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Adding that one can specify other files to be retrieved via the setting #89

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JPchico
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@JPchico JPchico commented Nov 25, 2023

Adding that one can specify other files to be retrieved via the settings. Addresses #88

@JPchico JPchico requested a review from sphuber November 25, 2023 16:37
@JPchico JPchico self-assigned this Nov 25, 2023
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codecov bot commented Nov 25, 2023

Codecov Report

Attention: 8 lines in your changes are missing coverage. Please review.

Comparison is base (12a4c95) 85.30% compared to head (3febf4c) 84.95%.
Report is 1 commits behind head on develop.

Files Patch % Lines
aiida_lammps/calculations/raw.py 41.66% 7 Missing ⚠️
aiida_lammps/calculations/base.py 75.00% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop      #89      +/-   ##
===========================================
- Coverage    85.30%   84.95%   -0.35%     
===========================================
  Files           19       19              
  Lines         1599     1615      +16     
===========================================
+ Hits          1364     1372       +8     
- Misses         235      243       +8     
Flag Coverage Δ
pytests 84.95% <50.00%> (-0.35%) ⬇️

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Implementation looks good, just a comment on the docs

@@ -34,4 +34,4 @@ LAMMPS can produce binary restart files which contain all the atomic positions,
- **structure**, ({class}`~aiida.orm.nodes.data.structure.StructureData`), *optional* - The output structure of the calculation.
- **remote_folder**, ({class}`~aiida.orm.nodes.data.remote.base.RemoteData`) - Folder in the remote machine where the calculation was performed.
- **remote_stash**, ({class}`~aiida.orm.nodes.data.remote.stash.base.RemoteStashData`), *optional* – Contents of the stash.source_list option are stored in this remote folder after job completion.
- **retrieved**, ({class}`~aiida.orm.nodes.data.folder.FolderData`) - Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `CalcInfo.retrieve_list`.
- **retrieved**, ({class}`~aiida.orm.nodes.data.folder.FolderData`) - Files that are retrieved by the daemon will be stored in this node. By default the stdout and stderr of the scheduler will be added, but one can add more by specifying them in `settings["additional_retrieve_list"] = ["foo", "bar"]`.
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Instead of explaining this option in the settings here, wouldn't it make more sense to actually add this to the explanation of the settings input itself? You also may want to add that wildcards are supported, i.e. you could add *.xml to retrieve all XML files for example

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Hi @sphuber ! Thanks for the comments, I have fixed them now, and added the explanation about wildcards with a link to the place in the aiida-core documentation where this is explained.

Adding that the settings can take a list of strings or a list of tuples.
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Thanks @JPchico all good. Just one typo left in the docs

docs/source/topics/calculations/base.md Outdated Show resolved Hide resolved
docs/source/topics/calculations/raw.md Outdated Show resolved Hide resolved
docs/source/topics/workflows/base.md Outdated Show resolved Hide resolved
docs/source/topics/workflows/md.md Outdated Show resolved Hide resolved
docs/source/topics/workflows/relax.md Outdated Show resolved Hide resolved
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JPchico commented Nov 28, 2023

@sphuber I think this is ready, if you have no objections I will merge this one.

JPchico and others added 5 commits November 28, 2023 12:19
Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
Co-authored-by: Sebastiaan Huber <mail@sphuber.net>
@JPchico JPchico merged commit 47b1a4d into aiidaplugins:develop Nov 28, 2023
@JPchico JPchico deleted the 88-add-an-explicit-way-to-get-extra-retrieved-files-in-the-calculations branch November 28, 2023 11:38
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