Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

helper functions to bootstrap from renv.lock 2 #356

Open
wants to merge 43 commits into
base: main
Choose a base branch
from

Commits on Oct 11, 2024

  1. * add renv_lock_pkgs() function

    ---
    
    `renv_lock_pkgs()` provides the basic functionality of getting the list
    of R packages present in an renv.lock file.
    It does NOT handle the versions of those packages or transitive
    dependencies not directly used in the project.
    RichardJActon committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    7061274 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    803bfd7 View commit details
    Browse the repository at this point in the history
  3. * add renv_lock_r_ver() function

    ---
    
    `renv_lock_r_ver()` retrieves the R version from an renv.lock file.
    RichardJActon committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    8387137 View commit details
    Browse the repository at this point in the history
  4. * add simple non-standard repo filtering to renv_lock_pkgs() function

    ---
    
    adds the `exclude_other_sources` option to `renv_lock_pkgs()` and
    defaults it to TRUE.
    This excludes packages from being returned if the do not have
    "Repository" as their value for "Source" in renv.lock the and throws a
    warning listing the excluded packages.
    This should exclude packages from sources like github which are not
    presently like to be packaged in nix.
    RichardJActon committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    701eafa View commit details
    Browse the repository at this point in the history
  5. * add renv2nix() function

    ---
    
    add `renv2nix()` wraps `rix()` and populates `r_ver`, `r_pkgs`,
    `git_pkgs`, and `local_r_pkgs` based on an `renv.lock` file.
    RichardJActon committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    2e74fcd View commit details
    Browse the repository at this point in the history
  6. * add return_rix_call argument to renv2nix() function

    ---
    
    The `return_rix_call` argument allows `renv2rix()` to return the call to
    the rix function instead of evaluating it, this allows or debugging the
    call.
    RichardJActon committed Oct 11, 2024
    Configuration menu
    Copy the full SHA
    8e4e0a2 View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    926102f View commit details
    Browse the repository at this point in the history

Commits on Oct 12, 2024

  1. Configuration menu
    Copy the full SHA
    700e014 View commit details
    Browse the repository at this point in the history
  2. * add renv_remote_pkgs() function, factors out generating `git_pkgs…

    …` information
    
    ---
    
    The `renv_remote_pkgs()` function takes a single renv.lock package entry
    as an argument, infers it's remote type and extracts the informaton
    necesary for `rix()`'s `git_pkgs` argument.
    
    This functionality was factored out of the `renv2nix()`, and the
    `method` argument added `renv2nix()` to allow for a future
    implementation of exact package version matching.
    RichardJActon committed Oct 12, 2024
    Configuration menu
    Copy the full SHA
    eed8e9a View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    e4b86ef View commit details
    Browse the repository at this point in the history

Commits on Oct 13, 2024

  1. Configuration menu
    Copy the full SHA
    be0ffa2 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    7c108be View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    c34d908 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    d75319d View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    bd52c7d View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    72f930e View commit details
    Browse the repository at this point in the history
  7. wrap overlong lines

    RichardJActon committed Oct 13, 2024
    Configuration menu
    Copy the full SHA
    de7dfb2 View commit details
    Browse the repository at this point in the history
  8. styler styling

    RichardJActon committed Oct 13, 2024
    Configuration menu
    Copy the full SHA
    730bad1 View commit details
    Browse the repository at this point in the history

Commits on Oct 14, 2024

  1. Configuration menu
    Copy the full SHA
    e7a5d08 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    ebb17b3 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    f717e9a View commit details
    Browse the repository at this point in the history

Commits on Oct 15, 2024

  1. Configuration menu
    Copy the full SHA
    0f9de72 View commit details
    Browse the repository at this point in the history
  2. * add renv_remote_pkgs()

    ---
    
    Returns a list of package information suitable to supply to the
    `git_pkgs` argument of `rix()`
    RichardJActon committed Oct 15, 2024
    Configuration menu
    Copy the full SHA
    68ebf8a View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    43137b9 View commit details
    Browse the repository at this point in the history

Commits on Oct 16, 2024

  1. Configuration menu
    Copy the full SHA
    7bd3d50 View commit details
    Browse the repository at this point in the history
  2. * remove renv_remote_pkg() refactoring into renv_remote_pkgs(), w…

    …ith type assertion handling
    
    ---
    
    Ability to allow remote type inference with error for unsupported types
    as well as to assert a remote type expected for all pkgs
    RichardJActon committed Oct 16, 2024
    Configuration menu
    Copy the full SHA
    d24730d View commit details
    Browse the repository at this point in the history

Commits on Oct 23, 2024

  1. Configuration menu
    Copy the full SHA
    753c30b View commit details
    Browse the repository at this point in the history
  2. switch to building lists of remote and repo packages

    simpler to work with than using logicals approach and fixes bug with NAs
    in `r_pkgs` in the previous approach.
    RichardJActon committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    1fa96f3 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    c8d2cb5 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    d54e044 View commit details
    Browse the repository at this point in the history
  5. styling fix

    RichardJActon committed Oct 23, 2024
    Configuration menu
    Copy the full SHA
    dc168a1 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    d953b4b View commit details
    Browse the repository at this point in the history
  7. Configuration menu
    Copy the full SHA
    3bda5ea View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2024

  1. Configuration menu
    Copy the full SHA
    4ef5f97 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    05cbf6b View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    ff69fe2 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    9c1f539 View commit details
    Browse the repository at this point in the history

Commits on Oct 29, 2024

  1. add some example 'real world' renv.lock files for use in testing

    These files come from some random projects of mine sampled from those
    generated with a few different versions of renv, and one which is a
    snapshot of the current rix package.
    RichardJActon committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    1fb1e48 View commit details
    Browse the repository at this point in the history
  2. fix bug where bioconductor is the source

    if source was not "Repository" `renv2nix()` looked for a remote, source
    can also be "Bioconductor" and not have a remote which resulted in an
    error as remote was empty when source was "Bioconductor"
    RichardJActon committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    adcb182 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    c0c7b3c View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    41343f3 View commit details
    Browse the repository at this point in the history

Commits on Nov 1, 2024

  1. renv2nix docs

    b-rodrigues committed Nov 1, 2024
    Configuration menu
    Copy the full SHA
    62d19ba View commit details
    Browse the repository at this point in the history

Commits on Nov 3, 2024

  1. Configuration menu
    Copy the full SHA
    078ac16 View commit details
    Browse the repository at this point in the history