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Sprint/refactor resubmit #1139

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Commits on Sep 4, 2023

  1. Added some temporary comments in workflow.py.

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Commits on Sep 6, 2023

  1. Started to add docstrings to workflow.py

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Commits on Sep 7, 2023

  1. Added a docstring to esm_plugin_mamager

    @nwieters
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  2. Some docstring changes in workflow.py

    @nwieters
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Commits on Oct 6, 2023

  1. Added comments to esm_plugin_manager

    @nwieters
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  2. Start to refactor workflow.

    @nwieters
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  3. Started to refactor workflow.py

    @nwieters
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Commits on Oct 16, 2023

  1. Placed the default definition of workflow phases in esm_software.../d… 

    …efauls.yaml .
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Commits on Oct 17, 2023

  1. Update src/esm_plugin_manager/esm_plugin_manager.py 

    Co-authored-by: Miguel <[email protected]>
    @nwieters @mandresm
    nwieters and mandresm authored Oct 17, 2023
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  2. Update src/esm_plugin_manager/esm_plugin_manager.py 

    Co-authored-by: Miguel <[email protected]>
    @nwieters @mandresm
    nwieters and mandresm authored Oct 17, 2023
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  3. Update src/esm_runscripts/workflow.py 

    Co-authored-by: Miguel <[email protected]>
    @nwieters @mandresm
    nwieters and mandresm authored Oct 17, 2023
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  4. Correcte syntax of docstrings.

    @nwieters
    nwieters committed Oct 17, 2023
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  5. Renamed default_workflow_phases entry in defaults.yaml

    @nwieters
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Commits on Oct 18, 2023

  1. Renamed workflow method, added property decorator and added test.

    @nwieters
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  2. Added a temporary workflow to awicm3.

    @nwieters
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Commits on Oct 20, 2023

  1. Added method to return a list of an attribute for all phases.

    @nwieters
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Commits on Oct 23, 2023

  1. Convert functions into methods, moved class variables to be instance … 

    …variables.
    @nwieters
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Commits on Oct 27, 2023

  1. Further developments until order_cluster.

    @nwieters
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Commits on Nov 3, 2023

  1. Further changes for workflow manager.

    @nwieters
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Commits on Nov 9, 2023

  1. Merge branch 'release' into sprint/workflow_manager

    @nwieters
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Commits on Nov 10, 2023

  1. Added prepend_newrun, skip_cluster, fixed next_submit entries.

    @nwieters
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Commits on Nov 13, 2023

  1. Reactivated function display_nicely.

    @nwieters
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Commits on Nov 14, 2023

  1. Added some flake8 style optimization.

    @nwieters
    nwieters committed Nov 14, 2023
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Commits on Nov 16, 2023

  1. Adapted the output for inspect (-i) workflow.

    @nwieters
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  2. Fix multiple phases in one cluster, fix batch_or_shell to be set by e… 

    …sm_tools.
    @nwieters
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Commits on Nov 17, 2023

  1. Added some further comments and added cluster info in display_workflo… 

    …w for inspect argument.
    @nwieters
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  2. Add new workflow attribute in defaults.yaml.

    @nwieters
    nwieters committed Nov 17, 2023
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  3. Reactivated function complete_clusters.

    @nwieters
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  4. Some changes for processing phases in awicm3.

    @nwieters
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Commits on Nov 20, 2023

  1. Update src/esm_runscripts/inspect.py 

    Co-authored-by: Miguel <[email protected]>
    @nwieters @mandresm
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  2. Merged default and user phase class, made phase a subclass of dict.

    @nwieters
    nwieters committed Nov 20, 2023
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  3. Fixed some of the workflow tests.

    @nwieters
    nwieters committed Nov 20, 2023
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  4. Added review suggestions.

    @nwieters
    nwieters committed Nov 20, 2023
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Commits on Nov 22, 2023

  1. Changed initialization of workflow and phases.

    @nwieters
    nwieters committed Nov 22, 2023
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  2. Changed initial config of default workflow phases.

    @nwieters
    nwieters committed Nov 22, 2023
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  3. Bugfix in error message.

    @nwieters
    nwieters committed Nov 22, 2023
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  4. Make next_run_triggered_by a keyword of phase (trigger_next_run) not … 

    …workflow.
    @nwieters
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  5. Bugfix if no phase trigger_next_run.

    @nwieters
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Commits on Nov 23, 2023

  1. Resolved function complete_cluster into other functions, fix next_sub… 

    …mit for clusters.
    @nwieters
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  2. Removed obsolete functions.

    @nwieters
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Commits on Nov 24, 2023

  1. (Re)moved redundant code, renamed function for collecting phases.

    @nwieters
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  2. Removed the possibility to set workflow keywords by user.

    @nwieters
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Commits on Nov 27, 2023

  1. Worked on workflow tests, and other minor changes to workflow.

    @nwieters
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Commits on Nov 28, 2023

  1. Fixed a bug in order_phases_and_clusters

    @nwieters
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  2. Added workflow tests for test examples (in documentation).

    @nwieters
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Commits on Nov 29, 2023

  1. Fixed test example_2, add preprocessing phase with adding newrun.

    @nwieters
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  2. Added test for workflow example 5.

    @nwieters
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Commits on Nov 30, 2023

  1. Added function to cluster phases after collecting them.

    @nwieters
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Commits on Dec 1, 2023

  1. Changes to pass all example tests.

    @nwieters
    nwieters committed Dec 1, 2023
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  2. Code optimizations

    @nwieters
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Commits on Dec 4, 2023

  1. Removed unused function.

    @nwieters
    nwieters committed Dec 4, 2023
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  2. Finished workflow tests.

    @nwieters
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  3. Changes in default workflow definition.

    @nwieters
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  4. Revive init_workflow funtion.

    @nwieters
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  5. Added my email to setup.py

    @nwieters
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  6. Added comments and docstrings.

    @nwieters
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  7. Merge branch 'release' into sprint/workflow_manager

    @nwieters
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Commits on Dec 7, 2023

  1. Some more code improvements.

    @nwieters
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Commits on Dec 8, 2023

  1. Small changes in some comments.

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Commits on Dec 12, 2023

  1. Remove calc of nproc in workflow.py.

    @nwieters
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  2. Remove keyword run_on_queue (not used) and give error by missing run_… 

    …after/run_before.
    @nwieters
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Commits on Dec 13, 2023

  1. Adapted log-file name and append mode.

    @nwieters
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  2. Removed run_on_queue from default phases.

    @nwieters
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  3. Removed run_on_queue.

    @nwieters
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  4. Added START and END statement to logfile of recipe steps.

    @nwieters
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  5. Added comments.

    @nwieters
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Commits on Dec 14, 2023

  1. Added comments.

    @nwieters
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  2. Change comment

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  3. Adde jobid to logfiles.

    @nwieters
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Commits on Dec 15, 2023

  1. Comment out unused functions.

    @nwieters
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Commits on Jan 15, 2024

  1. Added -s argument to read current_date; some code syntax optimisations.

    @nwieters
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  2. Test, to remove maybe_resumbit.

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Commits on Jan 23, 2024

  1. Test to remove jobtype setting in workflow.py

    @nwieters
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Commits on Feb 1, 2024

  1. comment and clean esm_software/esm_runscripts config files

    @mandresm
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  2. paetially refactoring of SimulationSetup.__init__ and some of the fun… 

    …ction of config_initialization.py
    @mandresm
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  3. restructure SimulationSetup.__init__: 1) the functions there do not c… 

    …all other functions (i.e. by looking at SimulationSetup.__init__ it is now clear what are the steps 2) redefine each steps in config_initialization.py so that each step has a single and well defined used and 3) collect all defaults variables defined in the functions from config_initialization.py and included them into a new general section in the configs/esm_software/esm_runscripts/defaults.yaml
    @mandresm
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  4. Merge branch 'release' into sprint/rearrange_prepexp

    @mandresm
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  5. Merge branch 'release' into sprint/rearrange_prepexp

    @mandresm
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  6. fix a bug in init_interactive_info that was afecting esm_master

    @mandresm
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Commits on Feb 2, 2024

  1. Added optional argument to _write_finalized_config.

    @nwieters
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  2. Merge branch 'sprint/rearrange_prepexp' of https://github.com/esm-too… 

    …ls/esm_tools into sprint/rearrange_prepexp
    @nwieters
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  3. Add docstring

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  4. add docstrings to all functions in config_initialization.py and to Si… 

    …mulationSetup in sim_objects.py
    @mandresm
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  5. Merge branch 'sprint/rearrange_prepexp' of https://github.com/esm-too… 

    …ls/esm_tools into sprint/rearrange_prepexp
    @mandresm
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  6. black formating of config_initialization.py and remove strings concat… 

    …enations with +
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  7. Put the esm_runscripts call via subprocess in its own prepexp revipe.

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  8. Merge branch 'sprint/rearrange_prepexp' of https://github.com/esm-too… 

    …ls/esm_tools into sprint/rearrange_prepexp
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  9. Small changes.

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Commits on Feb 12, 2024

  1. Added docstrings and refactoring _copy_preliminary_files_from_experim… 

    …ent_to_thisrun function in prepexp.py
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Commits on Feb 13, 2024

  1. Rename step in prepexp recipe, extract function that runs esm_runscri… 

    …pts in subprocess.
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Commits on Feb 14, 2024

  1. Bugfix

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  2. Small changes.

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Commits on Feb 15, 2024

  1. Merge branch 'sprint/rearrange_prepexp' into sprint/refactor_resubmit

    @nwieters
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  2. isort src/esm_runscripts/prepexp.py

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Commits on Feb 19, 2024

  1. Add comment in prepexp recipe.

    @nwieters
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  2. Added review suggestions.

    @nwieters
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  3. Changed condition for runscript update.

    @nwieters
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  4. Changed string concatenations to f-string format.

    @nwieters
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  5. Applied flake8 recommendations.

    @nwieters
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Commits on Feb 20, 2024

  1. Merge branch 'sprint/rearrange_prepexp' into sprint/refactor_resubmit

    @nwieters
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  2. Add flake8 recommondations.

    @nwieters
    nwieters committed Feb 20, 2024
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  3. Added workflow test.

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    nwieters committed Feb 20, 2024
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Commits on Feb 22, 2024

  1. Reactivate call of maybe_resubmit.

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    nwieters committed Feb 22, 2024
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  2. Implement new function to write run file.

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    nwieters committed Feb 22, 2024
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  3. Start to refactor maybe_resubmit function.

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    nwieters committed Feb 22, 2024
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  4. Add workflow methon to set the run command of each phase.

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    nwieters committed Feb 22, 2024
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  5. Add default cluster.

    @nwieters
    nwieters committed Feb 22, 2024
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