dkist-processing-common 11.1.0rc1__py3-none-any.whl → 11.2.0__py3-none-any.whl

dkist_processing_common/models/graphql.py

@@ -1,6 +1,7 @@
 """GraphQL Data models for the metadata store api."""
 from pydantic import BaseModel
 from pydantic import ConfigDict
+from pydantic import field_serializer
 from pydantic import field_validator
 from pydantic import Json
 
@@ -129,6 +130,10 @@ class RecipeRunResponse(GraphqlBaseModel):
             return RecipeRunConfiguration()
         return RecipeRunConfiguration.model_validate(value)
 
+    @field_serializer("configuration")
+    def _serialize_as_basemodel(self, config: RecipeRunConfiguration):
+        return config.model_dump()
+
 
 class RecipeRunMutationResponse(GraphqlBaseModel):
     """Recipe run mutation response."""

dkist_processing_common/tasks/assemble_movie.py

@@ -2,10 +2,10 @@
 import logging
 from abc import ABC
 from abc import abstractmethod
+from importlib.resources import files
 from typing import Literal
 
 import numpy as np
-import pkg_resources
 from matplotlib import colormaps
 from moviepy import VideoClip
 from PIL import Image
@@ -66,7 +66,7 @@ class AssembleMovie(WorkflowTaskBase, ABC):
     MINIMUM_DURATION = 10  # seconds
     MAXIMUM_DURATION = 60  # seconds
     FPS = 15
-    FONT_FILE = pkg_resources.resource_filename("dkist_processing_common", "fonts/Lato-Regular.ttf")
+    FONT_FILE = files("dkist_processing_common").joinpath("fonts/Lato-Regular.ttf")
     TEXT_MARGIN_PX = 5
     MPL_COLOR_MAP = "viridis"
 

dkist_processing_common/tasks/mixin/quality/_metrics.py

@@ -1365,13 +1365,22 @@ class _WavecalQualityMixin:
         wcs = WCS(best_fit_header)
         best_fit_wavelength = wcs.spectral.pixel_to_world(np.arange(input_spectrum.size))
 
+        finite_idx = (
+            np.isfinite(input_wavelength)
+            * np.isfinite(input_spectrum)
+            * np.isfinite(best_fit_wavelength)
+            * np.isfinite(best_fit_atlas)
+            * np.isfinite(normalized_residuals)
+            * np.isfinite(weight_data)
+        )
+
         data = {
-            "input_wavelength_nm": input_wavelength.to_value(u.nm).tolist(),
-            "input_spectrum": input_spectrum.tolist(),
-            "best_fit_wavelength_nm": best_fit_wavelength.to_value(u.nm).tolist(),
-            "best_fit_atlas": best_fit_atlas.tolist(),
-            "normalized_residuals": normalized_residuals.tolist(),
-            "weights": None if weights is None else weight_data.tolist(),
+            "input_wavelength_nm": input_wavelength.to_value(u.nm)[finite_idx].tolist(),
+            "input_spectrum": input_spectrum[finite_idx].tolist(),
+            "best_fit_wavelength_nm": best_fit_wavelength.to_value(u.nm)[finite_idx].tolist(),
+            "best_fit_atlas": best_fit_atlas[finite_idx].tolist(),
+            "normalized_residuals": normalized_residuals[finite_idx].tolist(),
+            "weights": None if weights is None else weight_data[finite_idx].tolist(),
         }
 
         self._record_values(values=data, tags=[Tag.quality(MetricCode.wavecal_fit)])

dkist_processing_common/tasks/write_l1.py

@@ -230,7 +230,13 @@ class WriteL1Frame(WorkflowTaskBase, MetadataStoreMixin, ABC):
         header = self.add_contributing_id_headers(header=header)
         header["MANPROCD"] = self.workflow_had_manual_intervention
         header["PRODUCT"] = self.compute_product_id(header["IDSOBSID"], header["PROCTYPE"])
-        # Spectral line keywords
+        return header
+
+    def add_spectral_line_headers(
+        self,
+        header: fits.Header,
+    ) -> fits.Header:
+        """Add datacenter table keys relating to spectral lines."""
         wavelength_range = self.get_wavelength_range(header=header)
         spectral_lines = get_spectral_lines(
             wavelength_min=wavelength_range.min,
@@ -364,6 +370,8 @@ class WriteL1Frame(WorkflowTaskBase, MetadataStoreMixin, ABC):
         header = self.add_doc_headers(header=header)
         # Add the dataset headers (abstract - implement in instrument task)
         header = self.add_dataset_headers(header=header, stokes=stokes_param)
+        # Add the spectral line headers
+        header = self.add_spectral_line_headers(header=header)
         # Remove any headers not contained in spec 214
         header = remove_spec_122_keys_and_spec_214_l0_keys(input_headers=header)
         # Remove any keys referring to axes that don't exist

dkist_processing_common/tests/test_quality_mixin.py

@@ -1201,12 +1201,16 @@ def wavecal_input_wavelength() -> u.Quantity:
 
 @pytest.fixture(scope="session")
 def wavecal_input_spectrum(wavecal_input_wavelength) -> np.ndarray:
-    return (wavecal_input_wavelength.value - wavecal_input_wavelength.size // 2) ** 2 + 10.0
+    spec = (wavecal_input_wavelength.value - wavecal_input_wavelength.size // 2) ** 2 + 10.0
+    spec[spec.size // 2] = np.nan
+    return spec
 
 
 @pytest.fixture(scope="session")
 def wavecal_weights(wavecal_input_wavelength) -> np.ndarray:
-    return np.arange(wavecal_input_wavelength.size)
+    weights = np.arange(wavecal_input_wavelength.size, dtype=float)
+    weights[0] = np.inf
+    return weights
 
 
 @pytest.fixture(scope="session")

dkist_processing_common/tests/test_workflow_task_base.py

@@ -2,12 +2,11 @@ import json
 import logging
 import re
 import tomllib
-from dataclasses import asdict
+from importlib.metadata import version
 from pathlib import Path
 from string import ascii_uppercase
 
 import pytest
-from pkg_resources import get_distribution
 from sqids import Sqids
 
 import dkist_processing_common
@@ -272,7 +271,7 @@ def test_library_versions(provenance_task, package_dependencies):
     #   installed packages.
     for package in package_dependencies:
         assert package in libraries
-        assert libraries[package] == get_distribution(package).version
+        assert libraries[package] == version(package)
 
 
 def test_record_provenance(provenance_task):

dkist_processing_common/tests/test_write_l1.py

@@ -677,7 +677,7 @@ def test_spectral_line_keys(write_l1_task, mocker, fake_gql_client):
         new=fake_gql_client,
     )
     task, _, header = write_l1_task
-    header = task.add_datacenter_headers(header=header, hdu_size=1024, stokes="I")
+    header = task.add_spectral_line_headers(header=header)
     assert header["SPECLN01"] == "Fe XIII (1079.8 nm)"
     assert header["SPECLN02"] == "He I (1083.0 nm)"
     assert header["NSPECLNS"] == 2

{dkist_processing_common-11.1.0rc1.dist-info → dkist_processing_common-11.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dkist-processing-common
-Version: 11.1.0rc1
+Version: 11.2.0
 Summary: Common task classes used by the DKIST science data processing pipelines
 Author-email: NSO / AURA <dkistdc@nso.edu>
 License: BSD-3-Clause

{dkist_processing_common-11.1.0rc1.dist-info → dkist_processing_common-11.2.0.dist-info}/RECORD

@@ -1,5 +1,4 @@
 changelog/.gitempty,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-changelog/255.misc.rst,sha256=Y0CIOQbdAK8Emlz6wQaX59hg1Hr9QDhDMv7-Z-OpbAU,255
 dkist_processing_common/__init__.py,sha256=490Fwm_GgqpwriQlsYfKcLUZNhZ6GkINtJqcYSIEKoU,319
 dkist_processing_common/config.py,sha256=IcpaD_NvHZU-aLlUNOTdRC4V7ADIvVQwrZ2dHhIr4NY,4247
 dkist_processing_common/manual.py,sha256=mrW__HupEZMYOxUxfKsdsTI3TfOrOrWHS9yXC_835W4,7023
@@ -27,7 +26,7 @@ dkist_processing_common/models/dkist_location.py,sha256=3cbN6As60tJa0uoOSNFNnz2s
 dkist_processing_common/models/fits_access.py,sha256=Au9JROwhVla9zb_u0dN8mIWiSJd_Pca0oOr4N1hN0HY,4113
 dkist_processing_common/models/flower_pot.py,sha256=59C5uGYKyMyncqQYxhzDZWl8k1DRZFB6s9RF-HFp9mY,5128
 dkist_processing_common/models/fried_parameter.py,sha256=ro_H2Eo3I88lRf1wJjZfTc_XOjhgLt4whIQR_sjAFbM,1609
-dkist_processing_common/models/graphql.py,sha256=RcFlSDTtV6TwHExb9Y89NhTfLMx2ysdqecY7kHuRwg0,5690
+dkist_processing_common/models/graphql.py,sha256=ahCGiDZlbx31_SFfOLyS-qzVzxYvd18zUEAGZWYGjCM,5874
 dkist_processing_common/models/input_dataset.py,sha256=stQa_lbFPr2tmOUpQgpDuwM0-DiIDV3zYwyawh01cKc,4172
 dkist_processing_common/models/message.py,sha256=DRW7Qhl01dF5KagcqLta5U-uzdOMewrsHvMatDT6jnk,1684
 dkist_processing_common/models/message_queue_binding.py,sha256=ROQ2ZQE3TCr4gVbz4WggvUSExAiWP8SD_GjjQl482M8,1012
@@ -54,7 +53,7 @@ dkist_processing_common/parsers/time.py,sha256=jcyhID_6ldkLZMBO9gqzYJ-oAD1kmFOTh
 dkist_processing_common/parsers/unique_bud.py,sha256=ht_1Oi1OL7otZOMXcoVilmDSYVCC7KZ7Fj-TfKDFcqw,3173
 dkist_processing_common/parsers/wavelength.py,sha256=Cb0opJmFRLQVPIMC5YRSDeygWjvQGS9avYrFhLsBekY,546
 dkist_processing_common/tasks/__init__.py,sha256=uH8DTiQP-cx4vMK53S4LYGZGmbip5s0kWORvZBrSNj8,624
-dkist_processing_common/tasks/assemble_movie.py,sha256=9K4sgXyRKaX7UsFBIs138pG3AtClwLLopYw3ZQY3ok4,12771
+dkist_processing_common/tasks/assemble_movie.py,sha256=6tb_vOwXZuQEhGBK8LoBaGnYQnpv_FiE9DVa_cLjreE,12771
 dkist_processing_common/tasks/base.py,sha256=k_IJR5sVV6ennX0sbeb0C6dciqshdY7CKjtWHy_adm8,13143
 dkist_processing_common/tasks/l1_output_data.py,sha256=IM-nvGaTM5r-z-9vHr2wovPVUpuNCah-cWIFMO2fcII,10576
 dkist_processing_common/tasks/output_data_base.py,sha256=CC1TnCrChi8_iuMymr425CJqpY4jCggnVUMfqzFkpnw,3682
@@ -64,7 +63,7 @@ dkist_processing_common/tasks/teardown.py,sha256=e4LKnphJDYDVDAez2tH7MxpZgCmxYsK
 dkist_processing_common/tasks/transfer_input_data.py,sha256=8dDOfnT46qavGW-6fy-FT9LVb0TXANSpk1WpACpWK70,5787
 dkist_processing_common/tasks/trial_catalog.py,sha256=Y3DKstRfMS8nWWtJFMB0MUVPlZ1jWS_2jhJGMWwxy50,8748
 dkist_processing_common/tasks/trial_output_data.py,sha256=ehuts_L_GrnTRsVNeoh1N2kgQhId6_FnrMEiJ_2X_Jc,6834
-dkist_processing_common/tasks/write_l1.py,sha256=EtCy7vltkZsZgoCAQybKgI35nmQncm0XrhIKxGJGSyc,22615
+dkist_processing_common/tasks/write_l1.py,sha256=KSb62iTYP21XBqIYVQVx6X8vhpcLn403EgGG4DJ2wag,22876
 dkist_processing_common/tasks/mixin/__init__.py,sha256=-g-DQbU7m1bclJYuFe3Yh757V-35GIDTbstardKQ7nU,68
 dkist_processing_common/tasks/mixin/globus.py,sha256=QAV8VElxMAqxJ2KSB_bJaraceovYfjHXjOdocrTCkIA,6592
 dkist_processing_common/tasks/mixin/interservice_bus.py,sha256=I7BUh0o8AEX-FZv7gxCts6is0uq9lycWjtTB2KqwBrU,1080
@@ -72,7 +71,7 @@ dkist_processing_common/tasks/mixin/metadata_store.py,sha256=yTKijpQ-tNx_H2V_9Hs
 dkist_processing_common/tasks/mixin/object_store.py,sha256=Vn4l2XuCimii9Fc3gM-pQGIkTKMv_ldqljlxkLesZLU,3236
 dkist_processing_common/tasks/mixin/quality/__init__.py,sha256=Bgu-DHW7yXLiehglldOCWluEkAP5qh0Hp1F30rh5NFw,383
 dkist_processing_common/tasks/mixin/quality/_base.py,sha256=U1AEhj6OtF4YEdTkKWcgmoH6zrz6tYNjNXnmVU24L70,8491
-dkist_processing_common/tasks/mixin/quality/_metrics.py,sha256=sQspAXoeSA2dQSX6wQuJKGON2XFilB5t29kNXhSLMmY,59844
+dkist_processing_common/tasks/mixin/quality/_metrics.py,sha256=kBZqvYvCKx0ar1tYw-f1AYNMORekqMERo73fsZS3QQU,60210
 dkist_processing_common/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dkist_processing_common/tests/conftest.py,sha256=xTmu87MZSPIcucg9UCH88OimdqgjE5VSc-n-fSFbtjI,22319
 dkist_processing_common/tests/mock_metadata_store.py,sha256=ZVxAtVoW8ayEceafeR8yJbGdFZsw13Eyf1Z2-rwGZDM,8260
@@ -95,7 +94,7 @@ dkist_processing_common/tests/test_parameters.py,sha256=kNzX89vfrNRJ8d9rusMVv4DM
 dkist_processing_common/tests/test_parse_l0_input_data.py,sha256=SMNV1qyQTvnMx94MCNsiA-RyS9uxaxIABEDDxsuVzqY,10629
 dkist_processing_common/tests/test_publish_catalog_messages.py,sha256=l6Wga1s2wNBIf4wGZ78ZIO_rtqjdidmtvlN9nMnQUAs,3222
 dkist_processing_common/tests/test_quality.py,sha256=vomy2YSPadKqJj2tG8sCs-UkQVvfKus7Cum7_Hpee4I,10257
-dkist_processing_common/tests/test_quality_mixin.py,sha256=NVpHCHVAO_kbM1hfgOCYYzq88zZP2jOEEjkOfaS8jcY,55120
+dkist_processing_common/tests/test_quality_mixin.py,sha256=Kaj4gFglRiWrYaL_USnsyK8-5-wrMQuG36nU8YSXus0,55229
 dkist_processing_common/tests/test_scratch.py,sha256=7f28FMiSskSNX-bkRSrpJf2u1HQIbSvYajbjkeGMF9s,16481
 dkist_processing_common/tests/test_stems.py,sha256=ini5dylLT5ioWKKWd1uu6kwx8Tf3aEnKKaGjf46a_GI,32649
 dkist_processing_common/tests/test_submit_dataset_metadata.py,sha256=LHEyjoIxJHXXssqKkr8Qn1NzzHD1FLJiD3lP8yaLiXU,3764
@@ -107,8 +106,8 @@ dkist_processing_common/tests/test_transfer_input_data.py,sha256=bLBQs7qiYKJz3MN
 dkist_processing_common/tests/test_transfer_l1_output_data.py,sha256=PVGDJBEUk4kAeu8ivrhlCE7yd29R18t9kZLFx-mpBwY,2063
 dkist_processing_common/tests/test_trial_catalog.py,sha256=y5SDjns8CoAY_Wr3pgkYwvRB-ieRXavbF5_2AZ4NFNM,6777
 dkist_processing_common/tests/test_trial_output_data.py,sha256=TUPycx_hDgyQj_k6xqDQXgS25yrz78vh78SArZHHm0g,12008
-dkist_processing_common/tests/test_workflow_task_base.py,sha256=Z5aPW5LQtS0UWJiYho4X0r-2gPLfzpkmMwfmaoFLjMg,10517
-dkist_processing_common/tests/test_write_l1.py,sha256=Uj6eOCcmfrTTfRY7pgkS2tqaWH_9RFDg8KAFRJCLSQw,28020
+dkist_processing_common/tests/test_workflow_task_base.py,sha256=pxdR_qBWINty82rRhSt_nhaC0g-wBMWMoF4R3RUWSXM,10465
+dkist_processing_common/tests/test_write_l1.py,sha256=LORwt8Eb2myfcFqNWTLNWERvZ1fAD9FgonzJEF76ABI,27996
 docs/Makefile,sha256=qnlVz6PuBqE39NfHWuUnHhNEA-EFgT2-WJNNNy9ttfk,4598
 docs/changelog.rst,sha256=S2jPASsWlQxSlAPqdvNrYvhk9k3FcFWNXFNDYXBSjl4,120
 docs/conf.py,sha256=FkX575cqTqZGCcLAjg2MlvE8Buj1Vt3CpHNgZxG256E,1890
@@ -117,7 +116,7 @@ docs/landing_page.rst,sha256=aPAuXFhBx73lEZ59B6E6JXxkK0LlxzD0n-HXqHrfumQ,746
 docs/make.bat,sha256=mBAhtURwhQ7yc95pqwJzlhqBSvRknr1aqZ5s8NKvdKs,4513
 docs/requirements.txt,sha256=Kbl_X4c7RQZw035YTeNB63We6I7pvXFU4T0Uflp2yDY,29
 licenses/LICENSE.rst,sha256=piZaQplkzOMmH1NXg6QIdo9wwo9pPCoHkvm2-DmH76E,1462
-dkist_processing_common-11.1.0rc1.dist-info/METADATA,sha256=dRRRLyGbSfnb7REoyDKxbfdrs8x9-iJelOzGHv9fcOg,7204
-dkist_processing_common-11.1.0rc1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-dkist_processing_common-11.1.0rc1.dist-info/top_level.txt,sha256=LJhd1W-Vn90K8HnQDIE4r52YDpUjjMWDnllAWHBByW0,48
-dkist_processing_common-11.1.0rc1.dist-info/RECORD,,
+dkist_processing_common-11.2.0.dist-info/METADATA,sha256=B6nAxP9DTElEykVWOBFt9SEAsq_CJS2NIxneZXBaj6c,7201
+dkist_processing_common-11.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+dkist_processing_common-11.2.0.dist-info/top_level.txt,sha256=LJhd1W-Vn90K8HnQDIE4r52YDpUjjMWDnllAWHBByW0,48
+dkist_processing_common-11.2.0.dist-info/RECORD,,

changelog/255.misc.rst

@@ -1,3 +0,0 @@
-Create a factory for custom `FakeGQLClient` used in tests.  The factory and associated default returns live in a
-new `mock_metadata_store.py` module in the tests directory.  `FakeGQLClient` is now a test fixture and does not need to
-be imported in tests.