funpack merge requestshttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests2020-02-28T16:23:51+00:00https://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/42Revise configuration files2020-02-28T16:23:51+00:00Tom NicholsRevise configuration files# Revise configuration files
In response to my own usage, I find the existing `fmrib.cfg` overly broad and involves too many different types of processes:
1. Default processing of UKB tables using FMRIB expertise/experience/decisio...# Revise configuration files
In response to my own usage, I find the existing `fmrib.cfg` overly broad and involves too many different types of processes:
1. Default processing of UKB tables using FMRIB expertise/experience/decisions
1. Selection of a large set of variables for output
1. Individual preferences; some, including high verbosity and use of extensive logging/documentation, will come down to a user's preference; some, are site-level decisions (e.g. default value for `num_jobs`)
In this PR I propose splitting in `fmrib.cfg` in the following files
* `fmrib.cfg` - A paired down file that just has recommended variable processing, and defines FMRIB categories (but doesn't select categories to process)
* `fmrib_cats.cfg` - The FMRIB categories that were previously always selected with use of `fmrib.cfg`
* `fmrib_logs.cfg` - Contains all options in `fmrib.cfg`, but adds maximal verbosity, logging and documentation file output.
* `local.cfg` - The local (maybe should be `site.cfg`?) that are global preferences that a local maintainer may wish to change.
This PR is really a WIP because to make use of these we really need two other modifications to `funpack` described in #13 and #14.https://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/36Make pared down UKB configuration, ukb.cfg2020-01-30T10:52:03+00:00Tom NicholsMake pared down UKB configuration, ukb.cfgSuggestion for pared down UKB configuration, aside from the many configuration choices in `fmrib.cfg`. Just not sure if there should be anything else in here... e.g. should `trust_types` be there? `import_all`? Also unsure about `date...Suggestion for pared down UKB configuration, aside from the many configuration choices in `fmrib.cfg`. Just not sure if there should be anything else in here... e.g. should `trust_types` be there? `import_all`? Also unsure about `date_format` & `time_format`, and `loader` options.https://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/33Rf/fmrib config2020-01-23T17:41:34+00:00Paul McCarthyRf/fmrib config# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/18Rf/categories2019-06-04T14:53:49+01:00Paul McCarthyRf/categories# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/16Mnt/tweaks2019-05-29T19:12:08+01:00Paul McCarthyMnt/tweaks# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/13RF: Summary file in FMRIB config2019-05-25T12:45:38+01:00Paul McCarthyRF: Summary file in FMRIB configPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/10Rf/sparsity categorical nan2019-05-16T17:47:45+01:00Paul McCarthyRf/sparsity categorical nan# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/9Bf/flatten hierarchical na2019-05-16T12:12:37+01:00Paul McCarthyBf/flatten hierarchical na# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/8Bf/non numeric2019-05-15T18:10:25+01:00Paul McCarthyBf/non numeric# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/7Rf/visit instancing2019-05-14T19:31:39+01:00Paul McCarthyRf/visit instancing# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/4CI: Fix zenodo upload2019-05-10T15:19:25+01:00Paul McCarthyCI: Fix zenodo uploadPaul McCarthyPaul McCarthyhttps://git.fmrib.ox.ac.uk/fsl/funpack/-/merge_requests/3MNT: Fix pytest/coverage config2019-05-10T13:13:54+01:00Paul McCarthyMNT: Fix pytest/coverage config# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` upd...# `funpack` merge request
Unless the maintainer is being sloppy, this merge request will not be accepted
unless the following criteria are met:
[ ] Unit tests pass
[ ] Changelog updated
[ ] Version number in `funpack/__init__.py` updated according to
[Semantic Versioning](https://semver.org) conventionsPaul McCarthyPaul McCarthy