Changelog • metabodecon

metabodecon 1.1.1

Development Branch:

API:

Fixed a bug in generate_lorentz_curves() that caused the function to always use file format “bruker”, even when file format “jcampdx” was specified.

Datasets:

Fixed filenames of samples in blood dataset (renamed from Bood_<nr> to blood_<nr>).
Renamed example_datasets/jcampdx/urine/urine.dx to example_datasets/jcampdx/urine/urine_1.dx and renamed example_datasets/bruker/urine/urine/ to example_datasets/bruker/urine/urine_1/. This was done because list.files seems to return different orderings for urine.dx and urine_2.dx in different operating systems, whereas urine_1.dx and urine_2.dx are sorted the same way everywhere. This makes it easier to write clear and concise test cases, because we don’t need to check for file ordering.

Documentation:

Testing:

Added unit tests for generate_lorentz_curves().
Enabled parallel processing for unit tests.
Created initial versions of tests/testthat/test-generate_lorentz_curves-[1-4].R.
Added generate_lorentz_curves_v2() to DESCRIPTION/Config/testthat/start-first.
Adjusted existing tests to use the updated version of example_datasets (sample urine was renamed to urine_1, as mentioned in above in section Datasets)

Internal:

Added functions %||%, msg() and msgf to R/util.R.
Added elements range_water_signal_ppm and signal_free_region to returned list of function deconvolute_spectrum.
Function with now prints error messages to stderr even if the message stream is redirected.
Copied function deconvolution() from R/MetaboDecon1D.R to R/main_v2.R as .deconvolute_spectrum.
Fixed order of params in deconvolution.
Fixed download_example_datasets(). Argument overwrite is passed correctly on to cache_example_datasets().
Changed URL of example datasets xds$url from https://github.com/spang-lab/metabodecon/releases/download/v1.0.2/example_datasets.zip to https://github.com/spang-lab/metabodecon/releases/download/v1.1.0/example_datasets.zip.
Improved cache_example_datasets(). Extraction now only is done if extract == TRUE AND the resulting folder does not yet exist (saves approx. 2-3s on each call). To overwrite a possible existing folder, argument overwrite can be set to TRUE.
Fixed formatting of test_helpers.R
Added linter config .lintr

API:

Improved function download_example_datasets() by adding caching and making it more stable
Replaced function get_data_dir() with datadir() and its helper functions datadir_persistent(), datadir_temp() and tempdir
Function get_data_dir() is now deprecated in favour of datadir()

Documentation:

Datasets:

Internal:

Added unit tests
Removed script check_package.R
Moved functions from util.R to datadir.R
Added grDevices, stats and utils as internal imports
Added lots of test helper functions in R/test_helpers.R
Added function generate_lorentz_curves_v2() which will replace generate_lorentz_curves() as soon as we have new features AND 100% backwards compatibility
Fixed bug in with() that caused get_datadir_mock() to be called after redirection took place causing unexpected message output
Fixed bug in datadir() that caused the resulting path to end with a slash on Unix-like systems and without a slash on Windows, if file was not specified
RUN_SLOW_TESTS is now set to TRUE for the CI pipeline

API:

Updated get_data_dir() to accept "blood" as new value for parameter dataset_name
Updated download_example_datasets() to download the datasets from the github repo instead of the old spang-lab repo

Documentation:

Removed table of contents from README.md as it’s a bit overkill for approx. 50 lines of text
Improved documentation

Internal:

Switched from MIT License to GPL-3 to match the license of the predecessor package MetaboDecon1D
Added docs folder to .gitignore. Reason: we changed all vignettes to pkgdown articles which will be displayed only at our Github Pages website and can be regenerated from folder vignettes upon deployment.
Created TODOS.md and added it to .Rbuildignore
Improved .gitignore