Changelog

Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]#

Template updates#

  • Do not ignore gitignore files in output/report directories of template (#63)

v0.10.0#

Template updates#

  • Improve instruction text in quarto template to get users started more quickly (#40)

  • Add .gitignore catch-all clauses for output and report folders in stages to not pick up data and repots being tracked via git (#46).

  • Every dso project is now also a uv project declaring Python dependencies in pyproject.toml. This makes it possible to use a different dso version per project and makes it easy to work with virtual Python environments (#52)

  • bash templates now include -euo pipefail settings, ensuring that stages fail early and return a nonzero error code if something failed (#59).

Fixes#

  • Remove vendored hiyapyco code since required changes were released upstream in v0.7.0 (#45).

  • None values in params.in.yaml can now be used to override anything, e.g. to disable watermarking only in a specific stage (#45).

  • Clean up existing *.rmarkdown files in quarto stage before running quarto render. This fixes issues with re-running quarto stages that failed in the previous attempt (#57).

  • DSO now respects a DSO_SKIP_CHECK_ASK_PRE_COMMIT environment variable. If it is set to anything that evaluates as True, we skip the check if pre-commit is installed. This was a requirement introduced by the R API package, see #50 (#58).

  • Improve logging for “missing path” warning during compile-config (#59).

  • Improve logging for missing parameters in dvc.yaml during get-config (#59).

  • Make sure internal calls to the dso pandocfilter use the same python and dso version as the parent command. This is important for the upcoming dso-mgr feature (#61).

v0.9.0#

New Features#

  • dso watermark now supports files in PDF format. With this change, quarto reports using the watermark feature can be rendered to PDF, too (#26).

Fixes#

  • Fix linting rule DSO001: It is now allowed to specify additional arguments in read_params(), e.g. quiet = TRUE (#36).

  • It is now possible to use Jinja2 interpolation in combination with !path objects (#36)

  • Improve error messages when dso get-config can’t find required input files (#36)

Documentation#

  • Documentation is now built via sphinx and hosted on GitHub pages: https://boehringer-ingelheim.github.io/dso/ (#35).

Template updates#

  • Make instruction comments in quarto template more descriptive (#33).

  • Include params.yaml in default project .gitignore. We decided to not track params.yaml in git anymore since it adds noise during code review and led to merge conflicts in some cases. In the future, a certain dso version will be tied to each project, improving reproducibility also without params.yaml files.

Migration advice#

  • Add params.yaml to your project-level .gitignore. Then execute find -iname "params.yaml" -exec git rm --cached {} \; to untrack existing params.yaml files.

v0.8.2#

Fixes#

  • Fixed params.yaml sorting issue - params.yaml order will be kept intact when using dso get-config

v0.8.1#

Fixes#

  • Fixed and issue with spaces in image filenames when watermarking a quarto document

v0.8.0#

New Features#

  • dso init and dso create folder now also work in existing directories. In such case missing files will be added from the template, but existing files are never overwritten.

  • There’s now a template for a bash stage available in dso create stage. The stage template needs can be specified via the --template flag, otherwise the user is prompted to choose a template.

  • dso now has flags to control logging verbosity. The default log-level is info. -q will set it to warning, -qq to error and -v to debug. The “quiet” option can also be activated by setting the environment variable DSO_QUIET=1 or DSO_QUIET=2.

  • dso exec and dso get-config now have a --skip-compile flag to disable automatic internal calls to dso compile-config. The flag can also be activated by setting the environment variable DSO_SKIP_COMPILE=1.

Fixes#

  • Fix that compile-config also compiles parents when in a directory without a params.in.yaml file.

  • The order of dictionaries is now preserved by dso get-config.

  • When running dso init or dso create, dso compile-config is now only executed after it was clearly communicated with the user that the project/stage/folder was successfully created.

  • Specifying a stylesheet using css via dso.quarto is now possible.

  • Adjusted the log level of some messages to more reasonable defaults. Some messages that were previously info messages are now debug messages and not shown by default.

  • When running dso repro, configuration is only compiled once and not recompiled when dso exec or dso get-config is called internally. This reduces runtime and redundant log messages.

v0.7.0#

  • Improved watermarking support

    • Added test cases for watermarking and the pandocfilter

    • Support for SVG images

    • There’s now a dso watermark command line interface to watermark specified image files. In the future this can be used to provide a custom plotting device in R that performs the watermarking.

    • Changed the watermark layout to use a tiled pattern which is less obstrusive and is guaranteed to cover the entire plot

    • The watermark is now fully configurable via params.in.yaml:

      dso:
    quarto:
        watermark:
            text: WATERMARK
            # change the visuals - Usually fine to stick with the default, but these are the options that can be changed
            tile_size: [100, 100]
            font_size: 12
            font_outline: 2
            font_color: black
            font_outline_color: "#AA111160"

  • Fix issue where dso was stuck in an infinity loop while searching for a config file. Now it should fail if it can’t be found. To realize this the funcitonality for searching parent folders for a certain file that was used in different places was refactored into a separate function.

v0.6.1#

  • Fix issue in dso get-config if multiple parameters have been used in a single line in deps:.

v0.6.0#

  • Add a dso lint command that performs consistency checks on dso projects. For now, only a single rule is implemented, but it can be easily extended. The rule:

    • DSO001: In a quarto stage, ensure dso::read_params is called and stage name is correct.

  • Logging information is now printed to STDERR instead of STDOUT

  • Add dso get-config <STAGE> which will compile and print the configuration for a given stage to STDOUT. Additionally, it filters the output to fields that are specified in dvc.yaml which forces the user to declare all dependencies in dvc.yaml.

  • Add automated watermarking of plots in quarto documents as experimental feature. For now, only png images are supported. To enable, add to params.in.yaml:

    • dso.quarto.watermark: a text to be shown as watermark.

    • dso.quarto.disclaimer.text: a text to be shown as disclaimer box.

    • dso.quarto.disclaimer.title: title of the disclaimer box.

    The disclaimer box is only shown if both text and title are set.

Migration advice#

  • Update dso-r to v0.3.0 to take advantage of dso get-config.

  • Add the following rule to your .pre-commit-config.yaml:

      - repo: local
      hooks:
      [...]
      - id: lint
          name: Run dso lint
          entry: dso lint --skip-compile
          language: system
          stages: [commit]

v0.5.0#

  • dso.before_script is now dso.quarto.before_script. This change has been made because different “exec” modules will likely need different setup-scripts (i.e. environment modules). If the script shall be shared nevertheless, this can be done with jinja templating.

  • It is now possible to specify bibliography files in params.in.config:dso.quarto.bibliography using !path.

  • Upon dso repro, the CLI asks once if the user wants to install the pre-commit hooks

Migration advice#

  • Move dso.before_script to dso.quarto.before_script in all your config files.

  • Update all quarto stages to depend only on params:dso.quarto instead of params:dso. This will avoid invalidating the cache unnecessarily.

  • add /.dso.json to your .gitignore file

v0.4.4#

  • Remove confirmation before overwriting a newer params.yaml file - It turned out not to work well with switching branches in git and led to way too many unnecessary questions.

  • Do not fail when dso.quarto is null in params.in.yaml (not all cases were addressed in v0.4.3)

v0.4.3#

  • Fix confirmation to overwrite params.yaml

  • Improve error message when dso exec quarto fails

  • Make pre-commit hooks verbose

  • Do not fail when dso.quarto is null in params.in.yaml

v0.4.2#

  • Update quarto template to include dso params as dependency

  • Reduce the number of false-positives when asking for confirmation to overwrite params.yaml

v0.4.1#

  • Allow a tolerance of 1s when comparing timestamps of params.in.yaml and params.yaml

v0.4.0#

  • Ask for confirmation before overwriting a newer params.yaml file

  • The log messages when compiling configuration files have improved

  • Added dso exec quarto, a convenient wrapper to execute quarto stages

    • Quarto configuration/headers will be read from params.yaml:qso.quarto

    • A shell snippet specified in params.yaml:dso.before_script will be executed before rendering the report. This is useful for setting up the environment, e.g. by loading modules

v0.3.1#

  • Update quarto template to be concordant with latest dso-r version

v0.3.0#

  • Updated quarto template to use dso code to load files

  • dso compile-config now optionally supports specifying a list of paths

  • Renamed dso create project to dso init

  • Added dso create folder in addition to dso create stage.

  • Currently only one template for dso init, dso create folder and dso create stage but prepared the project to easily support multiple templates in the future

  • Improved pre-commit config. Install it using pre-commit install in the project. It automatically performs some consistency checks and dvc pull/push/checkout.

v0.2.0#

  • It’s now possible to specify paths via the !path tag in params.in.yaml. These paths will be checked for existence and automatically resolved such that they are always relative to the compiled params.yaml files.

v0.1.0#

  • initial prototype

  • dso create command