feat: enable # fmt: off recognized by snakefmt

README.md

@@ -17,10 +17,10 @@ design and specifications of [Black][black].
 > `--diff` or `--check` options. See [Usage](#usage) for more details.
 
 > [!IMPORTANT]
-> **Recent Changes:** 
+> **Recent Changes:**
 > 1. **Rule and module directives are now sorted by default:** `snakefmt` will automatically sort the order of directives inside rules (e.g. `input`, `output`, `shell`) and modules into a consistent order. You can opt out of this by using the `--no-sort` CLI flag.
 > 2. **Black upgraded to v26:** The underlying `black` formatter has been upgraded to v26. You will see changes in how implicitly concatenated strings are wrapped (they are now collapsed onto a single line if they fit within the line limit) and other minor adjustments compared to previous versions.
-> 
+>
 > **Example of expected differences:**
 > ```python
 > # Before (Snakefmt older versions)
@@ -33,7 +33,7 @@ design and specifications of [Black][black].
 >         "b.txt",
 >     input:
 >         "a.txt",
-> 
+>
 > # After (Directives sorted, strings collapsed by Black 26)
 > rule example:
 >     input:
@@ -51,18 +51,23 @@ design and specifications of [Black][black].
   - [PyPi](#pypi)
   - [Conda](#conda)
   - [Containers](#containers)
+    - [Docker](#docker)
+    - [Singularity](#singularity)
   - [Local](#local)
 - [Example File](#example-file)
 - [Usage](#usage)
   - [Basic Usage](#basic-usage)
   - [Full Usage](#full-usage)
 - [Configuration](#configuration)
   - [Directive Sorting](#directive-sorting)
+  - [Format Directives](#format-directives)
 - [Integration](#integration)
-    - [Editor Integration](#editor-integration)
-    - [Version Control Integration](#version-control-integration)
-    - [Github Actions](#github-actions)
+  - [Editor Integration](#editor-integration)
+  - [Version Control Integration](#version-control-integration)
+  - [GitHub Actions](#github-actions)
 - [Plug Us](#plug-us)
+    - [Markdown](#markdown)
+    - [ReStructuredText](#restructuredtext)
 - [Changes](#changes)
 - [Contributing](#contributing)
 - [Cite](#cite)
@@ -313,6 +318,76 @@ This ordering ensures that the directives most frequently used in execution bloc
 
 You can disable this feature using the `--no-sort` flag.
 
+### Format Directives
+
+`snakefmt` supports inline comment directives to control formatting behaviour for specific regions of code.
+
+#### `# fmt: off` / `# fmt: on`
+
+Disables all formatting for the region between the two directives. The directives must appear at the same indentation level. A `# fmt: on` at a deeper indent than the matching `# fmt: off` has no effect.
+
+```python
+rule a:
+    input:
+        "a.txt",
+
+
+# fmt: off
+rule b:
+  input: "b.txt"
+  output:
+          "c.txt"
+# fmt: on
+
+
+rule c:
+    input:
+        "d.txt",
+```
+
+Note: inside `run:` blocks and other Python code, `# fmt: off` / `# fmt: on` is passed through to [Black][black] which handles it natively.
+
+#### `# fmt: off[sort]`
+
+Disables only directive sorting for the region, while still applying all other formatting. Useful when you want to preserve a custom directive order for a specific rule.
+
+```python
+# fmt: off[sort]
+rule keep_my_order:
+    output:
+        "result.txt",
+    input:
+        "source.txt",
+    shell:
+        "cp {input} {output}"
+# fmt: on[sort]
+```
+
+A plain `# fmt: on` (without `[sort]`) also ends a `# fmt: off[sort]` region.
+
+#### `# fmt: off[next]`
+
+Disables formatting for the single next Snakemake keyword block (e.g. `rule`, `checkpoint`, `use rule`). Only that one block is left unformatted; subsequent blocks are formatted normally.
+
+```python
+rule formatted:
+    input:
+        "a.txt",
+    output:
+        "b.txt",
+
+
+# fmt: off[next]
+rule unformatted:
+  input: "a.txt"
+  output: "b.txt"
+
+
+rule also_formatted:
+    input:
+        "a.txt",
+```
+
 #### Example
 
 `pyproject.toml`

snakefmt/formatter.py

@@ -65,7 +65,6 @@ def __init__(
         self.result: str = ""
         self.lagging_comments: str = ""
         self.no_formatting_yet: bool = True
-        self.sort_directives = sort_directives
         self.previous_result: str = ""
         self.keyword_spec: list[str] = []
         self.keywords: dict[str, str] = {}  # cache to sort
@@ -75,7 +74,7 @@ def __init__(
         if line_length is not None:
             self.black_mode.line_length = line_length
 
-        super().__init__(snakefile)  # Call to parse snakefile
+        super().__init__(snakefile, sort_directives=sort_directives)
 
     def get_formatted(self) -> str:
         return self.result
@@ -90,10 +89,13 @@ def flush_buffer(
         from_python: bool = False,
         final_flush: bool = False,
         in_global_context: bool = False,
+        exiting_keywords: bool = False,
     ) -> None:
         if len(self.buffer) == 0 or self.buffer.isspace():
             self.result += self.buffer
             self.buffer = ""
+            if exiting_keywords and self.no_formatting_yet and self.result.rstrip("\n"):
+                self.no_formatting_yet = False
             return
 
         if not from_python:
@@ -103,6 +105,9 @@ def flush_buffer(
         else:
             # Invalid python syntax, eg lone 'else:' between two rules, can occur.
             # Below constructs valid code statements and formats them.
+            if self.fmt_off_expected_indent:
+                self.buffer += self.fmt_off_expected_indent
+                self.fmt_off_expected_indent = ""
             re_match = contextual_matcher.match(self.buffer)
             if re_match is not None:
                 callback_keyword = re_match.group(2)
@@ -119,11 +124,13 @@ def flush_buffer(
                 )
                 formatted = self.run_black_format_str(to_format, self.block_indent)
                 re_rematch = contextual_matcher.match(formatted)
-                if re_rematch is None:
-                    raise ValueError(
-                        "contextual_matcher failed to match for the given "
-                        f"formatted string: {formatted}"
-                    )
+                assert re_rematch, (
+                    "This should always match as we just formatted it with the same "
+                    "regex. If this error is raised, it's a bug in snakefmt's "
+                    "handling of snakemake syntax. Please report this to the "
+                    "developers with the code so we can fix it: "
+                    "https://github.com/snakemake/snakefmt/issues"
+                )
                 if condition != "":
                     callback_keyword += re_rematch.group(3)
                 formatted = (
@@ -174,7 +181,7 @@ def process_keyword_param(
             context=param_context,
         )
         param_formatted = self.format_params(param_context)
-        if self.sort_directives and not in_global_context and self.keyword_spec:
+        if self.sort_off_indent is None and not in_global_context and self.keyword_spec:
             self.keywords[param_context.keyword_name] = self.result + param_formatted
             self.result = ""
         else:
@@ -188,13 +195,49 @@ def post_process_keyword(self):
         for keyword in self.keyword_spec:
             res = self.keywords.pop(keyword, "")
             self.previous_result += res
-        if self.keywords:
-            raise InvalidParameterSyntax(
-                "Unexpected keywords when sorted keywords: "
-                + (", ".join(self.keywords))
-            )
+        assert not self.keywords, (
+            "All directives should have been consumed; "
+            "if not, this is a bug in snakefmt's handling of snakemake syntax. "
+            "It must be the coder's fault, not the user's. "
+            "So please report this to the developers with the code so we can fix it: "
+            "https://github.com/snakemake/snakefmt/issues"
+        )
         self.result = self.previous_result + self.result
         self.previous_result = ""
+        # Keep no_formatting_yet when there is pending buffered content.
+        # This prevents premature separator insertion after fmt: off/on
+        # verbatim regions before the next flush occurs.
+        if self.no_formatting_yet and self.result.rstrip("\n") and not self.buffer:
+            self.no_formatting_yet = False
+
+    def handle_fmt_off_region(self, verbatim: str) -> None:
+        if self.no_formatting_yet:
+            self.result = self.result.lstrip("\n")
+        self.result += self.buffer
+        self.buffer = ""
+        if not verbatim:
+            return
+        # When fmt:off[next] is inside a Python block (e.g. `if 1:`), the
+        # directive ends up as a lagging_comment after flushing that block.
+        is_nested_next = self.fmt_off and self.fmt_off[1] == "next"
+        if self.lagging_comments:
+            # For nested fmt:off[next], add the same \n separator that
+            # process_keyword_context/add_newlines would normally provide
+            # before the first keyword inside the Python block.
+            if is_nested_next and not self.no_formatting_yet:
+                self.result += "\n"
+            self.result += self.lagging_comments
+            self.lagging_comments = ""
+        if self.fmt_off_preceded_by_blank_line:
+            if self.result and not self.result.endswith("\n\n"):
+                self.result += "\n"
+            self.fmt_off_preceded_by_blank_line = False
+        self.result += verbatim
+        # For fmt: off[next], mark that we've emitted content so the following
+        # block gets its normal blank-line separator.
+        # For fmt: off regions, treat verbatim as transparent to separator logic.
+        self.no_formatting_yet = not is_nested_next
+        self.last_recognised_keyword = ""
 
     def run_black_format_str(
         self,
@@ -216,7 +259,6 @@ def run_black_format_str(
             and len(string.strip().splitlines()) > 1
             and not no_nesting
         )
-
         if artificial_nest:
             string = f"if x:\n{textwrap.indent(string, TAB)}"