Changelog 2024ΒΆ
Note
π‘ LaminDB implements βmigration-based versioningβ. When upgrading your LaminDB installation to a new minor
version in major.minor.patch
, you also migrate your database via lamin migrate deploy
.
Get notified by watching releases for the lamindb, laminhub-public, and bionty GitHub repositories.
2024-09-05 db 0.76.5ΒΆ
π Fix
lamin save
for source code updates PR @falexwolfπ Allow login with Beta API key via CLI PR @fredericenard @Koncopd
2024-09-04 db 0.76.4ΒΆ
πΈ Make source code searchable Details & PR @falexwolf @chaichontat
π Fix marking latest transform as
is_latest
PR @falexwolf⨠Support lists as values in validation PR @sunnyosun
2024-08-30 db 0.76.3 | bionty 0.49ΒΆ
β¨ tiledbsoma
integration. Guide PR @Koncopd
Example
Create a tiledbsoma.Experiment
array store or append AnnData
objects to an existing store.
# create new versioned tiledbsoma.Experiment
artifact = ln.integrations.save_tiledbsoma_experiment(
adatas,
measurement_name="RNA"
)
# append to existing tiledbsoma.Experiment
revised_artifact = ln.integrations.save_tiledbsoma_experiment(
adatas,
measurement_name="RNA",
revises=artifact
)
Bionty updates.
More changes.
π Deprecate
Curate
in favor ofCurator
PR @sunnyosunπ₯ Remove
lamin register
and password argument oflamin login
PR PR @falexwolf
2024-08-26 hub 0.27ΒΆ
β¨ Instance overview page. @chaichontat
Screenshot
π Show Vitessce button next to dataset instead of VitessceConfig
file. @sunnyosun
ποΈ Much improved on-prem deployment. @fredericenard
2024-08-23 db 0.76.2ΒΆ
πΈ Simplify versioning. PR @falexwolf
Semantic version strings in .version
are now optional as in git.
For Artifact
& Transform
, you can now also create new versions by passing the key
argument.
artifact_v1 = ln.Artifact.from_df(df, key="my_datasets/my_study1.parquet").save()
# below automatically creates a new version of artifact_v1 because the `key` matches
artifact_v2 = ln.Artifact.from_df(df_updated, key="my_datasets/my_study1.parquet").save()
π Deprecate
is_new_version_of
argument in favor ofrevises
π Deprecate passing
version
to constructors; rather set.version
after creating records
More changes.
π Simpler icons PR @sunnyosun
2024-08-16 db 0.76.1ΒΆ
πΈ Overhauled context tracking experience with ln.context.track()
Details & PR @falexwolf @chaichontat
ln.context.uid = "FPnfDtJz8qbE0000" # <-- auto-generated by ln.context.track()
# track the execution of your notebook or script with inputs & outputs
ln.context.track()
What was the previous experience?
Now:
Previously:
How does it look on the hub?
If you donβt label with a semantic version tag, youβll get an auto-generated revision id.
β οΈ Breaking change: ln.track()
now returns None
instead of a Run
. Access the run via ln.context.run
instead.
More changes:
2024-08-14 db 0.76ΒΆ
β‘οΈ Add boolean field
IsVersioned.is_latest
to speed up queries for latest versions PR @falexwolf @fredericenard @chaichontatπ Fix length limitation for external hash parsing PR @falexwolf
β‘οΈ Speed up
BioRecord.import_from_source
PR @sunnyosunπ¨ Make more backward accessors private and type the rest PR @falexwolf
2024-08-10 hub 0.26ΒΆ
πΈ Backend search & filter via multiple relationships @chaichontat @fredericenard
β¨ Login via Microsoft @fredericenard
π Details in hover cards @chaichontat
2024-08-08 db 0.75.1ΒΆ
πΈ Improved the cellxgene_lamin
curation guide.
π Fixes for
lamindb.Curate
PR PR @sunnyosun⨠Allow excluding values in
Curate.validate
PR @sunnyosun
2024-08-08 bionty 0.48ΒΆ
New ontology versions.
2024-08-03 db 0.75ΒΆ
β¨ Track mutations of array stores. Guide PR @Koncopd
Artifacts that store mutable arrays can lead to non-reproducible queries.
To monitor reproduciblity and data lineage, mutations are now tracked when a context manager and
Artifact.open(mode="w")
fortiledbsoma
array stores is used:with artifact.open(mode="w") as array: # mutate `artifact` # `artifact` now points to a new version of the artifact with an updated hash
πΈ A better structured API. PR @falexwolf
πΈ Easier typing & maintenance of categorical fields via
typing.Literal
instead of Djangoβs migration-dependentCharField.choices
πΈ Less clutter in auto-complete
π All fields pointing to link records start with
links_
π Several fields for
Artifact
are now private via_
prefix:accessor
,key_is_virtual
,feature_values
,param_values
,hash_type
,previous_runs
π¨ More consistency
π Rename
Transform.parents
toTransform.predecessors
to disambiguate procedural/temporal from ontological/conceptual hierachiesπ¨ Feature names are now guaranteed to be unique in a lamindb instance
Feature.name
π¨ Consistent length of hash fields:
HASH_LENGTH=22
π Rename
input_of
toinput_of_runs
π¨
Transform.latest_report
is now a property point toTransform.latest_run.report
to simplify the schemaπ¨
Artifact.type
now defaults toNone
when passing apath
so that auxiliary files and folders arenβt labeled asdataset
πΈ Better definition of
Collection
π Rename fields
.artifact
to.meta_artifact
and.unordered_artifacts
to.artifacts
Iteration over an ordered
QuerySet
of artifacts is now possible via.ordered_artifacts
For collections that have a single data artifact, access it via
.data_artifact
ποΈ Towards searchable source code
π Rename
Transform.source_code
toTransform._source_code_artifact
Re-introduce
Transform.source_code
as a text field together with a fieldhash
Better storage management.
πΈ Enable deleting artifacts in all managed storage locations of the current instance PR @falexwolf
β»οΈ Do not write storage records to hub for local test instances PR @falexwolf
π Fix populating
storage.instance_uid
duringinit_instance
PR @falexwolf
Various updates.
2024-08-03 bionty 0.47ΒΆ
ποΈ Bionty is now a single Python package. PR PR PR PR PR
ποΈ
lnschema-bionty
andbionty-base
are integrated intobionty
πΈ Considerably simpler UX: see Manage biological registries PR @sunnyosun
β οΈ Migration: Once you load an instance, youβll be asked to uninstall lnschema_bionty
and lamin migrate deploy
On the SQL level, tables are now prefixed with
bionty_
instead oflnschema_bionty_
On the Django level, you can mount the
bionty
instead of thelnschema_bionty
apps
πΈ You can now import from in-house ontology sources. PR @sunnyosun
π Rename
PublicSource
toSource
&from_public
tofrom_source
Import from any parquet file into your registry, akin to how Bionty imports public ontology sources
User experience.
β‘ Performantly import bulk records via
.import_from_source()
πΈ More reliable
ontology_id
field recognition⨠Better error message for synonym duplications PR @Zethson
π¨
CellMarker.name
is now unique together withorganism
PR sunnyosun
New ontologies.
2024-07-26 hub 0.25ΒΆ
Overhauled the REST API: better performance and architecture.
β‘ Optimize query builder @fredericenard
β¨ GroupBy endpoint @fredericenard
β»οΈ Improved API schema @fredericenard @chaichontat
UI improvements.
π Add details in hover card @chaichontat
π Stop settings from flickering @chaichontat
2024-07-26 db 0.74.3ΒΆ
β‘ Speed up populating parent records by an order of magnitude, remove the parents
keyword (PR @sunnyosun).
Features.
β¨ Allow for multiple local storage locations with the same root path PR @falexwolf
β¨ Add
add_from_df
method toBioRecord
PR @sunnyosun
Chores.
β¬οΈ Upgrade to pydantic v2 PR @falexwolf
2024-07-22 db 0.74.2ΒΆ
The API is now cleaner and fields are typed.
Details
All users who donβt use Django outside of lamindb can set Djangoβs internal API that clutters the Record
name spaces by running: lamin set private-django-api
on the command line.
![](https://lamin-site-assets.s3.amazonaws.com/.lamindb/8uTijEvtSEh0zeeNvwZx.png)
πΈ Cleaner API PR @falexwolf @Koncopd
β¨ Add global
private-django-api
setting PR @falexwolfπ·οΈ Add types to fields PR @falexwolf
tiledbsoma
is now better supported.
Better names.
π Deprecate
Artifact.backed()
in favor ofArtifact.open()
PR @Koncopdπ Deprecate
Annotate
in favor ofCurate
PR @falexwolfπ Deprecate
Registry
in favor ofRecord
PR @falexwolf
Better documentation.
π Improve the curation guide PR PR @sunnyosun @falexwolf
π Improve the CLI docs PR @falexwolf
Security updates & bug fixes.
π Enable Ruff security rules (bandit) & CodeQL PR @Zethson
π Fix return values of
.save()
for a few classes PR @falexwolf
2024-07-01 hub 0.24ΒΆ
β¨ Add a checkbox for instance setting
keep-artifacts-local
PR @chaichontat @sunnyosun⨠New endpoint:
create-instance
PR @fredericenardπ More detailed feature view PR @chaichontat
β¨ Image preview PR @chaichontat
β¨ Artifact backlinks PR @chaichontat
2024-06-26 db 0.74.1ΒΆ
β»οΈ Refactor ln.settings
PR @falexwolf.
β¨ Pass custom names for scripts via
ln.settings.transform.name = "My script"
β οΈ
ln.settings.storage
returns aStorageSettings
object (root vialn.settings.storage.root
)
Features.
β¨ Support different join types in
QuerySet.df()
PR @insavchuk
Use cases.
π First version of tiledbsoma guide PR Koncopd
π First version of wandb guide PR felix0097
Docs.
π Update hub screenshots PR @sunnyosun
2024-06-20 db 0.74ΒΆ
β¨ You can now distinguish model-like and dataset-like artifacts via a type
field in the Artifact
registry.
πΈ Leverage
artifact.params.add_values()
to annotate model-like artifacts like you leverageartifact.features.add_values()
to annotate dataset-like artifactsποΈ Add
type
field toArtifact
, allow linking model-like artifacts against params, validate params akin to validating features, enable features-based annotation with non-ulabels PR @falexwolf
2024-06-13 db 0.73.2ΒΆ
π Fix clashing reverse accessors for
.previous_runs
and.run
PR @falexwolf
2024-06-05 db 0.73.1ΒΆ
ποΈ Instantly synchronize instance schema with the hub PR @fredericenard
π Fix generation of
uid
for manual Transform constructor PR @falexwolfπ₯ Deleting
artifact.stage()
in favor ofartifact.cache()
(was deprecated in 0.70.0)
2024-05-29 db 0.73.0ΒΆ
Annotating & querying by features improved:
β¨ Support non-categorical feature values PR @falexwolf
β¨ Annotate dict-style with features & values PR @falexwolf
β¨ Query by features via
.features.filter(key=value)
PR @falexwolfποΈ Feature values decoupled from feature sets PR @falexwolf
Example:
# annotate dict-style (feature & category names get validated)
artifact.features.add_values({
"species": "setosa",
"scientist": ["Barbara McClintock", "Edgar Anderson"],
"instrument": "Leica IIIc Camera",
"temperature": 27.6,
"study": "Study 0: initial plant gathering",
"is_awesome": True
})
# get the dict back
artifact.features.get_values()
# query by feature
ln.Artifact.features.filter(is_awesome=True)
Various improvements:
π Additional non-breaking constraints in the core schema PR @falexwolf
πΈ Make
.upload_from()
,.download_to()
, and.view_tree()
more user friendly PR @falexwolf PR @KoncopdπΈ More intuitive version updating dialogue PR @falexwolf
π Actually add tracking run for entities beyond Artifact & Collection PR @falexwolf
πΈ
ln.track()
returnsrun
PR @falexwolfπΈ Better duplicate detection and search PR @falexwolf
πΈ Prettier
.describe()
PR @falexwolfπΈ More interactivity in
lamin save
PR @falexwolfπΈ
create
flag in.from_values()
PR @falexwolfπΈ Better ordering of fields in dataframe & record representations PR @falexwolf
π Improved API reference: docs now show relationship attributes PR @falexwolf
2024-05-19 db 0.72.1ΒΆ
β¬οΈ Update bionty PR @sunnyosun
π Deal with migration errors when keep-artifacts-local is true PR @falexwolf
2024-05-19 db 0.72.0ΒΆ
β¨ Extend managed access for AWS S3 to arbitrary paths PR @Koncopd @fredericenard
β¨ Extended data lineage tracking PR @falexwolf
Now store all creating runs and all updating runs for any entity, not just for
Artifact
&Collection
, e.g., runs can now haveCellType
record outputsCode is simpler through inheritance from two new base classes:
TracksRun
andTracksUpdates
β»οΈ Briefer and richer syntax for denoting feature types, renamed
Feature.type
toFeature.dtype
, e.g., for categorical features, a valid type can be:cat[ULabel|bionty.Drug]
PR @falexwolf⨠Support non-categorical metadata PR @falexwolf
Track non-categorical features:
int
,float
,bool
,datetime
, lists & dictionaries stored in aFeatureValue
registryTrack arbitrary typed parameters for runs through a
Param
registry analogous to theFeature
registry: this replaces the hard-to-validate, hard-to-migrate, and hard-to-queryjson
field ofRun
ποΈ Refactor link models PR PR @falexwolf
All annotation-related links are now stratified by
Feature
: what held forULabel
now also holdsCellType
and all otherBionty
registriesIndicate whether semantic keys were used during validation to enable warnings upon renames
Protect artifact annotations rather than cascade delete them
More consistent naming of link models, e.g.,
ulabels.artifact_links
instead ofulabels.artifactulabel_set
Dropped linking
Bionty
entities directly againstCollection
Pruned & squashed migrations for faster instance creation
2024-05-14 db 0.71.3ΒΆ
π¨ Enable transfer when schema donβt match PR @sunnyosun
β¨ Get artifacts through the CLI PR @falexwolf
β‘οΈ Improve the speed of describe PR @sunnyosun
β»οΈ Refactor search PR @falexwolf
β¨ Introduce bulk update PR @falexwolf
πΈ No need to pass organism if validating on ids PR @sunnyosun
2024-05-07 db 0.71.2ΒΆ
β¨ Enable passing parameters to
ln.track()
PR @falexwolf
2024-05-07 db 0.71.1ΒΆ
πΈ Upload source code of scripts upon
ln.finish()
and no longer uponln.track()
PR @falexwolfπ¨ Make
features.add_feature_set
public PR @sunnyosunπ¨ Use the same
uid
for the same feature set in transfer PR @sunnyosunπ¨ Upon upload switch to virtual key PR @falexwolf
β»οΈ Extend valid suffixes to composite suffixes PR @falexwolf
π₯ Remove little-used
artifact.view_tree()
PR @falexwolf
2024-05-01 db 0.71.0ΒΆ
β¨ Manage multiple storage locations with integrity PR @falexwolf
πΈ Proper progress bars for upload and download PR @Koncopd
πΈ Make save return self PR @falexwolf
2024-04-24 db 0.70.4ΒΆ
β¨ Allow passing path to
.from_anndata
PR @sunnyosunπΈ In
.setup.delete()
, check for data deletion & delete from hub PR @falexwolfβ‘οΈ Speed up
latest_version
PR @falexwolfπΈ Better user feedback on folder-like artifacts PR @falexwolf
2024-04-22 db 0.70.3ΒΆ
πΈ Update metadata like description upon re-running PR @falexwolf
π Fix detection of AnnData in zarr and h5ad, refactor directory upload PR @Koncopd
πΈ Raise error if transforms of type notebook or script are passed manually PR @falexwolf
2024-04-19 db 0.70.2ΒΆ
β»οΈ In Vitessce integration, separate
VitessceConfig
from its referenced artifacts PR @falexwolfπΈ In
ln.finish()
, remove flagi_saved_the_notebook
PR @falexwolf
2024-04-18 db 0.70.1ΒΆ
π Fix
public_source
in inspect PR @sunnyosun
2024-04-17 db 0.70.0ΒΆ
πΈ Update data source in case transform is re-run PR @falexwolf
πΈ Enable to label transforms via
transform.ulabels
PR @falexwolfπ Deprecate
stage()
in favor ofcache()
PR @falexwolf
2024-04-12 db 0.69.10ΒΆ
β¨ Add
.obsm
and.layers
toMappedCollection
and renamelabel_keys
toobs_keys
PR @KoncopdπΈ Eliminate kwargs PR @sunnyosun
β¨ Introduce
Annotate.from_mudata
PR @sunnyosun
2024-04-08 db 0.69.9ΒΆ
π Fix clashes for multiple processes PR @falexwolf
2024-04-04 db 0.69.8ΒΆ
2024-04-03 db 0.69.7ΒΆ
β¨ Add ability to upload arbitrary files or folders from CLI PR @falexwolf
π Fix anndata backed mode incompatibility with scipy 1.13.0 f
2024-04-02 db 0.69.6ΒΆ
ποΈ Temp fix region for non-hosted buckets PR @sunnyosun
2024-03-30 db 0.69.5ΒΆ
β»οΈ Improve Annotate API PR PR @sunnyosun @falexwolf
β¨ Introduce
Registry.get()
andlamin get
(replaceslamin stage
) PR @falexwolf
2024-03-30 db 0.69.4ΒΆ
β»οΈ Add Vitessce integration PR @falexwolf
β»οΈ Refactor collections PR @falexwolf
2024-03-28 db 0.69.3ΒΆ
β¨ Introduce annotation flow via
Annotate.from_df
andAnnotate.from_anndata
PR 1 2 3 @sunnyosun
2024-03-26 db 0.69.2ΒΆ
2024-03-18 db 0.69.1ΒΆ
β¨ To try out, add lamindb.validation
with the Validator
class PR @sunnyosun
2024-03-17 db 0.69.0ΒΆ
Main new features:
β¨ Integrate lamindb with git PR PR @falexwolf
β¨ Introduce
ln.finish()
, track run finish times asrun.finished_at
, renamerun.run_at
torun.started_at
, upload notebooks duringln.finish()
PR @falexwolfπΈ Upload script source code and environment during
ln.track()
PR @falexwolf
Other changes:
β¨ Allow including simple related fields in
.df()
PR @falexwolfπ Move transform settings into settings PR @falexwolf
β¨ Add
latest_version
filter forQuerySet
PR @falexwolfπ Rename
transform.short_name
totransform.key
PR @falexwolfβ»οΈ Add a JSON field to
Run
PR @falexwolf
2024-03-11 db 0.68.2ΒΆ
πΈ Move transform & run artifacts into cache before uploading PR @falexwolf
πΈ More sensible transform types PR @falexwolf
π Rename
lnschema_lamin1
towetlab
PR @falexwolf
2024-03-08 db 0.68.1ΒΆ
πΈ You can now use
ln.connect()
to connect to a LaminDB instance PR @falexwolfπΈ You can no longer delete data from non-default storage locations, as these might be tracked in other instances PR @sunnyosun
πΈ Enable transferring data from local instances to remote instances PR @sunnyosun
2024-03-01 db 0.68.0ΒΆ
πΈ Decouple features linking from Artifact construction PR 1 2 3 @sunnyosun.
# default constructor for PathLike
artifact = ln.Artifact("mysc.h5ad", description="raw data")
# from_ constructors for other types
artifact = ln.Artifact.from_anndata(mysc_adata, description="raw data") # no longer links features
artifact = artifact.save()
# high-level feature linking
artifact.features.add_from_anndata(var_field=bt.Gene.ensembl_gene_id)
artifact.features.add_from_df()
# low-level feature linking
meta = ln.Feature.from_values(mysc_adata.obs.columns, field="name")
genes = bt.Gene.from_values(mysc_adata.var.ensembl_gene_id, field="ensembl_gene_id")
artifact.features.add(genes, slot="obs")
artifact.features.add(genes, slot="var")
# labels linking (no change)
labels = ln.ULabel.from_values(adata.obs.donor, field=...)
ln.save(labels)
artifact.labels.add(labels)
πΈ Can now use
ln.track()
withoutlamin track
PR @falexwolfπ
lamin stage
respects new URL design PR @falexwolfπ Rename
.dev
to.core
PR @falexwolf
2024-02-02 db 0.67.3ΒΆ
πΈ Can now import
bionty
instead oflnschema-bionty
PR @sunnyosunβ»οΈ Use Click for CLI PR @chaichontat
π¨ Make
Collection.save()
ACID PR @falexwolf⨠Add
add_to_version_family
PR @sunnyosunπ Transfer
collection.artifacts
PR @sunnyosun
2024-01-14 db 0.67.2ΒΆ
β¨ Enable staging notebooks & code using the CLI PR @falexwolf
2024-01-12 db 0.67.1ΒΆ
π Fix idempotency of
collection.save()
PR @falexwolfπΈ Disallow bulk-delete for Artifact, Transform & Collection PR @falexwolf
πΈ Init transform versions at 1 PR @falexwolf
β¨ Load json and html files PR @falexwolf
2024-01-11 db 0.67.0ΒΆ
π Rename
.bionty
to.public
,.from_bionty
to.from_public
PR @sunnyosun
2024-01-09 db 0.66.1ΒΆ
π Fix id matching in view_lineage PR @sunnyosun
β»οΈ Incorporate edge cases in
inner
andouter
join inCollection.mapped
PR @Koncopdπ¨ Not create organism records when calling
.bionty()
PR @sunnyosun
2024-01-07 db 0.66.0ΒΆ
πΈ Add anonymous access (now works without login) PR1386 @falexwolf
π¨ Introduce ordered collections and simplify
.mapped()
PR1390 @falexwolfπ Re-write quickstart PR1387 @falexwolf
2024-01-05 db 0.65.1ΒΆ
π©Ή Prepare a potential migration of the hub to Django PR1385 @falexwolf
πΈ Various improvements PR1384 @falexwolf
π©Ή Track suffix of requirements.txt PR1383 @falexwolf
β¨ Add outer join and categories caching to Collection.mapped PR1380 @Koncopd
β»οΈ Except memory error PR1382 @falexwolf
2024-01-02 db 0.65.0ΒΆ
π Rename
Dataset
toCollection
PR1377 @falexwolf⨠Track run environment PR1368 @falexwolf
β¨ Allow transfer from private instances PR1370 @falexwolf
πΈ Speed up transfer and enable transfer parents PR1371 @sunnyosun
π¨ Version based on
stem_uid
instead ofinitial_version_id
and replace__lamindb_uid_prefix__
with__transform_stem_uid__
PR1369 PR1375 PR1373 @bpenteado @falexwolfπ¨ Name
.lndb
files by instance id PR1372 @falexwolf
biontyΒΆ
Name |
PR |
Developer |
Date |
Version |
---|---|---|---|---|
π Rename |
2024-01-12 |
0.36.0 |
||
π Rename |
||||
π Rename |
2024-07-26 |
0.44.0 |
||
π¨ Do not add obsolete terms due to ontology_id duplication |
2024-07-25 |
|||
β‘οΈ Speed up parents |
2024-07-22 |
|||
π Rename registry to record |
2024-07-17 |
|||
β»οΈ Consciously use class method |
2024-07-10 |
|||
π Fix clashing reverse accessors between |
2024-06-13 |
0.43.0 |
||
β»οΈ Reformulate data lineage, remove json field from run |
2024-05-19 |
0.42.0 |
||
β»οΈ Protect gene, protein, cell_marker & pathway in their FeatureSet relationships |
2024-05-18 |
|||
ποΈ Naming conventions for link tables, protecting deletion in link tables, maintaining integrity upon label & feature renames |
2024-05-18 |
|||
β»οΈ Account for migrations in lnschema_core |
2024-05-17 |
|||
π₯ Prune migrations |
2024-05-16 |
|||
ποΈ Spell out link tables with |
2024-05-16 |
|||
π₯ Remove linking Collection to all Bionty entities |
2024-05-15 |
|||
β¨ Add sources |
2024-05-14 |
|||
π¨ Fix passing arguments to from_public |
2024-05-13 |
|||
π Fix organism |
2024-05-08 |
|||
ποΈ Fix public_source in inspect |
2024-04-18 |
|||
π Fix syncing public sources |
2024-04-11 |
|||
β¨ Add PublicSource.set_as_currently_used |
2024-03-14 |
0.41.4 |
||
βοΈ Fix encoding |
2024-01-12 |
0.38.4 |
||
ποΈ Re-encode PublicSource |
2024-01-10 |
0.38.3 |
||
π Rename .bionty to .public |
2024-01-09 |
|||
πΈ Do not create organism when calling bionty |
2024-01-08 |
|||
π Rename |
2023-12-23 |
0.37.0 |
||
π Rename |
2023-12-11 |
0.36.0 |
||
β¬οΈ Enabled ID conversion via return_field |
2023-12-02 |
|||
π Fix save parents with bionty_source |
2023-11-23 |
|||
β¨ Added functions to sync bionty source |
2023-11-16 |
0.35.1 |
||
π Rename FK organism to organisms in BiontySource |
2023-11-13 |
0.35.0 |
||
β¨ Add |
2023-10-23 |
0.34.0 |
||
π Rename |
2023-10-19 |
0.33.0 |
||
βοΈ Fix uid encoder |
2023-10-18 |
0.32.2 |
||
π Migrate to integer primary keys |
2023-10-13 |
0.32.0 |
||
π Mute repetitive warning for saving parents |
2023-09-20 |
0.31.2 |
||
β¬οΈ Silence download bar for <5MB files |
2023-09-08 |
0.31.1 |
||
π¨ Return |
2023-09-07 |
0.31.0 |
||
β¨ Allow non-default bionty sources in LaminDB |
2023-09-07 |
|||
β»οΈ Add DB-facing constructor |
2023-08-28 |
0.30.1 |
||
π¨ Make species not nullable in Gene, Protein, CellType |
2023-08-24 |
|||
β»οΈ Use |
2023-08-23 |
0.30.0 |
||
π Rename map_synonyms to standardize |
2023-08-16 |
0.29.5 |
||
π Rename ORM to Registry |
2023-08-05 |
|||
π Added stable_id to Gene |
2023-07-31 |
0.29.0 |
||
π Rename select to filter |
2023-07-31 |
|||
π¨ Switch biontysource id to hash id |
2023-07-25 |
0.28.2 |
||
πΈ New settings |
2023-07-25 |
0.28.1 |
||
π¨ Link all entities to files and datasets |
2023-07-24 |
0.28.0 |
||
π Replace |
2023-07-24 |
|||
βοΈ Fix docstrings |
2023-07-21 |
0.27.4 |
||
π¨ Make species name unique |
2023-07-21 |
|||
π¨ Gene table unique on ensembl id |
2023-07-18 |
0.27.0 |
||
π¨ Fix migration |
2023-07-18 |
|||
π Rename Readout to ExperimentalFactor |
2023-07-17 |
|||
πΈ Trigger instance loading for users |
2023-07-06 |
0.26.2 |
||
β‘οΈ Speed up parents ingestion |
2023-07-04 |
0.26.1 |
||
πΈ Add settings |
2023-06-30 |
0.25.4 |
||
ποΈ Allow bulk saving parents without causing conflicts |
2023-06-30 |
0.25.2 |
||
β¨ Added self-referential |
2023-06-29 |
0.25.0 |
||
β»οΈ Replaced ln.parse with orm.from_values |
2023-06-27 |
0.24.0 |
||
π Move add_synonym to BaseORM |
2023-06-22 |
0.23.5 |
||
β¬οΈ Fix synonyms duplication check |
2023-06-22 |
|||
ποΈ Do not check existing synonyms when db table is empty |
2023-06-20 |
|||
π¨ Create multiple records with .from_bionty |
2023-06-20 |
0.23.3 |
||
π Save to DB if record already exists for add_synonyms |
2023-06-20 |
0.23.2 |
||
π Fixed all related_names |
2023-06-20 |
0.23.1 |
||
π·οΈ Change name to a required field for ontology tables |
2023-06-19 |
0.23.0 |
||
π¨ Consolidate schema, remove non-crucial fields |
2023-06-16 |
0.22.0 |
||
π Rename |
2023-06-10 |
0.21.3 |
||
π Rename Featureset to FeatureSet |
2023-06-10 |
0.21.2 |
||
βͺ Change species uid to 4 char |
2023-06-09 |
0.21.1 |
||
π¨ Change on_delete to PROTECT |
2023-06-09 |
0.21.0 |
||
π¨ Remove unnecessary null=True, blank=True |
2023-06-08 |
0.19a6 |
||
β»οΈ Simplified species code |
2023-06-08 |
0.19a4 |
||
π Rename BiontyVersions to BiontySources |
2023-06-07 |
0.19a3 |
||
π Migrate |
2023-06-05 |
0.19a1 |
||
β¨ Added |
2023-06-02 |
0.18.3 |
||
β¨ Add |
2023-06-01 |
|||
π Must pass a species when creating record from lookup |
2023-05-30 |
0.18.2 |
||
β¨ Added |
2023-05-30 |
0.18.1 |
||
π Fix created_by_id in Readout |
2023-05-28 |
0.18.0 |
||
π¨ Change .bionty to a method |
2023-05-28 |
|||
π Default species to None and not pass to Bionty |
2023-05-27 |
0.18a6 |
||
π Fix 0.18.0 sqlite migration script |
2023-05-27 |
|||
β¨ Add |
2023-05-27 |
0.18a5 |
||
π Fix table name for id_encoder |
2023-05-27 |
|||
β¬οΈ Update lamindb and bionty versions |
2023-05-27 |
|||
π·οΈ Restored Optional type annotation |
2023-05-26 |
|||
ποΈ Remove SQL-level schema modules |
2023-05-25 |
0.18a2 |
||
π Fix last migration |
2023-05-25 |
0.17.1 |
||
π± Add CreatedBy and CreatedAt to all entities |
2023-05-25 |
0.17.0 |
||
π Rename bt.Entity to bt.Bionty |
2023-05-25 |
|||
β¬οΈ Upgrade to bionty 0.13 |
2023-05-09 |
0.16.4 |
||
β¨ Added synonyms field to CellMarker |
2023-05-09 |
0.16.3 |
||
π Fix dependencies |
2023-04-27 |
0.16.2 |
||
π¨ Move ._entity to private |
2023-04-27 |
0.16.1 |
||
π₯ Enable |
2023-04-24 |
0.16.0 |
||
β‘ Fix adding species |
2023-04-19 |
0.15.2 |
||
β¨ Add ._entity to knowledge class for features parsing |
2023-04-18 |
0.15.1 |
||
π¨ New design of the knowledge API |
2023-04-17 |
0.15.0 |
||
β»οΈ Refactor knowledge |
2023-03-28 |
0.14.0 |
||
β¨ Added Readout |
2023-03-27 |
0.13.0 |
||
π Move knowledge guide from lamindb here |
2023-03-27 |
|||
β¬οΈ Updated bionty and lamindb deps |
2023-03-27 |
0.12.2 |
||
π· Upgrade to latest cookiecutter |
2023-03-27 |
|||
π Fix |
2023-03-25 |
0.12.1 |
||
β»οΈ Switch to class property |
2023-03-24 |
0.12.0 |
||
β¨ Expose bionty functions with knowledge decorator |
2023-03-24 |
0.11.0 |
||
π Fix Readout population |
2023-03-23 |
0.10.1 |
||
β¬οΈ Update CellMarker columns for bionty 0.10 |
2023-03-21 |
0.10.0 |
||
β¨ Add CellLine, Pathway, Phenotype |
2023-03-21 |
0.9.0 |
||
π Fix CI |
2023-03-21 |
|||
β¬οΈ Upgrade to bionty 0.9.0 |
2023-03-20 |
0.8.1 |
||
π¨ Allow hashing external IDs |
2023-03-10 |
|||
β¬οΈ Stable release of bionty 0.8.0 |
2023-03-09 |
0.8.0 |
||
β¬οΈ Bionty>=0.8rc3 |
2023-03-09 |
0.8rc2 |
||
β¨ Use ontology_id as the id for Tissue, CellType, Disease |
2023-03-07 |
0.8.0rc1 |
||
β¬οΈ Upgrade bionty |
2023-03-06 |
|||
π₯ Remove migration files |
2023-02-14 |
0.7.0 |
||
β¬οΈ Upgrade and rename |
2023-02-14 |
0.6.9 |
||
π Fixed taxon_id type |
2023-01-17 |
0.6.8 |
||
β¬οΈ Upgrade dependencies |
2023-01-17 |
0.6.7 |
||
βͺ Revert the last PR |
2023-01-17 |
|||
π Fixed typo for postgres |
2023-01-16 |
0.6.6 |
||
π¨ Change |
2023-01-13 |
|||
π· Extend CI to py3.8-3.10 |
2023-01-12 |
|||
π Rename |
2023-01-05 |
|||
π Fix migration for sqlite |
2023-01-05 |
0.6.5 |
||
β»οΈ Treat link tables as in all other schema modules |
2023-01-05 |
0.6.4 |
||
π Move knowledge version tables into module |
2023-01-05 |
0.6.3 |
||
π§ͺ Added test for ontology autopopulate |
2022-12-09 |
|||
β Add migrations test |
2022-12-08 |
|||
β¨ Added bionty_version table |
2022-12-07 |
0.6.2 |
||
π¨ Updated bionty_versions |
2022-12-05 |
|||
β¨ Added |
2022-11-18 |
0.6.1 |
||
ποΈ Introduce relationships, move Features table to core |
2022-11-17 |
0.6.0 |
||
β‘ Implemented knowledge as a decorator |
2022-11-11 |
0.5.4 |
||
β¨ Added populator for ontologies |
2022-11-11 |
|||
β»οΈ Refactor knowledge population |
2022-11-06 |
|||
π Fixed postgres migration script |
2022-11-06 |
0.5.3 |
||
β¨ Use bionty to populate species |
2022-11-06 |
0.5.2 |
||
π Fix prefix |
2022-11-03 |
0.5.1 |
||
π¨ Modularize and capitalize |
2022-11-03 |
0.5.0 |
||
π¨ Updated cell marker id gen |
2022-10-25 |
0.4.5 |
||
βοΈ Updated species id to be 3 chars |
2022-10-24 |
0.4.4 |
||
π§βπ» Added naming convention |
2022-10-20 |
|||
π©Ή Fix type annotations of primary keys |
2022-09-29 |
0.4.3 |
||
βοΈ Changed ids to str |
2022-09-29 |
0.4.2 |
||
π± Added |
2022-09-27 |
0.4.1 |
||
π Update primary keys to universal ids |
2022-09-22 |
0.4.0 |
||
π Rename column in version table, add testdb, and migration script |
2022-09-22 |
0.3.1 |
||
β¨ Add migrations infra |
2022-09-22 |
0.3.0 |
||
π©Ή Added unique constraints |
2022-09-22 |
|||
π Fixed API ref |
2022-09-06 |
0.2.4 |
||
π¨ Import additional modules, species -> species_id |
2022-08-28 |
0.2.3 |
||
π Rename gene_symbol to symbol, protein_name to name |
2022-08-28 |
0.2.2 |
||
β¬οΈ Update schema to match bionty 0.2.0 |
2022-08-28 |
0.2.1 |
||
π Rename |
2022-08-19 |
0.2.0 |
||
π§ Add schema module id |
2022-08-18 |
|||
π± Updated the gene table to match new ensembl table |
2022-08-18 |
0.1.4 |
||
π¨ Changed type of |
2022-08-15 |
0.1.3 |
||
π Move |
2022-07-31 |
|||
β¨ Introduced featureset to replace geneset and proteinset |
2022-07-31 |
0.1.2 |
||
π¨ Changed |
2022-07-23 |
0.1.1 |
||
π Move code from |
2022-07-23 |
0.1.0 |
wetlabΒΆ
Name |
PR |
Developer |
Date |
Version |
---|---|---|---|---|
β»οΈ Model categoricals via simple |
2024-08-02 |
|||
β¨ Improved support for perturbations |
2024-07-29 |
|||
π Rename |
2024-03-08 |
0.27.0 |
nbprojectΒΆ
Name |
PR |
Developer |
Date |
Version |
---|---|---|---|---|
β¬οΈ Upgrade to pydantic v2 |
2024-07-23 |
|||
β‘οΈ Warn instead of raising the exception when ipylab is not installed |
2024-05-08 |
0.10.3 |
||
β»οΈ Make ipylab an optional dependency |
2024-05-06 |
|||
π Silence erroneous logging |
2024-02-27 |
0.10.1 |
||
πΈ Init version at 1 |
2024-01-11 |
0.10.0 |