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Unreleased / main

10.2.4 (2024-10-08)

  • Compatibility with SQLAlchemy 2. SQLAlchemy 1.4 remains supported.

10.2.0 (2024-08-14)

  • Update SQLAlchemy ORM models for ispyb-database v4.2.0.
  • Azure pipelines CI: Use ispyb-database schema v4.2.0

10.1.0 (2024-04-03)

  • Use context manager interface to open ispyb connection (#210 <#210>)
  • Update SQLAlchemy ORM models for ispyb-database v4.1.0.
  • Azure pipelines CI: Use ubuntu-22.04 and install mariadb-client package

10.0.0 (2024-01-10)

  • Update SQLAlchemy ORM models for ispyb-database v4.0.1. This drops some previously mapped tables and columns, so is a breaking change.
  • Update MXAcquisition class to use the stored procedure retrieve_grid_info_for_dc_v2.

9.0.0 (2023-12-06)

  • Replace use of procrunner with subprocess
  • Remove method insert_motion_correction_drift and related dictionary in the EMAcquisition class
  • Update SQLAlchemy ORM models for ispyb-database v3.0.0
  • Rename pixelsPerMicron to micronsPerPixel in dicts and retrieve_dc_grid result-set

8.0.1 (2023-06-07)

  • Require mysql-connector-python>=8.0.32 (#203)

8.0.0 (2023-05-15)

  • Update SQLAlchemy ORM models for ispyb-database v2.0.0
  • Remove mxacquisition.upsert_xray_centring_result (stored procedure removed in ispyb-database v2.0.0)

7.2.0 (2023-03-02)

  • Update SQLAlchemy ORM models for ispyb-database v1.35.0

7.1.2 (2023-01-26)

  • ispyb.job: bug fix for --new option, broken by removal of ispyb.model

7.1.0 (2023-01-18)

  • New method update_dc_append_comments available in the Acquisition and MXAcquisition classes
  • Update SQLAlchemy ORM models for ispyb-database v1.34.0

7.0.0 (2023-01-16)

  • Remove deprecated ispyb.model

6.13.0 (2022-11-03)

  • ispyb.job: bug fix - sweeps may start counting at 0
  • Added support for Python 3.11
  • Remove support for Python 3.6 (end-of-life on 2021-12-23)
  • Update SQLAlchemy ORM models for ispyb-database v1.33.0

6.12.1 (2022-10-05)

  • Pin mysql-connector-python version to 8.0.29

6.12.0 (2022-08-11)

  • Update SQLAlchemy ORM models for ispyb-database v1.31.0
  • Update insert_subsample_for_image_full_path() to use stored procedure v2 and add optional parameter experiment_type

6.11.0 (2022-04-21)

  • Update SQLAlchemy ORM models for ispyb-database v1.29.0
  • The ISPyB database ORM model version can now be interrogated via ispyb.sqlalchemy.__schema_version__.
  • Added support for Python 3.10

6.10.0 (2022-01-13)

  • Update SQLAlchemy ORM models for ispyb-database v1.28.0
  • ispyb.job is now less facility-specific and can handle recipe paths via a Zocalo configuration file (#162)

6.9.0 (2021-09-16)

  • Update SQLAlchemy ORM models for ispyb-database v1.27.0

6.8.0 (2021-09-03)

  • Correctly translate database stored procedure permission errors into ISPyBException #160

6.7.0 (2021-09-01)

  • Update SQLAlchemy ORM models for ispyb-database v1.26.0

6.6.0 (2021-08-13)

  • Update SQLAlchemy ORM models for ispyb-database v1.25.0
  • Support XML file with multiple AutoProcScalingContainers #155
  • Add ability to store values for the new column AutoProcScalingStatistics.resIOverSigI2 #157
  • Use new versions of stored procedures for ParticlePicker and ParticleClassification insert methods

6.5.0 (2021-07-08)

  • ispyb.last_data_collections_on is now more tolerant of data collections that do not have all fields populated.
  • Update SQLAlchemy ORM models for ispyb-database v1.23.1

6.4.0 (2021-05-25)

  • Update SQLAlchemy ORM models for ispyb-database v1.21.1

6.3.0 (2021-05-13)

  • Add insert methods for new cryo-EM tables. #150
  • Change ispyb.job so that new processing jobs can be created without specifying any sweeps. Useful for EM data collections.
  • ispyb.sqlalchemy.enable_debug_logging() will now log query times
  • When installed in a cctbx environment, force libtbx to generate dispatchers for ispby.* commands

6.2.0 (2021-04-19)

  • Fix bug preventing ispyb.last_data_collections_on from seeing new data collections in --follow mode
  • Update SQLAlchemy ORM models for ispyb-database v1.20.0
  • Adapt insert_motion_correction() to take parameters #147

6.1.1 (2021-04-13)

  • Fix issue with ispyb.job not starting

6.1.0 (2021-04-12)

  • ispyb.open() now supports reading the credentials file from the ISPYB_CREDENTIALS environment variable. The function's configuration_file parameter is now deprecated - positional arguments or credentials should be used instead.
  • A new ispyb.job command line tool allows the creation, viewing, and updating of processing jobs in ISPyB.
  • Silence SQLAlchemy relationship conflict warnings

6.0.2 (2021-04-06)

  • ispyb.sqlalchemy.url() is a function that generates the SQLAlchemy connection URL from the ISPyB configuration

6.0.1 (2021-03-16)

  • ispyb.sqlalchemy.enable_debug_logging() will log every SQL call before execution through the Python logging framework

6.0.0 (2021-03-05)

  • New ispyb.sqlalchemy module containing SQLAlchemy ORM models to interface with ISPyB
  • New ispyb.last_data_collections_on command-line interface to list the most recent data collections on the given beamlines
  • With the introduction of the SQLAlchemy models the existing ispyb.model has been deprecated and will not be developed further.
  • Refactored XRF mapping to work at scale #122
  • Functions marked for deprecation in v5.0 have been removed
  • Added support for Python 3.9

ISPyB API versions 5.x (2019-2021)

5.9.1 (2021-01-28)

  • Fix compatibility issue with newer versions of mysql-connector #116
  • Final version to support Python 2.7 and 3.5 #118

5.9.0 (2021-01-14)

  • New method insert_subsample_for_image_full_path #114 (requires ispyb-database 1.17.2)

5.8.1 (2020-11-22)

  • ispyb.model.sample_group bug fix obtaining linked dcids

5.8.0 (2020-11-10)

  • New method insert_phasing_analysis_results #111 (requires ispyb-database 1.15.0)

5.7.1 (2020-10-23)

  • Add ispyb.model.sample #110

5.7.0 (2020-10-06)

  • Add ispyb.model.samplegroup #104
  • Rewrite EM insert_ctf() to accept parameters #105

5.6.2 (2020-05-22)

  • Add ispyb.model.detector.Detector model #100

5.6.1 (2020-03-30)

  • Added method to retrieve container for a given sample ID #98
  • Add object model for containers

5.6.0 (2020-02-05)

  • Object model for Screening tables #91 and ImageQualityIndicators #95
  • set_role, new method to change the current role of the DB user. #94
  • New module for crystal imaging: xtalimaging #96
  • Add method to close additional future connections #88
  • mysql/mariadb IntegrityError is now translated to ISPyBException #97

5.5.0 (2020-01-07)

New methods:
  • upsert_program_message
  • upsert_sample_image_auto_score

5.4.1 (2019-11-12)

Fix segmentation fault when enabling the SQL future methods.

5.4.0 (2019-11-11)

Breaking change:

  • Database connection package changed from mysql-connector to mysql-connector-python

5.3.0 (2019-08-15)

New method:

  • retrieve_samples_not_loaded_for_container_reg_barcode, #85

5.2.0 (2019-06-17)

New methods:

  • retrieve_sessions_for_beamline_and_run, #75
  • retrieve_data_collection_group, #81

5.1.0 (2019-04-16)

Added more fields to the datacollection object model.

5.0.0 (2019-03-29)

Breaking changes:

  • configuration file section ispyb_mysql_sp renamed to ispyb_mariadb_sp
  • mxprocessing: upsert_program has been removed. Use upsert_program_ex instead.
  • processing interface: removed get_processing_job

Future breaking changes:

  • Exception classes renamed and moved from ispyb.exception into ispyb. Using previous exception classes will generate deprecation warnings.

New features:

  • Authorisation built into the queries for relevant stored procedures
  • New methods for:
    • storing x-ray centring results
    • retrieving persons on a session
    • un-assigning all containers on a certain beamline
  • New reconnection parameters in config file: reconn_attempts and reconn_delay
  • update_container_assign now returns the containerId and the new containerStatus