@platforma-open/milaboratories.3d-structure-prediction.software 1.0.3 → 1.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +348 -318
- package/CHANGELOG.md +22 -0
- package/Dockerfile +9 -0
- package/dist/artifacts/py-archive/archive.json +1 -1
- package/dist/artifacts/py-docker/docker_x64.json +1 -1
- package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
- package/package.json +1 -1
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.5.tgz +0 -0
- package/src_python/pdb_writer.py +6 -7
- package/src_python/run_immunebuilder.py +9 -15
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.3.tgz +0 -0
package/.turbo/turbo-build.log
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WARN Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.5 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
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#0 building with "default" instance using docker driver
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#10 19.94 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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#10 26.52 micromamba activate base
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#10 26.56 Cleaning index cache..
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#10 26.61 Cleaning lock files..
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#10 26.61 ───────────────────────────────────────────────────────────────
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#10 26.61 libgomp-15.2.0-he0feb66_19.conda 604kB
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#10 26.61 liblapack-3.11.0-7_h47877c9_openblas.conda 19kB
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#10 26.61 liblzma-5.8.3-hb03c661_0.conda 113kB
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#10 26.61 libnsl-2.0.1-hb9d3cd8_1.conda 34kB
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#10 26.61 libopenblas-0.3.33-pthreads_h94d23a6_0.conda 6MB
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#10 26.61 libsqlite-3.53.1-h0c1763c_0.conda 955kB
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#10 26.61 libstdcxx-15.2.0-h934c35e_19.conda 6MB
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#10 26.61 libstdcxx-ng-15.2.0-hdf11a46_19.conda 28kB
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#10 26.61 libuuid-2.42-h5347b49_0.conda 40kB
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#10 26.61 libxcrypt-4.4.36-hd590300_1.conda 100kB
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#10 26.61 libzlib-1.3.2-h25fd6f3_2.conda 64kB
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#10 26.61 mpi-1.0-openmpi.tar.bz2 4kB
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#10 26.61 ncurses-6.6-hdb14827_0.conda 919kB
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#10 26.61 numpy-2.4.3-py312h33ff503_0.conda 9MB
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#10 26.61 ocl-icd-2.3.3-hb9d3cd8_0.conda 107kB
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#10 26.61 ocl-icd-system-1.0.0-1.tar.bz2 4kB
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#10 26.61 opencl-headers-2025.06.13-hecca717_0.conda 56kB
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#10 26.61 openmm-8.3.1-py312h50c43f0_0.conda 13MB
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#10 26.61 openmpi-4.1.6-hc5af2df_101.conda 4MB
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#10 26.61 openssl-3.6.2-h35e630c_0.conda 3MB
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#10 26.61 packaging-26.2-pyhc364b38_0.conda 92kB
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#10 26.61 pdbfixer-1.12-pyhd8ed1ab_1.conda 546kB
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#10 26.61 pip-26.1.1-pyh8b19718_0.conda 1MB
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#10 26.61 python-3.12.10-h9e4cc4f_0_cpython.conda 31MB
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#10 26.61 python_abi-3.12-8_cp312.conda 7kB
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#10 26.61 readline-8.3-h853b02a_0.conda 345kB
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#10 26.61 scipy-1.17.1-py312h54fa4ab_0.conda 17MB
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#10 26.61 setuptools-82.0.1-pyh332efcf_0.conda 640kB
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#10 26.61 tk-8.6.13-noxft_h366c992_103.conda 3MB
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#10 26.61 tzdata-2025c-hc9c84f9_1.conda 119kB
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platforma-open.milaboratories.3d-structure-prediction.software.py-docker.7dca6668fe43: digest: sha256:4f2d5b7ba3a999e4d5fecccbc7f5e4aea1fb632f780b61ae50275645a1c63280 size: 4073
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package/CHANGELOG.md
CHANGED
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@@ -1,5 +1,27 @@
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# @platforma-open/milaboratories.3d-structure-prediction.software
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2
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## 1.0.5
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4
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5
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### Patch Changes
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+
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7
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- 4438d9d: Clarify NanoBodyBuilder2 usage in the settings panel: relabel the light chain dropdown as optional with a tooltip, and expand the mode-info alert to note that NanoBodyBuilder2 is camelid-VHH-trained, so for conventional heavy-only inputs (e.g. human bulk IGH-only) the produced structure has VHH-biased framework geometry.
|
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+
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9
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+
Drop the user-facing CPU and memory inputs (per-batch resources are fixed). Each prediction batch now requests 4 CPU cores and 4 GiB of memory.
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+
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+
Stop writing a wall-clock `prediction-date` REMARK into emitted PDBs. The timestamp made every PDB byte-different on every run, breaking the platforma backend's content-addressed caching — downstream nodes that consumed merged PDB ResourceMaps hit `CIDConflictError`. The other provenance REMARKs (immunebuilder version, torch seed, block version, numbering scheme) plus the seeded ensemble fully determine the prediction.
|
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+
|
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13
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+
Make the saved Python wrapper log byte-stable for identical inputs: drop the per-line UTC timestamp prefix and remove every wall-clock duration printed by `_log` (`predictor ready in Xs`, `predicted in Xs`, `elapsed=Xs`). The exec template saves stdout via `saveStdoutStream()` into the regular file output set, so its content hash flows into the resource CID; timestamped logs would re-introduce the same `CIDConflictError` failure mode as the PDB date.
|
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+
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+
Set `stepCache: 30 * times.minute` on the `processColumn` call so per-batch outputs stay reachable for the dedup/recovery path across project re-renders, matching the convention used by mixcr-clonotyping and miltenyi-tcr-bcr-clonotyping.
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Add the species selector (spec R44): `human | mouse | camelid | rat | rabbit | other`, default `human`. Species is included in the block subtitle (R56) alongside the engine. The mode-info banner now splits into two cases: when the species is `camelid` and the light chain is unset we treat it as a true VHH input (informational); for any other species combined with heavy-only input we surface a warning that NanoBodyBuilder2's framework geometry is biased away from conventional VH. A separate warning fires for ABodyBuilder2 runs on species outside the training distribution (anything other than human or mouse). Species is held in `BlockData` only — the workflow does not consume it yet, so switching species does not invalidate cached predictions. Upstream clonotyping blocks do not propagate species through PColumn specs today, so the selector is user-supplied; once upstream wires `pl7.app/species` onto the clonotype-axis domain, this block can pre-fill the default.
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## 1.0.4
|
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+
|
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### Patch Changes
|
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22
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+
|
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- 7a0fedd: Fix docker permissions
|
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|
## 1.0.3
|
|
4
26
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5
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|
### Patch Changes
|
package/Dockerfile
CHANGED
|
@@ -55,6 +55,15 @@ RUN pip install --no-cache-dir \
|
|
|
55
55
|
--extra-index-url https://download.pytorch.org/whl/cpu \
|
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-r /tmp/requirements.txt
|
|
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58
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+
# Pre-download model weights into the image. ImmuneBuilder otherwise writes
|
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|
+
# them into its own site-packages dir (/opt/conda/.../ImmuneBuilder/trained_model/)
|
|
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|
+
# on first use. That works locally because we're root, but cloud runtimes
|
|
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|
+
# run as a non-root user and hit PermissionError. Doing the download at
|
|
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|
+
# build time bakes ~400 MB of weights into the image and the runtime is
|
|
63
|
+
# read-only there, which is what we want.
|
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|
+
RUN python -c "from ImmuneBuilder import ABodyBuilder2, NanoBodyBuilder2; ABodyBuilder2(); NanoBodyBuilder2()" \
|
|
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|
+
&& chmod -R a+rX /opt/conda/lib/python3.12/site-packages/ImmuneBuilder/trained_model
|
|
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|
# Block sources (everything in src_python/).
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|
WORKDIR /app
|
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|
COPY . /app/
|
|
@@ -1 +1 @@
|
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1
|
-
{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.
|
|
1
|
+
{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.5.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.5.tgz"}
|
|
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|
|
|
1
|
-
{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
|
|
1
|
+
{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.7dca6668fe43","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
|
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1
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-
{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
|
|
1
|
+
{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.7dca6668fe43","entrypoint":["/usr/local/bin/_entrypoint.sh"],"cmd":["python","/app/run_immunebuilder.py"],"pkg":"/app"},"binary":{"type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.5.tgz","cmd":["python","{pkg}/run_immunebuilder.py"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-python-3:3.12.10-atls","type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.runenv-python-3.12.10-atls/main/1.2.7-{os}-{arch}.tgz","python-version":"3.12.10","envVars":[],"binDir":"bin"},"toolset":"pip","dependencies":{"requirements":"requirements.txt"}}}
|
package/package.json
CHANGED
package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.5.tgz
ADDED
|
Binary file
|
package/src_python/pdb_writer.py
CHANGED
|
@@ -3,9 +3,14 @@
|
|
|
3
3
|
ImmuneBuilder writes a standard PDB. Per spec R26/R28/R29 we need to:
|
|
4
4
|
- Clamp per-atom B-factor to [0.00, 99.99] to fit PDB `%6.2f` precision.
|
|
5
5
|
- Inject a TITLE line identifying the predictor.
|
|
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|
-
- Inject REMARK 99 PROVENANCE block (version, seed, block version
|
|
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|
+
- Inject REMARK 99 PROVENANCE block (version, seed, block version).
|
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7
7
|
- Inject REMARK 99 CDR* records with IMGT CDR ranges.
|
|
8
8
|
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|
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PDB content must be byte-stable for identical inputs so the platforma
|
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+
backend can cache and reuse downstream results — a wall-clock prediction
|
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|
+
timestamp would break every run's CID, so we omit it. The seed + version
|
|
12
|
+
fields plus the input sequences are sufficient to reproduce the prediction.
|
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|
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|
|
9
14
|
The cleanest approach is: let ImmuneBuilder write a temp PDB, then post-
|
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15
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process the lines — injecting REMARKs after TITLE and clamping B-factors on
|
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16
|
ATOM/HETATM lines in one pass.
|
|
@@ -13,7 +18,6 @@ ATOM/HETATM lines in one pass.
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from __future__ import annotations
|
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from datetime import datetime, timezone
|
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|
from pathlib import Path
|
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|
|
19
23
|
from numbering import IMGT_CDR_RANGES, cdr_ranges_in_pdb_notation
|
|
@@ -22,10 +26,6 @@ B_FACTOR_MIN = 0.00
|
|
|
22
26
|
B_FACTOR_MAX = 99.99
|
|
23
27
|
|
|
24
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|
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|
25
|
-
def _iso_now() -> str:
|
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|
-
return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
|
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|
-
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|
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|
def _clamp_b_factor(line: str) -> tuple[str, bool]:
|
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|
"""Clamp B-factor column on ATOM/HETATM lines. Returns (new_line, clamped)."""
|
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|
if not (line.startswith("ATOM") or line.startswith("HETATM")):
|
|
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|
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67
67
|
f"REMARK 99 PROVENANCE immunebuilder-version={immunebuilder_version}",
|
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|
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|
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|
-
f"REMARK 99 PROVENANCE prediction-date={_iso_now()}",
|
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|
f"REMARK 99 PROVENANCE numbering-scheme={numbering_scheme}",
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|
]
|
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@@ -51,22 +51,21 @@ import hashlib
|
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|
import json
|
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import os
|
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import sys
|
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import time
|
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|
import traceback
|
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56
55
|
from dataclasses import asdict, dataclass, field
|
|
57
|
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from datetime import datetime, timezone
|
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|
from pathlib import Path
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def _log(message: str) -> None:
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"""Line-buffered log entry to stderr.
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|
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|
-
|
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|
-
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|
+
The exec template saves the stdout stream as a regular file output, so
|
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63
|
+
the saved-file blob's content hash flows into the resource CID. Wall
|
|
64
|
+
clock timestamps and elapsed-time durations would make the saved log
|
|
65
|
+
byte-different on every run and break the platforma backend's
|
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|
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content-addressed caching. Keep log lines fully determined by inputs.
|
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67
|
"""
|
|
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|
-
|
|
69
|
-
print(f"[{ts}] {message}", file=sys.stderr, flush=True)
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|
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print(message, file=sys.stderr, flush=True)
|
|
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|
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|
from numbering import cdrh3_length as imgt_cdrh3_length
|
|
72
71
|
from numbering import extract_numbered_residues, vhh_hallmarks_present
|
|
@@ -407,9 +406,8 @@ def process_batch(
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|
407
406
|
_set_seed(seed)
|
|
408
407
|
if rows:
|
|
409
408
|
_log(f"loading {mode} ensemble (4 models)")
|
|
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|
-
predictor_t0 = time.time()
|
|
411
409
|
predictor = _load_predictor(mode)
|
|
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|
-
_log(
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|
+
_log("predictor ready")
|
|
413
411
|
else:
|
|
414
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|
predictor = None
|
|
415
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|
|
|
@@ -422,7 +420,6 @@ def process_batch(
|
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|
422
420
|
fail_count = 0
|
|
423
421
|
success_count = 0
|
|
424
422
|
cache_hits = 0
|
|
425
|
-
run_t0 = time.time()
|
|
426
423
|
|
|
427
424
|
for row_idx, row in enumerate(rows):
|
|
428
425
|
key = row.get(key_col, "")
|
|
@@ -455,12 +452,10 @@ def process_batch(
|
|
|
455
452
|
antibody = prediction_cache.get(cache_key)
|
|
456
453
|
if antibody is None:
|
|
457
454
|
try:
|
|
458
|
-
pred_t0 = time.time()
|
|
459
455
|
antibody = _predict_one(predictor, mode, sanitized.vh, sanitized.vl)
|
|
460
|
-
pred_dt = time.time() - pred_t0
|
|
461
456
|
prediction_cache[cache_key] = antibody
|
|
462
457
|
if (row_idx + 1) % log_every == 0 or row_idx == 0:
|
|
463
|
-
_log(f"{prefix} predicted
|
|
458
|
+
_log(f"{prefix} predicted")
|
|
464
459
|
except Exception as exc: # noqa: BLE001
|
|
465
460
|
fail_count += 1
|
|
466
461
|
_log(f"{prefix} FAIL ImmuneBuilder {type(exc).__name__}: {exc}")
|
|
@@ -563,11 +558,10 @@ def process_batch(
|
|
|
563
558
|
with open(summary_json, "w") as f:
|
|
564
559
|
json.dump(summary, f)
|
|
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560
|
|
|
566
|
-
elapsed = time.time() - run_t0 if rows else 0.0
|
|
567
561
|
_log(
|
|
568
562
|
f"done total={summary['totalRows']} succeeded={summary['succeeded']} "
|
|
569
563
|
f"failed={summary['failed']} confident={summary['confidentCount']} "
|
|
570
|
-
f"cache_hits={cache_hits}
|
|
564
|
+
f"cache_hits={cache_hits}"
|
|
571
565
|
)
|
|
572
566
|
if summary["byFailureReason"]:
|
|
573
567
|
for reason, n_fail in sorted(
|