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Install bifti in playground notebooks and playground CI - #203

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MRzeroCore now depends on bifti>=0.3.0, but the playground notebooks install MRzeroCore with --no-deps, so bifti never gets installed.

Changes

  • 18 playground notebooks (documentation/playground_mr0/**): added !pip install bifti --no-deps right after !pip install MRzeroCore --no-deps. Where a notebook silences that install with &> /dev/null, the new line does too.
  • .github/workflows/playground_test.yml: added pip install bifti (with dependencies) after the MRzeroCore install, since the CI environment starts empty and needs bifti's nibabel and requests.

Note

In the notebooks bifti is installed with --no-deps, like MRzeroCore. Colab already has nibabel and requests, and this keeps pip from upgrading Colab's numpy to the numpy>=2.5.1 that bifti asks for, which would force a runtime restart. If bifti really needs that numpy version, drop --no-deps from those lines.


Generated by Claude Code

MRzeroCore now depends on bifti, but the playground notebooks install
MRzeroCore with --no-deps, so bifti was missing.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01NHKPBcsb28ED47iXtFJjsC
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Simulation test: main (before) vs. this PR (after)

Sequence Status max mag NRMSE max phase RMSE max runtime Δ
mr0_DREAM_STE_seq ✅ 0.00e+00 0.00e+00 +0.4%
mr0_DWI_SE_EPI ✅ 0.00e+00 0.00e+00 +0.6%
mr0_EPI_2D_seq ✅ 0.00e+00 0.00e+00 +3.0%
mr0_FID_seq ✅ 0.00e+00 0.00e+00 +5.3%
mr0_FLASH_2D_seq ✅ 0.00e+00 0.00e+00 +1.1%
mr0_GRE_to_FLASH ⚠️ – – –
mr0_RARE_2D_seq ✅ 0.00e+00 0.00e+00 +10.7%
mr0_SE_CPMG_seq ✅ 0.00e+00 0.00e+00 +6.8%
mr0_STE_3pulses_5echoes_seq ✅ 0.00e+00 0.00e+00 +9.8%
mr0_TSE_2D_multi_shot_seq ✅ 0.00e+00 0.00e+00 +4.7%
mr0_bSSFP_2D_seq ✅ 0.00e+00 0.00e+00 +1.4%
mr0_diffusion_prep_STEAM_2D_seq ✅ 0.00e+00 0.00e+00 +9.1%
✅ mr0_DREAM_STE_seq: All tests passed.

mr0_DREAM_STE_seq

✅ mr0_DWI_SE_EPI: All tests passed.

mr0_DWI_SE_EPI

✅ mr0_EPI_2D_seq: All tests passed.

mr0_EPI_2D_seq

✅ mr0_FID_seq: All tests passed.

mr0_FID_seq

✅ mr0_FLASH_2D_seq: All tests passed.

mr0_FLASH_2D_seq

⚠️ mr0_GRE_to_FLASH: No comparison possible: [Errno 2] No such file or directory: '/home/runner/work/MRzero-Core/MRzero-Core/tests/simulation_test/ref_files/mr0_GRE_to_FLASH.seq.npz'
✅ mr0_RARE_2D_seq: All tests passed.

mr0_RARE_2D_seq

✅ mr0_SE_CPMG_seq: All tests passed.

mr0_SE_CPMG_seq

✅ mr0_STE_3pulses_5echoes_seq: All tests passed.

mr0_STE_3pulses_5echoes_seq

✅ mr0_TSE_2D_multi_shot_seq: All tests passed.

mr0_TSE_2D_multi_shot_seq

✅ mr0_bSSFP_2D_seq: All tests passed.

mr0_bSSFP_2D_seq

✅ mr0_diffusion_prep_STEAM_2D_seq: All tests passed.

mr0_diffusion_prep_STEAM_2D_seq

Workflow run — raw .npz data is attached as artifacts.

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