NEWS

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condathis 0.1.4

Release Date: Unreleased

Development Changelog: dev

Added

• New channel_priority argument in create_env() and install_packages() to control channel priority strategy.

• Condathis now support system installed micromamba binaries. For that we added 1 new option and 1 environment variable to control that behavior. condathis_micromamba_path and "CONDATHIS_MICROMAMBA_PATH" respectively. The order of discovey is as follows:

  • User override via getOption("condathis.micromamba_path")
  • User override via CONDATHIS_MICROMAMBA_PATH environment variable
  • condathis internal managed path (micromamba_bin_path())
  • R-in-conda: micromamba adjacent to R's own installation prefix
  • Active conda environment (CONDA_PREFIX)
  • condathis managed micromamba-env fallback
  • System PATH (Sys.which("micromamba"))

Changed

• Internal micromamba version bump to "2.6.2-1".

• clean_cache() now also removes any additional cache files created in the path reported by tools::R_user_dir(package = "condathis", which = "cache").

• Order of channels argument changed to have "conda-forge" as the first option as for using channel_priority = "strict" the order of the channels matters. Note that relying solely on channel order for priority is not recommended. Use explicit syntax like: bioconda::samtools==X.Y.Z for better guarantee of reproducibility.

• create_env() now properly parses MatchSpec version constraints strings to define if environment need to be recreated using new internal functions parse_match_spec() and version_spec_contains() to parse Conda MatchSpec and use VersionSpec to compare versions, following CEP29 and CEP33, respectively.

Fixed

• Fix error in create_env() when packages were specified with "channel::package" environment was always recreated.

condathis 0.1.3 (2025-11-08)

Release Date: 2025-11-07

Development Changelog: 0.1.3

Added

• New clean_cache() function to clean the local package cache.

• New verbose = "spinner" strategy to show only spinner animation in interactive sessions. Spinner is always silenced in non-interactive sessions.

Changed

• Internal micromamba version bump to "2.3.3-0".

• Argument verbose = TRUE is now converted to verbose = "output" by default in all exported functions.

• Argument verbose in create_env(), run(), run_bin(), and install_micromamba() are set to verbose = "output" by default. All internal calls to other functions are kept as "silent", unless when calling the user-facing function with verbose = "full".

• Argument verbose = "silent" now also silence the spinner animation in interactive sessions.

Fixed

• Ignore CONDA_ENVS_DIRS environment variable.

condathis 0.1.2 (2025-06-02)

Release Date: 2025-06-02

Development Changelog: 0.1.2

Added

• New stdin argument to run() and run_bin() functions, allowing input to be redirected via standard input (stdin) via a text file for commands that require it.

• Argument verbose included in install_micromamba() and other auxiliary functions, allowing message suppression in all package functions.

Changed

• Internal micromamba version bump to "2.1.1-0".

• with_sandbox_dir() now also defines temporary cache directory paths, using R_USER_CACHE_DIR and XDG_CACHE_HOME environment variables.

Fixed

• Fix parsing of error messages with curly braces in run() and run_bin(), in the rethrown error, when error = "cancel".

condathis 0.1.1 (2025-01-23)

Release Date: 2025-01-24

Development Changelog: 0.1.1

Changed

• Internal micromamba version bump to "2.0.5-0".

Fixed

• Fix error in run_bin() when error = "continue" and cmd is not on PATH nor in the environment. The expected behavior is to not fail (#23).

• Fix error in create_env() that would fail if debris from failed installation attempts were left in the environment path.

condathis 0.1.0 (2024-12-11)

Release Date: 2024-12-10

Development Changelog: 0.1.0

Added

• Initial submission to CRAN.
• New Package Logo.

Fixed

• run() always creates empty base environment if it does not exists yet.

condathis 0.0.8

Breaking changes

• env_exists() now error if no argument is supplied.

• The base directory path used for creating the environments is now controlled by tools::R_user_dir() and accepts R_USER_DATA_DIR, and XDG_DATA_HOME, respectively as environment variables that can control that path. On Unix/Linux it should be "${HOME}/.local/share/R/condathis".

• The default TMPDIR for all run() and run_bin() calls is cleaned after execution.

• All error messages are resurfaced in the exported function call instead of being thrown in the internal processx call.

• New classes were added to the error condition in most functions.

New features

• New with_sandbox_dir() allow for isolated tests and examples.

Minor improvements and fixes

• Improved error message in list_packages() when environment doesn't exist (#21).

• Improved message in install_packages().

• Spinner is only active when session is interactive.

condathis 0.0.7

New features

• install_micromamba() now tries to download an uncompressed version of the 'micromamba' binary if untar() fails because of missing bzip2 system library. (#10 and #14)

• New parse_output() parses lines output streams from run() results into character vectors.

• New run_bin() runs binary installed in a Conda environment without wrapping in micromamba run.

Minor improvements and fixes

• Internal micromamba version bump to "2.0.4-0".

• create_env() and remove_env() have improved output.

condathis 0.0.6

Breaking changes

• method = "auto" no longer exists. For backward compatibility will fall back to method = "native".
  • All container back-end methods were removed and method = "native" is the only method supported using just this package.
  • A method for supplying additional backends from other packages is planned to be implemented.

Minor improvements and fixes

• Remove dependency on dockerthis.

• Fix error in run() when verbose argument was not supplied.

condathis 0.0.5

Breaking changes

• verbose, levels TRUE and FALSE are now soft deprecated. For previous functionality "full" and "silent" should be used respectively.

New features

• run() now has error argument.

Minor improvements and fixes

• run() output now has class "condathis_run_output" with custom print method.
• run() now exposes stderr.
• verbose now accepts any of c("silent", "full", "cmd", "output"). TRUE and FALSE are deprecated but still kept for compatibility.
• Improved error handling in run() when invalid arguments are provided.

condathis 0.0.4

Breaking changes

• create_env() new argument default overwrite = FALSE, since the previous behavior would allow for the environment to always be overwritten. For previous behavior use overwrite = TRUE.

• Across the entire package verbose = FALSE is default.

New features

• New get_env_dir() retrieves path to environment v(0.0.3.9032).

• create_env() now has overwrite = FALSE argument v(0.0.3.9030).

• install_micromamba() now has micromamba_version argument (v0.0.3.9025).

• Add support for internal micromamba versions above v2.0 (v0.0.3.9024).

• New remove_env() created (v0.0.3.9012 #7).

Minor improvements and fixes

• native_cmd() now uses additional Environmental Variables for removing warnings when calling nested micromamba run (v0.0.3.9029 #13).

• Standardize argument order passed to micromamba, since v2.0, order of some arguments starts to conflict (v0.0.3.9027).

• On Windows, the "BAT" file used by micromamba run is renamed (v0.0.3.9026 #11).

• Internal micromamba version is upgraded to "2.0.2-0", fixes warnings about missing prefixes (v0.0.3.9028).

• The internal micromamba version is now fixed (currently "v2.0.1-0") (v0.0.3.9025).

• Use GitHub releases as the primary URL for installing micromamba (v0.0.3.9025).

• Move --no-rc and --no-env arguments to native_cmd() (v0.0.3.9024).

• Fix path handling in Windows (v0.0.3.9023).

• Add mode = "wb" to internal download.file() for handling binary downloads in Windows (v0.0.3.9023).

• list_envs() and list_packages() uses --no-rc internally (v.0.0.3.9022).

• create_env_*(), packages_search_*(), and install_packages() now uses --no-rc and --override-channels (v0.0.3.9020).

• Remove "defaults" channel (-c defaults) from all functions (v0.0.3.9020).

• create_env_*(), packages_search_*(), and install_packages() uses --no-channel-priority internally (v0.0.3.9019).