From 89fa9299498e3cc18dd869c7eb95dd0b5f180b4a Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Wed, 20 May 2026 09:27:15 -0400 Subject: [PATCH 1/3] fixed issue with unexpected shapes / types of volume variables Fix addresses scalar, pre-sized, and domain-less volume variables --- pyvcell/_internal/simdata/zarr_writer.py | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/pyvcell/_internal/simdata/zarr_writer.py b/pyvcell/_internal/simdata/zarr_writer.py index ac05ae3..090cc4d 100644 --- a/pyvcell/_internal/simdata/zarr_writer.py +++ b/pyvcell/_internal/simdata/zarr_writer.py @@ -144,21 +144,29 @@ def _get_domain_mask(dname: str) -> np.ndarray: # add volumetric functions for f in volume_functions: - func_data = f.evaluate(variable_bindings=bindings).reshape((num_z, num_y, num_x)) + evaluated_data = f.evaluate(variable_bindings=bindings) + is_pre_sized: bool = evaluated_data.shape == (num_z, num_y, num_x) + if evaluated_data.shape == (): # scalar value + func_data = np.zeros((num_z, num_y, num_x), dtype=evaluated_data.dtype) + func_data.fill(evaluated_data.min()) # min of a scalar value is the value itself. + else: + func_data = evaluated_data if is_pre_sized else evaluated_data.reshape((num_z, num_y, num_x)) z1[t, c, :, :, :] = func_data - domain_name = f.name.split("::")[0] - function_name = f.name.split("::")[1] + name_parts = f.name.split("::") + if len(name_parts) > 2: + raise ValueError(f"Volume function name `{f.name}` is not in the expected format") + domain_half: str = f.name.split("::")[0] if len(name_parts) == 2 else "" + name_half: str = f.name.split("::")[-1] if t == 0: channel_metadata.append({ "index": c, - "label": function_name, - "domain_name": domain_name, + "label": name_half, + "domain_name": domain_half, "min_values": [], "max_values": [], "mean_values": [], }) - domain_mask = _get_domain_mask(domain_name) - masked = func_data[domain_mask] + masked = func_data if len(domain_half) == 0 else func_data[_get_domain_mask(domain_half)] channel_metadata[c]["min_values"].append(float(np.min(masked))) channel_metadata[c]["max_values"].append(float(np.max(masked))) channel_metadata[c]["mean_values"].append(float(np.mean(masked))) From 2284ffb99637992ce729682bcd7b35414e2d4898 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Thu, 21 May 2026 11:30:31 -0400 Subject: [PATCH 2/3] increased range of python version --- pyproject.toml | 4 +- uv.lock | 513 ++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 509 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7fcd008..b59e50d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] name = "pyvcell" -version = "0.2.0" -requires-python = ">=3.12,<4.0" +version = "0.2.2" +requires-python = ">=3.11,<4.0" description = "This is the python wrapper for vcell modeling and simulation" repository = "https://github.com/virtualcell/pyvcell" documentation = 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