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Version 1.0.0 release PR - "Ardent adenine" #10

Merged
merged 77 commits into from
Aug 16, 2023
Merged

Version 1.0.0 release PR - "Ardent adenine" #10

merged 77 commits into from
Aug 16, 2023

Commits on Apr 13, 2023

  1. Johannes over-simplification

    @alneberg
    alneberg committed Apr 13, 2023
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  2. Tidying up a bit

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    alneberg committed Apr 13, 2023
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  3. Added back option to gzip output

    @alneberg
    alneberg committed Apr 13, 2023
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  4. Started adjusting the readme

    @alneberg
    alneberg committed Apr 13, 2023
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  5. Readme table formatting

    @alneberg
    alneberg committed Apr 13, 2023
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  6. more readme changes

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  7. Wrote the performance guide

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Commits on Apr 14, 2023

  1. Version 0.2.0

    @alneberg
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  2. Added background and for developers sections to README

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Commits on Apr 18, 2023

  1. Use file-format crate to check for gzipped file

    @alneberg
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  2. Added 'written by' to authors list in clap

    @alneberg
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  3. Failed splitting, cannot reach file_io from umi_external

    @alneberg
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Commits on Apr 20, 2023

  1. Managed to use modules

    @alneberg
    alneberg committed Apr 20, 2023
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  2. Added a gitignore

    @alneberg
    alneberg committed Apr 20, 2023
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Commits on May 3, 2023

  1. Adding some basic error handling.

    @MatthiasZepper
    MatthiasZepper committed May 3, 2023
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  2. Implemented some basic error handling.

    @MatthiasZepper
    MatthiasZepper committed May 3, 2023
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Commits on May 5, 2023

  1. Merge pull request #5 from alneberg/johannes_simple 

    Make Johannes' simplification the base for the new dev.
    @MatthiasZepper
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  2. Merge pull request #6 from MatthiasZepper/johannes-simplification 

    Some amendments to Johannes simplification
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    MatthiasZepper authored May 5, 2023
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  3. Further refactor: Subcommand structure to allow for easy addition of … 

    …further subcommands in later versions.
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  4. Implemented a simple counter for the records.

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Commits on May 8, 2023

  1. Switching the CLI arguments from strings to Option<PathBuf> and imple… 

    …mented an output overwrite check and prompt.
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  2. Cleaner code for output checks and suffix updates.

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  3. file_io::append_to_path() must work without owning the provided PathB… 

    …uf. Had do clone twice :-(
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  4. Finished autogeneration of the file name extension, used a Regex to m… 

    …odify the input file names if no output file names were given.
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Commits on May 9, 2023

  1. Implemented fixing the read numbers for both reads and using a custom… 

    … delimiter.
    @MatthiasZepper
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  2. Readme updates.

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    MatthiasZepper committed May 9, 2023
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Commits on May 25, 2023

  1. Fixing issues highlighted by Clippy.

    @MatthiasZepper
    MatthiasZepper committed May 25, 2023
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  2. Addressed the clippy warning 'Large size difference between variants'… 

    … for the ReadFile enum by introducing a <Box> around the compressed input. Also used a BufReader for the plain text file.
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Commits on Jun 2, 2023

  1. Readme updates.

    @MatthiasZepper
    MatthiasZepper committed Jun 2, 2023
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  2. Github unfortunately doesn't render simple style commands in the Readme.

    @MatthiasZepper
    MatthiasZepper committed Jun 2, 2023
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  3. Increase Logoheader size.

    @MatthiasZepper
    MatthiasZepper committed Jun 2, 2023
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  4. Merge pull request #7 from MatthiasZepper/further_refactor 

    Continued refactoring, approved by Johannes. Nearing release 0.2
    @MatthiasZepper
    MatthiasZepper authored Jun 2, 2023
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Commits on Jun 14, 2023

  1. Remove a possible .gz extension, if the --gzip/-z flag is not active.

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Commits on Jun 15, 2023

  1. Add the first unit test. More to come.

    @MatthiasZepper
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  2. Added more tests, this time for check_outputpath function

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    MatthiasZepper committed Jun 15, 2023
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Commits on Jul 6, 2023

  1. Consolidate nested if/else to match in file_io::check_outputpath().

    @MatthiasZepper
    MatthiasZepper committed Jul 6, 2023
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Commits on Jul 7, 2023

  1. Move extension handling and correction into new separate function.

    @MatthiasZepper
    MatthiasZepper committed Jul 7, 2023
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  2. Integrate a custom header.

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    MatthiasZepper committed Jul 7, 2023
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Commits on Jul 10, 2023

  1. Collapse else if clause in rectify_extension().

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    MatthiasZepper committed Jul 10, 2023
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  2. Add test data, 10 simulated reads pairs from Escherichia phage phiX17… 

    …4 genome (NC_001422.1).
    @MatthiasZepper
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  3. Replace tempdir crate with assert_fs.

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    MatthiasZepper committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. Make colors of the header optional.

    @MatthiasZepper
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  2. Refactor errors so they accept an optional path.

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  3. Consistently replace OutputFile with Result<OutputFile> in all functi… 

    …ons.
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  4. Add a new ReadWriteError to RuntimeErrors.

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  5. Write error messages to Stderr instead of Stdout and color with owo-c… 

    …olorize.
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  6. Created a custom error parsing for clap:Error enum that allows custom… 

    … styling of particular errors.
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Commits on Jul 12, 2023

  1. Again error styling.

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  2. Adapt the append_umi_to_path() function to additional edge cases with… 

    … hidden directories and hidden files.
    @MatthiasZepper
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  3. Write the first two integration tests.

    @MatthiasZepper
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  4. Add two more integration tests.

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  5. Refactor integration tests for clearer structure.

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  6. Added tests for gz file extension.

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  7. Add more integration tests: Existing and non-existing output.

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  8. Remove a needless_late_init warning from clippy in file_io.rs

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Commits on Jul 13, 2023

  1. Create validated output files to be used in tests and correct header … 

    …glitch in input.
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  2. Create TestResults struct to hold the paths to the validated program … 

    …outputs.
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  3. Wrote an auxiliary function verify_file_contents() for the tests, so … 

    …I can test if the output looks as expected.
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  4. Finished the integration tests to test file output.

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Commits on Jul 14, 2023

  1. Merge pull request #8 from MatthiasZepper 

    This PR adds extensive unit and integration tests and enables removal of an input `*.gz` extension if the output is not compressed.
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  2. Create new Testing workflow comprising Clippy and Tarpaulin.

    @MatthiasZepper
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  3. Devise a new release action that includes cross-plattform builds. Hea… 

    …vily inspired by/copied from Alex Hallam's tidy-viewer release action.
    @MatthiasZepper
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  4. Refurbish the Docker image build action.

    @MatthiasZepper
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  5. Change EventTriggers to test workflows in my fork.

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Commits on Jul 15, 2023

  1. Bugfixes in the GithubAction workflows. Fingers crossed...

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Commits on Jul 18, 2023

  1. Slight tweaks to the GithubActions and the Dockerfile.

    @MatthiasZepper
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  2. Switch to ructions from actions-rs, since the latter seem to be unmai… 

    …ntained.
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  3. Extract version from Cargo.toml with grep to have it in the filenames.

    @MatthiasZepper
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  4. Modify tarpaulin command to incluce integration tests

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  5. Update the Github Actions... 

    ...and unlock the YOLO batch from Github.
    @MatthiasZepper
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  6. Readme updates to inclue binaries and Docker.

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Commits on Jul 31, 2023

  1. Implement exceptions to the prompts for /dev/null and FIFOs.

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  2. Fix the 'all variants have the same postfix' warning. I appreciated t… 

    …he consistency, though.
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Commits on Aug 1, 2023

  1. Include instructions for singletons in README.md and change version t… 

    …o 1.0.0
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  2. Dropping support for implicit compressed output by specifing .gz exte… 

    …nsion. This will result in a more consistent behaviour.
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  3. Match on Ok() instead of Some() in rectify_extension() to avoid going… 

    … from Result to Option and back.
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Commits on Aug 14, 2023

  1. Typofix in README.md

    @alneberg
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