diff options
| -rw-r--r-- | NEWS | 10 | ||||
| -rw-r--r-- | snakemake.el | 135 |
2 files changed, 119 insertions, 26 deletions
@@ -1,5 +1,15 @@ NEWS -- history of user-visible changes -*- mode: org; -*- +* master (unreleased) + +** New features + +- ~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 ** New features diff --git a/snakemake.el b/snakemake.el index ab56ae5..99473fc 100644 --- a/snakemake.el +++ b/snakemake.el @@ -25,9 +25,9 @@ ;; `snakemake-popup', which you should consider giving a global key ;; binding. ;; -;; The popup currently includes four actions, all which lead to -;; `compile' being called with "snakemake ...". What's different -;; between the actions is how targets are selected. +;; The popup currently includes four actions, all which lead to a +;; Snakemake call. What's different between the actions is how +;; targets are selected. ;; ;; snakemake-build-targets-at-point ;; @@ -39,10 +39,9 @@ ;; names from Dired, Org links, and general text under point that ;; looks like a file name. ;; -;; snakemake-compile +;; snakemake-build ;; -;; This action leads to an interactive `compile' call that allows -;; you to edit the command before it is run. +;; This action allows you to edit the command before running it. ;; ;; It tries to guess what the target name should be, but it ;; doesn't verify if this target is actually a build target. This @@ -75,6 +74,10 @@ ;; which to look for a Snakefile if there isn't one in the current ;; directory. ;; +;; By default, commands are executed through `compile'. However, a +;; terminal can be created with `snakemake-term-start', in which case +;; commands are sent there instead. +;; ;; In addition to the popup commands, there are commands for showing ;; and saving the dependency graph of a target. The command ;; `snakemake-graph' displays the graph in a buffer. From this @@ -88,6 +91,7 @@ (require 'cl-lib) (require 'compile) +(require 'term) (require 'magit-popup) (require 'snakemake-mode) @@ -105,6 +109,11 @@ :type 'string :package-version '(snakemake-mode . "0.4.0")) +(defcustom snakemake-shell-file-name shell-file-name + "Program used by `ansi-term' to start a terminal." + :type 'string + :package-version '(snakemake-mode . "1.2.0")) + (defcustom snakemake-file-target-program (executable-find "snakemake-file-targets") "Program that returns newline-delimited list of output files." @@ -541,7 +550,14 @@ Snakemake-graph mode is a minor mode that provides a key, :keymap snakemake-graph-mode-map) -;;; Compilation commands +;;; Commands for calling Snakemake + +(defun snakemake--make-command (targets args) + (mapconcat #'identity + `(,snakemake-program ,@args "--" ,@targets) + " ")) + +;;;; Compilation interface (add-to-list 'compilation-error-regexp-alist 'snakemake) (add-to-list @@ -549,25 +565,79 @@ Snakemake-graph mode is a minor mode that provides a key, '(snakemake . ("^SyntaxError in line \\([0-9]+\\) of \\(.*[^A-z]Snakefile\\):$" 2 1))) -(defun snakemake--define-compile-command (targets args) - (mapconcat #'identity - `(,snakemake-program ,@args "--" ,@targets) - " ")) - (defun snakemake-compile-targets (targets args) "Run non-interactive `compile' with 'snakemake [ARGS] -- TARGETS'." (let ((default-directory (snakemake-snakefile-directory)) - (cmd (snakemake--define-compile-command targets args))) + (cmd (snakemake--make-command targets args))) (compile cmd) (push cmd compile-history))) +;;;; Terminal interface + +(defun snakemake-term--name () + (concat "snakemake-terminal: " (abbreviate-file-name default-directory))) + +(defun snakemake-term-process () + "Return the terminal process of the current directory." + (get-process (concat "*" (snakemake-term--name) "*"))) + +(defun snakemake-term-start () + "Start a terminal session for the current Snakefile directory. + +The main advantage of using a terminal is that it allows for a +persistent environment between Snakemake calls, which is useful +for running Snakemake in isolated environments created by tools +like Guix. + +To do so, `snakemake-shell-file-name' should be set to a script +that starts a shell with the desired environment. For example, +to set up an enviroment with Guix, `snakemake-shell-file-name' +could point to a script that runs + + guix environment -l manifest.scm --ad-hoc snakemake --pure" + (interactive) + (let ((default-directory (snakemake-snakefile-directory))) + (unless (snakemake-term-process) + (ansi-term snakemake-shell-file-name (snakemake-term--name))))) + +(defun snakemake-term-send (string) + "Send STRING to the terminal for the current directory." + (let* ((proc (or (snakemake-term-process) + (user-error "No active terminal. Start with %s" + (substitute-command-keys + "`\\[snakemake-term-start]'")))) + (buf (process-buffer proc))) + (unless (get-buffer-window buf) + (display-buffer buf)) + (term-send-string proc (concat string "\n")) + (with-current-buffer buf + (goto-char (process-mark proc))))) + +(defun snakemake-term-build-targets (targets args) + "Send 'snakemake [ARGS] -- TARGETS' to the terminal." + (let ((default-directory (snakemake-snakefile-directory))) + (snakemake-term-send (snakemake--make-command targets args)))) + +;;;; General interface + +(defun snakemake-build-targets (targets args) + "Run 'snakemake [ARGS] -- TARGETS'. +If a terminal is associated with the current Snakefile directory, +send the command there. Otherwise, run the command with +`compile'." + (funcall (if (snakemake-term-process) + #'snakemake-term-build-targets + #'snakemake-compile-targets) + targets + args)) + ;;;###autoload (defun snakemake-build-targets-at-point (&optional args) "Build target(s) at point without any prompts. $ snakemake [ARGS] -- <targets>" (interactive (list (snakemake-arguments))) - (snakemake-compile-targets + (snakemake-build-targets (or (snakemake-file-targets-at-point 'check) (snakemake-rule-at-point 'target) (user-error "No target found at point")) @@ -579,7 +649,7 @@ $ snakemake [ARGS] -- <targets>" $ snakemake [ARGS] -- <file>" (interactive (list (snakemake-arguments))) - (snakemake-compile-targets + (snakemake-build-targets (list (snakemake-read-file-target)) args)) @@ -589,24 +659,37 @@ $ snakemake [ARGS] -- <file>" $ snakemake [ARGS] -- <rule>" (interactive (list (snakemake-arguments))) - (snakemake-compile-targets + (snakemake-build-targets (list (snakemake-read-rule 'targets)) args)) ;;;###autoload -(defun snakemake-compile (&optional args) - "Read `compile' command for building targets. +(defun snakemake-build (&optional args) + "Read and run a Snakemake command for building targets. + +If a terminal is associated with the current Snakefile directory, +send the command there. Otherwise, run the command with +`compile'. + +To start a terminal for the current Snakefile directory, run +`\\[snakemake-term-start]'. $ snakemake [ARGS] -- <targets>" (interactive (list (snakemake-arguments))) - (let ((compile-command (snakemake--define-compile-command - (or (snakemake-file-targets-at-point) - (snakemake-rule-at-point) - (list "")) - args)) - (compilation-read-command t) + (let ((cmd (snakemake--make-command + (or (snakemake-file-targets-at-point) + (snakemake-rule-at-point) + (list "")) + args)) (default-directory (snakemake-snakefile-directory))) - (call-interactively #'compile))) + (if (snakemake-term-process) + (snakemake-term-send + (read-from-minibuffer "Command to send to terminal: " cmd)) + (let ((compile-command cmd) + (compilation-read-command t)) + (call-interactively #'compile))))) + +(define-obsolete-function-alias 'snakemake-compile 'snakemake-build "1.2.0") ;;;###autoload (autoload 'snakemake-popup "snakemake" nil t) (magit-define-popup snakemake-popup @@ -622,7 +705,7 @@ $ snakemake [ARGS] -- <targets>" '((?a "Allowed rules" "--allowed-rules " snakemake-read-rules) (?j "Number of jobs" "-j")) :actions - '((?c "Compile" snakemake-compile) nil nil + '((?c "Edit and run command" snakemake-build) nil nil (?p "Build target at point" snakemake-build-targets-at-point) (?f "Build file" snakemake-build-file-target) (?r "Build rule" snakemake-build-rule-target)) |