CHANGELOG.md

Latch SDK Changelog

2.52.4 - 2024-09-19

Changed

• Nextflow
  • Fix typo in Nextflow base image

2.52.3 - 2024-09-17

Changed

• Nextflow
  • Update nextflow base image to version v2.0.0

2.52.2 - 2024-09-04

Changed

• Nextflow
  • Update nextflow base image to version v1.1.8

2.52.1 - 2024-08-30

Fixed

• Move tty and termios imports to enable latch cp on Windows

2.52.0 - 2024-08-30

Fixed

• Make latch cp work on Windows without WSL

2.51.2 - 2024-08-27

Fixed

• Bump lytekit version to fix download of empty files

2.51.1 - 2024-08-21

Fixed

• Remove caching from tinyrequests module

2.51.0 - 2024-08-16

Added

• New task annotations for V100 GPU enabled nodes
  • @v100_x1_task: 1 V100 GPU
  • @v100_x4_task: 4 V100 GPUs
  • @v100_x8_task: 8 V100 GPUs

2.50.6 - 2024-08-15

Added

• The --chunk-size-mib to latch cp which allows users to configure the chunk size of uploads

Changed

• Lower the default chunk size for latch cp to 64 MiB
• latch cp now reuses connections for speed

2.50.5 - 2024-08-12

Fixed

• Fix a bug where GPU template selection wouldn't happen correctly in latch init

2.50.4 - 2024-08-09

Changed

• Nextflow
  • Update nextflow base image to version v1.1.7

2.50.3 - 2024-08-08

Fixed

• Nextflow
  • Normalize result paths before publishing results

2.50.2 - 2024-08-07

Dependencies

• lytekit 0.15.10 -> 0.15.11 which parallelizes file downloads from Latch Data

2.50.1 - 2024-08-05

Added

• Nextflow
  • Report workdir size on workflow completion

2.50.0 - 2024-08-02

Added

• Add git commit information to version string if exists

2.49.10 - 2024-08-02

Fixed

• Pin cryptography to remove warning messages when importing paramiko

2.49.9 - 2024-08-01

Fixed

• Better error messages when using latch exec on a task that is not yet running

2.49.8 - 2024-07-29

Fixed

• Nextflow
  • Indentation error in samplesheet constructor function call

2.49.7 - 2024-07-26

Changed

• Nextflow
  • Cleanup Nextflow logging
  • Update nextflow base image to version v1.1.6

2.49.6 - 2024-07-23

Added

• Ability to publish results to be displayed on executions Results page

2.49.5 - 2024-07-20

Added

• Add --cores parameter to latch cp

2.49.4 - 2024-07-19

Added

• allowed_tables argument to LatchParameter to constrain the set of registry tables selectable from a samplesheet parameter

2.49.3 - 2024-07-19

Added

• Ability to override the target workspace for registration using the LATCH_WORKSPACE env variable.

2.49.2 - 2024-07-18

Added

• Nextflow
  • Make EFS storage period configurable

2.49.1 - 2024-07-17

Fixed

• latch cp bug where directories containing symlinks would hang and not complete uploading

2.49.0 - 2024-07-17

Changed

• Nextflow
  • Update nextflow base image to version v1.1.5

2.48.9 - 2024-07-16

Added

• Nextflow
  • Make execution profile configurable via UI

2.48.8 - 2024-07-12

Changed

• Nextflow
  • Update nextflow base image to version v1.1.4

2.48.7 - 2024-07-11

Fixed

• Sync
  • Update objects with no ingress event

2.48.4 - 2024-07-10

Added

• Sync
  • Add option for number of cores

2.48.3 - 2024-07-08

Added

• Snakemake
  • Don't throw an exception on subprocess.CalledProcessError, sys.exit(1) instead to avoid polluting stdout with a traceback

Dependencies

• lytekit 0.15.9 -> 0.15.10 which removes unnecessary prints in exception wrappers

2.48.2 - 2024-07-06

Added

• Nextflow
  • ignore .git directory when copying /root to workdir

2.48.1 - 2024-07-05

Added

• Nextflow
  • use nextflow dockerfile instead of downloading the binary directly

2.48.0 - 2024-07-03

Added

• Nextflow
  • bump nf runtime version to 1.1.3

2.47.9 - 2024-07-02

Dependencies

• Use lytekit==0.15.9 which includes retries for file downloads

2.47.8 - 2024-06-29

Fixed

• latch sync upload in parallel
• latch sync missing normalize_path call
• latch sync cosmetic path display extra slash

2.47.7 - 2024-06-28

Fixed

• Timeout in tinyrequestst

2.47.6 - 2024-06-27

Fixed

• Snakemake + Nextflow
  • fix about page file validation

2.47.5 - 2024-06-26

Fixed

• Nextflow
  • remove storage_gib parameter from pvc provisioning request

2.47.4 - 2024-06-25

Added

• Nextflow
  • bump nf runtime version to 1.1.1

2.47.3 - 2024-06-25

Added

• Nextflow
  • bump nf runtime version to 1.1.0

2.47.2 - 2024-06-24

Added

• Snakemake
  • expose underlying Latch paths in config object

2.47.1 - 2024-06-22

Added

• Nextflow version 1.0.11

Fixed

• Snakemake
  • fix dataclass name collisions when generating metadata for Snakemake workflows

2.47.0 - 2024-06-20

Added

• Nextflow version 1.0.10

2.46.9 - 2024-06-20

Fixed

• Snakemake
  • fix metadata_root param for Snakemake workflows

2.46.8 - 2024-06-19

Added

• Nextflow
  • Support for relaunching from failed task using -resume flag

2.46.7 -- 2024-06-19

Fixed

• Nextflow
  • Bump Nextflow version to 1.0.8 to add retries on failure

2.46.6 - 2024-06-14

Added

• Nextflow + Snakemake
  • Add --metadata-root option to latch register

Fixed

• Nextflow
  • Bump Nextflow version to fix releasing workflow to different workspace

2.46.5 - 2024-06-13

Added

• Nextflow
  • Command to upgrade nextflow version

2.46.4 - 2024-06-13

Fixed

• Nextflow
  • Bump nextflow version to v1.0.4 -- fixes large file uploads

2.46.3 - 2024-06-12

Fixed

• Nextflow
  • Upload .nextflow.log on success and failure
  • Add tolerations to nextflow runtime task
  • Bump nextflow version to v1.0.2

2.46.2 - 2024-06-11

Added

• New error messages when trying to access registry projects/tables/records that don't exist.

2.46.1 - 2024-06-10

Removed

• Nextflow
  • Remove /finalize call at end of workflow

2.46.0 - 2024-06-10

Added

• Nextflow
  • Bump version from v1.0.0 to v1.0.1 -- resolves upload data corruption

2.45.8 - 2024-06-08

Fixed

• Nextflow
  • Fix default generation for parameters with type: typing.Optional[LatchFile,LatchDir]

2.45.7 - 2024-06-07

Added

• Nextflow
  • Support for About page
  • Pin Nextflow version to latch version (deprecate --redownload-dependencies)

Added

• Snakemake
  • Support for adding About page content from a markdown file

2.45.6 - 2024-06-04

Added

• Nextflow
  • Support for generating metadata from nextflow_schema.json
  • Command to generate Nextflow entrypoint without registering

Fixed

• Make LatchRule class a dataclass

2.45.5 - 2024-06-03

Added

• Support for uploading Nextflow workflows

2.45.4 - 2024-05-29

Changed

• TableUpdater.upsert_record no longer does file path resolution, and instead defers that operation to when the update commits. This drastically speeds up registry table updates to blob-type columns.

2.45.3 - 2024-05-28

Added

• Support selecting organization workspaces with latch workspace

2.45.2 - 2024-05-20

Dependencies

• Bump docker version to fix docker/docker-py#3256

2.45.0 - 2024-05-20

Fixed

• Latch resource limit on mem-512-spot should be 485 Gi instead of 490 Gi

2.44.0 - 2024-05-19

Fixed

• Accomodates the migration of personal workspaces to team workspaces.

2.43.3 - 2024-05-16

Fixed

• Snakemake
  • remove conversion of primitive types to string for input params
  • add support for output directories

2.43.2 - 2024-05-16

Fixed

• Circular import when importing latch constants

• Snakemake
  • support for running python scripts inside containers

2.43.1 - 2024-05-15

Fixed

• Cleanup toleration assignment

Added

• Support up to 126 cores and 975 GiB of memory in custom tasks

2.42.1 - 2024-05-08

Fixed

• Workflow identifier should be immutable per latch init
• Latch workspace does not display selected workspace when authenticated with workspace token
• Workspace id determination failing when authenticated with workspace token

2.42.0 - 2024-05-02

• Adding support for GCP mount paths

2.41.3 - 2024-04-29

Fixed

• Allow the use of **kwargs in dynamic resource allocation functions

2.41.2 - 2024-04-23

Fixed

• Snakemake
  • Namespace Snakemake execution outputs by execution name

2.41.1 - 2024-04-22

Fixed

• Snakemake
  • Add support for using directories as inputs to rules

2.41.0 - 2024-04-19

Added

• --wf-version flag to develop to use a container for a specific workflow version
• --disable-sync flag to develop to disable automatic syncing of local files. Useful for inspecting workflow code from a past version without overwriting with divergent local changes.

2.40.6 - 2024-04-12

Fixed

• Actually fix the issue where functions that use current_workspace would break if called from an execution

2.40.5 - 2024-04-09

Fixed

• bump flytekit version to 0.15.6 which fixes retries in dynamic resource allocation for map tasks

2.40.4 - 2024-04-09

Fixed

• Issue where functions that use current_workspace would break if called from an execution
• Issue where CLI commands that required an auth method would not print the correct error message if no auth was present

2.40.3 - 2024-04-09

• bump flytekit version to 0.15.5

2.40.2 - 2024-04-09

Fixed

• latch register failing when using launchplans with file or directory types

2.40.1 - 2024-04-06

Added

• add support for allocating task resources at runtime

2.40.0 - 2024-04-05

Fixed

• latch commands default to the user's default workspace instead of personal workspace

2.39.7 - 2024-04-03

Documentation

• latch cp
  • Commandline docstring states recursive default behavior.

2.39.6 - 2024-04-02

Fixed

• latch sync
  • prints error when case other than local -> remote is attempted

2.39.4 - 2024-03-11

Added

• Snakemake
  • Add container_args field in EnvironmentConfig

2.39.3 - 2024-03-07

Fixed

• Snakemake
  • fix bug where two rules with the same input parameter name causes JIT step to fail

2.39.3 - 2024-03-05

Fixed

• Fix bug where temporary SSH keys were getting added but not removed from the SSH Agent during workflow registration

2.39.2 - 2024-03-01

Fixed

• Fix bug LPath resolves to parent node if path does not exist

Deprecated

• latch mkdir command (replaced with latch mkdirp)
• latch rm command (replaced with latch rmr)
• latch touch
• latch open

2.39.1 - 2024-02-27

Added

• add LPath support for uploading and copying to non-existent directories
• clear LPath cache after modification operations such as rm and upload

Fixed

• skip symlinks that point to non-existent files when running latch cp

2.39.0 - 2024-02-21

Added

• add LPath implementation
• add support for registering workflows without Latch metadata

2.38.9 - 2024-02-14

Added

• Snakemake
  • add support for optional input parameters

2.38.8 - 2024-01-26

Fixed

• Snakemake
  • fix bug in ruleorder directive caused by block_content monkey patch returning None

2.38.7 - 2024-01-26

Fixed

• Snakemake
  • warn instead of error when config parameter type cannot be parsed in generate-metadata command

2.38.6 - 2024-01-26

Added

• Snakemake
  • support for config files with nested file paths
  • GPU support for non-container tasks
  • Add cores field to SnakemakeMetadata object

2.38.5 - 2024-01-22

Fixed

• Broken default in snakemake metadata which prevented registration of any workflow

2.38.4 - 2024-01-20

Added

• Snakemake
  • update defaults for conda + containers to False

2.38.3 - 2024-01-19

Added

• Snakemake
  • support for pulling images from private container registries
  • add config field for running tasks in conda and container environments

Fixed

• Snakemake
  • fix regression in 2.38.2 that caused failure to resolve upstream nodes for target files

2.38.2 - 2024-01-17

Added

• Snakemake
  • support for per-task containers in Snakemake workflow using the container directive

Fixed

• Snakemake
  • add _jit_register suffix when resolving Snakemake workflow name for latch develop
  • use variable_name_for_value instead of variable_name_for_file when resolving upstream jobs for target files

2.38.1 - 2024-01-15

Added

• The --open option to latch register, which if passed in, will open the workflow in the browser after successful registration

Fixed

• Snakemake
  • remove .latch directory copy from Dockerfile generation to avoid unexpected file overrides
  • limit pulp package version to < 2.8 to fix snakemake import failure

2.38.0 - 2024-01-13

Added

• The latch exec command to spawn a shell inside a running task.

2.37.1 - 2024-01-08

Added

• Snakemake
  • support for latch develop for JIT workflow

Fixed

• Snakemake
  • user input config overrides default config instead of merging
  • JIT workflow fails if the same keyword is used to define two different input parameters
  • fail to serialize snakemake_data when any params are defined as pathlib.Path

2.37.0 - 2023-12-11

Added

• rename_current_execution function which allows programmatic execution renaming.

2.36.11 - 2023-11-28

Added

• Snakemake
  • ability to cache snakemake tasks using the --cache-tasks option with latch register

Changed

• Minor aesthetic enhancements to latch workspace
  • the currently active workspace is now marked
  • the current selection is marked with a > for enhanced readability on terminals with limited color support

2.36.10 - 2023-11-17

Fixed

• Snakemake
  • bug in 2.36.9 where output directories would still fail to upload because of a missing pathlib.Path -> str conversion.

2.36.9 - 2023-11-16

Fixed

• Snakemake
  • bug where a snakemake task would fail to upload output directories

2.36.8 - 2023-11-14

Fixed

• Snakemake
  • bug where a snakemake workflow would only run successfully for the user who registered it

2.36.7 - 2023-11-13

Added

• Snakemake
  • added best effort display name parsing for generate-metadata
  • tasks now upload their intermediate outputs for better debugging

Fixed

• Snakemake
  • bug where update_mapping would iterate over the entirety of /root

2.36.6 - 2023-11-09

Added

• Added ability to skip version check using an env variable

2.36.5 - 2023-11-08

Fixed

• Bug in latch login where not having a token would prevent token generation

2.36.4 - 2023-10-25

Added

• Added ability to get a pandas Dataframe from a registry table.
• Added Multiselect to LatchAppearance
• Snakemake
  • fixed case where config values would not be populated correctly in the JIT workflow

Changed

• Better error messaging for both latch cp and latch mv.

2.36.3 - 2023-10-25

Fixed

• Bug where Python 3.8 clients would crash due to a broken type annotation

2.36.2 - 2023-10-25

Changed

• Snakemake
  • Log files are now marked as outputs - this enables rules to use logs of previous rules as inputs

2.36.1 - 2023-10-24

Changed

• latch mv now supports glob patterns (with the same restrictions as latch cp)

2.36.0 - 2023-10-23

Added

• latch.registry.record.Record.get_table_id method for querying the ID of the table containing a given registry record
• latch.registry.table.Table.get_project_id method for querying the ID of the project containing a given registry table

2.35.0 - 2023-10-21

Added

• Snakemake
  • Remote register support
  • download field for file inputs
  • config field for file inputs
  • Blanket support for parameters of any type via the SnakemakeParameter class
  • Support for generating a latch_metadata directory from a config.yaml with latch generate-metadata
  • Support for default values for parameters

Changed

• Snakemake
  • JIT register step no longer downloads input files by default
  • latch_metadata should now be a module (directory containing an __init__.py file), as opposed to just being a file

2.34.0 - 2023-10-04

Added

• Snakemake
  • directory modifier for input / outputs
  • Support temp by removing from compiled rules. All files / directories are temporary because they are deleted at the end of each job on Latch.
  • multiext output modifier
  • report output modifier
  • params in rules

Fixed

• Snakemake
  • Replace skipped rules with Ellipsis. Supports rules nested in conditionals where previously an empty block was produced.
  • Patched parser to generate compiled code for workflow.include calls Compiled workflow.include should carry print_compilation keyword (snakemake/snakemake#2469)
  • Detect use of conda keyword and install in image. This effectively supports wrapper/conda keywords.
  • Iterable, Generator cause issues as type hints when imported from collections.abc rather than typing

2.33.0 - 2023-09-29

Added

• Add latch sync for synchronization from local to remote directories that only uploads modified content

2.32.8 - 2023-09-07

Fixed

• Snakemake:
  • Better errors if Snakefile or latch_metadata.py file missing
  • Correct issues with snakemake example project

2.32.7 - 2023-09-07

Fixed

• Snakemake:

  • --snakemake for latch dockerfile command to generate Dockerfile with necessary instructions

  • Snakemake example for latch init

2.32.6 - 2023-09-07

Fixed

• A bug in latch develop where images for newly registered workflows could not be found.

2.32.5 - 2023-08-28

Fixed

• Snakemake:
  • Ignore global ruleorder directive
  • Ignore temporary condition on output values

2.32.4 - 2023-08-28

Fixed

• Fixed a bug in latch ls where datetime.isoformat was called on strings with timestamps (which is not supported on python < 3.11)

2.32.3 - 2023-08-26

Fixed

• Snakemake issues
  • bounded snakemake versions to prevent compatibility issues that arise in later versions
  • small bugs in list json encoder
  • mishandled http issues.

2.32.2 - 2023-08-25

Fixed

• Fixed latch ls to work with all latch URLs
• Fixed autocomplete bug where no completion results would be returned for longer paths

2.32.1 - 2023-08-24

Fixed

• Corrected dataclass import and removed multiprocessing logging from latch cp.

2.32.0 - 2023-08-23

Changed

• latch cp can now handle directories with up to 50k objects

Fixed

• Various vestigial bugs in latch develop that blocked certain users

2.31.1 - 2023-08-08

Changed

• Any CLI command will now display a message if no authentication token is found

2.31.0 - 2023-07-28

Changed

• latch stop-pod renamed to latch pods stop

2.30.0 - 2023-07-27

Added

• Support for python 3.11

Dependencies

• pinned lytekit to v0.15.2 to remove numpy + pandas + pyarrow dependencies
• pinned lytekitplugins-pods to v0.6.1 to remove dependency on numpy
• pinned latch-sdk-gql to 0.0.6 which supports 3.11
• pinned latch-sdk-config to 0.0.4 which supports 3.11

2.29.0 - 2023-07-26

Added

• stop-pod command to the CLI. Allows the user to stop a pod in which the CLI resides or to stop a pod using its id.

2.28.0 - 2023-07-25

Added

• Tasks explicitly request ephemeral storage
• custom_task and custom_memory_optimized_task allow selecting storage size
• custom_memory_optimized_task functionality merged into custom_task

Deprecated

• custom_memory_optimized_task

2.27.4 - 2023-07-18

Changed

• changed beta register implementation

2.27.3 - 2023-07-18

Dependencies

• pinned lytekit to v0.14.15 to bring in marshmallow-enum as a dependency.

2.27.2 - 2023-07-17

Fixed

• fixed bug where LatchFiles/LatchDirs would provide file:// URIs instead of Unix paths, which was causing errors in, e.g., calls to open().

2.27.1 - 2023-07-15

Fixed

• fixed bug where LatchFiles/LatchDirs wouldn't respect the workspace selected using latch workspace.

2.27.0 - 2023-07-15

Added

• Added .iterdir() method to LatchDir to iterate through subdirectories

2.26.2 - 2023-07-11

Fixed

• Fix unclosed file in lytekit upload code

2.26.1 - 2023-07-10

Fixed

• LatchFiles accessed through registry are downloaded to a file with the same name as the file on latch

2.26.0 - 2023-07-07

Changed

• Gated latch develop resource selection behind an environment variable due to its slow performance

Dependencies

• Added back several dependencies to allow the old latch develop infrastructure to work properly.

2.25.2 - 2023-07-05

Fixed

• Dockerfile generation uses \ escaping: fixes bug in Conda and R template

2.25.1 - 2023-06-28

Dependencies

• Upgraded paramiko dependency to >=3.2.0 which fixes a PKey issue.

2.25.0 - 2023-06-28

Changed

• latch register experimental features (2.24.xx) are now gated behind an environment variable, and by default we use the old (pre 2.24) register backend.

2.24.12 - 2023-06-27

Dependencies

• Upgraded lytekit to version 0.14.13 to support uploading files up to 5 TiB from within a task

2.24.11 - 2023-06-27

Fixed

• Internal bug in latch register which caused an API call to be made when not necessary, resulting in an irrelevant exception being thrown

2.24.10 - 2023-06-27

Fixed

• Bug in latch cp upload path where URLs would be generated but files would not be uploaded

2.24.9 - 2023-06-27

Changed

• Added client side rate limiting to latch cp upload API calls so as to not throttle our backend.

2.24.8 - 2023-06-27

Fixed

• latch register provision timeout bug
• catch KeyboardInterrupts during register provisioning
• updated latch-base image to fix docker-in-docker workflows which use the host machine's network interface

2.24.7 - 2023-06-26

Fixed

• latch develop and latch register provision timeout increased to 30 minutes

2.24.6 - 2023-06-26

Fixed

• latch develop and latch register SSH connections timeout on inactivity

2.24.5 - 2023-06-26

Fixed

• Bug in latch develop where rsync would continually flood stdout with requests to confirm host key authenticity

2.24.3 - 2023-06-24

Added

• Rename --no-glob option shorthand to -G for latch cp

Fixed

• Bug in latch register where SSH connections were going stale

2.24.0 - 2023-06-23

Added

• Glob support for latch cp
• latch cp autocomplete
• ability to choose task size in latch develop

Changed

• Backend implementations of latch register and latch develop

2.23.5 - 2023-06-19

Fixed

• Fix limits and imports

2.23.3 - 2023-06-19

Added

• Memory optimized task type

2.23.2 - 2023-06-14

Fixed

• Template generation bug in empty wfs

2.23.1 - 2023-06-12

Fixed

• NFCore template using wrong Latch version

2.22.5 - 2023-06-10

Added

• When a CLI command fails, metadata (latch version, current python, os info, etc) is printed.
• There is now a prompt on failure to generate a crash report. Previously reports were generated automatically which was slow and sometimes error-prone.

Fixed

• Bugs that broke support for Python 3.8 users:
  • Fixed imports of functools.cache
  • Fixed with statements with multiple contexts

Dependencies

• Removed unused packages
  • awscli
  • uvloop
  • prompt-toolkit

2.22.4 - 2023-06-08

Fixed

• catalogMultiCreateExperiments instead of catalogMultiUpsertExperiments in registry API

2.22.3 - 2023-06-08

Fixed

• catalogMultiCreateProjects instead of catalogMultiUpsertProjects in registry API

2.22.2 - 2023-06-08

Fixed

• workspace_id failing when file is empty

2.22.1 - 2023-06-05

Fixed

• latch cp failing when uploading a file into a directory without specifying the resulting filename.

2.22.0 - 2023-05-31

Fixed

• latch cp occasionally throwing an error when finalizing uploads for directories.

Added

• latch cp now supports remote -> remote copying (i.e. both source and destination are remote paths). This enables copying files across workspaces
• latch mv for moving remote files.

2.21.7 - 2023-05-29

Fixed

• Semver violation related to removed __init__.py files. These will happen again in the future but a proper major release will be created, communicated, and marketed.

2.21.6 - 2023-05-29

Dependencies

• Upgraded dependency lytekit to version 0.14.11.

2.21.5 - 2023-05-29

Fixed

• More imports in docker/NF-core template workflows have been updated to reflect the import changes outlined in the previous version.

2.21.4 - 2023-05-29

Fixed

• Imports in docker/NF-core template workflows have been updated to reflect the import changes outlined in the previous version.

2.21.3 - 2023-05-26

Added

• NFCore example workflow

Changed

• Replace docker example workflow with blastp

• Docker image selection when creating an empty workflow

• Workflow Name, Author Name prompts when creating an empty workflow

• latch cp has been rewritten and now allows for latch paths of the form

  • latch:///a/b/c
  • latch://xxx.account/a/b/c where xxx is the account ID
  • latch://shared.xxx.account/a/b/c
  • latch://shared/a/b/c
  • latch://mount/a/b/c
  • latch://xxx.node where xxx is the data ID (viewable in Latch Console)

Removed

• Unnecessary imports in __init__.py files have been removed. Statements like from latch.types import LatchFile will no longer work, and such objects should be imported from their defining files instead (in this example, the correct import is from latch.types.file import LatchFile)

2.19.11 - 2023-05-16

Fixed

• Revert an undocumented change that caused custom task settings to not work

2.19.10 - 2023-05-16

Fixed

• Typo in latch init R template

2.19.9 - 2023-05-12

Fixed

• latch cp should automatically detect file content type

2.19.8 - 2023-05-11

Fixed

• Registry API crashes when resolving paths if ~/.latch/workspace does not exist

2.19.7 - 2023-05-09

Added

• latch register will ask for confirmation unless --yes is provided on the command line

Changed

• latch register --remote is now the default. Use --no-remote to build the workflow image locally

Fixed

• latch register --remote will no longer ask for host key fingerprint verification

2.19.6 - 2023-05-08

Fixed

• Registry APIs should properly resolve files when using workspaces instead of always using the signer account

2.19.5 - 2023-05-06

Fixed

• latch workspace options should be ordered alphabetically

2.19.4 - 2023-05-04

Fixed

• Conda template registration issue and run in correct environment issue

Latch SDK Changelog

2.19.3 - 2023-04-26

Fixed

• Tasks stuck initializing on nodes that ran multiple tasks before

2.19.2 - 2023-04-24

Dependencies

• Upgrades lytekit to 0.14.10

2.19.1 - 2023-04-21

Changed

• latch cp now has a progress bar for downloads (previously they only showed for uploads)

2.19.0 - 2023-04-14

Added

• Functions for creating/deleting Projects and Tables, and creating Table columns in the Registry API

2.18.3 - 2023-04-12

Fixed

• Registry table updates should work with columns that have spaces in names

2.18.2 - 2023-04-11

Changed

• Improved Registry API __str__ and __repr__

2.18.1 - 2023-04-08

Fixed

• Registry API should work in an running asyncio event loop

2.18.0 - 2023-04-08

Added

• A new API for interacting with Latch Registry

Dependencies

• Added gql and aiohttp as dependencies

2.17.2 - 2023-04-07

Fixed

• Prevent latch cp from hitting the s3 part limits which causes large file uploads to fail

2.17.1 - 2023-04-05

Fixed

• Switched a dictionary union from |= notation to a manual for-loop to maintain support for Python 3.8.

2.17.0 - 2023-04-01

Added

• Option to disable default bulk execution mechanism when an alternative (e.g. using a samplesheet parameter) is supported by the workflow itself

2.16.0 - 2023-04-01

Added

• Verified Trim Galore adapter trimming workflow stub

2.15.1 - 2023-03-30

Fixed

• Custom tasks with less than 32 cores receiving incorrect toleration

2.15.0 - 2023-03-29

Added

• Verified MAFFT alignment workflow stub

2.14.2 - 2023-03-24

Fixed

• Parameter flow forks should preserve the order of branches

2.14.1 - 2023-03-21

Fixed

• latch commands which require authentication prompt user for token when no browser is present on machine

2.14.0 - 2023.03-18

Added

• SampleSheet metadata to LatchParameter -- allows for importing samples from Registry

2.13.5 - 2023-02-21

Fixed

• latch register ssh-keygen bug when .latch folder does not exist

2.13.4 - 2023-02-21

Dependencies

• Upgrades lytekit to 0.14.9

2.13.3 - 2023-02-21

Fixed

• Docker template uses correct base image

2.13.2 - 2023-02-21

Fixed

• Internal state file should be automatically created when running latch register and latch develop

Added

• latch init: Docker in Docker template workflow
• latch init: Docker base image
• Small, medium, and large tasks use the Sysbox runtime to run Docker and other system software within task containers

2.13.1 - 2023-02-17

Fixed

• Add latch/latch_cli/services/init/common to pypi release

2.13.0 - 2023-02-17

Added

• The latch dockerfile command which auto-generates a Dockerfile from files in the workflow directory.
• The latch init command can use base images with hardware acceleration using the --cuda and the --opencl flags
• The latch init command does not populate the workflow directory with a Dockerfile by default
• The latch init command will populate the workflow directory with a Dockerfile if passed --dockerfile
• The latch register and latch develop commands auto-generate a dockerfile from files in the workflow directory if no Dockerfile is present
• Documentation for the auto-generated Dockerfile feature

Fixed

• Quickstart tutorial is written factually
• Getting started docs are written factually

2.12.1 - 2023-02-08

Added

• latch develop documentation updates

Fixed

• latch develop throws error if user does not have rsync installed
• pip install latch installs the watchfiles package for latch develop

2.11.1 - 2023-01-25

Fixed

• LatchDir initialized with local path initialized to Path object fails on upload

2.12.0 - 2023-02-06

Added

• latch develop drops users directly into a shell in their docker environment. Local changes in the workflow directory and any subdirectories are automatically synced into the environment. Deleted local files are not deleted in the environment. However, any additions or modifications to files and directories are propagated.

Removed

• latch develop no longer drops user into REPL with multiple options -- it goes straight to a shell.

2.11.1 - 2023-01-25

Fixed

• LatchDir initialized with local path initialized to Path object fails on upload

2.11.0 - 2023-01-20

Added

• Use best practices in latch init templates
  • LatchOutputDir used to indicate output ___location on Latch
  • Regex rules used to validate files
  • Splits tasks into files
  • Include empty template
  • Remove yaml metadata from docstring
  • Use messages in examples
  • Error handling
  • Add LICENSE file
  • Add README file
• Allow user to select template in GUI or pass flag
• Allow user to run latch init .

Fixed

• LatchDir type transformer bug with Annotated types
  • LatchOutputDir is fixed

2.10.0 - 2023-01-14

Added

• The latch develop command, and with it an ecosystem supporting local development and faster debugging.
• The latch cp command now displays a x number of files out of n indicator and displays which stage of the download is going on (network request to get presigned urls vs downloading blob data).
• A new error that is thrown when there is an inconsistency between a LatchMetadata object and its associated workflow's parameters.
• The function get_secret which allows users to reference secrets they've uploaded to the Latch platform from within a workflow.

Deprecated

• The commands
  • latch rm,
  • latch mkdir, and
  • latch touch.
• The operators
  • left_join,
  • right_join,
  • inner_join,
  • outer_join,
  • group_tuple,
  • latch_filter, and
  • combine.

Removed

• Removed a broken SDK test (launching CRISPResso2)

Fixed

• requests library given higher version lower bound to fix warning with one of its dependencies
• lytekit version updated to
  • pin numpy to version 1.22 (breaking changes in later versions of this library)
  • have better behavior when downloading directories during local development
  • force retry on connection closed on file uploads (POST requests more generally)
• latch get-params will escape class attribute names (representation of Enum type) if they are python keywords
• latch preview now requires a directory argument instead of a workflow name argument, and now behaves consistently with regular parameter interface generation.
• The crash reporter now prints stack traces of caught exceptions in the correct order
• latch develop now throws an error when run on a workflow that hasn't been registered yet.
• Reworked how internal configs are stored, eschewing a flat dictionary of API endpoints in favor of a nested dataclass. This removes a small class of potential mistakes arising from misspelling, and gives the benefit of IDE intellisense.
• Made both configs singletons.

2.10.1 - 2023-01-18

Fixed

• Fixed issue with registering libraries containing nested imports used as subclasses (eg. torch )