Remove hard wrapping from all files touched by this PR

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: thompsonmj

docs/user-guide/io/cache.md

@@ -1,7 +1,6 @@
 # Cache
 
-TaxonoPy caches intermediate results (like parsed inputs and grouped entries) to
-speed up repeated runs on the same dataset.
+TaxonoPy caches intermediate results (like parsed inputs and grouped entries) to speed up repeated runs on the same dataset.
 
 ## Location
 
@@ -40,9 +39,6 @@ This keeps caches isolated across datasets and releases.
 - `--cache-stats` — show cache statistics and exit.
 - `--clear-cache` — remove cached objects.
 - `--refresh-cache` (resolve only) — ignore cached parse/group results.
-- `--full-rerun` (resolve only) — clear the input-scoped cache and remove
-  TaxonoPy-specific output files before rerunning. See [Reruns](reruns.md) for
-  full details.
+- `--full-rerun` (resolve only) — clear the input-scoped cache and remove TaxonoPy-specific output files before rerunning. See [Reruns](reruns.md) for full details.
 
-If you change input files or want to force a clean run, use `--refresh-cache` or
-`--full-rerun`.
+If you change input files or want to force a clean run, use `--refresh-cache` or `--full-rerun`.

docs/user-guide/io/index.md

@@ -1,8 +1,6 @@
 # IO
 
-TaxonoPy accepts CSV or Parquet inputs with the same schema. Use the pages below
-for the exact input columns, the structure of resolved/unsolved outputs, and how
-the cache supports provenance and transparency throughout the resolution process.
+TaxonoPy accepts CSV or Parquet inputs with the same schema. Use the pages below for the exact input columns, the structure of resolved/unsolved outputs, and how the cache supports provenance and transparency throughout the resolution process.
 
 - [Input](input.md)
 - [Output](output.md)

docs/user-guide/io/output.md

@@ -5,22 +5,13 @@ When you run `taxonopy resolve`, TaxonoPy writes two outputs for each input file
 - **Resolved**: `<input_name>.resolved.<csv|parquet>`
 - **Unsolved**: `<input_name>.unsolved.<csv|parquet>`
 
-The output directory mirrors the input directory structure. Output format is
-controlled by the `--output-format` flag (`csv` or `parquet`).
-
-TaxonoPy also writes a manifest file to the output directory before creating
-any other files. This manifest lists every file the run intends to produce and
-is used by `--full-rerun` to clean up precisely. Each command writes its own
-manifest (`taxonopy_resolve_manifest.json` and
-`taxonopy_common_names_manifest.json` respectively) so they coexist safely if
-both commands share an output directory. See [Reruns](reruns.md) for details.
-
-## What’s Inside
-
-Each output row corresponds to one input record. Resolved entries contain the
-standardized taxonomy where available, while unsolved entries preserve the
-original input ranks. Both outputs include resolution metadata such as status
-and strategy information.
+The output directory mirrors the input directory structure. Output format is controlled by the `--output-format` flag (`csv` or `parquet`).
+
+TaxonoPy also writes a manifest file to the output directory before creating any other files. This manifest lists every file the run intends to produce and is used by `--full-rerun` to clean up precisely. Each command writes its own manifest (`taxonopy_resolve_manifest.json` and `taxonopy_common_names_manifest.json` respectively) so they coexist safely if both commands share an output directory. See [Reruns](reruns.md) for details.
+
+## What's Inside
+
+Each output row corresponds to one input record. Resolved entries contain the standardized taxonomy where available, while unsolved entries preserve the original input ranks. Both outputs include resolution metadata such as status and strategy information.
 
 Running through the sample resolution results in the following core files:
 

docs/user-guide/io/reruns.md

@@ -2,9 +2,7 @@
 
 ## The Guard
 
-TaxonoPy checks for existing output before processing. If a prior run is
-detected for the current input, it exits with a warning rather than silently
-overwriting:
+TaxonoPy checks for existing output before processing. If a prior run is detected for the current input, it exits with a warning rather than silently overwriting:
 
 ```
 Existing cache (...) and/or output (...) detected for this input.
@@ -13,16 +11,12 @@ Rerun with --full-rerun to replace them.
 
 Detection uses two signals:
 
-- the presence of a `taxonopy_resolve_manifest.json` in the output directory
-  (written by any run using TaxonoPy v0.3.0 or later), or
-- `.resolved.*` files in the output directory root (legacy fallback for output
-  produced by earlier versions).
+- the presence of a `taxonopy_resolve_manifest.json` in the output directory (written by any run using TaxonoPy v0.3.0 or later), or
+- `.resolved.*` files in the output directory root (legacy fallback for output produced by earlier versions).
 
 ## `--full-rerun`
 
-`--full-rerun` is the explicit escape hatch through the guard. It clears the
-input-scoped cache namespace and removes all TaxonoPy-specific files from the
-output directory before proceeding.
+`--full-rerun` is the explicit escape hatch through the guard. It clears the input-scoped cache namespace and removes all TaxonoPy-specific files from the output directory before proceeding.
 
 ```console
 taxonopy resolve \
@@ -33,23 +27,17 @@ taxonopy resolve \
 
 ### What it touches
 
-- **Cache**: the namespace scoped to the current command, TaxonoPy version, and
-  input fingerprint. Other namespaces (different inputs, different versions) are
-  not affected.
-- **Output files**: only the files listed in `taxonopy_resolve_manifest.json`.
-  Any other files in the output directory are left untouched.
+- **Cache**: the namespace scoped to the current command, TaxonoPy version, and input fingerprint. Other namespaces (different inputs, different versions) are not affected.
+- **Output files**: only the files listed in `taxonopy_resolve_manifest.json`. Any other files in the output directory are left untouched.
 
 ### What it does not touch
 
-- Files not listed in the manifest — including any non-TaxonoPy files you have
-  placed in the output directory.
+- Files not listed in the manifest — including any non-TaxonoPy files you have placed in the output directory.
 - Cache namespaces from other runs.
 
 ### No manifest found
 
-If `--full-rerun` is used but no manifest is present (e.g. output from a
-pre-v0.3.0 run, or a manually populated directory), TaxonoPy logs a warning
-and proceeds without removing any files:
+If `--full-rerun` is used but no manifest is present (e.g. output from a pre-v0.3.0 run, or a manually populated directory), TaxonoPy logs a warning and proceeds without removing any files:
 
 ```
 --full-rerun: no manifest found in <output-dir>; no output files were removed.
@@ -59,13 +47,9 @@ The run then writes fresh output and a new manifest.
 
 ## The Manifest
 
-Every TaxonoPy run writes a manifest file to the output directory **before**
-creating any output. This means interrupted runs leave a complete record of
-what should be cleaned up — `--full-rerun` deletes exactly those files and
-nothing else.
+Every TaxonoPy run writes a manifest file to the output directory **before** creating any output. This means interrupted runs leave a complete record of what should be cleaned up — `--full-rerun` deletes exactly those files and nothing else.
 
-Manifest files are command-scoped so they coexist safely if multiple commands
-share an output directory:
+Manifest files are command-scoped so they coexist safely if multiple commands share an output directory:
 
 | Command | Manifest file |
 |---|---|
@@ -90,5 +74,4 @@ share an output directory:
 }
 ```
 
-All paths in `files` are relative to the output directory. `cache_namespace`
-is `null` for `common-names`, which does not use an input-scoped cache.
+All paths in `files` are relative to the output directory. `cache_namespace` is `null` for `common-names`, which does not use an input-scoped cache.

src/taxonopy/manifest.py

@@ -1,12 +1,8 @@
 """Manifest tracking for TaxonoPy output files.
 
-Each TaxonoPy command writes a manifest file to its output directory listing
-every file it intends to produce. The manifest is written before any output
-files are created, so interrupted runs leave a complete record of what should
-be cleaned up on the next --full-rerun.
+Each TaxonoPy command writes a manifest file to its output directory listing every file it intends to produce. The manifest is written before any output files are created, so interrupted runs leave a complete record of what should be cleaned up on the next --full-rerun.
 
-Manifest files are command-scoped to avoid collisions when multiple commands
-share an output directory.
+Manifest files are command-scoped to avoid collisions when multiple commands share an output directory.
 """
 
 import json
@@ -37,8 +33,7 @@ def get_intended_files_for_resolve(
 ) -> List[str]:
     """Return the full list of files a resolve run intends to write.
 
-    Delegates output path naming to compute_output_paths (single source of
-    truth in output_manager), then appends the fixed outputs.
+    Delegates output path naming to compute_output_paths (single source of truth in output_manager), then appends the fixed outputs.
 
     Args:
         input_path: The --input argument (file or directory).
@@ -63,9 +58,7 @@ def get_intended_files_for_common_names(
 ) -> List[str]:
     """Return the full list of files a common-names run intends to write.
 
-    Output files preserve the input directory structure, so paths are simply
-    the relative paths of the annotation files. No naming convention is
-    encoded here.
+    Output files preserve the input directory structure, so paths are simply the relative paths of the annotation files. No naming convention is encoded here.
 
     Args:
         annotation_dir: The --resolved-dir argument.
@@ -130,13 +123,7 @@ def read_manifest(output_dir: str, command: str) -> Optional[dict]:
     try:
         return json.loads(manifest_path.read_text())
     except (OSError, UnicodeDecodeError, json.JSONDecodeError) as exc:
-        logger.error(
-            "Cannot read manifest at '%s': %s -- automated rerun cleanup is not possible. "
-            "To proceed: fix or delete this file and remove previous TaxonoPy output files "
-            "from this output directory manually, or specify a new output directory with --output-dir.",
-            manifest_path,
-            exc,
-        )
+        logger.error("Cannot read manifest at '%s': %s -- automated rerun cleanup is not possible. To proceed: fix or delete this file and remove previous TaxonoPy output files from this output directory manually, or specify a new output directory with --output-dir.", manifest_path, exc)
         raise
 
 

src/taxonopy/output_manager.py

@@ -187,9 +187,7 @@ def _resolve_output_paths_for_input(
 ) -> Tuple[str, ...]:
     """Return absolute output file path(s) for a single input file.
 
-    This is the single source of truth for TaxonoPy output file naming.
-    Both the generate functions and compute_output_paths use it so that
-    naming convention changes need only be made here.
+    This is the single source of truth for TaxonoPy output file naming. Both the generate functions and compute_output_paths use it so that naming convention changes need only be made here.
 
     Args:
         input_file: Absolute path to the input file.
@@ -222,9 +220,7 @@ def compute_output_paths(
 ) -> List[str]:
     """Return intended output file paths (relative to output_dir) for a resolve run.
 
-    Used by the manifest system to record files before they are written.
-    Does not include fixed outputs such as resolution_stats.json or the
-    manifest file itself — callers are responsible for appending those.
+    Used by the manifest system to record files before they are written. Does not include fixed outputs such as resolution_stats.json or the manifest file itself — callers are responsible for appending those.
 
     Args:
         input_path: The --input argument (file or directory).