Prepare pyvcell for 2026 workshop: docs, remote simulation API, and client regeneration#35

Merged

jcschaff merged 24 commits intomainfrom

workshop-2026

Mar 19, 2026

Commits on Mar 19, 2026

documentation as guides and API docs
jcschaff
committed
extract SegmentedImageGeometry and fix image/analytic geometry rasterization

jcschaff
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claude
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add optional save_path parameter to plot methods

jcschaff
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claude
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add notebook-generated images to markdown guides and notebook execution tests

jcschaff
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claude
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add docs-execute-notebooks make target and gitignore notebook workspace

jcschaff
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claude
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fixed zarr_writer to consider domain masks when computing statistics
jcschaff
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improve models for complex-geometries and building-a-model guides
jcschaff
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regenerate vcell api python client
jcschaff
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fix API client bugs: base URL, Accept header, XML deserialization

jcschaff
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claude
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Add Version model to VCML pydantic models

jcschaff
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claude
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Add remote-simulations tutorial notebook and docs integration

jcschaff
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claude
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Update viz-concentrations image

jcschaff
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claude
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Use TensorStore to read remote N5 export results

jcschaff
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claude
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Add high-level convenience API for remote VCell simulations
jcschaff
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update poetry.lock for MacOS 15
jcschaff
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Fix ruff lint errors after rebase on main
jcschaff
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dded xvfb-run wrapper + xvfb install step to CI workflow
jcschaff
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zarr_writer (domain-masked stats) changed mean_values expected values
jcschaff
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write version objects to XML for biomodels and simulations, round trip
jcschaff
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Reformat regenerated API client after rebase
jcschaff
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Reformat docs and regenerate guide images after rebase
jcschaff
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Add Version XML write support for VCML roundtrip and fix mypy errors
jcschaff
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Fix tests: update expected values for domain-masked stats, use Agg backend
jcschaff
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lint error
jcschaff
committed

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Prepare pyvcell for 2026 workshop: docs, remote simulation API, and client regeneration#35

Prepare pyvcell for 2026 workshop: docs, remote simulation API, and client regeneration#35
jcschaff merged 24 commits intomainfrom
workshop-2026

Commits on Mar 19, 2026

documentation as guides and API docs

extract SegmentedImageGeometry and fix image/analytic geometry rasterization

add optional save_path parameter to plot methods

add notebook-generated images to markdown guides and notebook execution tests

add docs-execute-notebooks make target and gitignore notebook workspace

fixed zarr_writer to consider domain masks when computing statistics

improve models for complex-geometries and building-a-model guides

regenerate vcell api python client

fix API client bugs: base URL, Accept header, XML deserialization

Add Version model to VCML pydantic models

Add remote-simulations tutorial notebook and docs integration

Update viz-concentrations image

Use TensorStore to read remote N5 export results

Add high-level convenience API for remote VCell simulations

update poetry.lock for MacOS 15

Fix ruff lint errors after rebase on main

dded xvfb-run wrapper + xvfb install step to CI workflow

zarr_writer (domain-masked stats) changed mean_values expected values

write version objects to XML for biomodels and simulations, round trip

Reformat regenerated API client after rebase

Reformat docs and regenerate guide images after rebase

Add Version XML write support for VCML roundtrip and fix mypy errors

Fix tests: update expected values for domain-masked stats, use Agg backend

lint error