Merge branch 'master' into lsp-typespec

CHANGELOG.org

@@ -22,6 +22,7 @@
   * Fix zls wrong bin path
   * Add support for buf CLI ([[https://github.com/bufbuild/buf/releases/tag/v1.43.0][beta]])
   * Add fennel support
+  * Add support for [[https://github.com/nextflow-io/language-server][Nextflow]]
   * Add TypeSpec support
 
 ** 9.0.0

clients/lsp-nextflow.el

@@ -0,0 +1,139 @@
+;;; lsp-nextflow.el --- lsp-mode nextflow integration -*- lexical-binding: t; -*-
+
+;; Copyright (C) 2024 Edmund Miller
+
+;; Author: Edmund Miller
+;; Keywords: lsp, nextflow, groovy
+
+;; This program is free software; you can redistribute it and/or modify
+;; it under the terms of the GNU General Public License as published by
+;; the Free Software Foundation, either version 3 of the License, or
+;; (at your option) any later version.
+
+;; This program is distributed in the hope that it will be useful,
+;; but WITHOUT ANY WARRANTY; without even the implied warranty of
+;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;; GNU General Public License for more details.
+
+;; You should have received a copy of the GNU General Public License
+;; along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+;;; Commentary:
+
+;; LSP Clients for the Nextflow Programming Language.
+
+;;; Code:
+
+(require 'lsp-mode)
+(require 'f)
+
+(defgroup lsp-nextflow nil
+  "LSP support for nextflow, using nextflow-language-server."
+  :group 'lsp-mode
+  :link '(url-link "https://github.com/nextflow-io/language-server"))
+
+(defcustom lsp-nextflow-java-path "java"
+  "Path of the java executable."
+  :group 'lsp-nextflow
+  :type 'string)
+
+(defcustom lsp-nextflow-version "1.0.0"
+  "Version of Nextflow language server."
+  :type 'string
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0"))
+
+(defcustom lsp-nextflow-server-download-url
+  (format "https://github.com/nextflow-io/language-server/releases/download/v%s/language-server-all.jar"
+          lsp-nextflow-version)
+  "Automatic download url for lsp-nextflow."
+  :type 'string
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0"))
+
+(defcustom lsp-nextflow-server-file
+  (f-join lsp-server-install-dir "nextflow-language-server.jar")
+  "The path to the file in which `lsp-nextflow' will be stored."
+  :group 'lsp-nextflow
+  :risky t
+  :type 'file
+  :package-version '(lsp-mode . "9.0.0"))
+
+(defun lsp-nextflow-server-command ()
+  "Startup command for Nextflow language server."
+  `("java" "-jar" ,(expand-file-name lsp-nextflow-server-file)))
+
+(lsp-dependency 'nextflow-lsp
+                '(:system lsp-nextflow-server-file)
+                `(:download :url lsp-nextflow-server-download-url
+                  :store-path lsp-nextflow-server-file))
+
+;;
+;;; Settings
+
+;; (lsp-generate-settings "~/src/nf-core/vscode-language-nextflow/package.json" 'lsp-nextflow)
+
+(lsp-defcustom lsp-nextflow-debug nil
+  "Enable debug logging and debug information in hover hints."
+  :type 'boolean
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.debug")
+
+(lsp-defcustom lsp-nextflow-files-exclude [".git" ".nf-test" "work"]
+  "Configure glob patterns for excluding folders from being searched for
+Nextflow scripts and configuration files."
+  :type 'lsp-string-vector
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.files.exclude")
+
+(lsp-defcustom lsp-nextflow-formatting-harshil-alignment nil
+  "Use the [Harshil Alignment™️](https://nf-co.re/docs/contributing/code_editors_and_styling/harshil_alignment) when formatting Nextflow scripts and config files.
+
+*Note: not all rules are supported yet*"
+  :type 'boolean
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.formatting.harshilAlignment")
+
+(lsp-defcustom lsp-nextflow-java-home nil
+  "Specifies the folder path to the JDK. Use this setting if the extension cannot
+find Java automatically."
+  :type '(choice (const :tag "Auto" nil)
+          (directory :tag "Custom JDK path"))
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.java.home")
+
+(lsp-defcustom lsp-nextflow-suppress-future-warnings t
+  "Hide warnings for future changes, deprecations, and removals."
+  :type 'boolean
+  :group 'lsp-nextflow
+  :package-version '(lsp-mode . "9.0.0")
+  :lsp-path "nextflow.suppressFutureWarnings")
+
+;;
+;;; Client
+
+(lsp-register-client
+ (make-lsp-client
+  ;; FIXME
+  ;; :download-server-fn (lambda (_client callback error-callback _update?)
+  ;;                       (lsp-package-ensure 'nextflow-lsp callback error-callback))
+  :new-connection (lsp-stdio-connection #'lsp-nextflow-server-command)
+  :major-modes '(nextflow-mode)
+  :multi-root t
+  :activation-fn (lsp-activate-on "nextflow")
+  :priority -1
+  :initialized-fn (lambda (workspace)
+                    (with-lsp-workspace workspace
+                      (lsp--set-configuration
+                       (lsp-configuration-section "nextflow"))))
+  ;; TODO Handle preview dag
+  :server-id 'nextflow-lsp))
+
+(lsp-consistency-check lsp-nextflow)
+
+(provide 'lsp-nextflow)
+;;; lsp-nextflow.el ends here

docs/lsp-clients.json

@@ -686,6 +686,14 @@
     "installation": "npm install -g @mdx-js/language-server",
     "debugger": "Not available"
   },
+  {
+    "name": "nextflow",
+    "full-name": "Nextflow",
+    "server-name": "nextflow-language-server",
+    "server-url": "https://github.com/nextflow-io/language-server",
+    "installation-url": "https://github.com/nextflow-io/language-server#build",
+    "debugger": "Not available"
+  },
   {
     "name": "nginx",
     "full-name": "Nginx",

lsp-completion.el

@@ -755,6 +755,20 @@ The CLEANUP-FN will be called to cleanup."
   "Disable LSP completion support."
   (lsp-completion-mode -1))
 
+(defun lsp-completion-passthrough-try-completion (string table pred point)
+  (let* ((completion-ignore-case t)
+         (try (completion-basic-try-completion string table pred point))
+         (newstr (car try))
+         (newpoint (cdr try))
+         (beforepoint (and try (substring newstr 0 newpoint))))
+    (if (and beforepoint
+             (string-prefix-p
+              beforepoint
+              (try-completion "" table pred)
+              t))
+        try
+      (cons string point))))
+
 (defun lsp-completion-passthrough-all-completions (_string table pred _point)
   "Passthrough all completions from TABLE with PRED."
   (defvar completion-lazy-hilit-fn)
@@ -790,7 +804,7 @@ The CLEANUP-FN will be called to cleanup."
       (setf (alist-get 'lsp-capf completion-category-defaults) '((styles . (lsp-passthrough))))
       (make-local-variable 'completion-styles-alist)
       (setf (alist-get 'lsp-passthrough completion-styles-alist)
-            '(completion-basic-try-completion
+            '(lsp-completion-passthrough-try-completion
               lsp-completion-passthrough-all-completions
               "Passthrough completion."))
 

lsp-mode.el

@@ -182,7 +182,7 @@ As defined by the Language Server Protocol 3.16."
      lsp-graphql lsp-groovy lsp-hack lsp-haskell lsp-haxe lsp-idris lsp-java
      lsp-javascript lsp-jq lsp-json lsp-kotlin lsp-latex lsp-lisp lsp-ltex
      lsp-lua lsp-fennel lsp-magik lsp-markdown lsp-marksman lsp-mdx lsp-meson lsp-metals lsp-mint
-     lsp-mojo lsp-move lsp-mssql lsp-nginx lsp-nim lsp-nix lsp-nushell lsp-ocaml
+     lsp-mojo lsp-move lsp-mssql lsp-nextflow lsp-nginx lsp-nim lsp-nix lsp-nushell lsp-ocaml
      lsp-openscad lsp-pascal lsp-perl lsp-perlnavigator lsp-php lsp-pls
      lsp-purescript lsp-pwsh lsp-pyls lsp-pylsp lsp-pyright lsp-python-ms
      lsp-qml lsp-r lsp-racket lsp-remark lsp-rf lsp-roslyn lsp-rubocop lsp-ruby-lsp
@@ -836,6 +836,7 @@ Changes take effect only when a new session is started."
     (java-ts-mode . "java")
     (jdee-mode . "java")
     (groovy-mode . "groovy")
+    (nextflow-mode . "nextflow")
     (python-mode . "python")
     (python-ts-mode . "python")
     (cython-mode . "python")
@@ -1988,21 +1989,29 @@ want to watch."
          (not (lsp--string-match-any ignored-directories full-path)))))
 
 
-(defun lsp--all-watchable-directories (dir ignored-directories)
+(defun lsp--all-watchable-directories (dir ignored-directories &optional visited)
   "Traverse DIR recursively returning a list of paths that should have watchers.
-IGNORED-DIRECTORIES will be used for exclusions"
+IGNORED-DIRECTORIES will be used for exclusions.
+VISITED is used to track already-visited directories to avoid infinite loops."
   (let* ((dir (if (f-symlink? dir)
                   (file-truename dir)
-                dir)))
-    (apply #'nconc
-           ;; the directory itself is assumed to be part of the set
-           (list dir)
-           ;; collect all subdirectories that are watchable
-           (-map
-            (lambda (path) (lsp--all-watchable-directories (f-join dir path) ignored-directories))
-            ;; but only look at subdirectories that are watchable
-            (-filter (lambda (path) (lsp--path-is-watchable-directory path dir ignored-directories))
-                     (directory-files dir))))))
+                dir))
+         ;; Initialize visited directories if not provided
+         (visited (or visited (make-hash-table :test 'equal))))
+    (if (gethash dir visited)
+        ;; If the directory has already been visited, skip it
+        nil
+      ;; Mark the current directory as visited
+      (puthash dir t visited)
+      (apply #'nconc
+             ;; the directory itself is assumed to be part of the set
+             (list dir)
+             ;; collect all subdirectories that are watchable
+             (-map
+              (lambda (path) (lsp--all-watchable-directories (f-join dir path) ignored-directories visited))
+              ;; but only look at subdirectories that are watchable
+              (-filter (lambda (path) (lsp--path-is-watchable-directory path dir ignored-directories))
+                       (directory-files dir)))))))
 
 (defun lsp-watch-root-folder (dir callback ignored-files ignored-directories &optional watch warn-big-repo?)
   "Create recursive file notification watch in DIR.
@@ -3709,6 +3718,7 @@ disappearing, unset all the variables related to it."
                                                                    :json-false))))))
                    ,@(when lsp-lens-enable '((codeLens . ((refreshSupport . t)))))
                    ,@(when lsp-inlay-hint-enable '((inlayHint . ((refreshSupport . :json-false)))))
+                   (diagnostics . ((refreshSupport . :json-false)))
                    (fileOperations . ((didCreate . :json-false)
                                       (willCreate . :json-false)
                                       (didRename . t)
@@ -6947,6 +6957,8 @@ server. WORKSPACE is the active workspace."
                                  (fboundp 'lsp--lens-on-refresh))
                         (lsp--lens-on-refresh workspace))
                       nil)
+                     ((equal method "workspace/diagnostic/refresh")
+                      nil)
                      (t (lsp-warn "Unknown request method: %s" method) nil))))
     ;; Send response to the server.
     (unless (eq response 'delay-response)
@@ -9919,12 +9931,10 @@ In case the major-mode that you are using for "
   (let ((start-plain (make-temp-file "plain" nil ".el")))
     (url-copy-file "https://raw.githubusercontent.com/emacs-lsp/lsp-mode/master/scripts/lsp-start-plain.el"
                    start-plain t)
-    (async-shell-command
-     (format "%s -q -l %s %s"
-             (expand-file-name invocation-name invocation-directory)
-             start-plain
-             (or (buffer-file-name) ""))
-     (generate-new-buffer " *lsp-start-plain*"))))
+    (start-process "lsp-start-plain"
+                   (generate-new-buffer " *lsp-start-plain*")
+                   (expand-file-name invocation-name invocation-directory)
+                    "-q" "-l" start-plain (or (buffer-file-name) ""))))
 
 
 

mkdocs.yml

@@ -118,6 +118,7 @@ nav:
     - Move: page/lsp-move.md
     - MDX: page/lsp-mdx.md
     - MSSQL: https://emacs-lsp.github.io/lsp-mssql
+    - Nextflow: page/lsp-nextflow.md
     - Nginx: page/lsp-nginx.md
     - Nim: page/lsp-nim.md
     - Nix (nixd-lsp): page/lsp-nix-nixd.md