Move the regression and large-index tests into the pytest suite

scripts/test/README.md

@@ -11,23 +11,29 @@ From root:
 
     sh scripts/test/simple_tests.sh
 
-#### Regression tests
+#### pytest suite
 
-They use the Python3 infrastructure in the `scripts/test` subdirectory, including `bt2face.py`, `dataface.py` and `btdata.py`.
+The `test_*.py` modules in `scripts/test` exercise the `bowtie2`, `bowtie2-build` and `bowtie2-inspect` command lines, using small references generated from a fixed seed and the lambda phage example.  Shared helpers are in `bt2_helpers.py` and fixtures in `conftest.py`.  Requires Python 3 and `pytest`.  Set `BOWTIE2_BIN_DIR` to test binaries built somewhere else.
 
 From root:
 
-    python3 scripts/test/regressions.py --verbose
+    python3 -m pytest scripts/test
+
+#### Regression tests
+
+Tests for specific GitHub issues are in `scripts/test/test_regressions.py` and run as part of the pytest suite.  Val Antonescu originally set these up.
+
+From root:
 
-Val Antonescu originally set these up.
+    python3 -m pytest scripts/test/test_regressions.py
 
 #### Big index test
 
-Builds an index consisting of both human and mouse genomes, pushing the genome size above the 2^32 limit, and necessitating a "big" 64-bit index.  This takes a lot of time and RAM.
+`scripts/test/test_large_genome.py` aligns reads cut from beyond, and across, the 2^32 offset of a prebuilt large (`.bt2l`) index whose reference exceeds 2^32 bases, such as a combined human and mouse index.  Building such an index takes hours and tens of GB of memory, so the tests are skipped unless `BOWTIE2_LARGE_INDEX` names its prefix.  Running them needs enough memory to load that index.
 
 From root:
 
-    python3 scripts/test/large_idx.py --verbose
+    BOWTIE2_LARGE_INDEX=/path/to/hs_mm python3 -m pytest scripts/test/test_large_genome.py
 
 #### Randomized tests