Merge branch 'main' of github.com:sunpy/sunkit-image into pr/207

sunpy · Nov 13, 2024 · 88c4c85 · 88c4c85
2 parents da81f44 + 2ee3205
commit 88c4c85
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "67ea3b3815de57668e92dbe1fa2c3d033758d8f0",
+  "commit": "75f84c4adf1753af67967930c3335bc73bca9bf5",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -16,7 +16,8 @@
       "enable_dynamic_dev_versions": "y",
       "include_example_code": "n",
       "include_cruft_update_github_workflow": "y",
-      "_sphinx_theme": "alabaster",
+      "use_extended_ruff_linting": "y",
+      "_sphinx_theme": "sunpy",
       "_parent_project": "",
       "_install_requires": "",
       "_copy_without_render": [

diff --git a/.gitattributes b/.gitattributes
@@ -1,6 +1,7 @@
-*fits binary
 *fit binary
-*fts binary
 *fit.gz binary
+*fits binary
 *fits.gz binary
+*fts binary
 *fts.gz binary
+*npz binary
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -126,7 +126,6 @@ jobs:
           files: ./coverage.xml
 
   publish:
-    needs: [test, docs]
     # Build wheels on PRs only when labelled. Releases will only be published if tagged ^v.*
     # see https://github-actions-workflows.openastronomy.org/en/latest/publish.html#upload-to-pypi
     if: |
@@ -135,6 +134,7 @@ jobs:
         github.event_name == 'pull_request' &&
         contains(github.event.pull_request.labels.*.name, 'Run publish')
       )
+    needs: [test, docs]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@main
     with:
       python-version: '3.12'

diff --git a/.github/workflows/label_sync.yml b/.github/workflows/label_sync.yml
@@ -0,0 +1,23 @@
+name: Label Sync
+on:
+  workflow_dispatch:
+  schedule:
+    #        ┌───────── minute (0 - 59)
+    #        │ ┌───────── hour (0 - 23)
+    #        │ │ ┌───────── day of the month (1 - 31)
+    #        │ │ │ ┌───────── month (1 - 12 or JAN-DEC)
+    #        │ │ │ │ ┌───────── day of the week (0 - 6 or SUN-SAT)
+    - cron: '0 0 * * *' # run every day at midnight UTC
+
+# Give permissions to write issue labels
+permissions:
+  issues: write
+
+jobs:
+  label_sync:
+    runs-on: ubuntu-latest
+    name: Label Sync
+    steps:
+      - uses: srealmoreno/label-sync-action@850ba5cef2b25e56c6c420c4feed0319294682fd
+        with:
+          config-file: https://raw.githubusercontent.com/sunpy/.github/main/labels.yml
diff --git a/.github/workflows/sub_package_update.yml b/.github/workflows/sub_package_update.yml
@@ -21,14 +21,6 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: true
-      matrix:
-        include:
-          - add-paths: .
-            body: apply the changes to this repo.
-            branch: cruft/update
-            commit-message: "Automatic package template update"
-            title: Updates from the package template
-
     steps:
       - uses: actions/checkout@v4
 
@@ -55,25 +47,47 @@ jobs:
           echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
 
       - name: Run update if available
+        id: cruft_update
         if: steps.check.outputs.has_changes == '1'
         run: |
           git config --global user.email "${{ github.actor }}@users.noreply.github.com"
           git config --global user.name "${{ github.actor }}"
 
-          cruft update --skip-apply-ask --refresh-private-variables
+          cruft_output=$(cruft update --skip-apply-ask --refresh-private-variables)
+          echo $cruft_output
           git restore --staged .
 
-      - name: Create pull request
+          if [[ "$cruft_output" == *"Failed to cleanly apply the update, there may be merge conflicts."* ]]; then
+            echo merge_conflicts=1 >> $GITHUB_OUTPUT
+          else
+            echo merge_conflicts=0 >> $GITHUB_OUTPUT
+          fi
+
+      - name: Check if only .cruft.json is modified
+        id: cruft_json
         if: steps.check.outputs.has_changes == '1'
-        uses: peter-evans/create-pull-request@v6
+        run: |
+          git status --porcelain=1
+          if [[ "$(git status --porcelain=1)" == " M .cruft.json" ]]; then
+            echo "Only .cruft.json is modified. Exiting workflow early."
+            echo "has_changes=0" >> "$GITHUB_OUTPUT"
+          else
+            echo "has_changes=1" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Create pull request
+        if: steps.cruft_json.outputs.has_changes == '1'
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          add-paths: ${{ matrix.add-paths }}
-          commit-message: ${{ matrix.commit-message }}
-          branch: ${{ matrix.branch }}
+          add-paths: "."
+          commit-message: "Automatic package template update"
+          branch: "cruft/update"
           delete-branch: true
-          branch-suffix: timestamp
-          title: ${{ matrix.title }}
+          draft: ${{ steps.cruft_update.outputs.merge_conflicts == '1' }}
+          title: "Updates from the package template"
           body: |
-            This is an autogenerated PR, which will ${{ matrix.body }}.
-            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Package Template
+            This is an autogenerated PR, which will applies the latest changes from the [SunPy Package Template](https://github.com/sunpy/package-template).
+            If this pull request has been opened as a draft there are conflicts which need fixing.
+
+            **To run the CI on this pull request you will need to close it and reopen it.**
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,22 +1,6 @@
 repos:
-  - repo: https://github.com/PyCQA/docformatter
-    rev: master
-    hooks:
-      - id: docformatter
-        args: ["--in-place", "--pre-summary-newline", "--make-summary-multi"]
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        args:
-          [
-            "--in-place",
-            "--remove-all-unused-imports",
-            "--remove-unused-variable",
-          ]
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|extern.*|.rst|.md|docs/conf.py)$"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.3"
+    rev: "v0.7.3"
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -26,16 +10,12 @@ repos:
       - id: isort
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|sunkit_image/extern)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
-        exclude: ".*(.fits|.fts|.fit|.txt|.header|.csv)$"
-      - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
-      - id: end-of-file-fixer
-        exclude: ".*(.fits|.fts|.fit|.txt|.csv)$"
+        exclude: ".*(.fits|.fts|.fit|.header|.txt)$"
       - id: check-yaml
       - id: debug-statements
       - id: check-added-large-files
@@ -45,12 +25,17 @@ repos:
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|.json)$|^CITATION.rst$"
       - id: mixed-line-ending
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*)$"
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        args: [ "--write-changes" ]
   - repo: https://github.com/crate-ci/typos
-    rev: v1.23.1
+    rev: typos-dict-v0.11.35
     hooks:
       - id: typos
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.10.1"
+    rev: "v1.13.0"
     hooks:
       - id: mypy
         additional_dependencies: ["types-setuptools"]

diff --git a/.ruff.toml b/.ruff.toml
@@ -1,5 +1,5 @@
 target-version = "py310"
-line-length = 110
+line-length = 120
 exclude = [
   ".git,",
   "__pycache__",
@@ -8,30 +8,75 @@ exclude = [
 ]
 
 [lint]
-select = ["E", "F", "W", "UP", "PT"]
+select = [
+  "E",
+  "F",
+  "W",
+  "UP",
+  "PT",
+  "BLE",
+  "A",
+  "C4",
+  "INP",
+  "PIE",
+  "T20",
+  "RET",
+  "TID",
+  "PTH",
+  "PD",
+  "PLC",
+  "PLE",
+  "FLY",
+  "NPY",
+  "PERF",
+  "RUF",
+]
 extend-ignore = [
   # pycodestyle (E, W)
-  "E501", # LineTooLong                             # TODO! fix
+  "E501", # ignore line length will use a formatter instead
+  # pyupgrade (UP)
+  "UP038", # Use | in isinstance - not compatible with models and is slower
   # pytest (PT)
   "PT001", # Always use pytest.fixture()
   "PT004", # Fixtures which don't return anything should have leading _
-  "PT007", # Parametrize should be lists of tuples  # TODO! fix
-  "PT011", # Too broad exception assert             # TODO! fix
   "PT023", # Always use () on pytest decorators
+  # flake8-pie (PIE)
+  "PIE808", # Disallow passing 0 as the first argument to range
+  # flake8-use-pathlib (PTH)
+  "PTH123", # open() should be replaced by Path.open()
+  # Ruff (RUF)
+  "RUF003", # Ignore ambiguous quote marks, doesn't allow ' in comments
+  "RUF012", # Mutable class attributes should be annotated with `typing.ClassVar`
+  "RUF013", # PEP 484 prohibits implicit `Optional`
+  "RUF015", # Prefer `next(iter(...))` over single element slice
 ]
 
 [lint.per-file-ignores]
-# Part of configuration, not a package.
-"setup.py" = ["INP001"]
-"conftest.py" = ["INP001"]
+"setup.py" = [
+  "INP001", # File is part of an implicit namespace package.
+]
+"conftest.py" = [
+  "INP001", # File is part of an implicit namespace package.
+]
 "docs/conf.py" = [
-  "E402"  # Module imports not at top of file
+  "E402" # Module imports not at top of file
 ]
 "docs/*.py" = [
-  "INP001",  # Implicit-namespace-package. The examples are not a package.
+  "INP001", # File is part of an implicit namespace package.
+]
+"examples/**.py" = [
+  "T201", # allow use of print in examples
+  "INP001", # File is part of an implicit namespace package.
+]
+"__init__.py" = [
+  "E402", # Module level import not at top of cell
+  "F401", # Unused import
+  "F403", # from {name} import * used; unable to detect undefined names
+  "F405", # {name} may be undefined, or defined from star imports
+]
+"test_*.py" = [
+  "E402", # Module level import not at top of cell
 ]
-"__init__.py" = ["E402", "F401", "F403"]
-"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
 
 [lint.pydocstyle]
 convention = "numpy"
diff --git a/changelog/205.doc.rst b/changelog/205.doc.rst
@@ -1,2 +1,3 @@
 Added a new example for `sunkit_image.radial.rhef` at :ref:`sphx_glr_generated_gallery_radial_histogram_equalization.py`
-Added RFEF to :ref:`sphx_glr_generated_gallery_radial_gradient_filters.py` as a comparison to the other filters.
+
+Added RHEF to :ref:`sphx_glr_generated_gallery_radial_gradient_filters.py` as a comparison to the other filters.
diff --git a/changelog/215.bugfix.rst b/changelog/215.bugfix.rst
@@ -0,0 +1 @@
+Within `sunkit_image.enhance.mgn`, the input data is now cast to float32 to work around int/float being cast to each other causing an error.
diff --git a/changelog/215.trivial.rst b/changelog/215.trivial.rst
@@ -0,0 +1 @@
+Added unit tests with a JSOC cutout file.
diff --git a/changelog/231.breaking.rst b/changelog/231.breaking.rst
@@ -0,0 +1 @@
+All functions under (`sunkit_image.radial`) now have a settable fill value which now defaults to NaN instead of 0.
diff --git a/changelog/231.bugfix.rst b/changelog/231.bugfix.rst
@@ -0,0 +1 @@
+Improved the Radial Histogram Equalizing Filter (RHEF) (`sunkit_image.radial.rhef`) to work with images outside of SDO/AIA.
diff --git a/changelog/238.doc.rst b/changelog/238.doc.rst
@@ -0,0 +1 @@
+Added a new example showcasing advanced usage of Wavelets Optimized Whitening (WOW) at :ref:`sphx_glr_generated_gallery_advanced_wow.py`
diff --git a/changelog/243.breaking.rst b/changelog/243.breaking.rst
@@ -0,0 +1,3 @@
+The function ``set_attenuation_coefficients`` has been removed from the public API.
+
+Now you can pass in the inputs used by ``set_attenuation_coefficients`` directly into `sunkit_image.radial.fnrgf`, which now accepts ``mean_attenuation_range`` and ``std_attenuation_range``.