Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / fractal-analytics-platform/fractal-server issues and pull requests

#629 - Deleting Workflow Task properties after adding them

Issue - State: closed - Opened by jluethi over 1 year ago - 4 comments

#628 - Fix bug when running fractal-server with gunicorn and more than one worker

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: bug, maintenance

#624 - Can we request < 1 CPU per task?

Issue - State: closed - Opened by jluethi over 1 year ago - 2 comments
Labels: slurm

#622 - In FractalSlurmExecutor, make `working_dir` attribute required

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#621 - When should tasks write metadata files? Should they write them to disk at all?

Issue - State: closed - Opened by jluethi over 1 year ago - 2 comments
Labels: flexibility

#620 - Refactor logging to integrate uvicorn/gunicorn, fastapi, and fractal-server

Issue - State: open - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#618 - Update the `ApplyWorkflow.log` field also for successful worfklow runs

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments

#616 - Handle the case where workflow-apply fails because datasets have zero resources

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#615 - Further tests of overheads in new SLURM backend

Issue - State: closed - Opened by tcompa over 1 year ago - 12 comments
Labels: High Priority, slurm

#613 - Fix SlurmConfigError (Validation error)

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: High Priority, slurm

#611 - Include possibility to set (some?) SLURM-batching values per workflow

Issue - State: closed - Opened by tcompa over 1 year ago - 4 comments
Labels: backlog, slurm

#610 - Rename SLURM-batching related variables

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: slurm

#609 - Validate Fractal SLURM configuration file at server startup

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: slurm

#604 - Add `end_timestamp` to `ApplyWorkflow` (server)

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#602 - Review `validate_workflow_compatibility` error

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#599 - Out of memory errors

Issue - State: open - Opened by tcompa over 1 year ago - 4 comments
Labels: Priority, slurm

#597 - Multiple calls to `sudo cat` or `sudo ls` are slow

Issue - State: closed - Opened by tcompa over 1 year ago - 24 comments
Labels: slurm

#596 - Fix (or drop?) inconsistent project-name-uniqueness constraint

Issue - State: open - Opened by tcompa over 1 year ago - 6 comments
Labels: maintenance

#592 - Import `Task` default attributes `WorkflowTask` attributes

Issue - State: closed - Opened by tcompa over 1 year ago - 3 comments

#591 - Catch error in workflow-apply endpoint

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#583 - There is currently no simple way to remove one entry from `WorkflowTask.args`

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment

#581 - Review `SlurmConfig` to specify which attributes need to scale up with number of tasks

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: Priority, slurm

#580 - Expose *all* slurm configuration variables for each WorkflowTask

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: High Priority, slurm

#579 - Where is `n_ftasks_per_script` defined?

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: High Priority, slurm

#578 - Implement an executor fo multiple-tasks SLURM jobs

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: Priority, slurm

#577 - Where are `n_parallel_ftasks_per_script` and `n_ftasks_per_script` defined?

Issue - State: closed - Opened by tcompa over 1 year ago - 26 comments
Labels: Priority, slurm

#576 - New SLURM-configuration logic (where? in config files or in submission-script preparation?)

Issue - State: closed - Opened by tcompa over 1 year ago - 5 comments
Labels: Priority, slurm

#575 - Review `User` model

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#574 - Extract `LinkUserProject` from `project.py`, and add `User.project_list`

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#572 - Define expected sbatch script for parallel execution

Issue - State: closed - Opened by tcompa over 1 year ago - 15 comments
Labels: Priority, slurm

#571 - `project.user_member_list` is not populated

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: maintenance

#570 - Known sqlite issues

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment

#567 - Solves sqlite3.IntegrityError

Pull Request - State: closed - Opened by ychiucco over 1 year ago - 3 comments

#566 - Simplify `read_only` attributes

Issue - State: closed - Opened by tcompa over 1 year ago - 8 comments
Labels: maintenance

#560 - Fix `User`/`Project` models, due to unsupported UUID4 column in sqlite

Issue - State: closed - Opened by jluethi over 1 year ago - 7 comments
Labels: bug, Priority

#556 - [FMI deployment] task environment python executable simlink to server python leads to issues

Issue - State: open - Opened by jluethi over 1 year ago - 9 comments
Labels: bug, slurm, task collection

#550 - Review endpoint URLs

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: maintenance

#549 - Add `Task.docs_info` and `Task.docs_link`

Issue - State: closed - Opened by tcompa over 1 year ago - 7 comments
Labels: High Priority, july2023

#546 - Get rid of IDs from payload, move them to URLs

Issue - State: closed - Opened by tcompa over 1 year ago
Labels: maintenance

#543 - Consider upgrading to sqlalchemy2

Issue - State: closed - Opened by tcompa over 1 year ago - 1 comment
Labels: backlog

#541 - To-assess: should we remove the resource schema/table?

Issue - State: closed - Opened by tcompa over 1 year ago - 2 comments
Labels: v2

#528 - Add python 3.11 to CI

Issue - State: open - Opened by tcompa over 1 year ago - 6 comments
Labels: maintenance

#518 - Slurm GPU configuration

Issue - State: closed - Opened by jluethi over 1 year ago - 9 comments
Labels: slurm

#514 - Preliminary & final tasks around our core tasks?

Issue - State: closed - Opened by jluethi almost 2 years ago - 1 comment
Labels: flexibility

#513 - Add `Dataset.resource.info` column?

Issue - State: closed - Opened by tcompa almost 2 years ago - 4 comments
Labels: flexibility

#512 - Relax the reserved-keyword-argument constraint?

Issue - State: closed - Opened by tcompa almost 2 years ago - 2 comments
Labels: Priority, flexibility

#511 - When is history written?

Issue - State: open - Opened by jluethi almost 2 years ago
Labels: History

#509 - Who is in charge of writing the history?

Issue - State: closed - Opened by jluethi almost 2 years ago - 2 comments

#508 - Propagate history from db `Dataset` to ome-zarr

Issue - State: open - Opened by jluethi almost 2 years ago - 2 comments
Labels: flexibility, History

#507 - What is written as history?

Issue - State: closed - Opened by jluethi almost 2 years ago - 1 comment
Labels: flexibility

#506 - Fractal workflow history

Issue - State: open - Opened by jluethi almost 2 years ago - 1 comment
Labels: Priority, Overview, History

#505 - Use `Task.source` as a unique identifier

Issue - State: closed - Opened by tcompa almost 2 years ago - 1 comment
Labels: High Priority, Priority

#504 - Check traceback for errors raised through _slurm backend

Issue - State: closed - Opened by tcompa almost 2 years ago - 1 comment
Labels: backlog, maintenance, slurm

#498 - Tests fail if python3.8 is not installed

Issue - State: closed - Opened by tcompa almost 2 years ago - 5 comments
Labels: testing, maintenance

#493 - Define strategy for grouping tasks into slurm submissions

Issue - State: closed - Opened by jluethi almost 2 years ago - 3 comments
Labels: Priority, Overview, slurm

#492 - Failing gracefully when user fileshare runs out of space

Issue - State: closed - Opened by jluethi almost 2 years ago - 6 comments
Labels: slurm

#491 - Add additional options to sbatch submission: `-A` for accounts

Issue - State: closed - Opened by jluethi almost 2 years ago - 5 comments
Labels: maintenance

#488 - Remove fastapi-users-db-sqlmodel dependency

Issue - State: closed - Opened by tcompa almost 2 years ago - 8 comments
Labels: maintenance

#474 - Cleanup job folders to reduce number of files

Issue - State: open - Opened by tcompa almost 2 years ago - 12 comments

#454 - Use UUID4 everywhere?

Issue - State: closed - Opened by tcompa almost 2 years ago - 1 comment
Labels: backlog

#293 - Can we include a unicity constraint for `Task` attribute pair `(Task.name, Task.source)`?

Issue - State: closed - Opened by tcompa almost 2 years ago - 5 comments
Labels: backlog

#280 - SLURM backend should expose a `stop_workflow_execution` function

Issue - State: closed - Opened by tcompa about 2 years ago - 4 comments
Labels: High Priority

#276 - When are workflows linked to datasets?

Issue - State: closed - Opened by jluethi about 2 years ago - 3 comments

#262 - Restrictions for rerunning partial workflows

Issue - State: open - Opened by jluethi about 2 years ago
Labels: flexibility

#261 - Workflow submission scenarios

Issue - State: closed - Opened by jluethi about 2 years ago - 3 comments
Labels: High Priority, Overview, flexibility

#223 - Define private task

Issue - State: closed - Opened by jacopo-exact about 2 years ago - 6 comments
Labels: unclear

#220 - Replace `Dict[str, Any]` hint with some custom `Metadata`

Issue - State: closed - Opened by tcompa about 2 years ago - 1 comment
Labels: maintenance

#109 - Running a workflow on a subset of data

Issue - State: closed - Opened by tcompa about 2 years ago - 9 comments
Labels: Priority, flexibility

#108 - Write history file in each dataset

Issue - State: closed - Opened by tcompa about 2 years ago - 2 comments
Labels: Priority

#54 - handle db errors in endpoint

Issue - State: closed - Opened by jacopo-exact about 2 years ago - 1 comment
Labels: unclear

#16 - Validate workflow/task IO dependencies

Issue - State: closed - Opened by tcompa over 2 years ago - 3 comments
Labels: maintenance

#14 - Data lifecycle: Workflow Flexibility

Issue - State: closed - Opened by jluethi over 2 years ago - 9 comments
Labels: Overview, flexibility

#6 - Compound tasks

Issue - State: closed - Opened by tcompa about 2 years ago - 5 comments
Labels: flexibility

#5 - make dictionary updating safe

Issue - State: open - Opened by jacopo-exact about 2 years ago - 2 comments
Labels: bug, maintenance