MetaboDecon1D() that caused argument file_path to be interpreted as a relative path, even if it was an absolute path.read_spectrum() that caused argument raw to not be passed on to read_jcampdx().Finished the following tasks. For details about each task, see TODOS.md.
read_spectra()plot_spectrum()deconvolute_blood()-License, +Timestamps)generate_lorentz_curves()MetaboDecon1D() callscalc_prarp()API:
generate_lorentz_curves() that caused the function to always use file format "bruker", even when file format "jcampdx" was specified.Datasets:
Bood_<nr> to blood_<nr>).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:
generate_lorentz_curves().tests/testthat/test-generate_lorentz_curves-[1-4].R.generate_lorentz_curves_v2() to DESCRIPTION/Config/testthat/start-first.example_datasets (sample urine was renamed to urine_1, as mentioned in above in section Datasets)Internal:
%||%, msg() and msgf to R/util.R.range_water_signal_ppm and signal_free_region to returned list of function deconvolute_spectrum.with now prints error messages to stderr even if the message stream is redirected.deconvolution() from R/MetaboDecon1D.R to R/main_v2.R as .deconvolute_spectrum.deconvolution.download_example_datasets(). Argument overwrite is passed correctly on to cache_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.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.test_helpers.R.lintrAPI:
download_example_datasets() by adding caching and making it more stableget_data_dir() with datadir() and its helper functions datadir_persistent(), datadir_temp() and tempdirget_data_dir() is now deprecated in favour of datadir()Documentation:
Datasets:
misc/datasets to misc/example_datasetsmisc/examples/usage_example.R to misc/code_examples/sage_example.RInternal:
check_package.Rutil.R to datadir.RgrDevices, stats and utils as internal importsR/test_helpers.Rgenerate_lorentz_curves_v2() which will replace generate_lorentz_curves() as soon as we have new features AND 100% backwards compatibilitywith() that caused get_datadir_mock() to be called after redirection took place causing unexpected message outputdatadir() that caused the resulting path to end with a slash on Unix-like systems and without a slash on Windows, if file was not specifiedRUN_SLOW_TESTS is now set to TRUE for the CI pipelineAPI:
get_data_dir() to accept "blood" as new value for parameter dataset_namedownload_example_datasets() to download the datasets from the github repo instead of the old spang-lab repoDocumentation:
README.md as it's a bit overkill for approx. 50 lines of textInternal:
MetaboDecon1Ddocs 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.TODOS.md and added it to .Rbuildignore.gitignoreCONTRIBUTE.md (instead a section within README.md is used)