Fix scanner signature error and add binary signature verification

[albertx-wang]

• read_binary.py and write_binary.py:
  Added binary .bseq read/write support with MD5 signature serialization and deserialization.

• read_seq.py and write_seq.py:
  Updated text .seq signature handling. write_seq.py now computes the MD5 hash from raw file bytes before appending [SIGNATURE], and read_seq.py restores the signature metadata consistently when reading signed text files.

• verify_file_signature.py:
  Added a helper that recomputes the MD5 hash over the signed portion of text or binary Pulseq files and compares it with the stored signature, matching the MD5 verification behavior of MATLAB verifyFileSignature.m.

• sequence.py:
  Exposed read_binary() and write_binary() on Sequence, and added shared binary section codes used by binary IO and signature verification.

• test_binary_signature.py:
  Added binary signature roundtrip coverage for write_binary(), read_binary(), and verify_file_signature(), matching the binary signature roundtrip covered by MATLAB testBinarySignature.m.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
/home/runner/.local/lib/python3.12/site-packages/pypulseq
add_gradients.py	137	60	56%	44, 52, 58, 61, 75–86, 92, 125–128, 135–136, 155, 162, 167–263
add_ramps.py	36	36	0%	1–92
align.py	35	4	89%	41, 45, 69, 73
calc_duration.py	33	2	94%	43, 50
calc_ramp.py	220	216	2%	48–359
calc_rf_bandwidth.py	37	28	24%	45–81, 85–89
check_timing.py	96	29	70%	78, 82, 107, 180, 199, 232, 239, 249–293
compress_shape.py	30	1	97%	28
convert.py	40	8	80%	42, 48, 66, 72–73, 82, 88–89
event_lib.py	96	14	85%	6–9, 48–51, 70–71, 205–210
make_adc.py	98	14	86%	77, 80, 90–94, 97, 146, 149, 153, 159, 163, 202, 204, 206, 214
make_adiabatic_pulse.py	132	39	70%	208–212, 232–236, 244–245, 268, 274, 343–362, 466–475, 513–521
make_arbitrary_grad.py	53	15	72%	71, 74, 77, 80, 96–98, 107, 109, 117–121, 130
make_arbitrary_rf.py	75	63	16%	95–179
make_block_pulse.py	48	3	94%	121–125, 128
make_delay.py	9	1	89%	27
make_digital_output_pulse.py	16	2	88%	42, 50
make_extended_trapezoid.py	56	12	79%	67, 70, 76, 82, 85, 88, 91, 94, 116, 134, 136, 139
make_extended_trapezoid_area.py	104	4	96%	68, 71, 261, 264
make_gauss_pulse.py	73	20	73%	142–146, 149–173, 180, 183
make_label.py	22	4	82%	64, 66, 68, 75
make_sigpy_pulse.py	119	30	75%	12–13, 122, 125, 129, 166–170, 174, 177–178, 181–182, 197, 204, 209, 221, 224, 249–259, 273, 276, 306–316
make_sinc_pulse.py	70	10	86%	104, 110, 138–142, 146, 149–150, 153–154, 176
make_soft_delay.py	26	2	92%	107, 125
make_trapezoid.py	111	7	94%	177, 190, 196, 214, 232, 237, 255
make_trigger.py	16	2	88%	47, 55
opts.py	66	9	86%	78, 83, 102, 142, 166–170
points_to_waveform.py	9	1	89%	27
rotate.py	69	14	80%	15, 55, 66–69, 85–90, 112, 119–120
scale_grad.py	30	1	97%	65
sigpy_pulse_opts.py	26	7	73%	34–41
split_gradient.py	39	31	21%	46–103
split_gradient_at.py	70	27	61%	63–90, 110, 114, 118–120, 154–156
traj_to_grad.py	13	9	31%	26–40
verify_file_signature.py	58	26	55%	20, 29, 37, 41, 47, 54, 62–84
/home/runner/.local/lib/python3.12/site-packages/pypulseq/SAR
SAR_calc.py	5	1	80%	9
/home/runner/.local/lib/python3.12/site-packages/pypulseq/Sequence
block.py	469	79	83%	63, 66, 74, 80, 95, 103, 109, 120, 123, 126, 134, 139, 148, 159, 167, 207, 209, 213, 225, 274, 278, 294, 319–345, 382–385, 421–429, 436, 466–470, 512, 518, 551, 587–594, 611, 621, 647, 685, 703, 706, 724, 738, 765, 844, 881, 905
calc_grad_spectrum.py	81	76	6%	68–190
calc_pns.py	40	31	22%	45–96
ext_test_report.py	167	11	93%	79, 156, 167–168, 337–343
install.py	75	42	44%	31, 52, 69, 71, 112–131, 148, 181–184, 200–212, 254–278
parula.py	4	2	50%	19–86
read_binary.py	240	77	68%	15, 20, 22, 24, 66, 72, 76, 78–79, 81–82, 84–85, 87–88, 95, 119, 125–132, 141, 147–159, 197–203, 228–229, 245–249, 253–258, 262–266, 270–285
read_seq.py	400	39	90%	44–45, 110, 117, 130, 133–134, 138, 184, 228, 401, 422–439, 502, 505, 590, 614, 654, 685, 701–705, 712, 823, 834
sequence.py	656	128	80%	10–13, 109–119, 140–153, 207, 272–275, 322, 366, 442, 469–474, 511, 539–542, 633, 661–670, 682, 704, 745–748, 802, 840, 851–852, 858, 869, 875, 877, 885, 918–926, 1058, 1173, 1179, 1182, 1185, 1222, 1347–1360, 1418, 1440–1442, 1463, 1526, 1534, 1632, 1643–1656, 1725–1726, 1737–1755, 1779, 1809–1817, 1853, 1867–1877
write_binary.py	169	57	66%	25–28, 33–34, 39, 48, 70–77, 115–120, 123–131, 134–139, 142–147, 150–161, 185, 189
write_seq.py	362	7	98%	45, 77–79, 313, 347–349, 499
/home/runner/.local/lib/python3.12/site-packages/pypulseq/utils
cumsum.py	14	1	93%	17
paper_plot.py	63	58	8%	49–132
safe_pns_prediction.py	126	113	10%	50–87, 102–189, 197–214, 222, 244–250, 279–286, 310–336, 344–383, 396–411, 415
seq_plot.py	407	186	54%	22, 106, 138–139, 159, 176–178, 183–225, 235–242, 249–314, 318–324, 328–336, 359, 361, 363, 390–412, 457–458, 461–464, 487–496, 508, 525–535, 544–546, 565–567, 569–570, 572–573, 657–658, 674–691, 739–743
tracing.py	16	6	62%	33–34, 42, 54–55, 75
/home/runner/.local/lib/python3.12/site-packages/pypulseq/utils/siemens
asc_to_hw.py	58	53	9%	21–28, 48–106
readasc.py	59	7	88%	103–104, 110–111, 122–124
TOTAL	5686	1725	70%

Tests	Skipped	Failures	Errors	Time
1289	24 💤	0 ❌	0 🔥	4m 50s ⏱️

[mcencini]

Hi! Thanks for the PR. I noticed it fails on pre-commit, please make sure that the changes pass both pre-commit checks and tests before we start the review :)

[albertx-wang]

Hi! Thanks for the note!

The pre-commit issue was due to a missing Path import in test_binary_signature.py, which has now been fixed.

I originally changed the text .seq [SIGNATURE] comment block to more closely match the MATLAB formatting. However, that caused many differences against the existing expected-output .seq files. To avoid unnecessary expected-output churn, I restored the existing .seq signature comment format while keeping the corrected MD5 computation behavior.

[btasdelen]

Is there a reason hint ID logic here is different from the read_seq() and requires extra variables stored?

[albertx-wang]

The difference was to align with MATLAB’s binary read/write behavior. To avoid adding complexity here, I’ll move this into a separate PR.

[btasdelen]

I see. It was a conscious decision on our part to slightly deviate from Matlab Pulseq's logic. You can see the relevant discussion here #264. I think it is best to mimic read_seq() function to avoid any behavioral differences.

[albertx-wang]

Got it!

[btasdelen]

I don't know if any code out there uses this variable, but upstream Pulseq kept this as 'Text', so might be a better idea to keep it as 'Text', even though it is inconsistent capitalizaiton with 'bin'

[albertx-wang]

Thanks for catching this, I will keep it as Text for consistency!

[albertx-wang]

Thanks for the feedback and discussion. After discussing this, we think it would be cleaner for us to first submit a separate PR that only addresses the signature issue. We’ll keep that PR focused on the minimal signature fix, and split the other features into separate follow-up PRs.