
+precommit_task:
   only_if: ${SKIP_LINT_TASK} == ""
   << : *CREDITS_TEMPLATE
   auto_cancellation: true
-  name: "${CIRRUS_OS}: flake8 and black"
+  container:
+    image: python:3.8
+    cpu: 2
+    memory: 4G
+  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 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
+    - nox --session precommit
 
 
 #
-# Testing Full (Linux)
+# Testing (Linux)
 #
-test_full_task:
-  only_if: ${SKIP_TEST_FULL_TASK} == "" && ${SKIP_ALL_TEST_TASKS} == ""
+test_task:
+  only_if: ${SKIP_TEST_TASK} == ""
   << : *CREDITS_TEMPLATE
   matrix:
-    env:
-      PY_VER: 3.6
     env:
       PY_VER: 3.7
     env:
       PY_VER: 3.8
-  name: "${CIRRUS_OS}: py${PY_VER} tests (full)"
+  name: "${CIRRUS_OS}: py${PY_VER} tests"
   container:
     image: gcc:latest
     cpu: 6
@@ -182,46 +153,16 @@ test_full_task:
 
 
 #
-# Testing Documentation Gallery (Linux)
-#
-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)
+# Documentation Testing and Gallery (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:
+    PY_VER: 3.8
     MPL_RC_DIR: ${HOME}/.config/matplotlib
     MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
+  name: "${CIRRUS_OS}: py${PY_VER} doctests and gallery"
   << : *IRIS_TEST_DATA_TEMPLATE
   << : *LINUX_TASK_TEMPLATE
   tests_script:
@@ -236,22 +177,16 @@ doctest_task:
 
 
 #
-# Testing Documentation Link Check (Linux)
+# Documentation Link Check (Linux)
 #
 linkcheck_task:
   only_if: ${SKIP_LINKCHECK_TASK} == "" && ${SKIP_ALL_DOC_TASKS} == ""
   << : *CREDITS_TEMPLATE
-  matrix:
-    env:
-      PY_VER: 3.8
-  name: "${CIRRUS_OS}: py${PY_VER} doc link check"
-  container:
-    image: gcc:latest
-    cpu: 2
-    memory: 4G
   env:
+    PY_VER: 3.8
     MPL_RC_DIR: ${HOME}/.config/matplotlib
     MPL_RC_FILE: ${HOME}/.config/matplotlib/matplotlibrc
+  name: "${CIRRUS_OS}: py${PY_VER} link check"
   << : *LINUX_TASK_TEMPLATE
   tests_script:
     - export CONDA_OVERRIDE_LINUX="$(uname -r | cut -d'+' -f1)"

diff --git a/.flake8 b/.flake8
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -1 +1,13 @@
-See the [Developers Guide](https://scitools-iris.readthedocs.io/en/latest/index.html#development-index)
+# Contributing to Iris
+
+Want to contribute to Iris? But don't know where to start 🤔
+
+We recommend that you first checkout our advice to [First Time Contributors](https://github.com/SciTools/iris/issues/4133),
+which has some solid suggestions on where to begin.
+
+Otherwise, head over to our [Developers Guide on Getting Involved](https://scitools-iris.readthedocs.io/en/stable/developers_guide/contributing_getting_involved.html)
+for all the information you need to start on your Iris development journey.
+
+Still need help or advice?
+
+Then join us over on our [Iris GitHub Discussions](https://github.com/SciTools/iris/discussions). We'd love to hear from you!
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/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,2 +1,6 @@
 # reference: https://docs.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser
 blank_issues_enabled: false
+contact_links:
+  -  name: 💬 Iris GitHub Discussions
+     url: https://github.com/SciTools/iris/discussions
+     about: Engage with the Iris community to discuss your issue
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
@@ -7,31 +7,69 @@
 # pinned at specific versions.
 #
 # For environments that have changed, a pull request will be made and submitted
-# to the master branch
+# to the main branch
 
 name: Refresh Lockfiles
 
 
 on:
   workflow_dispatch:
+    inputs:
+      clobber:
+        description: |
+          Force the workflow to run, potentially clobbering any commits already made to the branch. 
+          Enter "yes" or "true" to run.
+        default: "no"
   schedule:
     # Run once a week on a Saturday night 
     - cron: 1 0 * * 6
 
 
 jobs:
 
+  no_clobber:
+    runs-on: ubuntu-latest
+    steps:
+      # check if the auto-update-lockfiles branch exists.  If it does, and someone other than
+      # the lockfile bot has made the head commit, abort the workflow.
+      # This job can be manually overridden by running directly from the github actions panel
+      # (known as a "workflow_dispatch") and setting the `clobber` input to "yes".
+      - uses: actions/script@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            if (context.eventName == "workflow_dispatch") {
+              const clobber = context.payload.inputs.clobber || "no";
+              if (["yes", "true", "y"].includes(clobber.trim().toLowerCase())) {
+                core.info("Manual override, continuing workflow, potentially overwriting previous commits to auto-update-lockfiles");
+                return
+              }
+            }
+            github.repos.getBranch({...context.repo, branch: "auto-update-lockfiles"}).then(res => {
+              const committer = res.data.commit.commit.committer;
+              if (committer && committer.name === "Lockfile bot") {
+                core.info("Lockfile bot was the last to push to auto-update-lockfiles. Continue.");
+              } else {
+                core.setFailed("New commits to auto-update-lockfiles since bot last ran. Abort!");
+              }
+            }).catch(err => {
+              if (err.status === 404) {
+                  core.info("auto-update-lockfiles branch not found, continue");
+              }
+            })
+
   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
+    needs: no_clobber
 
     strategy:
       matrix:
-        python: ['36', '37', '38']
+        python: ['37', '38']
 
     steps:
       - uses: actions/checkout@v2
@@ -62,14 +100,16 @@ jobs:
           path: artifacts
 
       - name: Update lock files in repo
-        run: | 
+        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
+          committer: "Lockfile bot <noreply@github.com>"
+          author: "Lockfile bot <noreply@github.com>"
           delete-branch: true
           branch: auto-update-lockfiles
           title: Update CI environment lockfiles

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