Auto-Organotypic 0.6.0__tar.gz

auto_organotypic-0.6.0/AGENTS.md

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+# Working in Auto-Organotypic
+
+## The analysis ships inside the package. Always.
+
+This package is downloaded by people who do not have this lab's Dropbox, its
+sibling projects, or its tuning folders. Anything the code does has to be *in
+the wheel*.
+
+That means, when you are asked to put an analysis into the pipeline:
+
+- **Write the code into a module of `src/auto_organotypic/`.** Do not import it from a
+  sibling project, do not read it off a path, do not load it from a file at run
+  time, and do not leave a comment saying where the real implementation lives.
+- **Declare every third-party import.** If it is reached on a default path, it
+  belongs in `[project] dependencies` — not in an extra. An extra is for a
+  capability a plain install does not need at all.
+- **Put constants, thresholds and accepted settings in the source**, not in a
+  JSON or CSV beside it. If data genuinely has to be a file, it goes inside the
+  package *and* into `[tool.setuptools.package-data]`, or it will be missing
+  from the wheel while working perfectly in your checkout.
+- A provenance comment naming where code came from is good. A provenance
+  comment standing *in place of* the code is the thing this rule exists for.
+
+`tests/test_self_contained.py` enforces all of the above, including by running
+the accepted outline in a subprocess with every undeclared module blocked. It
+was written after two real cases: an `import red_io` reaching for the tuning
+project, and scikit-image declared under an extra while the accepted outline
+needed it to draw a single slice. Both worked on the machine they were written
+on and on no other.
+
+## The outline is frozen
+
+`src/auto_organotypic/outline/` is accepted Round 6 attempt 7 of the Cry1-DIO-dLuc
+red-channel tuning project. Its numbers are not yours to tidy.
+
+Before and after **any** change under `outline/` or to `orientation.py`, run:
+
+    python -m pytest tests/test_automatic_scn_outline_parity.py
+
+Sixty tests, about three minutes, comparing generated labels against the frozen
+hand-checked evidence byte for byte. It needs that evidence: it is found at a
+sibling path automatically, or set `AUTO_ORGANOTYPIC_TUNING_ROOT`. **If it skips,
+you have no safety net — say so rather than proceeding quietly.**
+
+If you change a module under `outline/`, its recorded SHA256 in
+`outline/report.py` must be updated in the same commit, or `test_package.py`
+fails. That is deliberate: every report carries those hashes as the provenance
+of the mask it wrote.
+
+## Naming
+
+Modules are named for what they do, not for the project the code came from, and
+not with an `scn_` prefix — the package is already about the SCN. If a file does
+two jobs, it is two modules. This is why `_accepted_scn/scn_roi.py` and
+`_accepted_scn/red_measure.py` no longer exist.
+
+## Filenames written to disk are frozen even when code names change
+
+`batch_scn_outline_manifest.json` and `_automatic_scn_outline_report.json` keep
+their names through renames. Results already sitting in Dropbox are found by
+those names, and a resume is keyed on them.
+
+## A folder name distinguishes things that exist at the same time
+
+A stage key distinguishes things that replace each other. So a **trim** does not
+change any folder name — the window is a setting, like the channel, and the
+untrimmed result is the thing it replaces — and a **split** does, because both
+segments exist at once and would otherwise write to one folder. Segment folders
+are siblings, `outline/A1_baseline/`, never nested under the parent: split and
+unsplit recordings must sit at the same depth or every `traces/*/` glob breaks.
+
+The one exception to the rule above, and only because it is not a rename: a
+segment is a *new* file, and it is named for its folder —
+`segments/A1_baseline/A1_baseline.tif`, not the parent's stem with a suffix
+appended. Measured against a real output, the parent's stem is around 149
+characters and the path it leads to is already 17 characters past the 260
+Windows allows; appending reaches 33 over and naming the file for its folder
+comes in 65 under. This package survives being over the limit through
+`io.extended`; Fiji, Explorer, Excel and the sync client do not.
+
+## graphify
+
+This project has a graphify knowledge graph at graphify-out/.
+
+Rules:
+- Before answering architecture or codebase questions, read graphify-out/GRAPH_REPORT.md for god nodes and community structure
+- If graphify-out/wiki/index.md exists, navigate it instead of reading raw files
+- After modifying code files in this session, run `python3 -c "from graphify.watch import _rebuild_code; from pathlib import Path; _rebuild_code(Path('.'))"` to keep the graph current

auto_organotypic-0.6.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Jamie Malcolm, Brancaccio Lab, UK Dementia Research Institute
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

auto_organotypic-0.6.0/MANIFEST.in

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+# The parity evidence and the tests that read it travel in the sdist: without
+# them a download cannot check that the code in it is the accepted method.
+graft tests
+include LICENSE
+include AGENTS.md
+global-exclude __pycache__/*
+global-exclude *.py[cod]