@pikaa-ai/pikaa 0.3.1 → 0.3.4

package/skills/lab-hardware-cad/references/labware-adapters.md

@@ -1,190 +0,0 @@
-# Labware adapters, holders, and racks
-
-Parts that receive standard consumables: microplates, cuvettes, tubes, slides, dishes.
-
-The governing principle: **where a published standard exists, design to the standard; where it
-does not, require a measurement.** Microplate footprints are standardised. Well geometry, skirt
-profiles, tube dimensions, and lid fits are not.
-
-Verified dimensions live in `assets/standards.json`. Query them rather than copying numbers:
-
-```bash
-python scripts/check.py standards --show slas-microplate-footprint
-```
-
-## Microplates (ANSI/SLAS 1-4)
-
-Four documents split the plate geometry. All are ANSI-approved and were reaffirmed in 2012.
-
-| Document | Governs | Key numbers |
-| --- | --- | --- |
-| ANSI/SLAS 1-2004 | Footprint | 127.76 x 85.48 mm ±0.25; corner radius 3.18 ±1.6 mm |
-| ANSI/SLAS 2-2004 | Height | 14.35 ±0.25 mm, resting plane to top of perimeter wells |
-| ANSI/SLAS 3-2004 | Bottom outside flange | Short 2.41, medium 6.10, tall 7.62 mm, each ±0.38 |
-| ANSI/SLAS 4-2004 | Well positions | 96-well: 9.0 mm pitch, A1 at 14.38 mm from left, 11.24 mm from top |
-
-### Designing a plate pocket
-
-Three traps, in the order people fall into them.
-
-**1. Design to maximum material, not to nominal.** A plate at the top of tolerance is
-127.76 + 0.25 = 128.01 mm. A pocket cut at 127.76 + clearance will jam on roughly half the plates
-you try. Compute:
-
-```python
-plate_l_mm = 127.76      # ANSI/SLAS 1-2004 nominal
-plate_tol_mm = 0.25      # ANSI/SLAS 1-2004
-fit_clearance_mm = 0.40  # per side; FDM, see fabrication-limits.md
-pocket_l_mm = plate_l_mm + plate_tol_mm + 2 * fit_clearance_mm   # 128.81
-```
-
-**2. The corner radius tolerance is enormous — and it bounds the pocket radius from above,
-not below.** 3.18 ±1.6 mm means a real plate corner is anywhere from 1.58 to 4.78 mm. Get the
-direction right: a plate corner is **convex**, a pocket fillet is **concave material bulging
-inward**, so a *sharp* internal pocket corner always clears a rounded plate — the unused corner is
-empty space. It is a pocket fillet *larger* than the plate's corner radius that binds: the bulge
-occupies space the plate needs. Sizing the fillet to the plate's maximum corner radius is
-therefore exactly backwards — it binds every plate except those at the top of the corner
-tolerance.
-
-The safe options, best first:
-
-- **Corner relief** (a small slot or bore cut past each corner) — always clears, prints and mills
-  cleanly, and is the standard fix.
-- **Fillet no larger than the plate's minimum corner radius** (1.58 mm for SLAS plates) — clears
-  every conforming plate in every position.
-- A larger fillet only if `R ≤ r_min + ~3.4 × per-side clearance` — the geometry only recovers the
-  intrusion when the plate stays roughly centred, so treat this as a last resort and say so.
-
-```python
-with BuildPart() as pocket:
-    # ... pocket geometry ...
-    # relief bores just outside each pocket corner: clears any conforming corner radius
-    with Locations(*corner_relief_centres()):
-        Hole(radius=2.0)
-```
-
-**3. Height depends on the flange, not just the plate.** ANSI/SLAS 3 standardises three flange
-heights. A carrier that grips the flange must be told which one. Ask; do not assume medium.
-
-### Well grid
-
-For a part that must reach individual wells — a magnet block, a lid with access holes, a light
-guide — lay out from the plate's outline corner, not from the plate centre:
-
-```python
-a1_x_mm, a1_y_mm, pitch_mm = 14.38, 11.24, 9.0   # ANSI/SLAS 4-2004, 96-well
-locations = [
-    (a1_x_mm + pitch_mm * col, a1_y_mm + pitch_mm * row)
-    for row in range(8) for col in range(12)
-]
-```
-
-The standard's positional tolerance is a **0.70 mm diameter zone** around each nominal centre, not
-a ±0.70 mm band. A feature that must clear every well needs at least 0.35 mm of radial margin on
-top of your own process tolerance.
-
-384-well pitch is 4.5 mm and 1536-well pitch is 2.25 mm. **The A1 offsets for those formats in
-`standards.json` are marked unverified** — they were derived, not read from the document. Read
-ANSI/SLAS 4-2004 before relying on them.
-
-### What the standards do not fix
-
-Well diameter, well depth, well bottom shape (flat, round, conical), skirt height, lid geometry,
-optical bottom thickness, and deep-well plate height. All vary by manufacturer and product line.
-If the part touches any of these, get the vendor drawing or measure it.
-
-## Cuvettes
-
-The standard macro cuvette is a convention rather than a published standard, but it is close to
-universal: **12.5 x 12.5 mm external, 45 mm tall, 1.25 mm wall, 10 mm optical path**.
-
-Design notes:
-
-- Holders should be generous or compliant. Because no document fixes the tolerance, a 0.1 mm
-  interference fit designed against nominal will fail on some suppliers' cuvettes.
-- Semi-micro and micro cuvettes keep the 12.5 mm external footprint but change internal geometry
-  and often height. A holder designed for the external footprint accommodates all of them; one
-  designed around the sample volume does not.
-- Cuvettes are usually held with a spring or leaf on one face so the two optical faces register
-  against fixed datums. Copy that: locate on two adjacent faces, preload from the opposite corner.
-  A four-sided pocket with clearance lets the cuvette rotate and shifts the path length.
-- **Never print the optical path.** Printed surfaces scatter. The cuvette provides the optical
-  faces; the holder provides position only, and must not obstruct the beam window.
-
-## Tubes
-
-Tube dimensions are **not standardised** and differ measurably between suppliers, and often
-between product lines from the same supplier. Approximate outside diameters near the tube rim:
-
-| Tube | Approximate OD | Note |
-| --- | --- | --- |
-| 0.2 mL PCR | 6 mm | Often supplied in strips or as a 96-format plate |
-| 1.5 mL microcentrifuge | 11 mm | Rim is wider than the body; the body tapers |
-| 2.0 mL microcentrifuge | 11 mm | Same rim as 1.5 mL, taller body |
-| 15 mL conical | 17 mm | Cap is wider than the tube |
-| 50 mL conical | 30 mm | Cap is wider than the tube |
-
-**Treat every number in this table as a starting point for a first article, not a design input.**
-Ask the user for the supplier and catalogue number, or ask them to measure with calipers. Then
-design a rack that holds the tube by the **rim or the cap**, which is dimensionally stable, rather
-than by the tapered body, which is not.
-
-For a rack, the useful pattern is a through-hole sized to the body plus clearance and a counterbore
-that catches the rim, so the tube hangs rather than bottoms out.
-
-## Microscope slides and coverslips
-
-Standard slide: **75 x 25 mm, 1.0 mm thick** (ISO 8037-1 covers slide dimensions; thickness classes
-vary, and 1.0-1.2 mm is typical). Coverslips are specified by thickness number, not dimension:
-#1 is roughly 0.13-0.17 mm and #1.5 roughly 0.16-0.19 mm.
-
-Objective working distance is unforgiving. A holder that adds even 0.2 mm under the slide can put
-the sample outside a high-NA objective's working distance. Design slide holders so the slide
-registers directly against the stage datum, with the holder clamping from above.
-
-## Petri dishes and stage inserts
-
-Standard dish outside diameters are approximately 35, 60, 90, and 100 mm, but the flange profile
-and lid fit vary. Dishes are also slightly out of round. Locate on three points rather than a
-continuous circular pocket: a three-point nest is insensitive to ovality, a close-fitting bore is
-not.
-
-For stage inserts, the interface that matters is the **microscope stage opening**, which is
-instrument-specific and must be measured. Many stages accept a standard SLAS-footprint insert;
-confirm before assuming it.
-
-## Checks to run
-
-Declare the pocket in the model's `interfaces()` and let the check read it:
-
-```bash
-python scripts/gen.py carrier_model.py --outdir out/
-python scripts/check.py interfaces out/carrier.manifest.json
-```
-
-**Do not point `check.py fit` at the carrier's STEP.** `fit` measures the outer bounding box, which
-for a carrier is the outside of its walls — 6 mm larger than the pocket here — so it fails against
-the plate footprint no matter how correct the pocket is. The dimension that matters is internal, so
-it has to be declared, not measured from the envelope.
-
-To check the number by hand instead:
-
-```bash
-python scripts/check.py fit --standard slas-microplate-footprint \
-  --intent envelope --clearance 0.8 --value footprint_length=128.81
-```
-
-`--intent envelope` checks one-sided against maximum material condition, and `--clearance` is the
-total intended clearance: 0.40 mm per side is 0.80 mm. Passing means the pocket is the size you
-intended, not that the plate fits — only a test print shows that.
-
-Then always run `snapshot.py` and confirm the pocket is on the face you meant.
-
-## Sources
-
-- ANSI/SLAS 1-2004 (R2012) Footprint Dimensions — <https://www.slas.org/SLAS/assets/File/public/standards/ANSI_SLAS_1-2004_FootprintDimensions.pdf>
-- ANSI/SLAS 2-2004 (R2012) Height Dimensions — <https://www.slas.org/SLAS/assets/File/public/standards/ANSI_SLAS_2-2004_HeightDimensions.pdf>
-- ANSI/SLAS 3-2004 (R2012) Bottom Outside Flange Dimensions — <https://www.slas.org/SLAS/assets/File/public/standards/ANSI_SLAS_3-2004_BottomOutsideFlangeDimensions.pdf>
-- ANSI/SLAS 4-2004 (R2012) Well Positions — <https://www.slas.org/SLAS/assets/File/public/standards/ANSI_SLAS_4-2004_WellPositions.pdf>
-- SLAS microplate standards overview — <https://www.slas.org/education/ansi-slas-microplate-standards/>

package/skills/lab-hardware-cad/references/microfluidics.md

@@ -1,157 +0,0 @@
-# Microfluidic chips, molds, and flow cells
-
-Channel networks, soft-lithography molds, printed chips, gaskets, and manifolds.
-
-## First: decide what you are actually modelling
-
-This is the error that wastes the most time in microfluidic CAD. Three different objects get
-called "the chip":
-
-| Object | Channels are | Made by |
-| --- | --- | --- |
-| **Mold / master** | **Raised ridges** (positive relief) | Photolithography on a wafer, SLA print, or micromilling |
-| **Cast chip** | **Recessed grooves** (negative of the mold) | PDMS cast against the mold, then bonded to a substrate |
-| **Directly-fabricated chip** | **Recessed grooves or enclosed lumens** | Printed, milled, or laser-cut directly |
-
-A model that is correct as a chip is exactly wrong as a mold. Put the polarity in the module
-docstring and in a named parameter, and **verify it numerically, not by eye**: inverted polarity
-is invisible in the bounding box, the volume, and the validity check — and at typical channel
-scale (a 0.3 mm ridge on a 40+ mm part) it is invisible in an outline render too, because raised
-and recessed features draw the same edges. Declare it as geometry checks instead
-(`references/build123d-patterns.md`): a `material` region where the ridge must stand above the
-casting surface, and a `clear` region over the rest of that layer — a groove fails the first,
-an inverted full-area layer fails the second. For a one-off question,
-`check.py probe <step> --box ... --expect material` answers it without editing the model. State
-the measured relief height in the report. Use the snapshot for layout and connectivity, which
-it does show well.
-
-```python
-polarity = "mold"   # "mold" = raised ridges; "chip" = recessed grooves
-```
-
-If casting PDMS, the mold also needs a **surrounding wall or a casting frame** to contain the
-uncured polymer, and enough flat land around the features for the cast part to release.
-
-## Channel cross-section and aspect ratio
-
-Channels are usually rectangular because that is what planar fabrication produces. Two failure
-modes bound the aspect ratio, and both are geometric:
-
-- **Roof sag / collapse** — a channel much wider than it is tall has an unsupported ceiling. In
-  PDMS the roof bows down and can stick to the floor. Commonly cited guidance keeps
-  **width : height below roughly 10 : 1**; wide channels need support pillars.
-- **Sidewall collapse** — a mold ridge much taller than it is wide falls over or fails to release.
-  Keep **height : width below roughly 10 : 1** on the mold.
-
-Treat both as rules of thumb, not guarantees: the real limits depend on PDMS mixing ratio, cure
-schedule, and applied pressure. For anything load-bearing or high-pressure, prototype.
-
-Also keep **channel-to-channel spacing at least the channel height**, so the wall between two
-channels does not deflect or leak, and leave a flat **bonding land** — typically 1 mm or more of
-uninterrupted flat surface around the network perimeter — for plasma or adhesive bonding.
-
-## Minimum features by process
-
-Achievable feature size drives the entire design, and the range across processes is three orders
-of magnitude. Confirm against your specific tool before committing.
-
-| Process | Practical minimum channel | Notes |
-| --- | --- | --- |
-| SU-8 photolithography | ~1-10 µm wide, 1-200+ µm tall | The reference process for soft lithography. Feature height is set by spin speed and resist grade. |
-| Two-photon / µSLA | ~10-50 µm | Small build volume, slow, expensive. |
-| Desktop SLA / DLP | ~200-500 µm | Uncured resin is very hard to clear from smaller lumens. Enclosed channels below ~0.5 mm frequently print blocked. |
-| Micromilling | ~100 µm | Set by end-mill diameter; depth limited by tool aspect ratio. Leaves tool marks that scatter light. |
-| FDM | Not suitable for sealed channels | Layer porosity leaks. Use only for holders and manifolds. |
-| Laser-cut film / gasket | ~200 µm | Excellent for stacked-layer devices and gaskets. |
-
-**Design enclosed printed channels for drainage.** Every lumen needs a path for uncured resin to
-escape, and orientation on the build plate determines whether it drains. If the user is printing,
-say which way up.
-
-## Ports and tubing
-
-The port is where most chips leak. Options, roughly in order of how common they are in a research
-lab:
-
-- **Direct tubing insertion** — a bore slightly *under* the tubing OD so the tubing seals by
-  interference. For 1/16 inch OD tubing (1.5875 mm), a bore around 1.5 mm in PDMS is typical. This
-  works in elastomer and fails in rigid printed parts, which crack instead of gripping.
-- **Luer taper** — the standard syringe interface, a **6% taper** (ISO 80369-7 supersedes the
-  legacy ISO 594 series for medical use). Convenient, low pressure only. If you model a Luer taper,
-  get the profile from the standard, not from memory.
-- **Threaded fittings** — flat-bottom **1/4-28 UNF** is the common lab standard for low-pressure
-  fluidics; **10-32 coned** is used at higher pressures. These need a tapped or heat-set-insert
-  port and a matching flat sealing face.
-- **Barbs** — reliable with soft tubing and a clamp, bulky.
-
-Whichever you choose, the sealing surface must be **flat and normal to the port axis**. A port
-face left at a printed layer angle will not seal.
-
-## Dead volume
-
-Dead volume dominates the response time of any perfusion or gradient device, and it is trivially
-computable, so compute it rather than estimating:
-
-```
-V = pi * r^2 * L                # round tubing / bore
-V = w * h * L                   # rectangular channel
-```
-
-Report the volume of every connecting bore alongside the channel network volume. A 20 mm long
-1 mm bore holds ~15.7 µL, which is often larger than the entire channel network it feeds.
-
-## Flow regime sanity check
-
-Microfluidic flow is almost always laminar, but state it rather than assuming:
-
-```
-Re = rho * v * D_h / mu
-D_h = 2 * w * h / (w + h)       # hydraulic diameter, rectangular channel
-```
-
-For water in a 100 µm channel at 1 mm/s, Re is of order 0.1 — deeply laminar, so mixing is
-diffusive only. If the design depends on mixing, it needs a mixer geometry (serpentine,
-herringbone, or split-and-recombine); relying on turbulence will not work at these scales.
-
-Pressure drop for a rectangular channel scales steeply with the smaller dimension. **Halving
-channel height raises pressure drop by roughly an order of magnitude.** Check that the intended
-pump or syringe can actually deliver it before finalising the cross-section.
-
-## Material and optical constraints
-
-- **PDMS** absorbs small hydrophobic molecules and is gas-permeable. Both are sometimes features
-  (oxygenation in organ-on-chip) and sometimes fatal to an assay (drug studies).
-- **SLA resins** are frequently cytotoxic uncured and often still after a nominal cure. For cell
-  work, require post-cure plus a documented biocompatibility check, or use a different process.
-  See `references/fabrication-limits.md`.
-- **Autofluorescence** matters for any fluorescence readout. Most printed resins autofluoresce
-  strongly. Image through glass or a thin COC/COP film, not through printed material.
-- **Optical path**: printed and milled surfaces scatter. Any imaging window should be a bonded
-  coverslip or film, and the model must specify its thickness so the objective working distance
-  works out.
-
-## Checks to run
-
-```bash
-python scripts/gen.py chip_model.py --outdir out/
-python scripts/check.py facts out/chip.step
-python scripts/snapshot.py out/chip.step --out out/chip.png
-```
-
-`facts` gives the volume; compare it against your hand-computed channel volume as an independent
-check that the network is actually open and connected. A network modelled as a solid rather than a
-cavity shows up immediately as a volume far larger than expected.
-
-Then read the snapshot and confirm, explicitly:
-
-1. **Polarity** — ridges for a mold, grooves for a chip.
-2. Every port lands on the channel it should, and passes fully through to the surface.
-3. The bonding land is continuous around the network.
-4. No channel has been closed off or consumed by a fillet.
-
-## Sources
-
-- ISO 80369-7 (Luer connectors for intravascular applications) supersedes the ISO 594 series.
-  Obtain the taper profile from the standard itself.
-- Aspect-ratio and spacing guidance here is standard soft-lithography practice; the numerical
-  limits are rules of thumb and depend on material and process. Prototype before committing.

package/skills/lab-hardware-cad/references/optomechanics.md

@@ -1,148 +0,0 @@
-# Optomechanical mounts and breadboard hardware
-
-Parts that bolt to an optical table, join a cage system, hold an optic or a sample in a beam path,
-or carry a camera or objective.
-
-Verified dimensions are in `assets/standards.json`:
-
-```bash
-python scripts/check.py standards --show optical-breadboard-metric
-python scripts/check.py standards --show cage-system-30mm
-python scripts/check.py standards --show sm1-lens-tube-thread
-```
-
-## Ask which system before you model anything
-
-**Metric and imperial optical hardware are not interchangeable, and the difference is small enough
-to look like a rounding error and large enough to prevent assembly.**
-
-| | Metric | Imperial |
-| --- | --- | --- |
-| Grid pitch | 25.0 mm | 25.4 mm (1 inch) |
-| Tapped hole | M6 x 1.0 | 1/4-20 UNC |
-| Typical border | 12.5 mm | 12.7 mm |
-
-Over a four-hole span the grids differ by **1.6 mm** — far more than any clearance hole absorbs.
-There is no way to infer which the user has from the request. Ask. If the answer is unavailable,
-model the mounting features as **slots along the bolt line** rather than round holes, which
-tolerates both, and say that is what you did and why.
-
-## Mounting to the table
-
-- Use **clearance holes, not tapped holes**, in the part. The table is tapped; the part is
-  clearanced. For M6 use 6.6 mm (normal fit) in a printed part rather than 6.4 mm — printed holes
-  come out undersize.
-- **Counterbore for the screw head** if the part surface must stay clear: roughly 11 mm diameter
-  for an M6 socket head cap screw, 11.2 mm for 1/4-20.
-- **Never rely on more than two holes to locate a part.** Grid tolerance plus print tolerance means
-  a rigid four-hole pattern will bind. Round hole + slot is the standard fix: one hole locates, the
-  slot takes up the error.
-- Printed parts are compliant. For anything where pointing stability matters, a printed mount is a
-  prototyping aid, not a final part — thermal drift and creep in polymer are large compared with
-  optical alignment tolerances. Say so when recommending one.
-
-## Posts and pedestals
-
-Common conventions, which vary by vendor — **confirm against the catalogue before use**:
-
-- Imperial posts are Ø1/2 inch (12.7 mm), typically tapped 8-32 at one end with a 1/4-20 stud or
-  clearance at the other.
-- Metric posts are Ø12 mm, typically tapped M4 with an M6 interface to the table.
-- A post-holder plus post is height-adjustable but adds a compliant joint; a pedestal or a
-  solid machined riser is stiffer.
-
-**Beam height** is a project-wide constant, not a per-part choice. Every mount on the table must
-put its optic at the same height. Common conventions are 3 inches (76.2 mm) or 100 mm, but this is
-a lab-by-lab choice. Ask for the number, define it once as `beam_height_mm`, and derive every
-mount's optic centre from it.
-
-## 30 mm cage system
-
-The dominant convention for small free-space assemblies:
-
-- **Rod spacing 30.0 mm** on a square, centred on the optical axis.
-- **Rods Ø6 mm** (ER series).
-- Standard cage plates are 0.35 inch (8.9 mm) thick.
-
-For a custom cage plate: place four bores on a 30 mm square, put the aperture at the **centroid**
-of those four bores, and bore them for a free-sliding fit **at your process's clearance**
-(fabrication-limits.md): about 6.2 mm CNC, 6.4 mm SLA, 6.8 mm FDM. 6.1 mm is a reamed-metal
-number — printed bores come out undersize, and four bores on a common square over-constrain each
-other, so tighter is not better here. A cage plate that binds on the rods is worse than useless
-because it transmits stress into the whole assembly.
-
-Cage plates stack along the rods, so a custom plate's thickness directly consumes optical path
-length. Budget it.
-
-## Lens tube threads (SM series)
-
-**SM1 is a 1.035 inch-40 thread**, which holds Ø1 inch (25.4 mm) optics. That is a **0.635 mm
-pitch**.
-
-**Do not print SM threads.** A 0.635 mm pitch is at or below the practical resolution of FDM and
-marginal on desktop SLA; a printed SM1 thread will either not engage or will gall and shed
-particles into the beam path. Instead:
-
-- bore a clearance hole and use a purchased SM1 adapter or retaining ring, or
-- design for a threaded metal insert, or
-- clamp the optic directly with a retaining flange and screws.
-
-If the design truly requires a printed thread, say explicitly that it needs test printing and is
-likely to fail.
-
-## Holding an optic
-
-- **Never clamp an optic on its clear aperture.** Contact only the outer annulus of the face or the
-  edge. Define `clear_aperture_mm` as a named parameter and confirm in the snapshot that nothing
-  intrudes on it.
-- Three-point contact is kinematically correct and does not deform the optic. A continuous
-  circular seat over-constrains it and induces stress birefringence, which matters for
-  polarisation work.
-- Leave clearance for thermal expansion. A metal-in-polymer mount that is a press fit at 20 °C can
-  crack or bind across a temperature swing.
-- Retaining forces should be light and distributed. A single set screw pressing on glass is a way
-  to chip glass.
-
-## Stray light and scatter
-
-Geometry is not the whole design here, and a STEP file cannot show any of this:
-
-- Printed surfaces scatter strongly. Any surface that sees the beam should be baffled, angled away
-  from the optical axis, or treated.
-- **Black does not mean non-reflective.** Black resin and black filament are often quite specular.
-  Specify a genuinely absorbing surface treatment where it matters.
-- Thread and layer lines act as diffraction structures near a focus.
-- For fluorescence work, printed material near the sample can autofluoresce into the detection
-  path.
-
-Flag these to the user; do not silently assume a printed enclosure is light-tight.
-
-## Checks to run
-
-```bash
-python scripts/gen.py mount_model.py --outdir out/
-python scripts/check.py facts out/mount.step
-python scripts/check.py interfaces out/mount.manifest.json
-python scripts/snapshot.py out/mount.step --out out/mount.png
-```
-
-Declare the grid pitch, rod spacing, and bore diameters in the model's `interfaces()` against
-`optical-breadboard-metric`, `optical-breadboard-imperial`, or `cage-system-30mm`, so the check
-catches a 25.0-for-25.4 substitution rather than leaving it to a reader.
-
-There is still **no automatic bolt-pattern check** — the interface check compares dimensions, not
-hole positions. Compute the pattern in the model from a named `grid_pitch_mm` constant, and confirm
-in the snapshot that:
-
-1. All mounting holes are present and pass fully through.
-2. The optic aperture is centred where you intended, and unobstructed.
-3. Counterbores are on the accessible face.
-4. Nothing intrudes into the clear aperture or the beam path.
-
-## Sources
-
-- Thorlabs imperial and metric threading — <https://www.thorlabs.com/imperial-and-metric-threading>
-- Thorlabs standard 30 mm cage plates — <https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_ID=2273>
-- Thorlabs SM1 lens tube compatible cage plates — <https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=4114>
-- Post dimensions, beam heights, and vendor-specific thread conventions in this file are common
-  conventions rather than published standards. Confirm against the catalogue.

package/skills/lab-hardware-cad/references/validation.md

@@ -1,132 +0,0 @@
-# Pre-fabrication validation checklist
-
-Work through this before telling a user a part is ready to fabricate. Each item names the failure
-it catches, because a checklist without consequences gets skipped.
-
-## 1. Provenance
-
-- [ ] The STEP was produced by `gen.py` from the current model source.
-      *Catches: a stale artifact that no longer matches the code you just edited.*
-- [ ] A `*.manifest.json` exists alongside it, and its `source.sha256` matches the model file.
-      *Catches: silently editing an exported STEP, which makes the design unreproducible.*
-- [ ] The manifest's `interfaces` block lists every dimension a bundled standard covers, and its
-      values are the ones the model computed after any `--param` override. Empty is correct only
-      when nothing on the part mates with a bundled standard — and then every interface dimension
-      is named as unchecked in the report instead.
-      *Catches: a static `INTERFACES` list frozen at import, recording pre-override numbers; and
-      an interface that silently escaped checking.*
-- [ ] Every parameter in the model is named with units.
-      *Catches: the bare `12.7` nobody can later identify as half an inch.*
-
-```bash
-python scripts/gen.py part_model.py --outdir out/
-```
-
-## 2. Geometry is sound
-
-- [ ] `is_valid` is true.
-      *Catches: self-intersecting or non-manifold solids that slicers and CAM silently mangle.*
-- [ ] `solid_count` is what you expect — usually 1.
-      *Catches: a boolean that failed and left two disjoint lumps, or a feature floating free of
-      the body.*
-- [ ] Volume is plausible for the part's size and wall thickness.
-      *Catches: a cavity modelled solid, or a subtract that did nothing.*
-- [ ] Every geometric requirement in the request is declared in `checks()` and passes — clear
-      regions for what must pass through or fit in, material regions for what must remain,
-      bbox bounds for stated size limits.
-      *Catches: a recess that swallowed its screw seat, a pocket the mating part cannot enter,
-      a beam corridor with a wall in it, a feature a fillet silently ate — all invisible to
-      `is_valid` and the bounding box.*
-
-```bash
-python scripts/check.py facts out/part.step
-python scripts/check.py geometry out/part.step --model part_model.py
-```
-
-## 3. Interfaces
-
-- [ ] Every interface dimension has a written source: a standard ID, a vendor drawing, or a user
-      measurement. **None came from memory.**
-      *Catches: the single most expensive failure mode in this skill.*
-- [ ] Every interface covered by a standard is declared in the model's `interfaces()` and passes
-      `check.py interfaces`.
-      *Catches: an interface nobody checked because the outer bounding box could not see it.*
-- [ ] Features that receive a standardised component use `intent: "envelope"`.
-      *Catches: a pocket sized to nominal, which fits only the smaller half of conforming parts.*
-- [ ] Any standard entry marked `verified: false` was confirmed against the primary document, or
-      the user was told it is unconfirmed.
-      *Catches: propagating a derived number as if it were read from the standard.*
-- [ ] Metric vs imperial is confirmed where both exist, and no expression mixes them.
-      *Catches: the 25.0 vs 25.4 mm grid error, which accumulates to 1.6 mm over four holes.*
-- [ ] Interfaces not covered by any bundled standard — a vendor drawing, a measurement — were
-      reported to the user as unchecked, with the number and its source.
-      *Catches: a silent gap where the automatic check simply had nothing to say.*
-
-```bash
-python scripts/check.py interfaces out/part.manifest.json
-
-# one dimension by hand, when it is not declared in the model
-python scripts/check.py fit --standard <id> --intent envelope --clearance <mm> --value <dim>=<mm>
-```
-
-## 4. Fits and assembly
-
-- [ ] Every mating dimension has a deliberate clearance chosen for the process.
-      *Catches: nominal-to-nominal fits, which do not assemble.*
-- [ ] Multi-part assemblies were checked for interference.
-      *Catches: parts that overlap in CAD and therefore cannot exist together.*
-- [ ] Rigid multi-hole mounting patterns have at least one slot.
-      *Catches: a four-hole bolt pattern binding on accumulated tolerance.*
-
-```bash
-python scripts/check.py clearance out/a.step out/b.step --min 0.3
-```
-
-## 5. Manufacturability
-
-- [ ] Minimum wall and feature sizes are within the chosen process (`fabrication-limits.md`).
-- [ ] Print or machining orientation is stated, and load runs along layers, not across them.
-- [ ] Threads use inserts or captive nuts rather than printed threads, unless coarse.
-- [ ] Enclosed cavities have a drain path for resin, and support-free access where possible.
-- [ ] Milled internal corners have relief for the tool radius.
-
-## 6. Material
-
-- [ ] Material is compatible with the **cleaning agent**, not only the sample.
-      *Catches: acrylic crazing on 70% ethanol; PLA distorting in an autoclave.*
-- [ ] Sterilisation method is stated and the material actually survives it.
-- [ ] Anything contacting cells, tissue, or animals has a justified material, or contact is
-      designed out.
-      *Catches: assuming a printed resin part is cell-safe.*
-- [ ] Optical requirements — autofluorescence, scatter, transmission — are addressed if the part is
-      near a beam or a detector.
-
-## 7. Visual review — mandatory
-
-- [ ] A snapshot was rendered **and read** after the most recent generation.
-- [ ] Confirmed in the image: features on the intended faces; correct mold/chip polarity; every
-      port, bore, and boss present, inside the body, and passing through; nothing consumed by a
-      fillet; clear apertures unobstructed.
-
-```bash
-python scripts/snapshot.py out/part.step --out out/part.png
-```
-
-**This step is never waived by the numeric checks passing.** `is_valid: true` with a correct
-bounding box is fully consistent with a pocket cut on the wrong face or an inverted mold. Those
-errors are obvious in the picture and invisible in the numbers.
-
-## 8. Report
-
-Give the user, explicitly:
-
-1. Process and material, and why.
-2. Every interface dimension with its source and tolerance.
-3. Clearances chosen, and the fit class they came from.
-4. What the snapshot showed — described, not merely "a snapshot was generated".
-5. Every check that did not pass, and every dimension you could not verify.
-6. A recommendation to print a test coupon of the critical interface before committing to the full
-   part, whenever the design depends on a fit.
-
-State the unverified items plainly. A part list with one honest "this dimension needs
-confirmation" is far more useful than a confident one that is silently wrong.