Releases: nipype/pydra
Releases · nipype/pydra
0.12.1
- fixing
TaskBase.__call__
sosubmitter
is not overwritten - improving
checksum_states
so it doesn't calculate the content hash of big files for multiple times (usingfiles_hash
that keeps track of all the files) - removing output after task is run to save memory
- adding
Directory
,int
,float
,bool
,str
, andlist
to the types allowed byoutput_spec
ofShelloCommandTask
. - adding python 3.9 to GA
- fixing GA singularity workflow
0.12
- removing
checksum
fromsubmitter
andworkers
to avoid hash calculation before running the tasks (usinguid
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
andMultiOutputFile
to the pydra special types - fixing environment variable for GithubAction CI
- fixing
input_spec
forShellCommandTask
with thecontainer_info
, specbases
has to be changedDockerSpec
orSingularitySpec
in order to be used byDocker/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 fieldmetadata
, it can now useoutput_dir
, entireinputs
object or a specificfield
from theinputs
0.11
- fixing issues with quadratic memory increase for workflows with big splitters - removing
state_inputs
fromTask
(not used anymore) - allowing for directory with broken symlinks for an input
- fixing tests so could be run on a cluster (using
tmpdir
as acache_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
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 generate_output_updates, to be able to predict names of the generated outputs before running
Minor setup changes
- allows README to be displayed on pypi
- limits testing to valid pytests
0.9.1
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
andMultiOutObj
for a possible types ininput/output_spec
- fixing
copyfile_workflow
- setting proper
Workflow.output_spec
using tasks'output_spec
s - setting
output_dir
as a parent directory for all files created using the output templates - adding
requires
key tooutput_spec
's metadata in order to set conditions for creating a specific output field - adding
input_spec
andoutput_spec
as class attributes that could be rewritten in the init or in the child classes
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
andmessanger
- updating syntax to newer python
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 thestdlib pkgutil.extend_path
- moving readme to rst format
0.6.1
- Add
pydra.tasks
namespace package to enable separate packages ofTask
s to be installed intopydra.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