Merge branch 'main' into speed_up_repr_tiled

DKISTDC · Jan 6, 2025 · 231e89a · 231e89a
2 parents cf5125e + 5ad3fda
commit 231e89a
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Showing 18 changed files with 209 additions and 112 deletions.
diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "aec53b81aed2e7e534045e59303d82712fe82fb1",
+  "commit": "c60ccf2ddc71d3cf126cea15132a15da307864f7",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -10,13 +10,20 @@
       "author_name": "NSO / AURA",
       "author_email": "[email protected]",
       "project_url": "https://github.com/DKISTDC/dkist",
+      "github_repo": "DKISTDC/dkist",
+      "sourcecode_url": "https://github.com/DKISTDC/dkist",
+      "download_url": "https://pypi.org/project/dkist",
+      "documentation_url": "https://docs.dkist.nso.edu/projects/python-tools/en/stable/",
+      "changelog_url": "https://docs.dkist.nso.edu/projects/python-tools/en/stable/whatsnew/changelog.html",
+      "issue_tracker_url": "https://github.com/DKISTDC/dkist/issues",
       "license": "BSD 3-Clause",
       "minimum_python_version": "3.10",
       "use_compiled_extensions": "n",
       "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": "dkist",
       "_parent_project": "",
       "_install_requires": "",
       "_copy_without_render": [

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 +47,49 @@ 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 >> $GITHUB_OUTPUT
+          fi
+
+      - name: Check if only .cruft.json is modified
+        id: cruft_json
         if: steps.check.outputs.has_changes == '1'
+        run: |
+          git status --porcelain=1
+          if [[ "$(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"
+          labels: |
+            no changelog
           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
@@ -1,7 +1,7 @@
 repos:
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.9"
+    rev: "v0.8.3"
     hooks:
       - id: ruff
         args: ["--fix"]

diff --git a/.ruff.toml b/.ruff.toml
@@ -1,5 +1,5 @@
 target-version = "py310"
-line-length = 110
+line-length = 120
 exclude = [
   ".git,",
   "__pycache__",
@@ -10,65 +10,109 @@ exclude = [
 
 [lint]
 select = [
-  "F",
   "E",
+  "F",
   "W",
   "UP",
+  "PT",
+  "BLE",
+  # "A",
   "C4",
   "ICN",
   "G",
   "INP",
-  "PT",
   "Q",
   "RSE",
+  "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
   "E702",
   "E711",
   "E741",
   "F405",
   "F403",
   "F821",
   "F841",
+  # 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
-  # pyupgrade
-  "UP038", # Use | in isinstance - not compatible with models and is slower
   # Returns (RET)
   "RET502",  # Do not implicitly return None in function able to return non-None value
   "RET503",  # Missing explicit return at the end of function able to return non-None value
-  # Pathlib (PTH)
-  "PTH123",  # open() should be replaced by Path.open()
-  # Ruff
-  "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
-  "RUF013",  # PEP 484 prohibits implicit `Optional`
-  "RUF015",  # Prefer `next(iter(...))` over single element slice
+  # 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
+  "A001",
+  "BLE001",
+  "T201",
 ]
 "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
+  "B011",
+  "D",
+  "E402",
+  "PGH001",
+  "S101",
+]
+"dkist/logger.py" = [
+  "PTH",
+  "BLE001",
+]
+"dkist/tests/generate_*" = [
+  "T20",
+]
+"dkist/utils/sysinfo.py" = [
+  "T20",
+]
+"dkist/net/globus/auth.py" = [
+  "T201",
 ]
-"__init__.py" = ["E402", "F401", "F403"]
-"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
-"dkist/logger.py" = ["PTH"]
 
 [lint.flake8-import-conventions.extend-aliases]
 "astropy.units" = "u"

diff --git a/dkist/__init__.py b/dkist/__init__.py
@@ -17,7 +17,7 @@
     __version__ = "unknown"
 
 
-__all__ = ["TiledDataset", "Dataset", "load_dataset", "system_info", "conf"]
+__all__ = ["Dataset", "TiledDataset", "conf", "load_dataset", "system_info"]
 
 
 def write_default_config(overwrite=False):

diff --git a/dkist/_dev/scm_version.py b/dkist/_dev/scm_version.py
@@ -1,11 +1,11 @@
 # Try to use setuptools_scm to get the current version; this is only used
 # in development installations from the git repository.
-import os.path
+from pathlib import Path
 
 try:
     from setuptools_scm import get_version
 
-    version = get_version(root=os.path.join("..", ".."), relative_to=__file__)
+    version = get_version(root=Path('../..'), relative_to=__file__)
 except ImportError:
     raise
 except Exception as e:

diff --git a/dkist/data/sample.py b/dkist/data/sample.py
@@ -4,7 +4,7 @@
 
 from ._sample import _SAMPLE_DATASETS, VISP_HEADER, _get_sample_datasets
 
-__all__ = ["download_all_sample_data", *sorted(_SAMPLE_DATASETS.keys()), "VISP_HEADER"]
+__all__ = ["download_all_sample_data", *sorted(_SAMPLE_DATASETS.keys()), "VISP_HEADER"]  # noqa: PLE0604
 
 
 # See PEP 562 (https://peps.python.org/pep-0562/) for module-level __dir__()

diff --git a/dkist/dataset/utils.py b/dkist/dataset/utils.py
@@ -164,7 +164,7 @@ def pp_matrix(wcs):
     ----------
     wcs : `BaseHighLevelWCS` or `BaseLowLevelWCS`
     """
-    print(_get_pp_matrix(wcs))
+    print(_get_pp_matrix(wcs))  # noqa: T201
 
 
 def extract_pc_matrix(headers, naxes=None):

diff --git a/dkist/io/loaders.py b/dkist/io/loaders.py
@@ -14,7 +14,7 @@
 
 from dkist import log
 
-__all__ = ["BaseFITSLoader", "AstropyFITSLoader"]
+__all__ = ["AstropyFITSLoader", "BaseFITSLoader"]
 
 
 common_parameters = """

diff --git a/dkist/net/attrs.py b/dkist/net/attrs.py
@@ -12,13 +12,33 @@
 from sunpy.net.attr import Range as _Range
 from sunpy.net.attr import SimpleAttr as _SimpleAttr
 
-__all__ = ["PageSize", "Page", "Dataset", "WavelengthBand", "Embargoed", "Observable",
-           "Experiment", "Proposal", "TargetType", "Recipe",
-           "FriedParameter", "PolarimetricAccuracy", "ExposureTime",
-           "EmbargoEndTime", "BrowseMovie", "BoundingBox",
-           "SpectralSampling", "SpatialSampling", "TemporalSampling", "SummitSoftwareVersion",
-           "WorkflowName", "WorkflowVersion", "ObservingProgramExecutionID",
-           "InstrumentProgramExecutionID", "HeaderVersion"]
+__all__ = [
+    "BoundingBox",
+    "BrowseMovie",
+    "Dataset",
+    "EmbargoEndTime",
+    "Embargoed",
+    "Experiment",
+    "ExposureTime",
+    "FriedParameter",
+    "HeaderVersion",
+    "InstrumentProgramExecutionID",
+    "Observable",
+    "ObservingProgramExecutionID",
+    "Page",
+    "PageSize",
+    "PolarimetricAccuracy",
+    "Proposal",
+    "Recipe",
+    "SpatialSampling",
+    "SpectralSampling",
+    "SummitSoftwareVersion",
+    "TargetType",
+    "TemporalSampling",
+    "WavelengthBand",
+    "WorkflowName",
+    "WorkflowVersion",
+]
 
 
 # SimpleAttrs

diff --git a/dkist/net/client.py b/dkist/net/client.py
@@ -28,7 +28,7 @@
 from . import attrs as dattrs
 from .attr_walker import walker
 
-__all__ = ["DKISTQueryResponseTable", "DKISTClient"]
+__all__ = ["DKISTClient", "DKISTQueryResponseTable"]
 
 
 class DKISTQueryResponseTable(QueryResponseTable):

diff --git a/dkist/net/globus/endpoints.py b/dkist/net/globus/endpoints.py
@@ -11,7 +11,7 @@
 
 from .auth import ensure_globus_authorized, get_refresh_token_authorizer
 
-__all__ = ["get_data_center_endpoint_id", "get_endpoint_id", "get_directory_listing"]
+__all__ = ["get_data_center_endpoint_id", "get_directory_listing", "get_endpoint_id"]
 
 
 def get_transfer_client(force_reauth=False):

diff --git a/dkist/net/globus/tests/test_transfer.py b/dkist/net/globus/tests/test_transfer.py
@@ -130,7 +130,6 @@ def test_process_event_list(transfer_client, mock_task_event_list):
     assert all(isinstance(e, tuple) for e in events)
     assert all(all(isinstance(item, tuple) for item in e) for e in events)
 
-    print(events)
     assert len(json_events) == 1
     assert isinstance(json_events, tuple)
     assert isinstance(json_events[0], dict)

diff --git a/dkist/net/globus/transfer.py b/dkist/net/globus/transfer.py
@@ -15,7 +15,7 @@
 from .endpoints import (auto_activate_endpoint, get_data_center_endpoint_id,
                         get_endpoint_id, get_local_endpoint_id, get_transfer_client)
 
-__all__ = ["watch_transfer_progress", "start_transfer_from_file_list"]
+__all__ = ["start_transfer_from_file_list", "watch_transfer_progress"]
 
 
 def start_transfer_from_file_list(

diff --git a/dkist/utils/inventory.py b/dkist/utils/inventory.py
@@ -7,7 +7,7 @@
 
 from astropy.table import Table
 
-__all__ = ["dehumanize_inventory", "humanize_inventory", "INVENTORY_KEY_MAP"]
+__all__ = ["INVENTORY_KEY_MAP", "dehumanize_inventory", "humanize_inventory"]
 
 
 class DefaultMap(defaultdict):