Merge pull request #6 from peterk87/master

Release 1.2.0 - Fix process output popup issue and add some snippets

.gitignore

@@ -4,3 +4,5 @@ package-metadata.json
 .ipynb_checkpoints/
 *.ipynb
 *.pickle
+venv/
+.venv/

Nextflow.sublime-syntax

@@ -24,6 +24,14 @@ variables:
   single_dollar_interpolation_identifier: (?:{{unicode_letter}}|[a-zA-Z_])(?:{{unicode_letter}}|[a-zA-Z0-9_])*
 scope: source.nextflow
 contexts:
+  # else-pop and immediately-pop from https://forum.sublimetext.com/t/syntax-definitions-how-to-force-pop-out-of-the-stack/36376/4
+  # convenience contexts for popping context off stack
+  else-pop:
+    - match: (?=\S)
+      pop: true
+  immediately-pop:
+    - match: ''
+      pop: true
   main:
     - match: ^(#!).+$\n
       scope: comment.line.hashbang.nextflow
@@ -241,11 +249,12 @@ contexts:
         - meta_scope: meta.evaluation.ternary.nextflow
         - match: ":"
           scope: keyword.operator.ternary.expression-separator.nextflow
-        - include: nextflow-code
         - match: \}
           pop: true
         - match: $
           pop: true
+        - include: nextflow-code
+        - include: else-pop
     - match: "==~"
       scope: keyword.operator.match.nextflow
     - match: "=~"

VERSION

@@ -1 +1 @@
-1.1.0
+1.2.0

messages/1.2.0.txt

@@ -0,0 +1,9 @@
+=> 1.2.0
+
+Added:
+
+- snippets for process version YML and ch_versions mixing (ver), process modules config (withName)
+
+Fixed:
+
+- process popups hanging due to bad regex for getting output emit labels (https://github.com/nf-core/sublime/issues/5)

messages/install.txt

@@ -6,4 +6,4 @@ Thanks for using sublime-nextflow!
 
 If you want more info or have any issues, please see the Github page at:
 
-https://github.com/peterk87/sublime-nextflow
+https://github.com/nf-core/sublime

process_popups.py

@@ -10,7 +10,7 @@
 regex_input_section = re.compile(r'\s*input:\s*')
 regex_output_section = re.compile(r'\s*output:\s*')
 # regex to find output channels with emit
-regex_output_channel = re.compile(r'((?:.*,\s+)*.*),\s*emit:\s*(\w+)')
+regex_output_channel = re.compile(r'(.*?),\s*emit:\s*(\w+)', re.DOTALL)
 
 regex_take_section = re.compile(r'\s*take:\s*')
 regex_emit_section = re.compile(r'\s*emit:\s*')
@@ -140,7 +140,8 @@ def find_wf_emit_section(text: str, start: int, end: int) -> int:
 
 def get_output_channels(text: str, start: int, end: int) -> List[Tuple[str, str]]:
     out = []
-    for m in regex_output_channel.finditer(text[start:end]):
+    t = text[start:end]
+    for m in regex_output_channel.finditer(t):
         chan, emit = m.groups()
         chan = ''.join(x.strip() for x in chan.split('\n'))
         out.append((emit, chan))
@@ -178,6 +179,9 @@ def get_output_channel_emits(path: Path, proc_name: str) -> List[Tuple[str, str]
         return []
     proc_output_start = find_proc_output_section(text, proc_start, proc_end)
     proc_output_start += proc_start
+    next_section_match = re.search(r'(when:|exec:|script:|stub:)', text[proc_output_start:])
+    if next_section_match:
+        proc_end = proc_output_start + next_section_match.start()
     out = get_output_channels(text, proc_output_start, proc_end)
     if not out:
         out = output_section_lines(text, proc_output_start, proc_end)
@@ -341,7 +345,7 @@ def show_output_channel_popup(root_dir: Path, view: sublime.View, point: int) ->
                 output_channels_text = get_wf_emits(path, proc_name)
                 is_proc = False
         if not output_channels_text:
-            window.status_message(f'No input channels in {proc_name}!')
+            window.status_message(f'No output channels in {proc_name}!')
     else:
         for path in root_dir.rglob('**/*.nf'):
             output_channels_text = get_output_channel_emits(path, proc_name)

snippets/nextflow-ch_versions-mix.sublime-snippet

@@ -0,0 +1,7 @@
+<snippet>
+	<content><![CDATA[
+ch_versions = ch_versions.mix($1.out.versions${2:.first().ifEmpty(null)})$0
+]]></content>
+	<tabTrigger>ver</tabTrigger>
+	<scope>source.nextflow meta.definition.workflow.nextflow</scope>
+</snippet>

snippets/nextflow-modules-config.sublime-snippet

@@ -0,0 +1,17 @@
+<snippet>
+	<content><![CDATA[
+withName: '$1' {
+  ext.args = '$2'
+  publishDir = [
+    [
+      path: { "\${params.outdir}/$3" },
+      mode: params.publish_dir_mode,
+      saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+  ]
+}
+$0
+]]></content>
+	<tabTrigger>withName</tabTrigger>
+	<scope>source.nextflow meta.block.nextflow</scope>
+</snippet>

snippets/nextflow-versions-yml.sublime-snippet

@@ -0,0 +1,10 @@
+<snippet>
+	<content><![CDATA[
+cat <<-END_VERSIONS > versions.yml
+"\${task.process}":
+    $1: \\\$($1 --version | sed 's/$1 //')$0
+END_VERSIONS
+]]></content>
+	<tabTrigger>ver</tabTrigger>
+	<scope>source.nextflow meta.definition.process.nextflow string.quoted.double.block.nextflow</scope>
+</snippet>