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Recent Releases of pydra

pydra - 1.0a2

What's Changed

  • guard against empty shape arrays by setting initial value in reduce operations over state dimensions in State by @tclose in https://github.com/nipype/pydra/pull/818
  • add slurm dockerfile by @adi611 in https://github.com/nipype/pydra/pull/729
  • added guard against missing implicit helps in custom compose packages by @tclose in https://github.com/nipype/pydra/pull/819
  • doc: Use inner/outer splitter, analogize to zip/product by @effigies in https://github.com/nipype/pydra/pull/773
  • fixes ci-cd issues by @tclose in https://github.com/nipype/pydra/pull/832
  • Cli by @jadecci in https://github.com/nipype/pydra/pull/831
  • relaxed task definition validation to accept use cases found in ANTs, FSL, Freesurfer, etc... task packages by @tclose in https://github.com/nipype/pydra/pull/835

New Contributors

  • @jadecci made their first contribution in https://github.com/nipype/pydra/pull/831

Full Changelog: https://github.com/nipype/pydra/compare/1.0a1...1.0a2

- Python
Published by tclose 7 months ago

pydra - 1.0a1

What's Changed

  • Bump codecov/codecov-action from 2 to 5 by @dependabot in https://github.com/nipype/pydra/pull/774
  • Bump peaceiris/actions-gh-pages from 3 to 4 by @dependabot in https://github.com/nipype/pydra/pull/775
  • Doc string and glossary update by @tclose in https://github.com/nipype/pydra/pull/781
  • Touch-ups by @tclose in https://github.com/nipype/pydra/pull/787
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/788
  • Update CI to use build-and-inspect-python-package and tox-uv by @effigies in https://github.com/nipype/pydra/pull/782
  • [BUG] Remove pdb breakpoint and make single-op-splits robust to 1d shape by @ibevers in https://github.com/nipype/pydra/pull/758
  • handle ellipsis in type hashing by @tclose in https://github.com/nipype/pydra/pull/793
  • Bugfix-task-eq by @tclose in https://github.com/nipype/pydra/pull/794
  • Handle-none-outputs by @tclose in https://github.com/nipype/pydra/pull/790
  • chore(deps): bump astral-sh/setup-uv from 5 to 6 by @dependabot in https://github.com/nipype/pydra/pull/806
  • Serializing Task classes to/from dictionaries by @tclose in https://github.com/nipype/pydra/pull/792
  • Adds check to parsecommandline_template to catch options that don't have trailing field by @tclose in https://github.com/nipype/pydra/pull/795

New Contributors

  • @ibevers made their first contribution in https://github.com/nipype/pydra/pull/758

Full Changelog: https://github.com/nipype/pydra/compare/1.0a0...1.0a1

- Python
Published by tclose 10 months ago

pydra - 1.0a0

What's Changed

  • Develop: fixes for test_environments by @tclose in https://github.com/nipype/pydra/pull/769
  • Develop: Test specs by @tclose in https://github.com/nipype/pydra/pull/770
  • Test_submitter by @tclose in https://github.com/nipype/pydra/pull/771
  • Updated testshelltask, testshelltaskinputspec, testworkflow to new syntax by @tclose in https://github.com/nipype/pydra/pull/772
  • Implementation of proposed syntax changes by @tclose in https://github.com/nipype/pydra/pull/768

Full Changelog: https://github.com/nipype/pydra/compare/0.24...1.0a0

- Python
Published by tclose 11 months ago

pydra - 0.25

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/736
  • FIX: Add environment argument to TaskBase.runtask() and Workflow subclass by @ghisvail in https://github.com/nipype/pydra/pull/739
  • Handle None types by @tclose in https://github.com/nipype/pydra/pull/742
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/747
  • ENH: Add more complete format string implementation for argstrings by @tclose in https://github.com/nipype/pydra/pull/754
  • added nest_asyncio to install requires by @tclose in https://github.com/nipype/pydra/pull/501
  • Special handling of bytes_repr for mock filesets by @tclose in https://github.com/nipype/pydra/pull/743
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/753
  • fixes issues with super->sub-class auto-cast and handles MultiInputObj coercion by @tclose in https://github.com/nipype/pydra/pull/746

Full Changelog: https://github.com/nipype/pydra/compare/0.23...0.25

- Python
Published by djarecka over 1 year ago

pydra - 0.24

- Python
Published by djarecka over 1 year ago

pydra - 0.23

What's Changed

  • FIX: Type error in blocking task list, detailed exception message by @tclose in https://github.com/nipype/pydra/pull/623
  • REF: More detailed runtime checks for input spec by @ghisvail in https://github.com/nipype/pydra/pull/627
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/628
  • FIX: Provide templated fields to cmdline only when requirements are met by @ghisvail in https://github.com/nipype/pydra/pull/629
  • FIX: Allow any iterable for ShellOutSpec requires by @ghisvail in https://github.com/nipype/pydra/pull/631
  • FIX: Allow staticmethod be passed to callable metadata in ouput spec by @ghisvail in https://github.com/nipype/pydra/pull/632
  • CI: Add dependabot config by @ghisvail in https://github.com/nipype/pydra/pull/633
  • Build(deps): Bump actions/setup-go from 2 to 4 by @dependabot in https://github.com/nipype/pydra/pull/635
  • Build(deps): Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/nipype/pydra/pull/636
  • Build(deps): Bump actions/setup-python from 2 to 4 by @dependabot in https://github.com/nipype/pydra/pull/637
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/639
  • STY: Miscellaneous cleanups by @effigies in https://github.com/nipype/pydra/pull/645
  • No need for ignore words file now, also ignore afile by @yarikoptic in https://github.com/nipype/pydra/pull/678
  • MNT: Drop Python 3.7 support by @effigies in https://github.com/nipype/pydra/pull/669
  • Type checking and coercion by @tclose in https://github.com/nipype/pydra/pull/662
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/666
  • DOC: Fix linkcode resolving for attrs-defined classes by @ghisvail in https://github.com/nipype/pydra/pull/685
  • Fix DaskWorker and add GitHub Actions workflow for Dask tests by @adi611 in https://github.com/nipype/pydra/pull/686
  • Update Slurm container image in GitHub Actions workflow by @adi611 in https://github.com/nipype/pydra/pull/688
  • Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/nipype/pydra/pull/695
  • Typing bugfixes by @tclose in https://github.com/nipype/pydra/pull/687
  • Omit false output templates by @tclose in https://github.com/nipype/pydra/pull/693
  • Added handling of hashing of types with args and typing special forms by @tclose in https://github.com/nipype/pydra/pull/684
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/699
  • adding cache_dir to tests by @djarecka in https://github.com/nipype/pydra/pull/704
  • Env by @djarecka in https://github.com/nipype/pydra/pull/705
  • Update DOCKER_IMAGE tag in testslurm.yml by @adi611 in https://github.com/nipype/pydra/pull/697
  • Env by @djarecka in https://github.com/nipype/pydra/pull/706
  • Update .zenodo.json by @adi611 in https://github.com/nipype/pydra/pull/707
  • Draft: Adding new worker which uses PSI/J to run tasks by @adi611 in https://github.com/nipype/pydra/pull/694
  • adding the Singularity environment class by @djarecka in https://github.com/nipype/pydra/pull/711
  • [WIP] cleaning, fixing tests by @djarecka in https://github.com/nipype/pydra/pull/718
  • small fix by @djarecka in https://github.com/nipype/pydra/pull/721
  • small edits to the core by @djarecka in https://github.com/nipype/pydra/pull/722
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/nipype/pydra/pull/726
  • Bump actions/setup-go from 4 to 5 by @dependabot in https://github.com/nipype/pydra/pull/725
  • NF: Add Environment class, with initial Native/Docker implementations by @effigies in https://github.com/nipype/pydra/pull/516
  • Bump actions/download-artifact from 3 to 4 by @dependabot in https://github.com/nipype/pydra/pull/727
  • Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/nipype/pydra/pull/728
  • pre-commit updates and code fixes by @pre-commit-ci in https://github.com/nipype/pydra/pull/712
  • Test with Python 3.12 by @ghisvail in https://github.com/nipype/pydra/pull/730
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/731
  • Permit superclass to subclass lazy typing by @tclose in https://github.com/nipype/pydra/pull/696
  • BYO worker by @tclose in https://github.com/nipype/pydra/pull/733
  • Bugfix for optional output template files (i.e. of type Union[Path, bool]) when set to False by @tclose in https://github.com/nipype/pydra/pull/709
  • Hash change guards by @tclose in https://github.com/nipype/pydra/pull/698
  • Caching of file-set hashes by local path and mtimes by @tclose in https://github.com/nipype/pydra/pull/700
  • use exist_ok instead of explicit check for path exists when creating hash cache so it is multiprocess safe by @tclose in https://github.com/nipype/pydra/pull/735
  • updating to new version of auto by @djarecka in https://github.com/nipype/pydra/pull/738
  • Add note instead of catching and raising unhashable exception by @tclose in https://github.com/nipype/pydra/pull/734

New Contributors

  • @dependabot made their first contribution in https://github.com/nipype/pydra/pull/635
  • @yarikoptic made their first contribution in https://github.com/nipype/pydra/pull/678
  • @adi611 made their first contribution in https://github.com/nipype/pydra/pull/686

Full Changelog: https://github.com/nipype/pydra/compare/0.22...0.23

- Python
Published by djarecka almost 2 years ago

pydra - 0.23 Alpha

Motivation

Pre-release of type-checking/hashing changes (see #662) to allow them to be accessed from PyPI so a new version of Arcana can be released. A full release will be made once #682, #681, #683 have been addressed.

What's Changed

  • #662 - Type-checking/coercion; switch to use fileformats; more robust inputs hashing using functools.singledispatch (can handle sets)
  • #623 - List blocked tasks in error message when upstream nodes are not accessible due to hashing issues
  • #629 - FIX: Provide templated fields to cmdline only when requirements are met
  • #631 - FIX: Allow any iterable for ShellOutSpec requires
  • #636 - Build(deps): Bump actions/checkout from 2 to 3
  • #637 - Build(deps): Bump actions/setup-python from 2 to 4
  • #639 - [pre-commit.ci] pre-commit autoupdate #639
  • #645 - STY: Miscellaneous cleanups
  • #678 - No need for ignore words file now, also ignore afile
  • #669 - MNT: Drop Python 3.7 support

Full Changelog: https://github.com/nipype/pydra/compare/0.22...0.23a0

- Python
Published by tclose over 2 years ago

pydra - 0.22

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/608
  • MNT: Add git-archive support for setuptools_scm by @effigies in https://github.com/nipype/pydra/pull/609
  • CI: Enable testing for Python 3.11 on Windows by @ghisvail in https://github.com/nipype/pydra/pull/612
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/618
  • ENH: Add support for argstr formatting of any iterable by @ghisvail in https://github.com/nipype/pydra/pull/614
  • Add support for arbitrary mappings in a FunctionTask by @ghisvail in https://github.com/nipype/pydra/pull/565

Full Changelog: https://github.com/nipype/pydra/compare/0.21...0.22

- Python
Published by djarecka almost 3 years ago

pydra - 0.21

What's Changed

  • WIP-Adding software version retrieval by @rcali21 in https://github.com/nipype/pydra/pull/580
  • Working on adding entity_message by @rcali21 in https://github.com/nipype/pydra/pull/593
  • MNT: Migrate project to flit-scm by @ghisvail in https://github.com/nipype/pydra/pull/597
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/599
  • FIX: Enable testing with Python 3.11 by @ghisvail in https://github.com/nipype/pydra/pull/601
  • MNT: Prerelease updates by @effigies in https://github.com/nipype/pydra/pull/602
  • use cachedir instead of outputdir by @montesmariana in https://github.com/nipype/pydra/pull/538
  • Graph test by @djarecka in https://github.com/nipype/pydra/pull/603
  • Handling input fields checking for Mandatory and Mutually exclusive fields by @ablachair in https://github.com/nipype/pydra/pull/595
  • moving tests with xor to testshelltaskinputspec.py by @djarecka in https://github.com/nipype/pydra/pull/604

New Contributors

  • @montesmariana made their first contribution in https://github.com/nipype/pydra/pull/538
  • @ablachair made their first contribution in https://github.com/nipype/pydra/pull/595

Full Changelog: https://github.com/nipype/pydra/compare/0.20...0.21

- Python
Published by djarecka about 3 years ago

pydra - 0.20

What's Changed

  • Use inspect.getfullargspec instead of getargspec by @ghisvail in https://github.com/nipype/pydra/pull/568
  • Make Makefile compatible with macOS by @ghisvail in https://github.com/nipype/pydra/pull/567
  • Fix bug in inputs checksum before/after task run when deeply modifying objects by @tclose in https://github.com/nipype/pydra/pull/571
  • [FIX] Enable Workflow constructor to receive SpecInfo objects for input_spec parameter by @NicolasGensollen in https://github.com/nipype/pydra/pull/573
  • WIP: adding task input info by @rcali21 in https://github.com/nipype/pydra/pull/556
  • Update zenodo by @rcali21 in https://github.com/nipype/pydra/pull/578
  • [ENH] Add _graph_checksums to input_spec if missing by @NicolasGensollen in https://github.com/nipype/pydra/pull/584
  • changing sinngularity images by @djarecka in https://github.com/nipype/pydra/pull/589
  • Provide paths to ShellTask output files by @tclose in https://github.com/nipype/pydra/pull/585
  • Improve reporting of crash report location by @ghisvail in https://github.com/nipype/pydra/pull/564
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/551
  • More descriptive debugging graph errors and bugfix in values validator by @tclose in https://github.com/nipype/pydra/pull/581
  • fixing typo by @djarecka in https://github.com/nipype/pydra/pull/591
  • adding an Attribute Error to the exception for get_value by @djarecka in https://github.com/nipype/pydra/pull/592

New Contributors

  • @ghisvail made their first contribution in https://github.com/nipype/pydra/pull/568
  • @NicolasGensollen made their first contribution in https://github.com/nipype/pydra/pull/573
  • @rcali21 made their first contribution in https://github.com/nipype/pydra/pull/556

Full Changelog: https://github.com/nipype/pydra/compare/0.19...0.20

- Python
Published by djarecka over 3 years ago

pydra - 0.19

What's Changed

  • MNT: Require cloudpickle >= 2.0 by @effigies in https://github.com/nipype/pydra/pull/517
  • updating test pydra GA by @djarecka in https://github.com/nipype/pydra/pull/519
  • TST: Decrease divergence between Task/Workflow runtask by @mgxd in https://github.com/nipype/pydra/pull/518
  • simplifying ShellCommandTask.cmdline by @djarecka in https://github.com/nipype/pydra/pull/520
  • Use functools.wraps in task decorator by @tclose in https://github.com/nipype/pydra/pull/533
  • RF: Submitter logic. by @mgxd in https://github.com/nipype/pydra/pull/524
  • changed to sge/slurm checks, moving to utils by @djarecka in https://github.com/nipype/pydra/pull/537
  • disabling etelemetry for testing by @djarecka in https://github.com/nipype/pydra/pull/542
  • DOC: Use effigies fork of sphinxcontrib-versioning by @effigies in https://github.com/nipype/pydra/pull/544
  • removing res.output.stderr from docker tests by @djarecka in https://github.com/nipype/pydra/pull/543
  • Split command line using quote respecting shlex.split instead of ' '.split by @tclose in https://github.com/nipype/pydra/pull/545
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/534
  • function in outputfiletemplate by @djarecka in https://github.com/nipype/pydra/pull/553
  • allow more output types to use callables by @yibeichan in https://github.com/nipype/pydra/pull/557

New Contributors

  • @yibeichan made their first contribution in https://github.com/nipype/pydra/pull/557

Full Changelog: https://github.com/nipype/pydra/compare/0.18...0.19

- Python
Published by djarecka over 3 years ago

pydra - 0.18

What's Changed

  • Rf/state by @djarecka in https://github.com/nipype/pydra/pull/499
  • added filename to FileNotFoundError messages by @dafrose in https://github.com/nipype/pydra/pull/504
  • fixing two tests by @djarecka in https://github.com/nipype/pydra/pull/514
  • removing teststyle GA, we are using pre-commit by @djarecka in https://github.com/nipype/pydra/pull/515
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/511

New Contributors

  • @dafrose made their first contribution in https://github.com/nipype/pydra/pull/504

Full Changelog: https://github.com/nipype/pydra/compare/0.17...0.18

- Python
Published by djarecka almost 4 years ago

pydra - 0.17

What's Changed

  • Rerun errored by @chasejohnson3 in https://github.com/nipype/pydra/pull/483
  • adding a default name for shell tasks by @djarecka in https://github.com/nipype/pydra/pull/485
  • reverting adding absolute_path by @jw-96 in https://github.com/nipype/pydra/pull/489
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/nipype/pydra/pull/490
  • [fix] bringing back fname_presuffix and fixing copyfiles functions by @djarecka in https://github.com/nipype/pydra/pull/494
  • Ci/ci and pre-commit updates by @djarecka in https://github.com/nipype/pydra/pull/493
  • changing repo for sphinxcontrib-versioning by @djarecka in https://github.com/nipype/pydra/pull/495
  • [FIX] Gracefully handle empty input_spec arg passed to Workflow init by @tclose in https://github.com/nipype/pydra/pull/497
  • Prevent recursive attr->dict conversion of FunctionTask inputs by @tclose in https://github.com/nipype/pydra/pull/503
  • Sun Grid Engine: SGEWorker by @chasejohnson3 in https://github.com/nipype/pydra/pull/472
  • Fixes SerialWorker Implementation by @tclose in https://github.com/nipype/pydra/pull/507

New Contributors

  • @pre-commit-ci made their first contribution in https://github.com/nipype/pydra/pull/490
  • @tclose made their first contribution in https://github.com/nipype/pydra/pull/497

Full Changelog: https://github.com/nipype/pydra/compare/0.16.2...0.17

- Python
Published by djarecka about 4 years ago

pydra - 0.16.2

  • small changes to exceptions

- Python
Published by djarecka over 4 years ago

pydra - 0.16.1

  • better support for one element splitter

- Python
Published by djarecka over 4 years ago

pydra - 0.16

  • fixing command line for tasks wit splitter and templates in the inputs
  • adding absolute_path option to output spec
  • adding formatter to format input before adding it to the command line (similar to callable but for inputs)

- Python
Published by djarecka over 4 years ago

pydra - 0.15.1

  • fixing output files names with wildcard
  • fixing argstr with f-string

- Python
Published by djarecka over 4 years ago

pydra - 0.15

  • fixing copyfile input
  • adding flexibility to position of the shell task fields
  • Simplify output_spec definition and population
  • Various adjustments to ShellCommandTask
  • adding full traceback to the error files
  • updating Ubuntu for CI
  • fixing templates with float formatting and multiple fields
  • fixing hashing function for numpy objects
  • fixing call function for Workflow
  • adding container dimension concept to the split method
  • adding LazyField for MultiInputFiles
  • fixing issues with SoftFileLock with asyncio
  • style and black updates
  • fixing connections with multiple inputs

- Python
Published by djarecka almost 5 years ago

pydra - 0.14.1

  • reverting some changes to hash_value function, the part for arbitrary object didn't work well

- Python
Published by djarecka about 5 years ago

pydra - 0.14

  • fixing MultiInputObject in the input_spec
  • fixing numpy objects hashing
  • small improvements to the run method for Workflow (moving some part to the softlock file block)

- Python
Published by djarecka about 5 years ago

pydra - 0.13

  • changing the way of getting event loop with asyncio - more robust solution that should work even if get_event_loop raise an error
  • adding option to specify a name of Directory using output_file_template

- Python
Published by djarecka about 5 years ago

pydra - 0.12.1

  • fixing TaskBase.__call__ so submitter is not overwritten
  • improving checksum_states so it doesn't calculate the content hash of big files for multiple times (using files_hash that keeps track of all the files)
  • removing output after task is run to save memory
  • adding Directory, int, float, bool, str, and list to the types allowed by output_spec of ShelloCommandTask.
  • adding python 3.9 to GA
  • fixing GA singularity workflow

- Python
Published by djarecka about 5 years ago

pydra - 0.12

  • removing checksum from submitter and workers to avoid hash calculation before running the tasks (using uid instead)
  • saving the hash values for files to avoid content hash recalculation (the content is recalculated only if the time of the last modification has changed)
  • adding MultiInputFile and MultiOutputFile to the pydra special types
  • fixing environment variable for GithubAction CI
  • fixing input_spec for ShellCommandTask with the container_info, spec bases has to be changed DockerSpec or SingularitySpec in order to be used by Docker/SingularityTask
  • fixing automatic binding detections for ContainerTask that have files as input (is_local_file is now slightly more robust that work for input that has more complex type in the spec)
  • expanding callable function used in field metadata, it can now use output_dir, entire inputs object or a specific field from the inputs

- Python
Published by djarecka about 5 years ago

pydra - 0.11

  • fixing issues with quadratic memory increase for workflows with big splitters - removing state_inputs from Task (not used anymore)
  • allowing for directory with broken symlinks for an input
  • fixing tests so could be run on a cluster (using tmpdir as a cache_dir, so pytest can be run with --basetemp)
  • fixing cache_Dir setting for worflows used as nodes
  • fixing Submitter._run_workflow so it doesn't stop when there are still tasks in the graph, will try getting runnable tasks for another 60s (in case the previous tasks finished, but the results are still not available to read)
  • fixing template formatting for files from ShellCommandTask, so it works for directories that have dots in the name
  • fixing tests that were resubmitting tasks to the queue

- Python
Published by djarecka over 5 years ago

pydra - 0.10

  • disable etelemetry in tests
  • removing old pip (10.0.1) from testing (removing testallowfail from GA workflows)
  • removing min_requirements
  • adding rescheduling to the slurm worker for all jobs that are CANCELLED, TIMEOUT, or PREEMPTED
  • adding generateoutputupdates, to be able to predict names of the generated outputs before running

- Python
Published by djarecka over 5 years ago

pydra - Minor setup changes

  • allows README to be displayed on pypi
  • limits testing to valid pytests

- Python
Published by satra over 5 years ago

pydra - 0.9.1

  • fixing issue with checksum_states performance (it doesn't run self.state.prepare_states if not needed)

- Python
Published by satra over 5 years ago

pydra - 0.9

  • moving from Travis to Github Actions for CI
  • fixing issues with numpy.arrays provided as input fields
  • adding a combiner option for dotfiles and graphs plots
  • refactoring the input classes (adding FunctionSpec)
  • adding MultiInpObj and MultiOutObj for a possible types in input/output_spec
  • fixing copyfile_workflow
  • setting proper Workflow.output_spec using tasks' output_specs
  • setting output_dir as a parent directory for all files created using the output templates
  • adding requires key to output_spec's metadata in order to set conditions for creating a specific output field
  • adding input_spec and output_spec as class attributes that could be rewritten in the init or in the child classes

- Python
Published by djarecka over 5 years ago

pydra - 0.8

  • refactoring template formatting for input_spec
  • fixing issues with input fields with extension (and using them in templates)
  • adding simple validators to input spec (using `attr.validator)
  • adding create_dotfile for workflows, that creates graphs as dotfiles (can convert to other formats if dot available)
  • adding a simple user guide with input_spec description
  • expanding docstrings for State, audit and messanger
  • updating syntax to newer python

- Python
Published by djarecka over 5 years ago

pydra - 0.7

  • refactoring the error handling by padra: improving raised errors, removing nodes from the workflow graph that can't be run
  • refactoring of the input_spec: adapting better to the nipype interfaces
  • switching from pkg_resources.declare_namespace to the stdlib pkgutil.extend_path
  • moving readme to rst format

- Python
Published by djarecka over 5 years ago

pydra - 0.6.1

  • Add pydra.tasks namespace package to enable separate packages of Tasks to be installed into pydra.tasks.
  • Raise error when task or workflow name conflicts with names of attributes, methods, or other tasks already added to workflow
  • Mention requirements.txt in README

- Python
Published by effigies over 5 years ago

pydra - 0.6

  • removing the tutorial to a separate repo
  • adding windows tests to codecov
  • accepting None as a valid output from a FunctionTask, also for function that returns multiple values
  • fixing slurm error files
  • adding wf._connection to checksum
  • allowing for updates of wf._connections
  • editing output, so it works with numpy.arrays
  • removing to_job and pickling task instead (workers read the tasks and set the proper input, so the multile copies of the input are not kept in the memory)
  • adding standalone function load_and_run that can load and run a task from a pickle file
  • removing create_pyscript and simplifying the slurm worker
  • improving error reports in errors flies
  • fixing make_class so the Output is properly formatted

- Python
Published by djarecka over 5 years ago

pydra - 0.5

  • fixing hash_dir function
  • adding get_available_cpus to get the number of CPUs available to the current process or available on the system
  • adding simple implementation for BoshTask that uses boutiques descriptor
  • adding azure to CI
  • fixing code for windows
  • etelementry updates
  • adding more verbose output for task result - returns values or indices for input fields
  • adding an experimental implementation of Dask Worker (limited testing with ci)

- Python
Published by djarecka almost 6 years ago

pydra - 0.4

  • reorganization of the State class, fixing small issues with the class
  • fixing some paths issues on windows os
  • adding osx and window sto the travis runs (right now allowing for failures for windows)
  • adding PydraStateError for exception in the State class
  • small fixes to the hashing functions, adding more tests
  • adding hash_dir to calculate hash for Directory type

- Python
Published by djarecka almost 6 years ago

pydra - 0.3.1

  • passing wf.cache_locations to the task
  • using rerun from submitter to all task
  • adding test_rerun and propagate_rerun for workflows
  • fixing task with a full combiner
  • adding cont_dim to specify dimensionality of the input variables (how much the input is nested)

- Python
Published by djarecka almost 6 years ago

pydra - 0.3

  • adding sphinx documentation
  • moving from dataclasses to attrs
  • adding container flag to the ShellCommandTask
  • fixing cmdline, command_args and container_args for tasks with states
  • adding CONTRIBUTING.md
  • fixing hash calculations for inputs with a list of files
  • using attr.NOTHING for input that is not set

- Python
Published by djarecka about 6 years ago

pydra - 0.2.2

supporting tuple as a single element of an input

- Python
Published by djarecka about 6 years ago

pydra - 0.2.1

  • fixing: nodes with states and input fields (from splitter) that are empty were failing

- Python
Published by djarecka about 6 years ago

pydra - 0.2

  • big changes in ShellTask, DockerTask and SingularityTask

    • customized input specification and output specification for Tasks
    • adding singularity checks to Travis CI
    • binding all input files to the container

  • changes in Workflow

    • passing all outputs to the next node: lzout.all_
    • fixing inner splitter

  • allowing for splitter and combiner updates

  • adding etelementry support

- Python
Published by djarecka about 6 years ago

pydra - 0.1

  • Core dataflow creation and management API
  • Distributed workers:
    • concurrent futures
    • SLURM
  • Notebooks for Pydra concepts

- Python
Published by djarecka over 6 years ago

pydra - 0.0.1

Initial Pydra Dataflow Engine release.

- Python
Published by effigies over 7 years ago