Merge remote-tracking branch 'upstream/main'

.circleci/codecov_upload.sh

@@ -0,0 +1,9 @@
+#!/bin/bash -e
+curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
+curl -Os https://uploader.codecov.io/latest/linux/codecov
+curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
+curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
+gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
+shasum -a 256 -c codecov.SHA256SUM
+chmod +x codecov
+./codecov "$@"

.circleci/config.yml

@@ -12,7 +12,7 @@ skip-check: &skip-check
   command: bash .circleci/early_exit.sh
 
 merge-check: &merge-check
-  name: Check if we need to merge upstream master
+  name: Check if we need to merge upstream main
   command: |
     if [[ -n "${CIRCLE_PR_NUMBER}" ]]; then
       git fetch origin --tags
@@ -24,15 +24,15 @@ apt-run: &apt-install
   name: Install apt packages
   command: |
     sudo apt update
-    sudo apt install -y graphviz build-essential libopenjp2-7 python3-dev
+    sudo apt install -y libopenjp2-7
 
 jobs:
   figure:
     parameters:
       jobname:
         type: string
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.10
     environment:
       TOXENV=<< parameters.jobname >>
     steps:
@@ -42,19 +42,22 @@ jobs:
       - run: *merge-check
       - run: *apt-install
       - run: pip install --user -U tox tox-pypi-filter
-      - run: tox
-      - run: curl -s https://codecov.io/bash | bash
+      - run: tox -v
+      - run:
+          name: Running codecov
+          command: bash -e .circleci/codecov_upload.sh -f ".tmp/${TOXENV}/coverage.xml"
       - store_artifacts:
           path: .tmp/<< parameters.jobname >>/figure_test_images
       - run:
           name: "Image comparison page is available at: "
           command: echo "${CIRCLE_BUILD_URL}/artifacts/${CIRCLE_NODE_INDEX}/.tmp/${TOXENV}/figure_test_images/fig_comparison.html"
+
   deploy-reference-images:
     parameters:
       jobname:
         type: string
     docker:
-      - image: circleci/python:3.8
+      - image: cimg/python:3.10
     environment:
       TOXENV: << parameters.jobname >>
       GIT_SSH_COMMAND: ssh -i ~/.ssh/id_rsa_b1c8b094a8ec67162b0f18a949a6b1db
@@ -72,8 +75,9 @@ jobs:
       - run: git config --global user.email "ndcube@circleci" && git config --global user.name "ndcube Circle CI"
       - run: git clone [email protected]:sunpy/sunpy-figure-tests.git --depth 1 -b ndcube-${CIRCLE_BRANCH} ~/sunpy-figure-tests/
       # Generate Reference images
-      - run: pip install --user -U tox codecov tox-pypi-filter
-      - run: tox -- --mpl-generate-path=/home/circleci/sunpy-figure-tests/figures/$TOXENV | tee toxlog
+      - run: pip install --user -U tox tox-pypi-filter
+      - run: rm -rf /home/circleci/sunpy-figure-tests/figures/$TOXENV/*
+      - run: tox -v -- --mpl-generate-path=/home/circleci/sunpy-figure-tests/figures/$TOXENV | tee toxlog
       - run: |
           hashlib=$(grep "^figure_hashes.*\.json$" toxlog)
           cp ./ndcube/visualization/tests/$hashlib /home/circleci/sunpy-figure-tests/figures/$TOXENV/
@@ -87,25 +91,26 @@ jobs:
 
 workflows:
   version: 2
+
   figure-tests:
     jobs:
       - figure:
           name: << matrix.jobname >>
           matrix:
             parameters:
               jobname:
-                - "py38-figure"
-                - "py39-figure-devdeps"
+                - "py310-figure"
+                - "py310-figure-devdeps"
+
       - deploy-reference-images:
           name: baseline-<< matrix.jobname >>
           matrix:
             parameters:
               jobname:
-                - "py38-figure"
-                - "py39-figure-devdeps"
+                - "py310-figure"
+                - "py310-figure-devdeps"
           requires:
-            - "py38-figure"
-            - "py39-figure-devdeps"
+            - << matrix.jobname >>
           filters:
             branches:
               only:

.github/workflows/ci.yml

@@ -3,7 +3,8 @@ name: CI
 on:
   push:
     branches:
-      - '*'
+      - 'main'
+      - '*.*'
       - '!*backport*'
     tags:
       - 'v*'
@@ -27,19 +28,20 @@ jobs:
       coverage: codecov
       toxdeps: tox-pypi-filter
       envs: |
-        - linux: py310
+        - linux: py311
 
   test:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
+      default_python: '3.9'
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
       envs: |
-        - macos: py38
+        - macos: py310
         - windows: py39
-        - linux: py38-oldestdeps
+        - linux: py39-oldestdeps
         - linux: build_docs
           posargs: ''
           pytest: false
@@ -49,15 +51,19 @@ jobs:
               - graphviz
 
   cron:
-    if: github.event_name == 'workflow_dispatch'
+    if: |
+      github.event_name == 'workflow_dispatch' || (
+        github.event_name == 'pull_request' &&
+        contains(github.event.pull_request.labels.*.name, 'Run cron CI')
+      )
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
-      default_python: '3.8'
+      default_python: '3.9'
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
       envs: |
-        - linux: py39-devdeps
+        - linux: py311-devdeps
         - linux: py39-conda
           libraries: ''
 
@@ -71,6 +77,7 @@ jobs:
     needs: [test]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
     with:
+      python-version: '3.9'
       test_extras: 'dev'
       test_command: 'pytest -p no:warnings --doctest-rst -m "not mpl_image_compare" --pyargs ndcube'
       submodules: false
@@ -88,3 +95,4 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           homeserver: ${{ secrets.matrix_homeserver }}
           roomid: '!TWSJXVpyflnZOzmSQz:matrix.org'
+          ignore_pattern: '.*Load tox.*'

.github/workflows/scheduled_builds.yml

@@ -9,13 +9,13 @@ on:
     #        │ │ ┌───────── day of the month (1 - 31)
     #        │ │ │ ┌───────── month (1 - 12 or JAN-DEC)
     #        │ │ │ │ ┌───────── day of the week (0 - 6 or SUN-SAT)
-    - cron: '0 7 * * *'  # Every day at 07:00 UTC
+    - cron: '0 7 * * 1'  # Every day at 07:00 UTC
 
 jobs:
   dispatch_workflows:
     runs-on: ubuntu-latest
     steps:
       - run: gh workflow run ci.yml --repo sunpy/ndcube --ref main
-      - run: gh workflow run ci.yml --repo sunpy/ndcube --ref 2.0
+      - run: gh workflow run ci.yml --repo sunpy/ndcube --ref 2.1
     env:
       GITHUB_TOKEN: ${{ secrets.WORKFLOW_TOKEN }}

.gitignore

@@ -208,7 +208,7 @@ ndcube/_compiler.c
 ndcube/_version.py
 docs/_build
 docs/generated
-docs/api/
+docs/api
 examples/**/*.asdf
 examples/**/*.csv
 figure_test_images*

.mailmap

@@ -8,3 +8,9 @@ Aoife Maria Ryan <[email protected]> aoife <[email protected]>
 Baptiste Pellorce <[email protected]> Baptiste PELLORCE <[email protected]>
 Baptiste Pellorce <[email protected]> Baptiste Pellorce <37335327+BaptistePellorceAstro@users.noreply.github.com>
 Yash Sharma <[email protected]> Yash <[email protected]>
+Laura Hayes <[email protected]> hayesla <[email protected]>
+Marcus Hughes <[email protected]> jmbhughes <[email protected]>
+Ricky O'Steen <[email protected]> Ricky O'Steen <[email protected]>
+Kris Stern <[email protected]> Kris Stern <[email protected]>
+Matthew J. West <[email protected]> Dr Matthieu Wes <[email protected]>
+Will Barnes <[email protected]> Will Barnes <[email protected]>

.pre-commit-config.yaml

@@ -1,77 +1,23 @@
 repos:
-  # The warnings/errors we check for here are:
-  # E101 - mix of tabs and spaces
-  # E11  - Fix indentation.
-  # E111 - 4 spaces per indentation level
-  # E112 - 4 spaces per indentation level
-  # E113 - 4 spaces per indentation level
-  # E121 - Fix indentation to be a multiple of four.
-  # E122 - Add absent indentation for hanging indentation.
-  # E123 - Align closing bracket to match opening bracket.
-  # E124 - Align closing bracket to match visual indentation.
-  # E125 - Indent to distinguish line from next logical line.
-  # E126 - Fix over-indented hanging indentation.
-  # E127 - Fix visual indentation.
-  # E128 - Fix visual indentation.
-  # E129 - Fix visual indentation.
-  # E131 - Fix hanging indent for unaligned continuation line.
-  # E133 - Fix missing indentation for closing bracket.
-  # E20  - Remove extraneous whitespace.
-  # E211 - Remove extraneous whitespace.
-  # E231 - Add missing whitespace.
-  # E241 - Fix extraneous whitespace around keywords.
-  # E242 - Remove extraneous whitespace around operator.
-  # E251 - Remove whitespace around parameter '=' sign.
-  # E252 - Missing whitespace around parameter equals.
-  # E26  - Fix spacing after comment hash for inline comments.
-  # E265 - Fix spacing after comment hash for block comments.
-  # E266 - Fix too many leading '#' for block comments.
-  # E27  - Fix extraneous whitespace around keywords.
-  # E301 - Add missing blank line.
-  # E302 - Add missing 2 blank lines.
-  # E303 - Remove extra blank lines.
-  # E304 - Remove blank line following function decorator.
-  # E305 - expected 2 blank lines after class or function definition
-  # E305 - Expected 2 blank lines after end of function or class.
-  # E306 - expected 1 blank line before a nested definition
-  # E306 - Expected 1 blank line before a nested definition.
-  # E401 - Put imports on separate lines.
-  # E402 - Fix module level import not at top of file
-  # E502 - Remove extraneous escape of newline.
-  # E701 - Put colon-separated compound statement on separate lines.
-  # E711 - Fix comparison with None.
-  # E712 - Fix comparison with boolean.
-  # E713 - Use 'not in' for test for membership.
-  # E714 - Use 'is not' test for object identity.
-  # E722 - Fix bare except.
-  # E731 - Use a def when use do not assign a lambda expression.
+# The warnings/errors we check for here are:
   # E901 - SyntaxError or IndentationError
   # E902 - IOError
   # F822 - undefined name in __all__
   # F823 - local variable name referenced before assignment
-  # W291 - Remove trailing whitespace.
-  # W292 - Add a single newline at the end of the file.
-  # W293 - Remove trailing whitespace on blank line.
-  # W391 - Remove trailing blank lines.
-  # W601 - Use "in" rather than "has_key()".
-  # W602 - Fix deprecated form of raising exception.
-  # W603 - Use "!=" instead of "<>"
-  # W604 - Use "repr()" instead of backticks.
-  # W605 - Fix invalid escape sequence 'x'.
-  # W690 - Fix various deprecated code (via lib2to3).
+  # Others are taken care of by autopep8
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.0.0
     hooks:
       - id: flake8
         args:
           [
             "--count",
             "--select",
-            "E101,E11,E111,E112,E113,E121,E122,E123,E124,E125,E126,E127,E128,E129,E131,E133,E20,E211,E231,E241,E242,E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,E401,E402,E502,E701,E711,E712,E713,E714,E722,E731,E901,E902,F822,F823,W191,W291,W292,W293,W391,W601,W602,W603,W604,W605,W690",
+            "E901,E902,F822,F823",
           ]
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|__init__.py)$"
-  - repo: https://github.com/myint/autoflake
-    rev: v1.4
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v2.2.1
     hooks:
       - id: autoflake
         args:
@@ -80,27 +26,38 @@ repos:
             "--remove-all-unused-imports",
             "--remove-unused-variable",
           ]
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|__init__.py|sunpy/extern|docs/conf.py)$"
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md|__init__.py)$"
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["--sp", "setup.cfg"]
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|cm/__init__.py|sunpy/extern|docs/conf.py)$"
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
+  - repo: https://github.com/hhatto/autopep8
+    rev: v2.0.4
+    hooks:
+    -   id: autopep8
+        args: ["--in-place","--max-line-length", "200"]
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|.rst|.md)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
-        exclude: ".*(.fits|.fts|.fit|.txt)$"
+        exclude: ".*(.fits|.fts|.fit|.header|.txt)$"
       - id: check-yaml
       - id: debug-statements
       - id: check-added-large-files
+        args: ['--enforce-all','--maxkb=1054']
       - id: end-of-file-fixer
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
       - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*)$"
-
+        exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        args: ['--config setup.cfg']
 ci:
   autofix_prs: false

.readthedocs.yml

@@ -1,9 +1,16 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-4.10"
+  jobs:
+    pre_install:
+      - git update-index --assume-unchanged .rtd-environment.yml docs/conf.py
+
+conda:
+  environment: .rtd-environment.yml
+
 sphinx:
   builder: html
   configuration: docs/conf.py
@@ -13,5 +20,6 @@ python:
    install:
      - method: pip
        extra_requirements:
-          - dev
+        - all
+        - docs
        path: .

.rtd-environment.yml

@@ -0,0 +1,7 @@
+name: rtd_ndcube
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+  - graphviz!=2.42.*,!=2.43.*

.sunpy-template.yml

@@ -1,13 +1,13 @@
 default_context:
   package_name: ndcube
   module_name: ndcube
-  short_description: A package for multi-dimensional contiguious and non-contiguious coordinate aware arrays.
+  short_description: A package for multi-dimensional contiguous and non-contiguous coordinate aware arrays.
   author_name: The SunPy Community
   author_email: [email protected]
   license: BSD 2-Clause
   project_url: http://docs.sunpy.org/projects/ndcube/
   github_repo: sunpy/ndcube
-  minimum_python_version: 3.7
+  minimum_python_version: 3.9
   use_compiled_extensions: n
   include_example_code: n
   _provide_setuppy_fallback: y