History
Unreleased / main
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 procedureretrieve_grid_info_for_dc_v2
.
9.0.0 (2023-12-06)
Replace use of
procrunner
withsubprocess
Remove method
insert_motion_correction_drift
and related dictionary in theEMAcquisition
classUpdate SQLAlchemy ORM models for
ispyb-database
v3.0.0Rename
pixelsPerMicron
tomicronsPerPixel
in dicts andretrieve_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 ofispyb.model
7.1.0 (2023-01-18)
New method
update_dc_append_comments
available in theAcquisition
andMXAcquisition
classesUpdate 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 0Added 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 parameterexperiment_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
#155Add ability to store values for the new column
AutoProcScalingStatistics.resIOverSigI2
#157Use new versions of stored procedures for
ParticlePicker
andParticleClassification
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 timesWhen 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
modeUpdate 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’sconfiguration_file
parameter is now deprecated - positional arguments orcredentials
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 ISPyBNew
ispyb.last_data_collections_on
command-line interface to list the most recent data collections on the given beamlinesWith 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)
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)
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. #94New 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:
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 toispyb_mariadb_sp
mxprocessing:
upsert_program
has been removed. Useupsert_program_ex
instead.processing interface: removed
get_processing_job
Future breaking changes:
Exception classes renamed and moved from
ispyb.exception
intoispyb
. 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
andreconn_delay
update_container_assign
now returns the containerId and the new containerStatus