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NEWS

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NEWS – history of user-visible changes -*- mode: org; -*-

master (unreleased)

  • The ‘localrule’ keyword (new in Snakemake v7.25.0) is now recognized.

v2.0.0

  • Support for Emacs versions older than 26.1 has been dropped.
  • The Magit Popup command snakemake-popup has been rewritten as a transient, snakemake. snakemake.el now depends on Transient rather than Magit Popup.
  • The --jobs argument in the snakemake transient has been replaced by --cores to follow upstream changes. --cores is bound to -c, and --use-conda has been moved from -c to -C.
  • Snakemake’s new module syntax (added in v6.0) is now supported.
  • Additional Snakemake keywords are now recognized: ‘containerized’ (new in Snakemake v6.0.0), ‘default_target’ (new in Snakemake v6.15.0), ‘handover’ (new in Snakemake v6.2.0), ‘name’ (new in Snakemake v5.31.0), and ‘notebook’ (new in Snakemake v5.10.0).
  • The snakemake-compile command, marked obsolete in v1.2.0 in favor of snakemake-build, has been removed.

v1.8.0

  • Additional Snakemake keywords are now recognized: ‘envmodules’ (new in Snakemake v5.9.0), ‘envvars’ (new in v5.11.0), ‘container’ (new in v5.11.0), and ‘cache’ (new in v5.12.0).

v1.7.0

  • The ‘multiext’ built-in (new in Snakemake v5.8.2) is now recognized.
  • The font-lock handling has been updated to be compatible with python.el changes in Emacs 27.

v1.6.0

  • Checkpoints (new in Snakemake v5.4) are now recognized.

v1.5.0

  • snakemake-popup now includes --use-conda.
  • Additional Snakemake keywords are now recognized: ‘group’ keyword (new in Snakemake v5.0), report (both the keyword and function; new in Snakemake v5.1), and ‘localrules’.

v1.4.0

  • The ‘cwl’ keyword (new in Snakemake v4.8.0), ‘pipe’ (new in Snakemake v5.2.0), ‘directory’ (new in Snakemake v5.2.0), and ‘ancient’ built-in are now recognized.
  • The minimum Emacs version is now specified as 24.5. Although the previous specification was a looser “24”, Snakemake’s indentation function is incompatible with Emacs 24.4 and below.

v1.3.0

  • The ‘singularity’ keyword (new in Snakemake v4.2.0) is now recognized.
  • “.smk” has been added as a suffix for Snakemake files.

v1.2.0

  • snakemake-popup commands learned to call Snakemake through a terminal rather than through compile. This allows a persistent environment to be maintained between Snakemake calls, which is useful for running Snakemake in isolated environments created by tools like Guix.

v1.1.0

  • The ‘conda’ keyword (new in Snakemake v3.9.0) is now recognized.

v1.0.0

  • The ‘wildcard_constraints’ keyword (new in Snakemake v3.8.0) is now recognized.

v0.5.0

  • New command snakemake-graph-this-file displays the graph for the first rule of the current file. Similar functionality is available from snakemake-graph, which supports graphing any target in the file, but you may find the new command useful if your workflow involves frequently using Snakemake’s --snakefile option.
  • New function snakemake-mode-setup-mmm configures MMM mode to highlight string-embedded R code. (Contributed by Endre Bakken Stovner.)
  • “.rules” has been added as a suffix for Snakemake files.
  • beginning-of-defun and end-of-defun implementations for rule blocks are now defined.
  • Rule blocks are now recognized by add-log-current-defun.

v0.4.0

  • New library snakemake.el provides a popup interface for running Snakemake from Emacs.
  • New command snakemake-graph displays the graph of dependencies for a rule. (Thanks to Endre Bakken Stovner for the idea and initial implementation.)
  • “.snakefile” has been added as a suffix for Snakemake files.
  • Anonymous rule blocks are now supported.
  • The ‘wrapper’ keyword is now recognized.

v0.3.0

  • The keywords ‘configfile’, ‘onsuccess’, ‘onerror’, ‘log’, and ‘benchmark’, ‘script’, ‘shadow’, as well as the ‘touch’ function, are now recognized.
  • Indentation for field values starting on the line below a field key is now supported. New variable snakemake-indent-value-offset controls the offset for the value and replaces the variable snakemake-indent-run-offset. If these values are continued on another line, indentation cycling now includes a step that indents according to Python mode.
  • snakemake-compile-rule can now pass the ‘–touch’ flag to snakemake.
  • The Imenu index now includes Python mode items in addition to rule blocks.
  • Errors in Snakefiles are now highlighted in complilation buffers.

v0.2.0

  • Both the executable and flags for the Snakemake compile-command are now customizable.
  • New command snakemake-compile-rule runs Snakemake with the rule at point as the target.
  • Subworkflow blocks are now supported.
  • The ‘ruleorder’ keyword is now recognized.