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7297532
cli and gui runs were not aligned.
odcambc Apr 9, 2026
4c7d5cf
shift to uv
odcambc Apr 9, 2026
086179c
update env docs
odcambc Apr 9, 2026
6fec9ad
let's split this out a little.
odcambc Apr 10, 2026
a504e63
Update and fix tests for architecture changes
odcambc May 20, 2026
829481d
Make devcontainer canonical
odcambc May 20, 2026
0606a85
Consolidate architecture tests under tests/unit/
odcambc May 20, 2026
cd0f5ad
Extract DIMPLE class + addgene into DIMPLE/core.py
odcambc May 21, 2026
8fff7b4
Complete DIMPLE.py module migration
odcambc May 21, 2026
c3f901f
Fix DIS sequences not being registered causing runs to crash
odcambc May 21, 2026
1dfeab9
Introduce the oligo Pool object (Pool migration, Phase 1)
odcambc May 21, 2026
6c77492
Rename OLS -> pool for vendor neutrality
odcambc May 21, 2026
5af82e2
Flip qc + fragment_layout config reads to pool.config (Pool Phase 2)
odcambc May 21, 2026
a1fc3ae
Flip orchestrator + primers + oligo_assembly to pool.config (Pool Pha…
odcambc May 21, 2026
77881b7
Flip core.py __init__ + breaksites to pool.config (Pool Phase 2 done)
odcambc May 21, 2026
22e7331
Convert addgene-caller tests to explicit config (Pool Phase 3)
odcambc May 21, 2026
0393925
Convert DIS test + runners to explicit config (Pool Phase 3)
odcambc May 21, 2026
7adc3fb
Delete config scaffolding: DIMPLE class is now a pure gene object (Po…
odcambc May 21, 2026
d1a76ca
Fix stale PRIMER_BUFFER_BASE comment (Pool Phase 3)
odcambc May 21, 2026
f6ac739
Devcontainer update
odcambc May 22, 2026
edbd0c0
pytest in vscode settings
odcambc May 22, 2026
c3be2ac
attributes not sent to runners
odcambc May 23, 2026
f40efee
env and gitingore tweak
odcambc May 24, 2026
56988a1
clean up unused/unimplemented code, catch a few bugs, cleanup unneede…
odcambc May 24, 2026
e97fcdb
update test info in readme
odcambc May 24, 2026
67d6578
refresh lockfile
odcambc May 24, 2026
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Original file line number Diff line number Diff line change
@@ -1,18 +1,15 @@
{
"name": "DIMPLE Python 3.12",
"image": "mcr.microsoft.com/devcontainers/python:3.12-bookworm",
// Installs DIMPLE + dev extras
"postCreateCommand": "pip install --upgrade pip && pip install -e '.[dev]'",
"customizations": {
"vscode": {
"extensions": [
"ms-python.python",
"ms-python.vscode-pylance",
"ms-toolsai.jupyter"
],
"settings": {
"python.testing.pytestEnabled": true,
"python.testing.pytestArgs": ["tests"]
}
]
}
},
"features": {
Expand Down
8 changes: 6 additions & 2 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,4 +1,6 @@
### Python ###
.venv/

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
Expand All @@ -21,7 +23,9 @@ ipython_config.py


### VisualStudioCode ###
.vscode/
# Use `.vscode/*`, NOT `.vscode/`: git never descends into an ignored
# *directory*, so with `.vscode/` the `!` un-ignore lines below would be dead.
# `.vscode/*` ignores the contents while still allowing specific files back in.
.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
Expand All @@ -36,4 +40,4 @@ ipython_config.py
# Virtual environments
.venv/
venv/
env/
env/
3 changes: 3 additions & 0 deletions .vscode/settings.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
{
"python.testing.pytestEnabled": true
}
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