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Looper v1.8.0 Release #487

Merged
merged 249 commits into from
Jun 6, 2024
Merged

Looper v1.8.0 Release #487

merged 249 commits into from
Jun 6, 2024

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donaldcampbelljr
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@donaldcampbelljr donaldcampbelljr commented Mar 21, 2024 •
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Addresses Issues for https://github.com/pepkit/looper/milestone/13

A couple issues on milestone 1.8.0 are still outstanding but they are lower priority. If they are not solved by EOD Friday, they will be moved to 1.9.0: https://github.com/pepkit/looper/milestone/15

simeoncarstens and others added 30 commits January 14, 2024 19:54
@simeoncarstens
Add pydantic-argparse dependency
ad03377
@simeoncarstens
Add pydantic model scaffold for top-level parser
1b08809
@simeoncarstens
Add entrypoint
bbf3c75
@simeoncarstens
Add scaffold for dynamic command model generation
d2ac184
@simeoncarstens
Validate type of default field
44fa244
@simeoncarstens
Allow None as value next to allowed argument types
7b9273a
@simeoncarstens
[WIP] Add missing arguments for hello_looper to run
2333870
@simeoncarstens
Add cli_pydantic.py script to setuptools scripts
2ecef80
@simeoncarstens
Rework design
bed8292 
- make arguments inherit from `pydantic.fields.FieldInfo` and augment
them with a `name` attribute
- make a `Command` class that generates a `pydantic` model with the
arguments the command takes
- make commands take lists of specific arguments they take instead of
having arguments know by which commands they are supported
@simeoncarstens @zz1874
Fix typo
dfb07cf 
Co-authored-by: Zhihan Zhang <[email protected]>
@zz1874
Use **kwargs in Argument and ArgumentEnum
bc5c78f
@zz1874 @nsheff
Update looper/cli_pydantic.py
c4a20d9 
Co-authored-by: Nathan Sheffield <[email protected]>
@zz1874
Polish docstring of class Argument
c45deb9
@simeoncarstens @zz1874
Explicitly list default and description as args for Argument
82f84d8 
Co-authored-by: Zhihan Zhang <[email protected]>
@simeoncarstens @zz1874
Refactor into separate module
1e6620f 
Co-authored-by: Zhihan Zhang <[email protected]>
@simeoncarstens @zz1874
Add CONFIG_FILE argument
71593e4 
Co-authored-by: Zhihan Zhang <[email protected]>
@simeoncarstens
Add pydantic fields
b990e62
@simeoncarstens
Add a with_reduced_default method to Argument
74e89db 
This method returns the same data, but with the `default`
tuple (<type>, <value>) replaced by only <value>. This allows
`Argument`s to be used when directly defining `pydantic` models
instead of using `create_model()`.
@simeoncarstens
Add SETTINGS argument
a498889
@simeoncarstens
Converted manual pep_config option into Argument
b20ab57
@simeoncarstens
Converted manual output_dir option into Argument
5753a2a
@simeoncarstens
Converted manual config_file option into Argument
da94064
@simeoncarstens
Converted manual sample_pipeline_interfaces option into Argument
6a6c28d
@simeoncarstens
Converted manual project_pipeline_interfaces option into Argument
6dcf3dd
@simeoncarstens
Converted manual amend option into Argument
88b1fcf
@simeoncarstens
Converted manual sel_flag option into Argument
6e8aa34
@simeoncarstens
Converted manual exc_flag option into Argument
1339d42
@simeoncarstens
Make sample_pipeline_interfaces optional
2aa3a03
@simeoncarstens
Make project_pipeline_interfaces optional
c9974c4
@simeoncarstens
Make amend optional
bb10f1b
@donaldcampbelljr
bump pipestat req to 0.9.2a1
25d5d6a
@donaldcampbelljr
set multi_pipelines to True so that sample and project pipelines can …
e1b3aef 
…be reported to the same results.yaml file.
@donaldcampbelljr
Add warning for mismatched pipeline names
f63e1ca
@donaldcampbelljr
bump peppy req to 0.40.2 for issue #458
318b8fe
@donaldcampbelljr
update changelog #458
a0e1167
@donaldcampbelljr
refactor _set_pipestat_namespace
e95b62a
@donaldcampbelljr
remove unused code, finish Destroyer refactor
2e1d136
@donaldcampbelljr
refactor func names
55eb51f
@donaldcampbelljr
remove unnecessary variable duplication
60d807c
@donaldcampbelljr
remove commented code
f476e68
@donaldcampbelljr
add "--project" argument back to Looper
64c81f1
@donaldcampbelljr
refactor obtaining results_file_path during pipestat configuration cr…
ba7f03e 
…eation
@donaldcampbelljr
remove commented code
19d3130
@donaldcampbelljr
remove print statements, change info to debug
5c9ea75
@donaldcampbelljr
ensure we are checking for project level pipestat configuration if us…
c1825c1 
…ing --project
@donaldcampbelljr
reduce looper verbosity by switching to logger.debug in some places
5411139
@donaldcampbelljr
bumbp pipestat req to v0.9.2
d4f576c
@donaldcampbelljr
Merge branch 'dev' into dev_492_refactor_pipestat
4ec9bed
@donaldcampbelljr
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@donaldcampbelljr donaldcampbelljr merged commit 1c17c88 into master Jun 6, 2024
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@nsheff nsheff Awaiting requested review from nsheff

@khoroshevskyi khoroshevskyi Awaiting requested review from khoroshevskyi

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4 participants
@donaldcampbelljr @simeoncarstens @zz1874 @nsheff