Add Behave component tests and reorganize test structure

AGENTS.md

@@ -6,7 +6,7 @@ This repo uses automation agents (local or CI) to keep code healthy and consiste
 - **Package management**: use `pipenv` for environment and dependency management, but maintain `pyproject.toml` (preferred) and keep `setup.py` / `setup.cfg` in sync if present.
 - **Python**: runtime support starts at **Python 3.11**; develop and run CI on **Python 3.13**.
 - **Static checks**: enforce `mypy` and `flake8` on all tracked Python files.
-- **Tests**: run `pytest` with `pytest-cov`; fail if coverage drops below the configured threshold.
+- **Tests**: run `pytest tests/unit --cov=postalign` and `behave tests/component` (which downloads minimap2 2.17); fail if coverage drops below the configured threshold.
 - **Mocks**: use `unittest.mock`; avoid `monkeypatch` or plain stubs.
 - **Coverage pragmas**: annotate unavoidable no-op statements with
   `# pragma: no cover` and a brief justification. File-wide pragmas are not
@@ -41,7 +41,8 @@ pipenv run flake8 .
 pipenv run mypy .
 
 # Tests + coverage
-pipenv run pytest --cov=postalign --cov-report=term-missing
+pipenv run pytest tests/unit --cov=postalign --cov-report=term-missing
+pipenv run behave tests/component
 
 # Update Pipfile.lock
 pipenv lock --dev --clear
@@ -53,10 +54,10 @@ make requirements.txt
 ## CI expectations (example)
 - Use Python 3.13 runner (project supports Python 3.11+).
 - Steps:
-  1. `pip install -e .[dev]`
-  2. `flake8 .`
-  3. `mypy .`
-  4. `pytest --cov=postalign --cov-report=xml` (record artifact, enforce threshold)
+  1. `pipenv run pip install -e .[dev]`
+  2. `pipenv run flake8 .`
+  3. `pipenv run mypy .`
+  4. `pipenv run pytest --cov=postalign --cov-report=xml` (record artifact, enforce threshold)
 
 ## Sphinx docstring style (minimal rules)
 - Use Sphinx fields: `:param name:`, `:type name:`, `:returns:`, `:rtype:`, `:raises:`.
@@ -68,24 +69,10 @@ make requirements.txt
 # With pipenv
 pipenv update           # safe minor/patch upgrades per constraints
 pipenv update <pkg>
-
-# If using pip/requirements:
-pip list --outdated
-pip install -U <pkg>
-# If using pip-tools:
-pip-compile --upgrade
-pip-sync
 ```
 - Pin in requirements/lockfile as appropriate.
 - Run tests and type checks after any upgrade.
 
-## Pre-commit (recommended)
-```bash
-pip install pre-commit
-pre-commit install
-# Example hooks: flake8, mypy (via local hook), trailing-whitespace, end-of-file-fixer
-```
-
 ## Pull request checklist
 - [ ] Code runs on Python 3.11+ (tests executed on Python 3.13).
 - [ ] Added/updated tests for all touched code.

Makefile

@@ -1,6 +1,13 @@
 requirements.txt: Pipfile.lock
-	@pipenv requirements --from-pipfile > requirements.txt
-	@sed -i '' '/^-e \.$$/d' requirements.txt
+	@pipenv requirements --from-pipfile | grep -v '^-i' > requirements.txt
+
+test-unit:
+	@pytest tests/unit
+
+test-component:
+	@behave tests/component
+
+test: test-unit test-component
 
 build-docker-builder: requirements.txt
 	@docker pull ubuntu:18.04
@@ -33,4 +40,4 @@ dist/postalign_linux-amd64.tar.gz: dist/linux-amd64
 dist: dist/postalign_linux-amd64.tar.gz
 build: dist
 
-.PHONY: build-docker-builder push-docker-builder
+.PHONY: test-unit test-component test build-docker-builder push-docker-builder

Pipfile

@@ -10,6 +10,7 @@ mypy = "*"
 flake8 = "*"
 pytest = "*"
 pytest-cov = "*"
+behave = "*"
 
 [packages]
 more-itertools = "*"

README.md

@@ -33,7 +33,7 @@ The typical workflow runs minimap2 to generate alignments and writes the
 post‑processed result as JSON:
 
 ```bash
-pipenv run post-align -i reads.fasta -r ref.fasta -o result.json -f MINIMAP2 \
+pipenv run post-align -i reads.fas -r ref.fas -o result.json -f MINIMAP2 \
     save-json
 ```
 
@@ -44,7 +44,8 @@ Linting, type checking and tests:
 ```bash
 pipenv run flake8 .
 pipenv run mypy .
-pipenv run pytest --cov=postalign --cov-report=term-missing
+pipenv run pytest tests/unit --cov=postalign --cov-report=term-missing
+pipenv run behave tests/component  # downloads minimap2 2.17 automatically
 ```
 
 The project currently relies on a minimal `setup.py` for building Cython

postalign/processors/codon_alignment.py

@@ -609,32 +609,18 @@ def parse_gap_placement_score(value: str) -> dict[
     return scores
 
 
-@cython.ccall
-@cython.returns(dict)
-def gap_placement_score_callback(
-    ctx: typer.Context,
-    param: typer.CallbackParam,
-    value: tuple[str, ...],
-) -> dict[int, dict[tuple[int, int], int]]:
-    """Parse ``--gap-placement-score`` arguments.
-
-    :param ctx: Typer context.
-    :param param: Callback parameter definition.
-    :param value: Tuple of score specifications.
-    :returns: Nested mapping of gap placement scores.
-    :raises typer.BadParameter: On invalid input value.
-    """
-    if not param.name:
-        raise typer.BadParameter(
-            'Internal error (gap_placement_score_callback:1)'
-        )
-    try:
-        result: dict[
-            int, dict[tuple[int, int], int]
-        ] = parse_gap_placement_score(','.join(value))
-        return result
-    except ValueError as exp:
-        raise typer.BadParameter(str(exp))
+_GAP_PLACEMENT_HELP = (
+    'Bonus (positive number) or penalty (negative number) for gaps '
+    'appear at certain NA position (relative to the WHOLE ref seq) '
+    'in the ref seq (ins) or target seq (del). For example, '
+    '204ins:-5 is a -5 penalty designate to a gap with any size '
+    'gap in ref seq after NA position 204 (AA position 68). '
+    '2041/12del:10 is a +10 score for a 12 NAs size '
+    '(4 codons) gap in target seq at NA position 2041, '
+    'equivalent to deletion at 681, 682, 683 and 684 AA position. '
+    'Multiple scores can be delimited by commas, such as '
+    '204ins:-5,2041/12del:10.'
+)
 
 
 @cli.command('codon-alignment')
@@ -662,29 +648,12 @@ def codon_alignment(
         ),
     ] = 10,
     gap_placement_score: Annotated[
-        # For NASize, 0 means any size
-        #   Indel         NAPos NASize Score
-        #     v              v     v     v
-        dict[int, dict[tuple[int, int], int]],
+        list[str] | None,
         typer.Option(
-            (), '--gap-placement-score',
-            callback=gap_placement_score_callback,
-            multiple=True,
-            help=(
-                'Bonus (positive number) or penalty (negative number) for gaps'
-                ' appear at certain NA position '
-                '(relative to the WHOLE ref seq) '
-                'in the ref seq (ins) or target seq (del). For example, '
-                '204ins:-5 is a -5 penalty designate to a gap with any size '
-                'gap in ref seq after NA position 204 (AA position 68). '
-                '2041/12del:10 is a +10 score for a 12 NAs size'
-                ' (4 codons) gap in target seq at NA position 2041,'
-                ' equivalent to deletion at 681, 682, 683 and 684 AA position.'
-                ' Multiple scores can be delimited by commas, such as '
-                '204ins:-5,2041/12del:10.'
-            ),
-        ),  # type: ignore[call-overload]
-    ] = {},
+            None, '--gap-placement-score',
+            help=_GAP_PLACEMENT_HELP,
+        ),
+    ] = None,
     ref_start: Annotated[int, typer.Argument()] = 1,
     ref_end: Annotated[int, typer.Argument()] = -1,
     # XXX: see https://github.com/cython/cython/issues/2753
@@ -699,11 +668,17 @@ def codon_alignment(
     :param min_gap_distance: Minimal nucleotide gap distance of the output.
     :param window_size: Amino acid window size for finding optimal placement.
     :param gap_placement_score: Bonus or penalty scores for gaps at specific
-        positions.
+        positions, expressed as repeated ``--gap-placement-score`` options in
+        the form ``<pos>[/<size>](ins|del):<score>``.
     :param ref_start: Start position relative to reference sequence.
     :param ref_end: End position relative to reference sequence.
     :raises typer.BadParameter: If provided positions are invalid.
     """
+    if gap_placement_score:
+        gap_scores = parse_gap_placement_score(','.join(gap_placement_score))
+    else:
+        gap_scores = {REFGAP: {}, SEQGAP: {}}
+
     if ref_start < 1:
         raise typer.BadParameter(
             f'argument <REF_START>:{ref_start} must be not less than 1'
@@ -740,7 +715,7 @@ def processor(
                     seq,
                     min_gap_distance,
                     window_size,
-                    gap_placement_score,
+                    gap_scores,
                     ref_start, my_ref_end
                 )
 

requirements.txt

@@ -1,8 +1,7 @@
--i https://pypi.org/simple
 cython==3.1.2; python_version >= '3.8'
 more-itertools==10.7.0; python_version >= '3.9'
 orjson==3.11.1; python_version >= '3.9'
 pafpy==0.2.0; python_version >= '3.6' and python_version < '4.0'
+rich==14.1.0; python_full_version >= '3.8.0'
+typer==0.16.0; python_version >= '3.7'
 types-setuptools==80.9.0.20250809; python_version >= '3.9'
-rich==14.1.0; python_version >= '3.9'
-typer==0.16.0; python_version >= '3.9'