Docs: shorter README and clearer guides

README.md

@@ -6,17 +6,18 @@
 
 gtfparse
 ========
-Parsing tools for GTF (gene transfer format) files.
-
+Read GTF (gene transfer format) annotations into a pandas DataFrame, with one
+row per feature and attribute values such as gene and transcript IDs expanded
+into columns.
 
 ## Install
 
 ```sh
 python -m pip install gtfparse
 ```
 
-Python 3.9 or later is required. Version 3 uses pandas and PyArrow; Polars
-output is optional and requires `gtfparse[polars]`.
+Python 3.9 or later is required. For optional Polars output, install
+`gtfparse[polars]`.
 
 ## Read an annotation and find genes
 
@@ -62,5 +63,6 @@ it is not the gene ID. The ninth GTF field supplies attributes such as
 - [Version 3 migration and optional Polars output](docs/guides/migration.md)
 - [Complete API reference](docs/reference.md)
 
-Build with `python -m pip install -r requirements-docs.txt` and `./docs.sh`.
-Run `python scripts/check_docs_examples.py` to verify the printed examples.
+To build the documentation locally, run
+`python -m pip install -r requirements-docs.txt` and `./docs.sh`.
+`python scripts/check_docs_examples.py` checks the printed example output.

docs/guides/progress.md

@@ -1,24 +1,10 @@
 # Report parsing progress
 
 Pass `progress_callback(stage, completed, total)` to `read_gtf` to connect
-parsing to your own progress UI. The callback runs synchronously; exceptions
-from it stop parsing and propagate to the caller. Without a callback, gtfparse
-does not display a progress bar or add a progress-library dependency.
+parsing to your own progress UI. Without a callback, gtfparse does not display
+a progress bar or add a progress-library dependency.
 
-| Stage | Reports |
-| --- | --- |
-| `read` | `(0, None)` before loading/filtering the file; `(rows, rows)` after it succeeds |
-| `attributes` | `(0, rows)`, then every 10,000 rows, then `(rows, rows)` |
-| `convert` | `(0, None)` before output conversion/transforms; `(rows, rows)` after success |
-
-Counts refer to rows retained after `features` filtering, not bytes or overall
-percentages. `None` means the total is unknown: loading and conversion expose
-only stage boundaries, so use an indeterminate indicator during those steps.
-Attribute expansion is omitted when `expand_attribute_column=False`. A stage
-that fails does not emit completion. An empty filtered result is supported;
-its attributes stage emits a single `(0, 0)` event. Empty input files raise `gtfparse.ParsingError`.
-
-For example, with the optional `tqdm` package installed:
+This example requires the optional `tqdm` package and your own GTF file:
 
 ```python
 from gtfparse import read_gtf
@@ -37,9 +23,26 @@ with tqdm(unit="rows") as bar:
     df = read_gtf("gene_annotations.gtf", progress_callback=show_progress)
 ```
 
+## Stages and counts
+
+| Stage | Reports |
+| --- | --- |
+| `read` | `(0, None)` before loading/filtering the file; `(rows, rows)` after it succeeds |
+| `attributes` | `(0, rows)`, then every 10,000 rows, then `(rows, rows)` |
+| `convert` | `(0, None)` before output conversion/transforms; `(rows, rows)` after success |
+
+Counts refer to rows retained after `features` filtering, not bytes or overall
+percentages. `None` means the total is unknown: loading and conversion expose
+only stage boundaries, so use an indeterminate indicator during those steps.
+Attribute expansion is omitted when `expand_attribute_column=False`.
+
+The callback runs synchronously; exceptions from it stop parsing and propagate
+to the caller. A stage that fails does not emit completion. An empty filtered
+result is supported; its attributes stage emits a single `(0, 0)` event. Empty
+input files raise `gtfparse.ParsingError`.
+
+## Lower-level functions
+
 `parse_gtf` reports the `read` stage, `parse_gtf_and_expand_attributes` reports
 `read` and `attributes`, `parse_gtf_pandas` reports `read` and `convert`, and
 `expand_attribute_strings` reports only `attributes` using the same callback.
-
-Quoted attribute values preserve spaces, semicolons, and apostrophes. Raw
-attributes (`expand_attribute_column=False`) retain their original quote marks.

docs/index.md

@@ -9,8 +9,8 @@ attribute values such as gene and transcript IDs expanded into columns.
 python -m pip install gtfparse
 ```
 
-Python 3.9 or later is required. Version 3 uses pandas and PyArrow; Polars
-output is optional and requires `gtfparse[polars]`.
+Python 3.9 or later is required. For optional Polars output, install
+`gtfparse[polars]`.
 
 ## Read an annotation and find genes
 
@@ -59,6 +59,8 @@ features = read_gtf("annotations.gtf.gz", features={"gene", "transcript"})
 The `features` option filters row types while reading. Compressed inputs are
 detected from their contents. Attribute expansion does not turn every row into
 a gene or automatically supply missing parent features.
+Quoted attribute values preserve spaces, semicolons, and apostrophes. Raw
+attributes (`expand_attribute_column=False`) retain their original quote marks.
 
 Continue with [filter and write annotations](guides/annotations.md), then
 [progress callbacks](guides/progress.md) or [version 3 migration](guides/migration.md).

gtfparse/__init__.py

@@ -24,7 +24,7 @@
 )
 from .write_gtf import write_gtf
 
-__version__ = "3.0.3"
+__version__ = "3.0.4"
 
 __all__ = [
     "GENCODE_BIOTYPE_ALIASES",

tasks/todo.md

@@ -512,10 +512,12 @@ after the modern stack is verified. Update PR branches without publishing.
 - [x] Inspect PR heads, current master and version requirements.
 - [x] Preserve current code while resolving the version conflict.
 - [x] Run lint, tests and documentation checks on #93.
-- [ ] Incorporate #93 in #95 and verify its separate patch bump.
-- [ ] Update the PR branches and close superseded #74.
+- [x] Incorporate #93 in #95 and verify its separate patch bump.
+- [x] Update both PR branches. Closing superseded #74 is the final remote step.
 
 ## Review
 
 PR #93: lint passed, all 213 tests passed, all three executable documentation
 examples passed, and the strict MkDocs build passed.
+PR #95: merged the refreshed parent; version 3.0.4, lint, 213 tests, and the
+strict MkDocs build passed.