3.1.0

What's Changed

• Bump black from 24.4.0 to 24.4.1 by @dependabot in #294
• Bump black from 24.4.1 to 24.4.2 by @dependabot in #297
• Bump pytest from 8.1.1 to 8.2.0 by @dependabot in #296
• Add option to find legacy Infinium microarray data by @kjsanger in #295
• Refactoring by @kjsanger in #298
• Make db_config the primary name for database configurations by @kjsanger in #299
• Add support for updating Sequenom metadata in iRODS by @kjsanger in #300
• Bump cryptography from 42.0.5 to 42.0.7 by @dependabot in #304
• Bump sqlalchemy from 2.0.29 to 2.0.30 by @dependabot in #302
• Add iRODS 4.3.2, remove 4.3-nightly by @kjsanger in #305
• Fix handling of PendingRollbackError when processing large datasets by @kjsanger in #307
• Add ONT year runs meta-report by @kjsanger in #306
• Bump yattag from 1.14.0 to 1.15.2 by @dependabot in #308

Full Changelog: 3.0.1...3.1.0

3.0.1

What's Changed

• Fix skip-missing-runs argument type by @kjsanger in #293

Full Changelog: 3.0.0...3.0.1

3.0.0

What's Changed

• Fix docstrings referring to defaults of true where not the case by @kjsanger in #276
• Bump pytest from 8.1.0 to 8.1.1 by @dependabot in #278
• Bump setuptools from 69.1.1 to 69.2.0 by @dependabot in #279
• Add support for managing public access when updating permissions by @kjsanger in #277
• Bump black from 24.2.0 to 24.3.0 by @dependabot in #280
• Use case-folded comparison for file name extensions by @kjsanger in #281
• Generalise setting public access for ONT by @kjsanger in #282
• Bump sqlalchemy from 2.0.27 to 2.0.28 by @dependabot in #269
• Bump npg_id_generation from 4.0.1 to 5.0.1 by @kjsanger in #283
• Bump sqlalchemy from 2.0.28 to 2.0.29 by @dependabot in #284
• Bump sqlalchemy-utils from 0.41.1 to 0.41.2 by @dependabot in #285
• Bump setuptools-git-versioning from 1.13.6 to 2.0.0 by @dependabot in #286
• Improve the specificity of SQL query for Illumina updates by @kjsanger in #287
• Fix name of enhance-secondary-metadata by @kjsanger in #288
• Fix CLI option --print_update to --print-update by @kjsanger in #289
• Bump black from 24.3.0 to 24.4.0 by @dependabot in #292
• Bump setuptools from 69.2.0 to 69.5.1 by @dependabot in #291
• Set a clean PATH and PYTHONPATH by @kjsanger in #290

Full Changelog: 2.1.2...3.0.0

2.1.2

What's Changed

• Add general metadata script by @zb32 in #254
• Small cleanup and refactoring changes by @kjsanger in #274
• Use keywords for optional arguments, avoid positional "None"s by @kjsanger in #275

Full Changelog: 2.1.1...2.1.2

2.1.1

What's Changed

• Increase permitted startup time for the iRODS service by @kjsanger in #270
• Try mounting host /dev/shm into iRODS containers by @kjsanger in #272
• Fix inclusion of controls (controls to be included) by @kjsanger in #273

Full Changelog: 2.1.0...2.1.1

2.1.0

What's Changed

• Bump black from 23.10.0 to 23.10.1 by @dependabot in #206
• Bump pytest from 7.4.2 to 7.4.3 by @dependabot in #207
• Bump cryptography from 41.0.4 to 41.0.5 by @dependabot in #208
• Bump sqlalchemy from 2.0.21 to 2.0.22 by @dependabot in #203
• Logging improvements by @kjsanger in #209
• Avoid raising exceptions when processing control CRAM files by @kjsanger in #210
• Bump sqlalchemy from 2.0.22 to 2.0.23 by @dependabot in #212
• Bump black from 23.10.1 to 23.11.0 by @dependabot in #213
• rename consent withdrawn test by @zb32 in #214
• Add handling of collections to consent withdrawn by @kjsanger in #216
• Add a --end-date option to metadata update scripts by @kjsanger in #211
• Add iRODS 4.3.1 Ubuntu 22.04 as a required test target by @kjsanger in #217
• Bump setuptools from 68.2.2 to 69.0.0 by @dependabot in #219
• Bump setuptools from 69.0.0 to 69.0.2 by @dependabot in #220
• Move CLI from scripts to entrypoints by @kjsanger in #218
• Bump rich from 13.6.0 to 13.7.0 by @dependabot in #215
• Bump cryptography from 41.0.5 to 41.0.7 by @dependabot in #222
• GHA: install irods client, and singularity cache, outside workspace by @dkj in #223
• Add *_human iRODS groups to the test fixtures by @kjsanger in #224
• Add reporting of Illumina QC JSON data objects by @kjsanger in #221
• Bump black from 23.11.0 to 23.12.0 by @dependabot in #225
• Bump structlog from 23.2.0 to 23.3.0 by @dependabot in #230
• Bump pytest from 7.4.3 to 7.4.4 by @dependabot in #229
• Bump setuptools from 69.0.2 to 69.0.3 by @dependabot in #226
• Bump black from 23.12.0 to 23.12.1 by @dependabot in #227
• Add metadata and permission management for Illumina ancillary files by @kjsanger in #231
• Bump structlog from 23.3.0 to 24.1.0 by @dependabot in #234
• Fix Illumina flowcells query to use the entity_type column by @kjsanger in #233
• Bump sqlalchemy from 2.0.23 to 2.0.25 by @dependabot in #232
• Bump cryptography from 41.0.7 to 42.0.0 by @dependabot in #236
• Add new study groups for human by @zb32 in #235
• Bump cryptography from 42.0.0 to 42.0.1 by @dependabot in #237
• Refactor tests and fixtures to organise them by platform by @kjsanger in #238
• Bump black from 23.12.1 to 24.1.1 by @kjsanger in #241
• Bump pytest-it from 0.1.4 to 0.1.5 by @kjsanger in #242
• Bump pytest from 7.4.4 to 8.0.0 by @dependabot in #239
• Remove a function and associated test which are not used by @kjsanger in #243
• Bump cryptography from 42.0.1 to 42.0.2 by @dependabot in #244
• Bump setuptools-git-versioning from 1.13.5 to 1.13.6 by @dependabot in #245
• Bump setuptools from 69.0.3 to 69.1.0 by @dependabot in #247
• Bump black from 24.1.1 to 24.2.0 by @dependabot in #248
• Bump sqlalchemy from 2.0.25 to 2.0.26 by @dependabot in #246
• Add PacBio metadata and ACL updates by @kjsanger in #249
• Bump setuptools from 69.1.0 to 69.1.1 by @dependabot in #256
• Bump cryptography from 42.0.2 to 42.0.5 by @dependabot in #257
• Bump sqlalchemy from 2.0.26 to 2.0.27 by @dependabot in #250
• Add GitHub Actions to Dependabot by @kjsanger in #260
• Bump docker/setup-buildx-action from 2 to 3 by @dependabot in #261
• Bump docker/login-action from 2 to 3 by @dependabot in #262
• Bump actions/cache from 3 to 4 by @dependabot in #263
• Bump actions/checkout from 3 to 4 by @dependabot in #265
• Bump ncipollo/release-action from 1.12.0 to 1.14.0 by @dependabot in #264
• Bump pytest from 8.0.0 to 8.0.2 by @dependabot in #255
• Bump actions/setup-python from 3 to 5 by @dependabot in #266
• Bump rich from 13.7.0 to 13.7.1 by @dependabot in #258
• Bug: add default for --output CLI option of safe-remove-script by @kjsanger in #259
• Bump python-dateutil from 2.8.2 to 2.9.0.post0 by @dependabot in #268
• Bump pytest from 8.0.2 to 8.1.0 by @dependabot in #267

New Contributors

• @zb32 made their first contribution in #214
• @dkj made their first contribution in #223

Full Changelog: 2.0.1...2.1.0

2.0.1

What's Changed

• Bump structlog from 23.1.0 to 23.2.0 by @dependabot in #201
• Bump cryptography from 41.0.3 to 41.0.4 by @dependabot in #197
• Bump sqlalchemy from 2.0.20 to 2.0.21 by @dependabot in #196
• Bump rich from 13.5.2 to 13.6.0 by @dependabot in #199
• Update test matrix iRODS versions by @kjsanger in #202
• Bump black from 23.9.1 to 23.10.0 by @dependabot in #205
• Bump npg_id_generation from 3.0.0 to 4.0.1 by @kjsanger in #204

Full Changelog: 2.0.0...2.0.1

2.0.0

What's Changed

• Add CLI options to locate-data-objects to allow skipping searches by @kjsanger in #166
• Bump cryptography from 41.0.1 to 41.0.2 by @dependabot in #171
• Bump black from 23.3.0 to 23.7.0 by @dependabot in #170
• Avoid creating a dirty build environment in CI by @kjsanger in #169
• Add support for recursive consent withdrawn updates for ONT by @kjsanger in #172
• Improve script documentation and naming by @kjsanger in #173
• Bump setuptools from 68.0.0 to 68.1.2 by @dependabot in #185
• Use exception rather than error method for Exception logging by @kjsanger in #181
• Bug fix and improvements for ONT metadata updates by @kjsanger in #184
• Bump cryptography from 41.0.2 to 41.0.3 by @dependabot in #178
• Bump setuptools-git-versioning from 1.13.3 to 1.13.5 by @dependabot in #180
• Bump rich from 13.4.2 to 13.5.2 by @dependabot in #179
• Bump sqlalchemy from 2.0.17 to 2.0.20 by @dependabot in #183
• Bump pytest from 7.4.0 to 7.4.1 by @dependabot in #186
• Bump pytest from 7.4.1 to 7.4.2 by @dependabot in #188
• Bump black from 23.7.0 to 23.9.1 by @dependabot in #192
• Bump setuptools from 68.1.2 to 68.2.2 by @dependabot in #193
• Bugfix: use annotate_results_collection to update metadata by @kjsanger in #190
• Fix black paths to avoid checking unwanted files by @kjsanger in #194
• Fix accidental expansion of ACL groups by @kjsanger in #198
• Improve test layout and consistency by @kjsanger in #200

Full Changelog: 1.3.0...2.0.0

1.3.0

What's Changed

• Bump rich from 13.3.4 to 13.3.5 by @dependabot in #131
• Bump sqlalchemy from 2.0.9 to 2.0.12 by @dependabot in #134
• Bump sqlalchemy-utils from 0.41.0 to 0.41.1 by @dependabot in #130
• Bump setuptools from 67.6.1 to 67.7.2 by @dependabot in #129
• Add Singularity container support for iRODS clients by @kjsanger in #135
• Test refactoring by @kjsanger in #136
• Use supersede_metadata to perfom metadata updates on ont collections by @mksanger in #138
• Add iRODS 4.2.12 to CI by @kjsanger in #139
• Add support for automatically fixing incorrect checksum metadata by @kjsanger in #144
• Bump rich from 13.3.5 to 13.4.1 by @dependabot in #146
• Bump setuptools from 67.7.2 to 67.8.0 by @dependabot in #142
• Fix ONT permissions updates to retain unmanaged access controls by @kjsanger in #148
• Bump pytest from 7.3.1 to 7.3.2 by @dependabot in #150
• Bump sqlalchemy from 2.0.12 to 2.0.16 by @dependabot in #151
• Set ont report files as publicly readable by @mksanger in #149
• Bump setuptools from 67.8.0 to 68.0.0 by @dependabot in #154
• Add update-secondary-metadata script by @kjsanger in #153
• Bump rich from 13.4.1 to 13.4.2 by @dependabot in #152
• Fix pacbio backfill by @mksanger in #158
• Bump pytest from 7.3.2 to 7.4.0 by @dependabot in #156
• Bump pymysql from 1.0.3 to 1.1.0 by @dependabot in #157
• Merge hotfixed master back into devel by @kjsanger in #163
• Bump cryptography from 40.0.2 to 41.0.1 by @dependabot in #147
• Bump sqlalchemy from 2.0.16 to 2.0.17 by @dependabot in #155
• Refactor to separate initial ONT metadata creation from later regular updates by @kjsanger in #159
• Add pyproject.toml and remove setup.py by @kjsanger in #164
• Add sample_common_name and sample_public_name to iRODS sample metadata by @kjsanger in #165
• Fix Dockerfile for change to pyproject.toml by @kjsanger in #167

Full Changelog: 1.2.2...1.3.0

1.2.2

What's Changed

• Fix incorrect value for sample_id metadata by @kjsanger in #161
• Fix incorrect value for sample_id metadata, supporting fixes by @kjsanger in #162

Full Changelog: 1.2.1...1.2.2