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Merge main #19

Merged
merged 431 commits into from
Dec 3, 2024
Merged

Merge main #19

merged 431 commits into from
Dec 3, 2024

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fhernandezvivanco
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  • Merges the upstream mxcubecore develop branch into the Australian Synchtrotron main Branch
  • Updates the Aperture class which was refectored in the upstream branch

marcus-oscarsson and others added 30 commits July 8, 2024 14:18
Bumps [certifi](https://github.com/certifi/python-certifi) from 2023.5.7 to 2024.7.4.
- [Commits](certifi/python-certifi@2023.05.07...2024.07.04)

---
updated-dependencies:
- dependency-name: certifi
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [zipp](https://github.com/jaraco/zipp) from 3.15.0 to 3.19.1.
- [Release notes](https://github.com/jaraco/zipp/releases)
- [Changelog](https://github.com/jaraco/zipp/blob/main/NEWS.rst)
- [Commits](jaraco/zipp@v3.15.0...v3.19.1)

---
updated-dependencies:
- dependency-name: zipp
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
* Removed Device and Equipment objects and replaced them with HardwareObject

* Removed Device and Equipment objects and replaced them with HardwareObject for configuration files

* Fixed ISARA test

* Fixed device_uri tags
Bumps [setuptools](https://github.com/pypa/setuptools) from 67.8.0 to 70.0.0.
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v67.8.0...v70.0.0)

---
updated-dependencies:
- dependency-name: setuptools
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
The CatsMaintMockup does not inherit Equipment class anymore.
Don't import devtools module for the test collection queue entry.
Mxcube-core does not list devtools package as a dependency.

Also remove unused import of HardwareRepository.
New MachInfo hardware object, for using at BioMAX and MicroMAX.

Based on older HWO used at BioMAX, but updated to follow the
new AbstractMachineInfo API.
 - mark python 3.11.* as supported for this package.
 - require later version of greenlet package, as version 1.1.3
   does not work with python 3.11.
 - require later versions of gevent and gipc packages, to statisfy
   greenlet 3.* requirmets.
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github-actions bot commented Dec 2, 2024

Coverage

Coverage Report •
FileStmtsMissCoverMissing
mxcubecore
   BaseHardwareObjects.py54013375%63–67, 136, 166–174, 304, 626, 647, 664–668, 701–708, 733, 740–741, 750, 795–802, 822, 844, 872, 880, 942, 951, 991, 998, 1041, 1045–1048, 1066–1081, 1091–1093, 1103–1105, 1133, 1141–1145, 1148, 1165–1168, 1171–1177, 1180–1185, 1188, 1192–1196, 1206, 1209–1217, 1220–1224, 1231–1234, 1237, 1264–1267, 1270–1277, 1280–1284, 1287–1299, 1302–1304, 1307, 1310, 1313–1317, 1336, 1340, 1343, 1347, 1351, 1355, 1359, 1363
   CommandContainer.py46621454%102–103, 226–227, 386–397, 403–414, 430–438, 459–460, 470–471, 477–488, 496–517, 534–535, 547, 555, 597–598, 653–670, 673–684, 690–701, 716–724, 746–747, 757–758, 766–852, 857–874, 880–891, 902–903, 913–978
   HardwareObjectFileParser.py2418764%50–61, 106, 110–111, 120–134, 137–138, 173, 185, 221, 230, 232, 236, 249–250, 261, 265, 278–279, 284–288, 290–295, 297–298, 308–311, 335, 346, 361–368, 372–374, 390–391, 406–407, 416–419, 430–442, 447–452, 460, 469, 475–480, 491, 494
mxcubecore/Command
   Epics.py1199223%27–28, 45–81, 86–138, 141–147, 151–158, 162, 173–179, 189, 192, 195, 198–204, 211–220, 223, 226, 229, 232
   Exporter.py1449038%46–51, 79–84, 91, 95–96, 100, 104–105, 109, 116–119, 126–151, 160, 164–178, 187–191, 194–203, 213, 220, 236–247, 251–256, 263–264, 271, 278
   Mockup.py281450%42–45, 48, 51, 54, 57, 62–65, 68, 71–72, 76
   Pool.py1651650%21–290
   Sardana.py2872870%24–524
   Spec.py63630%21–120
   Taco.py88880%21–186
   Tango.py1809746%48–49, 60–64, 67–80, 83–99, 106–107, 111, 115, 119, 124–138, 143, 188–195, 210–225, 231–234, 241–243, 251–256, 260–273, 276–290, 324–325, 332, 334, 336, 342–355, 358, 361
   Tine.py1541540%21–310
mxcubecore/Command/exporter
   ExporterClient.py1168527%57–64, 71–80, 87–96, 103–105, 117–132, 143–151, 159–163, 171–175, 184–191, 200–201, 210–216, 225–232
   ExporterStates.py21210%24–50
   MDEvents.py1491490%1–250
   StandardClient.py21617718%50, 57–66, 82–96, 100–104, 108–114, 118–127, 134–138, 142–144, 155–184, 195–212, 219–222, 226, 230–236, 243–244, 248–290, 297–303, 312–324, 333–345, 356–360
mxcubecore/HardwareObjects
   Attenuators.py28280%21–60
   BeamInfo.py98980%22–254
   Beamline.py32711365%157–171, 272–279, 311, 333, 377, 388, 410, 466, 478, 489, 504, 548, 559, 572, 594, 605, 616, 627, 638, 649, 660, 672, 687, 698, 711, 722, 737, 748, 759, 775, 791, 808–893, 900–910, 913, 916–927
   BeamlineActions.py2102100%1–329
   Bliss.py35350%5–94
   BlissActuator.py31310%11–55
   BlissEnergy.py58580%38–146
   BlissHutchTrigger.py84840%1–135
   BlissMotor.py77770%29–199
   BlissMotorWPositions.py69690%1–119
   BlissNState.py88880%31–173
   BlissShutter.py61610%33–141
   Cats90.py6986980%22–1532
   CatsBessy.py2582580%1–480
   CatsMaint.py2952950%15–840
   CentringMath.py1581580%1–252
   DataPublisher.py1351350%19–397
   DozorOnlineProcessing.py31310%21–82
   EDNACharacterisation.py3123120%1–520
   EMBLFlexHCD.py3903900%31–699
   EMBLFlexHarvester.py1631630%28–327
   ESRFLIMS.py1061060%1–204
   EdnaWorkflow.py1731730%1–269
   Energy.py1121120%1–202
   ExporterMotor.py1061060%38–267
   ExporterNState.py68680%32–181
   FlexHCD.py4194190%1–725
   FlexHCDMaintenance.py74740%5–204
   GenericDiffractometer.py70636149%50–62, 130, 352–353, 363–366, 369–389, 394–395, 397, 402–403, 431–440, 448, 461–477, 481–482, 487–489, 499–501, 518, 521, 523, 525, 527, 529, 531, 535, 627, 632–634, 644, 658–663, 670, 677, 684, 692–714, 720–726, 730, 736, 742, 748, 754, 758, 764, 775–782, 801–802, 806–807, 815, 823, 828–856, 861–883, 887–904, 910–941, 949–976, 982–1018, 1022, 1026, 1036–1039, 1047–1086, 1090, 1094–1100, 1111, 1139, 1147–1148, 1155–1161, 1169–1172, 1180–1186, 1192–1197, 1203–1204, 1210, 1216–1220, 1226–1240, 1249, 1255, 1259, 1269–1281, 1285–1299, 1305, 1311, 1315, 1318, 1325, 1337–1348, 1352–1354, 1358–1359, 1363–1364, 1372, 1391–1396, 1402–1404, 1410–1435, 1441, 1447, 1450, 1454, 1458, 1461, 1464, 1467–1468, 1471–1489, 1492–1508, 1511–1514
   Grob.py10100%1–14
   GrobMotor.py72720%1–101
   GrobSampleChanger.py1571570%4–254
   Harvester.py2712710%43–735
   HarvesterMaintenance.py97970%24–289
   ICATLIMS.py3013010%1–705
   ISARAMaint.py1031883%42–46, 68, 109–111, 190, 201, 203, 210–219
   LdapAuthenticator.py1011010%7–188
   Lima2Detector.py2102100%1–405
   LimaEigerDetector.py1351350%5–319
   LimaJungfrauDetector.py1121120%1–217
   LimaPilatusDetector.py1851850%1–346
mxcubecore/HardwareObjects/ANSTO
   Diffractometer.py3243240%1–819
   ExporterMotor.py1021020%1–324
   ExporterNState.py65650%1–152
   redis_client.py2122120%1–554
mxcubecore/HardwareObjects/ANSTO/prefect_flows
   abstract_flow.py31310%1–146
   grid_scan_flow.py1191190%1–347
   prefect_client.py69690%1–221
   screening_flow.py23230%1–151
mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas
   grid_scan.py26260%1–34
   screening.py37370%1–95
mxcubecore/HardwareObjects/Gphl
   CollectEmulator.py1911910%25–379
   GphlMessages.py6456450%22–1367
   GphlQueueEntry.py29290%25–65
   GphlWorkflow.py134113410%24–3053
   GphlWorkflowConnection.py6436430%23–1315
   Transcal2MiniKappa.py1061060%23–292
TOTAL62821577188% 

Tests Skipped Failures Errors Time
2005 0 💤 0 ❌ 0 🔥 2m 12s ⏱️

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Review focused on @fhernandezvivanco commits.

@fhernandezvivanco fhernandezvivanco merged commit 5f6e44e into main Dec 3, 2024
10 of 11 checks passed
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