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# Sphinx build info version 1 | ||
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. | ||
config: 542912f80ce34c063298eb7c8e368ec9 | ||
tags: 645f666f9bcd5a90fca523b33c5a78b7 |
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# Sphinx build info version 1 | ||
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. | ||
config: 542912f80ce34c063298eb7c8e368ec9 | ||
tags: 645f666f9bcd5a90fca523b33c5a78b7 |
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Library API (application programmer interface) | ||
============================================== | ||
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.. automodule:: pydra | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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Subpackages | ||
----------- | ||
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.. toctree:: | ||
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api/pydra.engine | ||
api/pydra.mark | ||
api/pydra.tasks | ||
api/pydra.utils |
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pydra.engine.audit module | ||
========================= | ||
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.. automodule:: pydra.engine.audit | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.boutiques module | ||
============================= | ||
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.. automodule:: pydra.engine.boutiques | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.core module | ||
======================== | ||
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.. automodule:: pydra.engine.core | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.graph module | ||
========================= | ||
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.. automodule:: pydra.engine.graph | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.helpers module | ||
=========================== | ||
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.. automodule:: pydra.engine.helpers | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.helpers\_file module | ||
================================= | ||
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.. automodule:: pydra.engine.helpers_file | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.helpers\_state module | ||
================================== | ||
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.. automodule:: pydra.engine.helpers_state | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine package | ||
==================== | ||
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.. automodule:: pydra.engine | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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Submodules | ||
---------- | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
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pydra.engine.audit | ||
pydra.engine.boutiques | ||
pydra.engine.core | ||
pydra.engine.graph | ||
pydra.engine.helpers | ||
pydra.engine.helpers_file | ||
pydra.engine.helpers_state | ||
pydra.engine.specs | ||
pydra.engine.state | ||
pydra.engine.submitter | ||
pydra.engine.task | ||
pydra.engine.workers |
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pydra.engine.specs module | ||
========================= | ||
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.. automodule:: pydra.engine.specs | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.state module | ||
========================= | ||
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.. automodule:: pydra.engine.state | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.submitter module | ||
============================= | ||
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.. automodule:: pydra.engine.submitter | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.task module | ||
======================== | ||
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.. automodule:: pydra.engine.task | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.engine.workers module | ||
=========================== | ||
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.. automodule:: pydra.engine.workers | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.mark.functions module | ||
=========================== | ||
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.. automodule:: pydra.mark.functions | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.mark package | ||
================== | ||
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.. automodule:: pydra.mark | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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Submodules | ||
---------- | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
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pydra.mark.functions |
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pydra.tasks package | ||
=================== | ||
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.. automodule:: pydra.tasks | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.utils.messenger module | ||
============================ | ||
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.. automodule:: pydra.utils.messenger | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.utils.profiler module | ||
=========================== | ||
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.. automodule:: pydra.utils.profiler | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: |
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pydra.utils package | ||
=================== | ||
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.. automodule:: pydra.utils | ||
:members: | ||
:undoc-members: | ||
:show-inheritance: | ||
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Submodules | ||
---------- | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
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pydra.utils.messenger | ||
pydra.utils.profiler |
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Release Notes | ||
============= | ||
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0.8.0 | ||
----- | ||
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* 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 | ||
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0.7.0 | ||
----- | ||
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* 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 | ||
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0.6.2 | ||
----- | ||
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* Use pkgutil to declare ``pydra.tasks`` as a namespace package, ensuring better support for | ||
editable mode. | ||
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0.6.1 | ||
----- | ||
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* Add ``pydra.tasks`` namespace package to enable separate packages of ``Task``\s 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 | ||
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0.6 | ||
--- | ||
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* removing the tutorial to a `separate repo <https://github.com/nipype/pydra-tutorial>`__ | ||
* 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 multiple 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 | ||
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0.5 | ||
--- | ||
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* 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) | ||
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0.4 | ||
--- | ||
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* 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 | ||
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0.3.1 | ||
----- | ||
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* 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) | ||
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0.3 | ||
--- | ||
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* 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 | ||
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0.2.2 | ||
----- | ||
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* supporting tuple as a single element of an input | ||
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0.2.1 | ||
----- | ||
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* fixing: nodes with states and input fields (from splitter) that are empty were failing | ||
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0.2 | ||
--- | ||
|
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* big changes in ``ShellTask``, ``DockerTask`` and ``SingularityTask`` | ||
* customized input specification and output specification for ``Task``\s | ||
* 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 | ||
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0.1 | ||
--- | ||
|
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* Core dataflow creation and management API | ||
* Distributed workers: | ||
* concurrent futures | ||
* SLURM | ||
* Notebooks for Pydra concepts | ||
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0.0.1 | ||
----- | ||
|
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Initial Pydra Dataflow Engine release. |
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