ayar 0.1.0__tar.gz

ayar-0.1.0/.gitignore

@@ -0,0 +1,6 @@
+__pycache__/
+*.egg-info/
+dist/
+build/
+.pytest_cache/
+*.npz

ayar-0.1.0/LICENSE

@@ -0,0 +1,202 @@
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ayar-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: ayar
+Version: 0.1.0
+Summary: Assay your spike-sorted finding before you publish: detect sorting artifacts and test whether your result survives them.
+Author-email: Aslan Satary Dizaji <aslansatary@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: electrophysiology,kilosort,neuropixels,neuroscience,quality control,reproducibility,spike sorting,spikeinterface
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.9
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# ayar
+
+**Assay your spike-sorted finding before you publish.**
+
+*Ayar* (Persian عیار, Turkish *ayar*, Azerbaijani *əyar*) is the fineness of gold: how much of
+it is the real thing. `ayar` asks the same question of a result built on sorted spikes:
+how much of it is neuroscience, and how much is the spike sorter?
+
+Tools such as SpikeInterface quality metrics, Bombcell and UnitRefine judge **units**.
+`ayar` judges the **finding**. It reads the output of any sorter (Kilosort, MountainSort,
+SpyKING CIRCUS, ... via Phy folders or a plain `.npz` bundle), flags sorting artifacts
+that can manufacture or hide an effect, then re-computes *your* analysis without the
+flagged units and tells you whether your numbers survive.
+
+`ayar` does not sort spikes and does not prove a finding is right. It tests whether
+specific, known artifacts can explain it.
+
+```
+pip install ayar
+```
+
+Python 3.10+, depends only on numpy and scipy, runs on a CPU.
+
+## Thirty seconds
+
+```bash
+ayar synth demo.npz                                  # a session with planted artifacts
+ayar scan demo.npz --finding ayar.examples:condition_contrast
+```
+
+```
+ERROR   DRIFT_CONFOUND  unit 16: rate follows detection loss (r=0.94; up to 50% of spikes
+                        below threshold in the worst window)
+ERROR   DUPLICATE_UNIT  95% of unit 41's spikes have a unit 17 spike within ±0.25 ms (229x
+                        chance): likely one neuron counted twice
+ERROR   OVERLAP_HOLE    units 42 and 43 fire within ±0.5 ms 13% as often as expected from
+                        the 2-10 ms flanks (37 vs 295, p=1.6e-80)
+...
+finding audit: ayar.examples:condition_contrast
+  number                 remove units flagged by    n    baseline   after   change  random-drop q95  verdict
+  frac_units_suppressed  DRIFT_CONFOUND             3        0.06       0     100%               6%  SENSITIVE
+  mean_contrast_hz       DUPLICATE_UNIT             2       2.277    2.05      10%               8%  ROBUST
+  ...
+  frac_units_suppressed: SENSITIVE - depends on the flagged units beyond what random removals explain
+```
+
+In this synthetic block-design session, every "suppressed" unit was a drifting unit losing
+spikes below threshold: there was no suppression at all.
+
+On your own data:
+
+```bash
+ayar scan path/to/kilosort_output/ --finding my_analysis.py:main --events events.npz
+```
+
+`ayar scan` exits with status 1 when it finds an error-level artifact or a finding that is
+SENSITIVE or FLIPPED, so it can gate a pipeline or CI job (`--fail-on warning|never`).
+
+## Your finding is a function
+
+A finding is any function of a bundle that returns a number or a dict of numbers: the
+numbers you would put in a paper.
+
+```python
+import ayar
+
+def main(bundle):
+    trains = bundle.trains()                     # {unit_id: spike times in s}
+    ev = bundle.events                           # ev.times, ev.labels
+    ...
+    return {"decoding_accuracy": acc, "frac_tuned": frac}
+
+report = ayar.scan(ayar.load("kilosort_output/"), finding=main)
+print(report)
+report.finding_verdicts        # {'decoding_accuracy': 'robust', 'frac_tuned': 'sensitive'}
+report.to_json()
+```
+
+For each detector that raised flags, `ayar` removes the implicated units (the duplicate
+copy, one unit of each hole pair, the drifting unit), recomputes the finding, and compares
+the change with **random-drop controls**: the same number of *unflagged* units removed at
+random, 20 times. A change counts against the artifact only if it is bigger than what
+dropping arbitrary units does.
+
+| verdict | meaning |
+|---|---|
+| `robust` | changes by less than 10 % |
+| `nonspecific` | changes, but no more than random removals (95th percentile) |
+| `shifted` | moves beyond random removals, by 10-25 % |
+| `sensitive` | moves beyond random removals, by 25 % or more |
+| `flipped` | changes sign, which random removals almost never do |
+| `failed` | your function raised an error on the reduced bundle |
+
+`ayar.examples` has two finding templates: `condition_contrast` (two-condition rate effect)
+and `zero_lag_synchrony` (synchrony between neighbouring units).
+
+## Detectors
+
+| code | needs | what it catches | why it matters |
+|---|---|---|---|
+| `DUPLICATE_UNIT` | spike times | two units sharing most spikes within ±0.25 ms, far above chance | one neuron counted twice: inflated N, double weight in averages and decoders, fake zero-lag correlation |
+| `OVERLAP_HOLE` | spike times (depths restrict to neighbours) | a gap near zero lag in a nearby pair's cross-correlogram, tested against the 2-10 ms flanks (Poisson, Bonferroni) | the sorter dropped overlapping spikes, or one neuron was split in two: synchrony is underestimated |
+| `DRIFT_CONFOUND` | amplitudes or depths | firing rate that tracks spike amplitude, depth, or estimated detection loss (amplitude-cutoff per window) over the session | apparent rate changes are spikes lost below threshold; raised to **error** when conditions are ordered in time, because the loss then looks like a condition effect |
+
+Each flag carries a code, a severity, the units, the evidence, why it matters and a fix.
+Every threshold is named and can be overridden (`--set dup_window_ms=0.4`, or
+`ayar.DEFAULTS.override(...)`). When a check cannot run, or runs on only some units,
+`ayar` says so under *not checked* instead of guessing.
+
+## Evidence tiers
+
+* **Tier 0: spike times.** Duplicate and overlap detectors run (all pairs, capped at 20,000
+  pairs).
+* **Tier 1: plus amplitudes and/or depths.** Pair tests are restricted to neighbouring units
+  (100 µm), and the drift detector runs.
+* **Tier 2: plus the raw recording** (hybrid ground truth, re-sorting). Planned.
+
+## Input: the bundle
+
+```python
+b = ayar.from_phy("kilosort4_output/")            # spike_times/clusters/amplitudes/positions, labels
+b = ayar.from_arrays(times_s, clusters, amplitudes=amps, spike_depths=depths,
+                     events=ayar.Events(trial_times, trial_labels))
+b.save("session.npz")                             # plain npz, readable with numpy alone
+```
+
+`from_phy` keeps units labelled `good` or `mua` (curated labels win over Kilosort's), reads
+depths from `spike_positions.npy` (Kilosort 4) or `cluster_info.tsv` (Phy), and takes the
+sample rate from `params.py`.
+
+## Self-validation
+
+`ayar validate` plants artifacts in synthetic sessions, together with **controls** that
+must not be flagged: pairs driven by genuine common input (a real cross-correlogram peak)
+and units whose true rate ramps over the session at constant amplitude. Then it scores
+every detector.
+
+```
+ayar validate --sessions 20 --seed 100
+
+  detector         planted  found  false ctrl alarms sensitivity precision
+  DUPLICATE_UNIT        40     40      0           0        1.00      1.00
+  OVERLAP_HOLE          40     40      0           0        1.00      1.00
+  DRIFT_CONFOUND        60     55      1           0        0.92      0.98
+
+  finding audit: in 19 session(s) drift manufactured 'suppressed' units; ayar called that
+  number SENSITIVE or FLIPPED in 19
+```
+
+These numbers are measured on ayar's own synthetic data, whose artifacts are cleaner than
+real ones. They show that the detectors do what they claim, not how often they fire on real
+recordings.
+
+## Limitations (v0.1)
+
+* Research prototype. Thresholds are calibrated on synthetic sessions, not yet on public
+  datasets with ground truth.
+* Drift is detected per unit from rate-amplitude-depth co-variation. Units with few spikes
+  (fewer than ~600) get only the weaker amplitude/depth trend test and are reported as
+  partly checked.
+* The finding audit removes units; it does not yet repair them (merge duplicates, restrict
+  drifting units to their stable epoch).
+* `OVERLAP_HOLE` cannot yet tell missed overlaps from a split unit; both are reported.
+* The audit calls your function about 20 times per detector. Use `--set audit_controls=0`
+  to skip controls when the function is slow.
+
+## Roadmap
+
+* **v0.2**: SpikeInterface `SortingAnalyzer` and NWB adapters; `SPLIT_UNIT` and
+  `CONTAMINATION_TUNING` detectors; curation-threshold multiverse.
+* **v0.3**: multiverse across sorters (Kilosort 4, MountainSort 5, SpyKING CIRCUS 2) with
+  unit matching; single-file HTML report; provenance through
+  [daftar](https://pypi.org/project/daftar/).
+* **v0.4**: validation on public recordings (IBL, Allen, DANDI).
+
+## Family
+
+`ayar` sits with [daftar](https://pypi.org/project/daftar/) (provenance),
+[raftaar](https://pypi.org/project/raftaar/), [tarjuman](https://pypi.org/project/tarjuman/)
+(NeuroML to Jaxley), [miras](https://pypi.org/project/miras/) (study-design
+identifiability), [baghban](https://pypi.org/project/baghban/) (Bonsai workflow checks) and
+[ayna](https://pypi.org/project/ayna/) (are your inferred dynamics real?).
+
+## Author
+
+Aslan Satary Dizaji
+
+## License
+
+Apache 2.0

ayar-0.1.0/README.md

@@ -0,0 +1,190 @@
+# ayar
+
+**Assay your spike-sorted finding before you publish.**
+
+*Ayar* (Persian عیار, Turkish *ayar*, Azerbaijani *əyar*) is the fineness of gold: how much of
+it is the real thing. `ayar` asks the same question of a result built on sorted spikes:
+how much of it is neuroscience, and how much is the spike sorter?
+
+Tools such as SpikeInterface quality metrics, Bombcell and UnitRefine judge **units**.
+`ayar` judges the **finding**. It reads the output of any sorter (Kilosort, MountainSort,
+SpyKING CIRCUS, ... via Phy folders or a plain `.npz` bundle), flags sorting artifacts
+that can manufacture or hide an effect, then re-computes *your* analysis without the
+flagged units and tells you whether your numbers survive.
+
+`ayar` does not sort spikes and does not prove a finding is right. It tests whether
+specific, known artifacts can explain it.
+
+```
+pip install ayar
+```
+
+Python 3.10+, depends only on numpy and scipy, runs on a CPU.
+
+## Thirty seconds
+
+```bash
+ayar synth demo.npz                                  # a session with planted artifacts
+ayar scan demo.npz --finding ayar.examples:condition_contrast
+```
+
+```
+ERROR   DRIFT_CONFOUND  unit 16: rate follows detection loss (r=0.94; up to 50% of spikes
+                        below threshold in the worst window)
+ERROR   DUPLICATE_UNIT  95% of unit 41's spikes have a unit 17 spike within ±0.25 ms (229x
+                        chance): likely one neuron counted twice
+ERROR   OVERLAP_HOLE    units 42 and 43 fire within ±0.5 ms 13% as often as expected from
+                        the 2-10 ms flanks (37 vs 295, p=1.6e-80)
+...
+finding audit: ayar.examples:condition_contrast
+  number                 remove units flagged by    n    baseline   after   change  random-drop q95  verdict
+  frac_units_suppressed  DRIFT_CONFOUND             3        0.06       0     100%               6%  SENSITIVE
+  mean_contrast_hz       DUPLICATE_UNIT             2       2.277    2.05      10%               8%  ROBUST
+  ...
+  frac_units_suppressed: SENSITIVE - depends on the flagged units beyond what random removals explain
+```
+
+In this synthetic block-design session, every "suppressed" unit was a drifting unit losing
+spikes below threshold: there was no suppression at all.
+
+On your own data:
+
+```bash
+ayar scan path/to/kilosort_output/ --finding my_analysis.py:main --events events.npz
+```
+
+`ayar scan` exits with status 1 when it finds an error-level artifact or a finding that is
+SENSITIVE or FLIPPED, so it can gate a pipeline or CI job (`--fail-on warning|never`).
+
+## Your finding is a function
+
+A finding is any function of a bundle that returns a number or a dict of numbers: the
+numbers you would put in a paper.
+
+```python
+import ayar
+
+def main(bundle):
+    trains = bundle.trains()                     # {unit_id: spike times in s}
+    ev = bundle.events                           # ev.times, ev.labels
+    ...
+    return {"decoding_accuracy": acc, "frac_tuned": frac}
+
+report = ayar.scan(ayar.load("kilosort_output/"), finding=main)
+print(report)
+report.finding_verdicts        # {'decoding_accuracy': 'robust', 'frac_tuned': 'sensitive'}
+report.to_json()
+```
+
+For each detector that raised flags, `ayar` removes the implicated units (the duplicate
+copy, one unit of each hole pair, the drifting unit), recomputes the finding, and compares
+the change with **random-drop controls**: the same number of *unflagged* units removed at
+random, 20 times. A change counts against the artifact only if it is bigger than what
+dropping arbitrary units does.
+
+| verdict | meaning |
+|---|---|
+| `robust` | changes by less than 10 % |
+| `nonspecific` | changes, but no more than random removals (95th percentile) |
+| `shifted` | moves beyond random removals, by 10-25 % |
+| `sensitive` | moves beyond random removals, by 25 % or more |
+| `flipped` | changes sign, which random removals almost never do |
+| `failed` | your function raised an error on the reduced bundle |
+
+`ayar.examples` has two finding templates: `condition_contrast` (two-condition rate effect)
+and `zero_lag_synchrony` (synchrony between neighbouring units).
+
+## Detectors
+
+| code | needs | what it catches | why it matters |
+|---|---|---|---|
+| `DUPLICATE_UNIT` | spike times | two units sharing most spikes within ±0.25 ms, far above chance | one neuron counted twice: inflated N, double weight in averages and decoders, fake zero-lag correlation |
+| `OVERLAP_HOLE` | spike times (depths restrict to neighbours) | a gap near zero lag in a nearby pair's cross-correlogram, tested against the 2-10 ms flanks (Poisson, Bonferroni) | the sorter dropped overlapping spikes, or one neuron was split in two: synchrony is underestimated |
+| `DRIFT_CONFOUND` | amplitudes or depths | firing rate that tracks spike amplitude, depth, or estimated detection loss (amplitude-cutoff per window) over the session | apparent rate changes are spikes lost below threshold; raised to **error** when conditions are ordered in time, because the loss then looks like a condition effect |
+
+Each flag carries a code, a severity, the units, the evidence, why it matters and a fix.
+Every threshold is named and can be overridden (`--set dup_window_ms=0.4`, or
+`ayar.DEFAULTS.override(...)`). When a check cannot run, or runs on only some units,
+`ayar` says so under *not checked* instead of guessing.
+
+## Evidence tiers
+
+* **Tier 0: spike times.** Duplicate and overlap detectors run (all pairs, capped at 20,000
+  pairs).
+* **Tier 1: plus amplitudes and/or depths.** Pair tests are restricted to neighbouring units
+  (100 µm), and the drift detector runs.
+* **Tier 2: plus the raw recording** (hybrid ground truth, re-sorting). Planned.
+
+## Input: the bundle
+
+```python
+b = ayar.from_phy("kilosort4_output/")            # spike_times/clusters/amplitudes/positions, labels
+b = ayar.from_arrays(times_s, clusters, amplitudes=amps, spike_depths=depths,
+                     events=ayar.Events(trial_times, trial_labels))
+b.save("session.npz")                             # plain npz, readable with numpy alone
+```
+
+`from_phy` keeps units labelled `good` or `mua` (curated labels win over Kilosort's), reads
+depths from `spike_positions.npy` (Kilosort 4) or `cluster_info.tsv` (Phy), and takes the
+sample rate from `params.py`.
+
+## Self-validation
+
+`ayar validate` plants artifacts in synthetic sessions, together with **controls** that
+must not be flagged: pairs driven by genuine common input (a real cross-correlogram peak)
+and units whose true rate ramps over the session at constant amplitude. Then it scores
+every detector.
+
+```
+ayar validate --sessions 20 --seed 100
+
+  detector         planted  found  false ctrl alarms sensitivity precision
+  DUPLICATE_UNIT        40     40      0           0        1.00      1.00
+  OVERLAP_HOLE          40     40      0           0        1.00      1.00
+  DRIFT_CONFOUND        60     55      1           0        0.92      0.98
+
+  finding audit: in 19 session(s) drift manufactured 'suppressed' units; ayar called that
+  number SENSITIVE or FLIPPED in 19
+```
+
+These numbers are measured on ayar's own synthetic data, whose artifacts are cleaner than
+real ones. They show that the detectors do what they claim, not how often they fire on real
+recordings.
+
+## Limitations (v0.1)
+
+* Research prototype. Thresholds are calibrated on synthetic sessions, not yet on public
+  datasets with ground truth.
+* Drift is detected per unit from rate-amplitude-depth co-variation. Units with few spikes
+  (fewer than ~600) get only the weaker amplitude/depth trend test and are reported as
+  partly checked.
+* The finding audit removes units; it does not yet repair them (merge duplicates, restrict
+  drifting units to their stable epoch).
+* `OVERLAP_HOLE` cannot yet tell missed overlaps from a split unit; both are reported.
+* The audit calls your function about 20 times per detector. Use `--set audit_controls=0`
+  to skip controls when the function is slow.
+
+## Roadmap
+
+* **v0.2**: SpikeInterface `SortingAnalyzer` and NWB adapters; `SPLIT_UNIT` and
+  `CONTAMINATION_TUNING` detectors; curation-threshold multiverse.
+* **v0.3**: multiverse across sorters (Kilosort 4, MountainSort 5, SpyKING CIRCUS 2) with
+  unit matching; single-file HTML report; provenance through
+  [daftar](https://pypi.org/project/daftar/).
+* **v0.4**: validation on public recordings (IBL, Allen, DANDI).
+
+## Family
+
+`ayar` sits with [daftar](https://pypi.org/project/daftar/) (provenance),
+[raftaar](https://pypi.org/project/raftaar/), [tarjuman](https://pypi.org/project/tarjuman/)
+(NeuroML to Jaxley), [miras](https://pypi.org/project/miras/) (study-design
+identifiability), [baghban](https://pypi.org/project/baghban/) (Bonsai workflow checks) and
+[ayna](https://pypi.org/project/ayna/) (are your inferred dynamics real?).
+
+## Author
+
+Aslan Satary Dizaji
+
+## License
+
+Apache 2.0

ayar-0.1.0/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["hatchling>=1.18"]
+build-backend = "hatchling.build"
+
+[project]
+name = "ayar"
+version = "0.1.0"
+description = "Assay your spike-sorted finding before you publish: detect sorting artifacts and test whether your result survives them."
+readme = "README.md"
+license = "Apache-2.0"
+requires-python = ">=3.10"
+authors = [{ name = "Aslan Satary Dizaji", email = "aslansatary@gmail.com" }]
+keywords = [
+    "neuroscience", "electrophysiology", "spike sorting", "neuropixels",
+    "kilosort", "spikeinterface", "quality control", "reproducibility",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+]
+dependencies = ["numpy>=1.23", "scipy>=1.9"]
+
+[project.optional-dependencies]
+dev = ["pytest>=7"]
+
+[project.scripts]
+ayar = "ayar.cli:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ayar"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]