Merge pull request #253 from snakemake/feat/inputflags

feat: adapt to Snakemake 8 and 9 (add inputflags, outputflags, storage directive support, remove version and subworkflow directive support)

Author: johanneskoester

Diff for: .gitignore

@@ -141,3 +141,4 @@ tmp_work
 .python-version
 tags
 .vimspector.json
+poetry.lock

Diff for: poetry.lock

@@ -14,7 +14,7 @@ keywords = ["python", "snakemake", "code", "formatter", "parser", "workflow", "m
 snakefmt = 'snakefmt.snakefmt:main'
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.11"
 click = "^8.0.0"
 black = "^24.3.0"
 toml = "^0.10.2"
@@ -24,7 +24,12 @@ importlib_metadata = {version = ">=1.7.0,<5.0", python = "<3.8"}
 pytest = "^7.4.4"
 pytest-cov = "^4.1.0"
 flake8 = "^7.0"
-snakemake = "<8.0"
+# Always set this to the latest Snakemake version with grammar changes.
+# This way, the testcases for grammar completeness ensure that the formatter is always
+# up-to-date with the latest Snakemake.
+# TODO: implement a bot action that auto-creates a bumping PR on every Snakemake
+# release.
+snakemake = ">=9.1.1"
 isort = "^5.1.0"
 pynvim = "~0.4.3"
 

Diff for: pyproject.toml

@@ -371,7 +371,7 @@ def format_params(self, parameters: ParameterSyntax) -> str:
         if p_class is InlineSingleParam:
             inline_fmting = True
 
-        result = f"{used_indent}{parameters.keyword_name}:"
+        result = f"{used_indent}{parameters.keyword_line}:"
         if inline_fmting:
             result += " "
             prepended_comments = ""

Diff for: snakefmt/formatter.py

@@ -34,7 +34,6 @@ class PythonCode(Vocabulary):
     threads=Context(None, InlineSingleParam),
     resources=Context(None, ParamList),
     priority=Context(None, InlineSingleParam),
-    version=Context(None, SingleParam),
     log=Context(None, ParamList),
     message=Context(None, SingleParam),
     benchmark=Context(None, SingleParam),
@@ -79,14 +78,7 @@ class SnakeModule(Vocabulary):
         meta_wrapper=Context(None, SingleParam),
         prefix=Context(None, SingleParam),
         replace_prefix=Context(None, SingleParam),
-    )
-
-
-class SnakeSubworkflow(Vocabulary):
-    spec = dict(
-        snakefile=Context(None, SingleParam),
-        workdir=Context(None, SingleParam),
-        configfile=Context(None, SingleParam),
+        name=Context(None, InlineSingleParam),
     )
 
 
@@ -102,7 +94,6 @@ class SnakeGlobal(Vocabulary):
         ruleorder=Context(None, InlineSingleParam),
         rule=Context(SnakeRule, KeywordSyntax),
         checkpoint=Context(SnakeRule, KeywordSyntax),
-        subworkflow=Context(SnakeSubworkflow, KeywordSyntax),
         localrules=Context(None, NoKeyParamList),
         onstart=Context(PythonCode, KeywordSyntax),
         onsuccess=Context(PythonCode, KeywordSyntax),
@@ -112,7 +103,11 @@ class SnakeGlobal(Vocabulary):
         container=Context(None, InlineSingleParam),
         containerized=Context(None, InlineSingleParam),
         scattergather=Context(None, ParamList),
+        inputflags=Context(None, NoKeyParamList),
+        outputflags=Context(None, NoKeyParamList),
         module=Context(SnakeModule, KeywordSyntax),
         use=Context(SnakeUseRule, KeywordSyntax),
         resource_scopes=Context(None, KeywordSyntax),
+        conda=Context(None, InlineSingleParam),
+        storage=Context(None, ParamList),
     )

Diff for: snakefmt/parser/grammar.py

@@ -365,6 +365,22 @@ def __init__(
     def validate_keyword_line(self, snakefile: TokenIterator):
         self.token = next(snakefile)
 
+        if self.keyword_name == "storage":
+            self.validate_named_keyword_line(snakefile)
+        else:
+            self.validate_anonymous_keyword_line(snakefile)
+
+    def validate_named_keyword_line(self, snakefile: TokenIterator):
+        if not is_colon(self.token):
+            if self.token.type != tokenize.NAME:
+                NotAnIdentifierError(self.line_nb, self.token.string, self.keyword_line)
+            self.keyword_line += f" {self.token.string}"
+            self.token = next(snakefile)
+        if not is_colon(self.token):
+            ColonError(self.line_nb, self.token.string, self.keyword_line)
+        self.token = next(snakefile)
+
+    def validate_anonymous_keyword_line(self, snakefile: TokenIterator):
         if not is_colon(self.token):
             ColonError(self.line_nb, self.token.string, self.keyword_line)
         self.token = next(snakefile)

Diff for: snakefmt/parser/syntax.py

@@ -4,6 +4,7 @@
 errors arise, as tested in test_parser.py.
 """
 
+import textwrap
 from io import StringIO
 from unittest import mock
 
@@ -1457,3 +1458,17 @@ def test_shell_indention_long_line(self):
         formatter = setup_formatter(snakecode)
 
         assert formatter.get_formatted() == snakecode
+
+
+class TestStorage:
+    def test_storage(self):
+        code = textwrap.dedent(
+            """
+            storage http_local:
+                provider="http",
+                keep_local=True,
+            """
+        )
+        formatter = setup_formatter(code)
+
+        assert formatter.get_formatted() == code

Diff for: tests/test_formatter.py

@@ -31,11 +31,6 @@ def test_module_context_completeness(self):
         existing_keywords = set(grammar.SnakeModule.spec)
         self.check_completeness(target_keywords, existing_keywords)
 
-    def test_subworkflow_context_completeness(self):
-        target_keywords = set(parser.Subworkflow.subautomata)
-        existing_keywords = set(grammar.SnakeSubworkflow.spec)
-        self.check_completeness(target_keywords, existing_keywords)
-
     def test_use_rule_context_completeness(self):
         target_keywords = set(parser.UseRule.subautomata)
         existing_keywords = set(grammar.SnakeUseRule.spec)