History

Unreleased / master

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