Bump hictkpy to v1.0.0

pyproject.toml

@@ -43,7 +43,7 @@ requires-pyhton = ">=3.9"
 dependencies = [
     "bioframe >0.7, <1",
     "h5py >3, <4",
-    "hictkpy >=0.0.5, <1",
+    "hictkpy[scipy] >=1, <2",
     "matplotlib >=3.8, <4",
     "numpy >=1.26, <2",
     "pandas >=2.0, <3",

src/stripepy/main.py

@@ -40,14 +40,14 @@ def main():
     configs_input, configs_thresholds, configs_output = cli.parse_args()
 
     # Data loading:
-    c, chr_starts, chr_ends, bp_lengths = others.cmap_loading(configs_input["contact-map"], configs_input["resolution"])
+    f, chr_starts, chr_ends, bp_lengths = others.cmap_loading(configs_input["contact-map"], configs_input["resolution"])
 
     # Remove existing folders:
     configs_output["output_folder"] = f"{configs_output['output_folder']}/{configs_input['resolution']}"
     IO.remove_and_create_folder(configs_output["output_folder"])
 
     # Extract a list of tuples where each tuple is (index, chr), e.g. (2,'chr3'):
-    c_pairs = others.chromosomes_to_study(list(c.chromosomes().keys()), bp_lengths, MIN_SIZE_CHROMOSOME)
+    c_pairs = others.chromosomes_to_study(list(f.chromosomes().keys()), bp_lengths, MIN_SIZE_CHROMOSOME)
 
     # Create HDF5 file to store candidate stripes:
     hf = h5py.File(f"{configs_output['output_folder']}/results.hdf5", "w")
@@ -73,11 +73,7 @@ def main():
         if configs_input["roi"] is not None:
             IO.create_folders_for_plots(f"{configs_output['output_folder']}/plots/{this_chr}")
 
-        # Extract current chromosome (only the upper-triangular part is stored by hictkpy!):
-        I = c.fetch(this_chr).to_coo().tolil()
-        I += I.T
-        I.setdiag(I.diagonal() / 2)
-        I = I.tocsr()
+        I = f.fetch(this_chr).to_csr("full")
 
         # RoI:
         RoI = others.define_RoI(

src/stripepy/others.py

@@ -7,30 +7,37 @@
 from . import IO
 
 
-def cmap_loading(path, resolution):
-    # Retrieve metadata:
-    file_name, file_ext = os.path.splitext(path)
-    file_format = file_ext.lower()[1:]  # Remove the dot from the extension and convert to lowercase
-
-    if file_format == "cool" or file_format == "hic":
-        c = hictkpy.File(path, resolution)
-    elif file_format == "mcool":
-        c = hictkpy.File(f"{path}::/resolutions/{resolution}", resolution)
-    else:
-        raise ValueError("Unsupported file format: " + file_format)
+def cmap_loading(path: os.PathLike, resolution: int):
+    try:
+        if not isinstance(resolution, int):
+            raise TypeError("resolution must be an integer.")
+
+        if resolution <= 0:
+            raise ValueError("resolution must be greater than zero.")
+
+        if hictkpy.is_scool_file(path):
+            raise RuntimeError(".scool files are not currently supported.")
+        if hictkpy.is_cooler(path):
+            f = hictkpy.File(path)
+            if f.resolution() != resolution:
+                raise RuntimeError(f"expected {resolution} resolution, found {f.resolution()}.")
+        else:
+            f = hictkpy.MultiResFile(path)[resolution]
+    except RuntimeError as e:
+        raise RuntimeError(f'error opening file "{path}"') from e
 
     # Retrieve metadata:
     chr_starts = [0]  # left ends of each chromosome  (in matrix coordinates)
     chr_ends = []  # right ends of each chromosome (in matrix coordinates)
     chr_sizes = []  # integer bp lengths, one per chromosome
-    for _, bp_length in c.chromosomes().items():
+    for bp_length in f.chromosomes().values():
         chr_sizes.append(bp_length)
         chr_ends.append(chr_starts[-1] + int(np.ceil(bp_length / resolution)))
         chr_starts.append(chr_ends[-1])
         # print(f"{chr_starts[-2]}-{chr_ends[-1]}-{chr_sizes[-1]}")
     chr_starts.pop(-1)
 
-    return c, chr_starts, chr_ends, chr_sizes
+    return f, chr_starts, chr_ends, chr_sizes
 
 
 def chromosomes_to_study(chromosomes, length_in_bp, min_size_allowed):

src/stripepy/utils/evaluate.py

@@ -976,7 +976,7 @@ def recoverable_anchors_recognition(
         path2GT = f"{base_path}/MoDLE-benchmark/"
         file_name = f"{file_name_base}_{contact_density}_{noise}"
         path2mcool = f"{base_path}/MoDLE-benchmark/data/{file_name}/"
-        c = hictkpy.File(f"{path2mcool}{file_name}.mcool::resolutions/{resolution}", resolution)
+        c = hictkpy.File(f"{path2mcool}{file_name}.mcool", resolution)
         c_names = list(c.chromosomes().keys())
         c_ids = list(range(len(c_names)))
         c_pairs = list(zip(c_ids, c_names))
@@ -1116,7 +1116,7 @@ def recoverable_anchors_classification(
         path2GT = f"{base_path}/MoDLE-benchmark/"
         file_name = f"{file_name_base}_{contact_density}_{noise}"
         path2mcool = f"{base_path}/MoDLE-benchmark/data/{file_name}/"
-        c = hictkpy.File(f"{path2mcool}{file_name}.mcool::resolutions/{resolution}", resolution)
+        c = hictkpy.File(f"{path2mcool}{file_name}.mcool", resolution)
         c_names = list(c.chromosomes().keys())
         c_ids = list(range(len(c_names)))
         c_pairs = list(zip(c_ids, c_names))

test/test_others.py

@@ -31,7 +31,6 @@ def _generate_singleres_test_file(
     if chromosomes is None:
         chromosomes = _generate_chromosomes()
 
-    # TODO remove str() after upgrading to hictkpy v1.0.0
     writer = htk.cooler.FileWriter(str(path), resolution=resolution, chromosomes=chromosomes)
     writer.add_pixels(pd.DataFrame({"bin1_id": [0], "bin2_id": [0], "count": 1}))
     writer.finalize()
@@ -48,39 +47,41 @@ def _discretize(v: List[int], factor: int) -> List[int]:
 
 
 class TestCmapLoading:
-    # TODO revise error messages
     def test_invalid_paths(self, tmpdir):
         tmpdir = pathlib.Path(tmpdir)
-        with pytest.raises(Exception, match="Unsupported file format:"):
+        with pytest.raises(RuntimeError):
             cmap_loading(tmpdir / "foo", 5000)
 
     def test_invalid_formats(self, tmpdir):
         invalid_file = pathlib.Path(__file__).resolve()
         folder = pathlib.Path(tmpdir)
-        with pytest.raises(Exception, match="Unsupported file format:"):
+        with pytest.raises(RuntimeError):
             cmap_loading(invalid_file, 5000)
 
-        with pytest.raises(Exception, match="Unsupported file format:"):
+        with pytest.raises(RuntimeError):
             cmap_loading(folder, 5000)
 
     def test_invalid_resolutions(self, tmpdir):
-        invalid_resolutions = [-1, 0, 1000.0, 5000]
         with tempfile.NamedTemporaryFile(dir=tmpdir) as clr:
             clr.close()
             path_to_clr = _generate_singleres_test_file(pathlib.Path(clr.name), 1000)
 
-            for res in invalid_resolutions:
-                with pytest.raises(Exception):
-                    cmap_loading(path_to_clr, res)
+            with pytest.raises(RuntimeError):
+                cmap_loading(path_to_clr, 5000)
+            with pytest.raises(TypeError, match="must be an integer"):
+                cmap_loading(path_to_clr, 1000.0)
+            with pytest.raises(ValueError, match="must be greater than zero"):
+                cmap_loading(path_to_clr, -1)
+            with pytest.raises(ValueError, match="must be greater than zero"):
+                cmap_loading(path_to_clr, 0)
 
     def test_valid_files(self, tmpdir):
         tmpdir = pathlib.Path(tmpdir)
         chromosomes = {"A": 100_000, "B": 50_000, "C": 10_000}
         resolution = 1000
         path_to_clr = _generate_singleres_test_file(tmpdir / "test.cool", resolution, chromosomes)
 
-        # TODO remove str() after upgrading to hictkpy v1.0.0
-        f, starts, ends, sizes = cmap_loading(str(path_to_clr), resolution)
+        f, starts, ends, sizes = cmap_loading(path_to_clr, resolution)
         assert f.resolution() == 1000
         assert len(starts) == len(chromosomes)
         assert len(starts) == len(ends)
@@ -94,6 +95,5 @@ def test_valid_files(self, tmpdir):
         assert ends == _discretize([100_000, 150_000, 160_000], resolution)
         assert sizes == list(chromosomes.values())
 
-        # TODO enable after merging https://github.com/paulsengroup/StripePy/pull/4
-        # with pytest.raises(Exception):
-        #     cmap_loading(path_to_clr, resolution + 1)
+        with pytest.raises(Exception):
+            cmap_loading(path_to_clr, resolution + 1)