Merge branch 'benchmarking' into fitsioloader-plus-new-benchmark

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "6d6729b22066ef890e70c37438da70cac33e03b4",
+  "commit": "c79fc5bff74958e24c9a925a330b8d3aa138f4ce",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/codspeed.yml

@@ -15,7 +15,11 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
-      - run: python -m pip install .[tests] pytest-codspeed fitsio
+      - run: python -m pip install .[tests] pytest-codspeed 'numpy<2' fitsio
+      - run: |
+          parfive https://g-a36282.cd214.a567.data.globus.org/user_tools_tutorial_data/BKPLX_stokesI.tar
+          mkdir -p $HOME/dkist_data/BKPLX
+          tar -xv -f BKPLX_stokesI.tar --directory $HOME/dkist_data/BKPLX
       - name: Run benchmarks
         uses: CodspeedHQ/action@v2
         with:

.github/workflows/sub_package_update.yml

@@ -28,11 +28,6 @@ jobs:
             branch: cruft/update
             commit-message: "Automatic package template update"
             title: Updates from the package template
-          - add-paths: .cruft.json
-            body: reject these changes for this repo.
-            branch: cruft/reject
-            commit-message: "Reject this package template update"
-            title: Reject new updates from package template
 
     steps:
       - uses: actions/checkout@v4
@@ -42,7 +37,7 @@ jobs:
           python-version: "3.11"
 
       - name: Install Cruft
-        run: python -m pip install cruft
+        run: python -m pip install git+https://github.com/Cadair/cruft@patch-p1
 
       - name: Check if update is available
         continue-on-error: false

.gitignore

@@ -76,6 +76,7 @@ instance/
 docs/_build/
 # automodapi
 docs/api
+docs/sg_execution_times.rst
 
 # PyBuilder
 .pybuilder/

.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: "v0.3.5"
+    rev: "v0.4.8"
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -26,10 +26,10 @@ repos:
       - id: mixed-line-ending
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|.asdf|.json|.hdr)$"
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         args: [ "--write-changes", "-D", "-", "-D", ".codespell-dict.txt"]
 ci:
   autofix_prs: false
-  autoupdate_schedule: "weekly"
+  autoupdate_schedule: "quarterly"

CHANGELOG.rst

@@ -378,7 +378,7 @@ Bug Fixes
 Trivial/Internal Changes
 ------------------------
 
-- Migate to the asdf 2.8+ ``Converter`` interface, this bumps various
+- Migrate to the asdf 2.8+ ``Converter`` interface, this bumps various
   dependencies but should have no effect on reading or writing asdf files. (`#152 <https://github.com/DKISTDC/dkist/pull/152>`_)
 
 

dkist/conftest.py

@@ -338,3 +338,9 @@ def visp_dataset_no_headers(tmp_path_factory):
         with open(vispdir / "test_visp_no_headers.asdf", mode="wb") as afo:
             afo.write(gfo.read())
     return load_dataset(vispdir / "test_visp_no_headers.asdf")
+
+
+@pytest.fixture(scope="session")
+def real_visp(tmp_path_factory):
+    vispdir = Path.home() / "dkist_data" / "BKPLX"
+    return load_dataset(vispdir)

dkist/net/attrs.py

@@ -301,10 +301,10 @@ def __init__(self, bottom_left, *, top_right=None, width: _u.deg = None,
         bottom_left = bottom_left.transform_to(_Helioprojective(observer="earth"))
         top_right = top_right.transform_to(_Helioprojective(observer="earth"))
 
-        self.hpc_bounding_box_arcsec = ((bottom_left.Tx.to_value(_u.arcsec),
-                                         bottom_left.Ty.to_value(_u.arcsec)),
-                                        (top_right.Tx.to_value(_u.arcsec),
-                                         top_right.Ty.to_value(_u.arcsec)))
+        self.hpc_bounding_box_arcsec = ((float(bottom_left.Tx.to_value(_u.arcsec)),
+                                         float(bottom_left.Ty.to_value(_u.arcsec))),
+                                        (float(top_right.Tx.to_value(_u.arcsec)),
+                                         float(top_right.Ty.to_value(_u.arcsec))))
 
         self.search_type = search
 

dkist/tests/test_benchmarks.py

@@ -35,6 +35,6 @@ def plot_and_save_fig(ds=visp_dataset_no_headers, axes=axes):
 
 
 @pytest.mark.benchmark
-def test_dataset_compute_data(benchmark, small_visp_dataset):
-
-    benchmark(small_visp_dataset.data.compute)
+def test_dataset_compute_data(benchmark, real_visp):
+    ds = real_visp[0, :5]
+    benchmark(ds.data.compute)

dkist/utils/inventory.py

@@ -77,7 +77,7 @@ def __missing__(self, key):
 
 
 def _key_clean(key):
-    key = re.sub("[%s]" % re.escape(string.punctuation), "_", key)
+    key = re.sub(f"[{re.escape(string.punctuation)}]", "_", key)
     key = key.replace(" ", "_")
     key = "".join(char for char in key
                     if char.isidentifier() or char.isnumeric())

pyproject.toml

@@ -48,12 +48,12 @@ tests = [
   "pytest-doctestplus",
   "pytest-cov",
   "pytest-remotedata",
-  "pytest-cov",
   "pytest-mock",
   "pytest-mpl",
   "pytest-httpserver",
   "pytest-filter-subpackage",
   "pytest-benchmark",
+  "pytest-xdist",
   "hypothesis",
   "tox",
   "pydot",
@@ -85,6 +85,7 @@ zip-safe = false
 include-package-data = true
 
 [tool.setuptools.packages.find]
+exclude = ["dkist._dev*"]
 
 [tool.setuptools_scm]
 write_to = "dkist/_version.py"

pytest.ini

@@ -14,17 +14,23 @@ norecursedirs =
     .history
     dkist/extern
 doctest_plus = enabled
-doctest_optionflags = NORMALIZE_WHITESPACE FLOAT_CMP ELLIPSIS
+doctest_optionflags =
+    NORMALIZE_WHITESPACE
+    FLOAT_CMP
+    ELLIPSIS
 text_file_format = rst
-addopts = --doctest-rst  -p no:unraisableexception -p no:threadexception
-markers =
-    online: marks this test function as needing online connectivity.
-    figure: marks this test function as using hash-based Matplotlib figure verification. This mark is not meant to be directly applied, but is instead automatically applied when a test function uses the @sunpy.tests.helpers.figure_test decorator.
-    benchmark: marks this test as a benchmark
 # Disable internet access for tests not marked remote_data
 remote_data_strict = True
 asdf_schema_root = dkist/io/asdf/resources/
 asdf_schema_tests_enabled = true
+markers =
+    online: marks this test function as needing online connectivity.
+    figure: marks this test function as using hash-based Matplotlib figure verification. This mark is not meant to be directly applied, but is instead automatically applied when a test function uses the @sunpy.tests.helpers.figure_test decorator.
+    benchmark: marks this test as a benchmark
+addopts =
+    --doctest-rst
+    -p no:unraisableexception
+    -p no:threadexception
 filterwarnings =
     # Turn all warnings into errors so they do not pass silently.
     error
@@ -52,7 +58,7 @@ filterwarnings =
     # debugging.
     ignore:the imp module is deprecated in favour of importlib:DeprecationWarning:ipykernel.iostream
     # Ignore warnings about asdf versions
-    ignore:File.*asdf.extension.BuiltinExtension.*:asdf.exceptions.AsdfWarning
+    ignore:File.*asdf.extension.BuiltinExtension.*
     # pytest / asdf interaction
     ignore:The .* argument to AsdfSchemaFile is deprecated
     # gwcs main has the wrong version number: https://github.com/spacetelescope/gwcs/issues/399
@@ -71,7 +77,7 @@ filterwarnings =
     ignore:The loop argument is deprecated since Python 3.8, and scheduled for removal in Python 3.10.
     ignore:Subclassing validator classes is not intended to be part of their public API
     # Ignore warning so gwcs 0.18.3 can load
-    ignore:Converter handles multiple tags for this extension:asdf.exceptions.AsdfWarning
+    ignore:Converter handles multiple tags for this extension
     # https://github.com/pandas-dev/pandas/issues/54466
     ignore:\nPyarrow will become a required dependency of pandas in the next major release of pandas:DeprecationWarning
     # This seems to be coming out of pandas

tox.ini

@@ -8,9 +8,9 @@ envlist =
     py{310,311,312}
     py312-devdeps
     py310-oldestdeps
+    py312-benchmarks
     build_docs{,-notebooks}
     codestyle
-    benchmarks
 
 [testenv]
 pypi_filter = https://raw.githubusercontent.com/sunpy/sunpy/main/.test_package_pins.txt
@@ -34,8 +34,6 @@ set_env =
     MPLBACKEND = agg
     COLUMNS = 180
     devdeps: PIP_EXTRA_INDEX_URL = https://pypi.anaconda.org/astropy/simple https://pypi.anaconda.org/scientific-python-nightly-wheels/simple
-    # Define the base test command here to allow us to add more flags for each tox factor
-    PYTEST_COMMAND = pytest -vvv -r fEs --pyargs dkist --cov-report=xml --cov=dkist --cov-config={toxinidir}/.coveragerc {toxinidir}/docs --benchmark-skip
 deps =
     # For packages which publish nightly wheels this will pull the latest nightly
     devdeps: astropy>=0.0.dev0
@@ -59,15 +57,22 @@ commands_pre =
     pip install fitsio
     pip freeze --all --no-input
 commands =
-    # To run different commands for different factors exclude the factor from the default command like this
-    # !online: {env:PYTEST_COMMAND} {posargs}
-    # Then specify a specific one like this
-    # online: {env:PYTEST_COMMAND} --remote-data=any {posargs}
-    {env:PYTEST_COMMAND} \
+    # To amend the pytest command for different factors you can add a line
+    # which starts with a factor like `online: --remote-data=any \`
+    # If you have no factors which require different commands this is all you need:
+    pytest \
+    -vvv \
+    -r fEs \
+    --pyargs dkist \
+    --cov-report=xml \
+    --cov=dkist \
+    --cov-config={toxinidir}/.coveragerc \
+    {toxinidir}/docs \
     online: --remote-data=any \
-    # It's not possible to test the new schemas with the oldest dependencies
-    # as the new schemas require new dependent schemas
-    oldestdeps: -o asdf_schema_tests_enabled=false
+    !benchmarks: --benchmark-skip \
+    benchmarks: -m benchmark \
+    benchmarks: --benchmark-autosave \
+    oldestdeps: -o asdf_schema_tests_enabled=false \
     {posargs}
 
 [testenv:codestyle]
@@ -89,11 +94,15 @@ extras =
 commands =
     pip freeze --all --no-input
     # Disable parallel here due to https://github.com/astropy/astropy/issues/14916
-    !notebooks: sphinx-build -j 1 --color -W --keep-going -b html -d _build/.doctrees . _build/html -D nb_execution_mode=off {posargs}
-    notebooks: sphinx-build -j 1 --color -W --keep-going -b html -d _build/.doctrees . _build/html {posargs}
+    sphinx-build \
+    -j 1 \
+    --color \
+    -W \
+    --keep-going \
+    -b html \
+    -d _build/.doctrees \
+    . \
+    _build/html \
+    !notebooks: -D nb_execution_mode=off \
+    {posargs}
     python -c 'import pathlib; print("Documentation available under file://\{0\}".format(pathlib.Path(r"{toxinidir}") / "docs" / "_build" / "index.html"))'
-
-[testenv:benchmarks]
-description = Run benchmarks on PR and compare against main to ensure there are no performance regressions
-allowlist_externals=git
-commands = {env:PYTEST_COMMAND} -m benchmark --benchmark-autosave