added EUST2, EUSTAPF#2
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Pull request overview
This PR adds support for two additional plate designs (EUST2 and EUSTAPF) by shipping their layout matrices as package resources and exposing them via the CLI’s --plate_design option. It also removes a set of legacy/duplicate matrix files from the repository-level config/ directory.
Changes:
- Add EUST2 and EUSTAPF drug / concentration / dilution matrices under
amygda/config/. - Register
EUST2andEUSTAPFas valid--plate_designchoices in the CLI. - Delete repository-level
config/*-matrix.txtfiles (now redundant withamygda/config/*resource loading).
Reviewed changes
Copilot reviewed 22 out of 22 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| config/UKMYC6-drug-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/UKMYC6-dilution-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/UKMYC6-conc-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/UKMYC5-drug-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/UKMYC5-dilution-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/UKMYC5-conc-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/GPALL1F-drug-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/GPALL1F-dilution-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/GPALL1F-conc-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/GB1ECSDP-drug-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/GB1ECSDP-dilution-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/GB1ECSDP-conc-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/CHNMCMM2-drug-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/CHNMCMM2-dilution-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| config/CHNMCMM2-conc-matrix.txt | Removed legacy repository-level matrix file (package uses amygda/config/*). |
| amygda/config/EUSTAPF-drug-matrix.txt | Adds EUSTAPF drug layout matrix as package resource. |
| amygda/config/EUSTAPF-dilution-matrix.txt | Adds EUSTAPF dilution index matrix as package resource. |
| amygda/config/EUSTAPF-conc-matrix.txt | Adds EUSTAPF concentration matrix as package resource. |
| amygda/config/EUST2-drug-matrix.txt | Adds EUST2 drug layout matrix as package resource. |
| amygda/config/EUST2-dilution-matrix.txt | Adds EUST2 dilution index matrix as package resource. |
| amygda/config/EUST2-conc-matrix.txt | Adds EUST2 concentration matrix as package resource. |
| amygda/cli.py | Exposes EUST2/EUSTAPF via CLI validation; minor formatting-only refactors. |
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| VALID_PLATE_DESIGNS = { | ||
| "UKMYC5", | ||
| "UKMYC6", | ||
| "GPALL1F", | ||
| "CHNMCMM2", | ||
| "GB1ECSDP", | ||
| "EUST2", | ||
| "EUSTAPF", | ||
| } |
Contributor
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Added a parametrized smoke test test_initialize_plate_layout_for_new_designs in commit eabc116. It covers both EUST2 (2 POS controls) and EUSTAPF (3 POS controls), asserting the 8×12 matrix shape and presence of POS in drug_names.
Agent-Logs-Url: https://github.com/fowler-lab/amygda/sessions/0408133a-838e-49c9-beff-fa7411dcfe12 Co-authored-by: philipwfowler <7090790+philipwfowler@users.noreply.github.com>
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