diff --git a/README.md b/README.md index 44e0723..5f15b88 100644 --- a/README.md +++ b/README.md @@ -91,3 +91,4 @@ scripts/ ``` Each round's `data/` directory is generated locally and gitignored. +This is Venkat's PR diff --git a/pyproject.toml b/pyproject.toml index b854c3c..2559e5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,10 @@ version = "0.1.0" description = "Python Performance Lab: Sharpening Your Instincts — PyCon US 2026 tutorial" readme = "README.md" requires-python = ">=3.13" -dependencies = ["numpy>=2.0"] +dependencies = [ + "numpy>=2.0", + "regex>=2026.5.9", +] [dependency-groups] dev = ["pytest>=8.0", "pytest-codspeed>=5.0.1"] diff --git a/rounds/1_histogram/solution.py b/rounds/1_histogram/solution.py index dffbee5..b110736 100644 --- a/rounds/1_histogram/solution.py +++ b/rounds/1_histogram/solution.py @@ -8,7 +8,14 @@ def compute_histogram(path: str) -> dict[bytes, int]: """Frequency of every 2-byte bigram in the file at ``path``.""" - # TODO: remove this delegation and write your own implementation here. - from .baseline import compute_histogram as _baseline + with open(path, "rb") as f: + data = f.read() - return _baseline(path) + bytes_mat = [[0] * 256 for _ in range(256)] + + for i in range(len(data) - 1): + bytes_mat[data[i]][data[i + 1]] += 1 + + counts = {bytes([i, j]): c for i in range(256) for j in range(256) if (c := bytes_mat[i][j])} + + return counts diff --git a/rounds/3_dna/solution.py b/rounds/3_dna/solution.py index 8b917da..1a09608 100644 --- a/rounds/3_dna/solution.py +++ b/rounds/3_dna/solution.py @@ -6,6 +6,24 @@ """ from .baseline import find_matches as _baseline +import regex +from multiprocessing.pool import ThreadPool + +def match(record, pattern_str): + if not record.strip(): + return None, [] + + # split record ID + lines = record.split("\n") + record_id = lines[0].strip() + sequence = "".join(lines[1:]).replace(" ", "") + + # regex pattern match, get position if match + match_inds = [] + for match in regex.finditer(pattern_str, sequence, overlapped=True): + match_inds.append(match.start()) + + return record_id, match_inds def find_matches(fasta_path: str, pattern: bytes) -> list[tuple[str, list[int]]]: @@ -13,5 +31,19 @@ def find_matches(fasta_path: str, pattern: bytes) -> list[tuple[str, list[int]]] Returns ``[(record_id, [positions...]), ...]`` in file order. """ - # TODO: remove this delegation and write your own implementation here. - return _baseline(fasta_path, pattern) + pattern_str = pattern.decode("ascii") + with open(fasta_path, "r") as f: + text = f.read() + + results = [] + records = text.split(">") + args = [(record, pattern_str) for record in records] + + with ThreadPool(10) as pool: + + for record_id, match_inds in pool.starmap(match, args): + if len(match_inds) > 0: + # append to results + results.append((record_id, match_inds)) + + return results diff --git a/uv.lock b/uv.lock index dced559..1fb9f43 100644 --- a/uv.lock +++ b/uv.lock @@ -115,6 +115,7 @@ version = "0.1.0" source = { virtual = "." } dependencies = [ { name = "numpy" }, + { name = "regex" }, ] [package.dev-dependencies] @@ -124,7 +125,10 @@ dev = [ ] [package.metadata] -requires-dist = [{ name = "numpy", specifier = ">=2.0" }] +requires-dist = [ + { name = "numpy", specifier = ">=2.0" }, + { name = "regex", specifier = ">=2026.5.9" }, +] 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