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NF: Add Environment class, with initial Native/Docker implementations #516

Merged
merged 39 commits into from
Jan 29, 2024
Merged

NF: Add Environment class, with initial Native/Docker implementations #516

merged 39 commits into from
Jan 29, 2024

Commits on Sep 7, 2023

  1. NF: Add Environment class, with initial Native/Docker implementations

    @effigies
    effigies committed Sep 7, 2023
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  2. TEST: Add basic test for native environment

    @effigies
    effigies committed Sep 7, 2023
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  3. FIX: import and arg

    @effigies
    effigies committed Sep 7, 2023
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  4. removing resetting self.output_ to None (not sure why it was needed)

    @djarecka @effigies
    djarecka authored and effigies committed Sep 7, 2023
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  5. implementing execute for the Docker env; changes to the ShellCommandT… 

    …ask; adding tests (more tests needed)
    @djarecka @effigies
    djarecka authored and effigies committed Sep 7, 2023
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  6. updating docker tests; fixing issue with working directory for docker

    @djarecka @effigies
    djarecka authored and effigies committed Sep 7, 2023
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  7. adding need docker to the tests

    @djarecka @effigies
    djarecka authored and effigies committed Sep 7, 2023
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  8. FIX: Bad rebase

    @effigies
    effigies committed Sep 7, 2023
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  9. RF: Rewrite _check_input with FileSets

    @effigies
    effigies committed Sep 7, 2023
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  10. FIX: Missing argument

    @effigies
    effigies committed Sep 7, 2023
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  11. FIX: Get mode

    @effigies
    effigies committed Sep 7, 2023
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  12. TEST: Update tests to be typing-friendly

    @effigies
    effigies committed Sep 7, 2023
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Commits on Sep 16, 2023

  1. Merge branch 'rf/environments' of https://github.com/nipype/pydra int… 

    …o env
    @djarecka
    djarecka committed Sep 16, 2023
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Commits on Sep 17, 2023

  1. Update pydra/engine/task.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Sep 17, 2023
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  2. Update pydra/engine/task.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Sep 17, 2023
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Sep 17, 2023
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  4. Merge branch 'rf/environments' of https://github.com/nipype/pydra int… 

    …o env
    @djarecka
    djarecka committed Sep 17, 2023
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  5. removing temporary old env, some renaming

    @djarecka
    djarecka committed Sep 17, 2023
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  6. Merge pull request #705 from djarecka/env 

    Env
    @djarecka
    djarecka committed Sep 17, 2023
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Commits on Sep 18, 2023

  1. adding environment to run_el for slurm worker

    @djarecka
    djarecka committed Sep 18, 2023
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Commits on Sep 19, 2023

  1. cleaning DockerTask remains

    @djarecka
    djarecka committed Sep 19, 2023
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  2. Merge pull request #706 from djarecka/env 

    Env
    @djarecka
    djarecka committed Sep 19, 2023
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Commits on Oct 5, 2023

  1. adding the Singularity environment class

    @djarecka
    djarecka committed Oct 5, 2023
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  2. Merge pull request #711 from djarecka/env 

    adding the Singularity environment class
    @djarecka
    djarecka committed Oct 5, 2023
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Commits on Oct 28, 2023

  1. removing psi plugin from one test

    @djarecka
    djarecka committed Oct 28, 2023
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Commits on Nov 2, 2023

  1. creating Container class

    @djarecka
    djarecka committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. cleaning: removing ContainerTask and ContainerSpec

    @djarecka
    djarecka committed Nov 3, 2023
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  2. adding xarg to env command, changing output_cpath to root used in the… 

    … bindings
    @djarecka
    djarecka committed Nov 3, 2023
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  3. Merge pull request #718 from djarecka/env 

    [WIP] cleaning, fixing tests
    @djarecka
    djarecka committed Nov 3, 2023
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Commits on Nov 15, 2023

  1. Update pydra/engine/environments.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Nov 15, 2023
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  2. Update pydra/engine/environments.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Nov 15, 2023
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  3. Update pydra/engine/environments.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Nov 15, 2023
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  4. Update pydra/engine/tests/test_specs.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Nov 15, 2023
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  5. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Nov 15, 2023
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  6. Update pydra/engine/environments.py 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @djarecka @effigies
    djarecka and effigies committed Nov 15, 2023
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  7. small fix

    @djarecka
    djarecka committed Nov 15, 2023
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  8. Merge pull request #721 from djarecka/env 

    small fix
    @djarecka
    djarecka committed Nov 15, 2023
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  9. small edits to the core

    @djarecka
    djarecka committed Nov 15, 2023
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  10. Merge pull request #722 from djarecka/env 

    small edits to the core
    @djarecka
    djarecka committed Nov 15, 2023
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