Changelog#
0.3.0-dev2#
Released on 2024-04-24 - GitHub - PyPI
What's Changed
- cicd: use ruff for autoformatting by @jsstevenson in #292
- test: suppress noisy boto logs by default by @jsstevenson in #300
- feat!: use wags-tails for data acquisition by @jsstevenson in #303
- style: update ruff version by @jsstevenson in #316
- docs: add description metadata by @jsstevenson in #315
- docs: incorporate latest template elements by @jsstevenson in #322
- style: pin ruff version from template by @jsstevenson in #323
- cicd: reorganize QC checks by @jsstevenson in #324
- cicd: require priority label on PR by @jsstevenson in #325
- docs: fix api reference link in readme by @korikuzma in #327
- fix: handle password param in postgres connection by @nickzoic in #333
New Contributors
Full Changelog: 0.3.0-dev1...0.3.0-dev2
0.3.0-dev1#
Released on 2023-10-20 - GitHub - PyPI
What's Changed
- cicd: add Ruff and Black by @jsstevenson in #253
- feat!: merge concepts and source dynamodb tables by @jsstevenson in #258
- feat!: remove search result formatting options by @jsstevenson in #261
- feat!: use vrs 2.0-alpha core gene model in /normalize by @korikuzma in #252
- feat!: update data acquisition methods by @jsstevenson in #262
- feat: update HGNC license by @jsstevenson in #263
- fix: correct gene info file glob typo by @jsstevenson in #265
- fix: catch ETL module import errors by @jsstevenson in #268
- fix: set response_model_exclude_none=True in /normalize by @korikuzma in #273
- cicd: add gh action for closing issue on staging branch by @korikuzma in #276
- docs: incorporate Alex feedback by @jsstevenson in #269
- test: add basic route tests by @jsstevenson in #277
- build: modernize build configs by @jsstevenson in #271
- refactor: remove unused error handling by @jsstevenson in #280
- cicd: update release.yaml (publish python distribution to pypi) by @korikuzma in #284
- docs: update VRS compliance by @korikuzma in #287
- build: define build system by @jsstevenson in #288
- build: properly pin pydantic v2 major version by @korikuzma in #290
Full Changelog: 0.3.0-dev0...0.3.0-dev1
0.1.40-dev1#
Released on 2023-10-05 - GitHub - PyPI
What's Changed
- fix: catch ETL module import errors by @jsstevenson in #249
- docs: fix documentation link by @Rajdeep1311 in #257
- fix: correct gene info file glob typo by @jsstevenson in #266
- feat: update HGNC license by @jsstevenson in #267
- cicd: add gh action for closing issue on staging branch by @korikuzma in #275
- test: add basic route tests by @jsstevenson in #278
- build: modernize build configs by @jsstevenson in #279
- build: update ga4gh.vrsatile.pydantic version by @korikuzma in #281
- cicd: update release.yaml (publish python distribution to pypi) by @korikuzma in #283
New Contributors
- @Rajdeep1311 made their first contribution in #257
Full Changelog: v0.1.40-dev0...0.1.40-dev1
0.3.0-dev0#
Released on 2023-09-08 - GitHub - PyPI
What's Changed
- feat: add get_all_records DB method by @jsstevenson in #231
- build!: use vrs-python for VRS 2.0-alpha models by @korikuzma in #239
- refactor!: Remove ChromosomeLocation + SequenceLocation classes by @korikuzma in #245
Full Changelog: v0.2.10...0.3.0-dev0
v0.1.40-dev0#
Released on 2023-09-08 - GitHub - PyPI
What's Changed
- cicd: add Ruff and Black by @jsstevenson in #232
- refactor: use isinstance instead of type() check by @jsstevenson in #243
- feat!: store source metadata in concepts table by @jsstevenson in #233
- feat!: remove search result formatting options by @jsstevenson in #244
- feat!: update data acquisition methods by @jsstevenson in #236
- docs: incorporate Alex feedback by @jsstevenson in #242
Full Changelog: v0.1.39...v0.1.40-dev0
v0.1.39#
Released on 2023-07-21 - GitHub - PyPI
What's Changed
- feat: add get_all_records DB method by @jsstevenson in #230
Full Changelog: v0.1.38...v0.1.39
v0.2.10#
Released on 2023-07-21 - GitHub - PyPI
What's Changed
- docs: make separate sphinx docs by @jsstevenson in #190
- feat: add DB status check entrypoint by @jsstevenson in #196
- fix: remove duplicate xrefs from merged records by @jsstevenson in #197
- fix: prevent redundant/incorrect AWS confirmation checks by @jsstevenson in #198
- docs: touch up query API documentation by @jsstevenson in #199
- perf: improve PG normalized concept deletion by @jsstevenson in #201
- build: separate dependency groups by use case by @jsstevenson in #203
- fix!: use more precise name for CLI source option by @jsstevenson in #205
- docs: provide readthedocs integration by @jsstevenson in #208
- docs: expand base template and improve descriptions by @jsstevenson in #211
- docs: add more usage details by @jsstevenson in #213
- feat: optionally define dynamo table names via environment variable by @jsstevenson in #214
- test: update test data by @jsstevenson in #223
- ci: use latest pip in sphinx test (metaschema) by @jsstevenson in #221
- doc: preserve arg defaults in docs by @jsstevenson in #225
- chore: add PyPI metadata (metaschema) by @jsstevenson in #229
- feat: provide strand in normalized record (metaschema) by @jsstevenson in #228
Full Changelog: 0.2.9...v0.2.10
v0.1.38#
Released on 2023-07-21 - GitHub - PyPI
What's Changed
- ci: use latest pip in sphinx test by @jsstevenson in #219
- fix: preserve arg defaults in docs by @jsstevenson in #218
- test: update test data by @jsstevenson in #222
- feat: provide strand in normalized record by @jsstevenson in #226
- chore: add PyPI metadata by @jsstevenson in #224
Full Changelog: v0.1.37...v0.1.38
v0.1.37#
Released on 2023-06-27 - GitHub - PyPI
What's Changed
- fix!: use more precise name for CLI source option by @jsstevenson in #204
- docs: provide readthedocs integration by @jsstevenson in #207
- docs: expand base template and improve descriptions by @jsstevenson in #209
- docs: add more usage details by @jsstevenson in #210
- feat: optionally define dynamo table names via environment variable by @jsstevenson in #212
Full Changelog: 0.1.36...v0.1.37
0.1.36#
Released on 2023-05-08 - GitHub - PyPI
What's Changed
- feat: add DB status check entrypoint by @jsstevenson in #191
- fix: prevent redundant/incorrect AWS confirmation checks by @jsstevenson in #193
- fix: remove duplicate xrefs from merged records by @jsstevenson in #194
- docs: touch up query API documentation by @jsstevenson in #192
- perf: improve PG normalized concept deletion by @jsstevenson in #195
- build: separate dependency groups by use case by @jsstevenson in #202
Full Changelog: 0.1.35...0.1.36
0.1.35#
Released on 2023-04-21 - GitHub - PyPI
What's Changed
VRS 1.3 introduced in this release
- build: update ga4gh packages to use VRS 1.3 models by @korikuzma in #189
Full Changelog: 0.1.34...0.1.35
0.2.9#
Released on 2023-04-18 - GitHub - PyPI
What's Changed
- test: incorporate latest source updates to test cases by @jsstevenson in #173
- refactor: rename SEQREPO_DATA_PATH --> SEQREPO_ROOT_DIR (staging) by @korikuzma in #187
- feat: support PostgreSQL as optional storage backend by @jsstevenson in #183
Full Changelog: v0.2.8...0.2.9
0.1.34#
Released on 2023-04-18 - GitHub - PyPI
What's Changed
- feat: support PostgreSQL as optional storage backend by @jsstevenson in #169
- docs: make separate sphinx docs by @jsstevenson in #182
- refactor: rename SEQREPO_DATA_PATH --> SEQREPO_ROOT_DIR by @korikuzma in #186
Full Changelog: 0.1.33...0.1.34
0.1.33#
Released on 2023-03-31 - GitHub - PyPI
What's Changed
- test: incorporate latest source updates to test cases by @jsstevenson in #171
- build: update ga4gh.vrs version to ~= 0.7.8 by @korikuzma in #180
Full Changelog: 0.1.32...0.1.33
v0.2.8#
Released on 2023-02-07 - GitHub - PyPI
What's Changed
- build: update dev dependencies (staging) by @korikuzma in #168
Full Changelog: v0.2.7...v0.2.8
0.1.32#
Released on 2023-02-07 - GitHub - PyPI
What's Changed
- build: update dev dependencies by @korikuzma in #167
Full Changelog: v0.1.31...0.1.32
v0.1.31#
Released on 2023-01-05 - GitHub - PyPI
What's Changed
- remove ebextensions (main) by @korikuzma in #154
- feat: ensure test and aws env vars are not set at same time (main) by @korikuzma in #160
- build: do not pin exact version for ga4gh.vrsatile.pydantic by @korikuzma in #162
- build: unpin exact version of ga4gh.vrs (main) by @korikuzma in #164
Full Changelog: v0.1.30...v0.1.31
v0.2.7#
Released on 2023-01-05 - GitHub - PyPI
What's Changed
- remove ebextensions (staging) by @korikuzma in #155
- feat: ensure test and aws env vars are not set at same time (staging) by @korikuzma in #159
- build: update ga4gh versions (staging) by @korikuzma in #163
Full Changelog: v0.2.6...v0.2.7
v0.1.30#
Released on 2022-10-27 - GitHub - PyPI
What's Changed
- fix: return all locations in response (#126, #152) by @korikuzma in #153
Full Changelog: v0.1.29...v0.1.30
v0.1.29#
Released on 2022-10-26 - GitHub - PyPI
What's Changed
- fix: move SOURCE_CLASS to cli (main branch) by @korikuzma in #149
- refactor!: remove elastic beanstalk work on main branch by @korikuzma in #151
Full Changelog: v0.1.28...v0.1.29
v0.2.6#
Released on 2022-10-25 - GitHub - PyPI
What's Changed
- refactor!: remove elastic beanstalk work by @korikuzma in #150
Full Changelog: v0.2.5...v0.2.6
v0.2.5#
Released on 2022-10-24 - GitHub - PyPI
What's Changed
- ci: resolve action version warnings by @jsstevenson in #139
- build: separate out etl (dev) dependencies on staging by @korikuzma in #143
- refactor: how vrs chromosome/sequence locations are stored in dynamodb (staging) by @korikuzma in #145
- fix: move SOURCE_CLASS to cli (staging branch) by @korikuzma in #148
Full Changelog: v0.2.3...v0.2.5
v0.1.28#
Released on 2022-10-24 - GitHub - PyPI
What's Changed
- build: separate out etl (dev) dependencies on main by @korikuzma in #142
- refactor: how vrs chromosome/sequence locations are stored in dynamodb by @korikuzma in #144
Full Changelog: v0.1.27...v0.1.28
v0.2.3#
Released on 2022-09-28 - GitHub - PyPI
What's Changed
- feat: return all source locations in normalize response (#126) by @korikuzma in #138
Full Changelog: v0.2.2...v0.2.3
v0.2.2#
Released on 2022-09-23 - GitHub - PyPI
What's Changed
- refactor: update ga4gh vrsatile pydantic (gene_id --> gene) by @korikuzma in #137
Full Changelog: v0.2.1...v0.2.2
v0.2.1: #
Released on 2022-08-26 - GitHub - PyPI
- refactor: allow for nonprod tables to be used when EB_ENV_TYPE is set
v0.2.0: #
Released on 2022-08-24 - GitHub - PyPI
- fix: catch KeyErrors in seqrepo
- refactor: update models + fix seqrepo key error
- refactor: add condition for using nonprod db
v0.1.27: #
Released on 2022-05-11 - GitHub - PyPI
- Add
/normalize_unmerged
- Use correct SourceName value type in unmerged normalized records
- Create Zenodo record
v0.1.26: #
Released on 2022-04-11 - GitHub - PyPI
- Remove elastic beanstalk dependencies
- Allow SEQREPO_DATA_PATH to be set by environment variable
- Extract biotype / gene type from sources
- Use latest source data
v0.1.25: #
Released on 2022-04-06 - GitHub - PyPI
- Set use_enum_values in pydantic class configs
- response_datetime is a str in ServiceMeta
v0.1.24: #
Released on 2021-12-30 - GitHub - PyPI
- Add url to openapi contact info
- Return all results in
search
rather than the highest match
v0.1.23: #
Released on 2021-11-18 - GitHub - PyPI
- Unpin ga4gh.vrs and ga4gh.vrsatile.pyantic versions + update
v0.1.22: #
Released on 2021-11-04 - GitHub - PyPI
- Update package requirements
- Set SEQREPO_DATA_PATH value to /usr/local/share/seqrepo/latset
v0.1.21: #
Released on 2021-10-09 - GitHub - PyPI
- PROJECT_ROOT --> APP_ROOT
- Use gene_id rather than gene value object in gene descriptor
- normalize method always returns NormalizeService object
v0.1.20: #
Released on 2021-09-08 - GitHub - PyPI
- Use python 3.8
- Return Pydantic service classes in search and normalize methods
v0.1.19: #
Released on 2021-09-07 - GitHub - PyPI
- Update schema examples
- Fix bug where operations opened at the same time
v0.1.18: #
Released on 2021-08-31 - GitHub - PyPI
- Use ga4gh.vrsatile.pydantic classes
- Fix one off bug in SequenceInterval
v0.1.17: #
Released on 2021-08-13 - GitHub - PyPI
- Set type in ChromosomeLocation and SequenceLocation
- Cleaning up validators in schemas
v0.0.16: #
Released on 2021-08-12 - GitHub - PyPI
- Catch and log pydantic validation errors when loading sources
- Only download Ensembl data file if version is not found
v0.1.15: #
Released on 2021-08-09 - GitHub - PyPI
- Add previous_symbols to extensions
- Fix chromosome spelling / return dictionary for query instead of list
v0.1.14: #
Released on 2021-08-09 - GitHub - PyPI
- _id is optional field for Location
0.1.13: #
Released on 2021-08-06 - GitHub - PyPI
- Adding validators to schemas
v0.1.11: #
Released on 2021-08-04 - GitHub - PyPI
- Add normalize endpoint
- Update sources to extract most recent version
v0.1.10: #
Released on 2021-06-30 - GitHub - PyPI
- Add service meta to response
- Search by xref
- Add item type attribute
- other_id -> xref, xref -> associated_with
- Capture previous gene identifiers from NCBI
- Adds Dockerfile
v0.1.5: #
Released on 2021-03-31 - GitHub - PyPI
- Fix search endpoint with only partial sources loaded
- Remove unused requirements to fix EB instance
v.0.1.4: #
Released on 2021-03-30 - GitHub - PyPI
- Fixing environment variables for production EB
v0.1.3: #
Released on 2021-03-29 - GitHub - PyPI
- Add CLI Class back
- Use one environment variable for production EB instance