Code

Miscellaneous#266

Code

Merged

thalassemia merged 54 commits intomasterCovertLab/vEcoli:masterfrom tweaksCovertLab/vEcoli:tweaksCopy head branch name to clipboardDec 12, 2024

+4,392-1,159

Commits

Commits on Dec 3, 2024

• Use all available Sherlock partitions

  thalassemia

  committed
  85081c2

• Try different lineage seed for rich media Jenkins test

  thalassemia

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  92cfb5f

• Go back to running ParCa as separate SLURM job

  thalassemia

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  5cc766d

• Honor lineage seed setting

  thalassemia

  committed
  5152889

Commits on Dec 4, 2024

• Automatic unique index generation

  thalassemia

  committed
  a1662b0

• Remove full process parallelization because it is currently not practical

  thalassemia

  committed
  bb278a1

Commits on Dec 5, 2024

• Convert unique molecules back to normal Numpy arrays for JSON

  thalassemia

  committed
  a8156b3

• Fix mypy errors

  thalassemia

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  62b17e1

• Clarify unique indices and fix chromosome segment unique indices

  thalassemia

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  5d48139

• Fit RNA deg Km with minimization

  thalassemia

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  75d1499

Commits on Dec 6, 2024

• 64-bit Jax and sweet spot minimization tolerance

  thalassemia

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  7b068a7

Commits on Dec 7, 2024

• Start setting up uv install

  thalassemia

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  42b296d

• Use uv everywhere, including docs

  thalassemia

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  26e3179

• Use uv for container images and remove hvplot dependency

  thalassemia

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  b724113

• Replace Jax with lightweight Autograd

  thalassemia

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  9c786d6

• Try Debian image with uv

  thalassemia

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  a6ffd1c

• Add project dir for Singularity image

  thalassemia

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  f9962a0

• Install git and use gcc

  thalassemia

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  17dcd91

• Add temporary flag while waiting for stochastic-arrow 1.1.0

  thalassemia

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  4265a8a

• No persistent cache on Cloud Build

  thalassemia

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  1cbe75a

• Clarify ortools constraint

  thalassemia

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  7cbf34e

• No cache for WCM Docker build

  thalassemia

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  cc0dfd4

• Use gcc for WCM image

  thalassemia

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  ae08c46

• Fix Altair plot syntax

  thalassemia

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  5b7365c

• Fix fold change plot

  thalassemia

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  60987a4

• WCM image should use non-editable install

  thalassemia

  committed
  1d7ecc5

• Make container build scripts sh compliant

  Show description for 8586f58
  thalassemia

  committed
  8586f58

• Remove requirements.txt now that we use uv

  thalassemia

  committed
  a7bb125

• Use Python 3.12 Debian slim base image

  thalassemia

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  d098ed0

• Fix publish dir substitution

  thalassemia

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  ada3416

• Strip container image of unnecessary files

  thalassemia

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  6274a3c

• Add procps to container images

  thalassemia

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  289ab2e

• Fix gcloud build substitution

  thalassemia

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  62e4b58

• Try Kaniko cache

  thalassemia

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  f527fc5

• Remove data dir from package installation

  thalassemia

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  e79bc23

• Move murein strand length distribution to flat files

  thalassemia

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  6e809a2

• Try editable install to fix cython modules

  thalassemia

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  3621487

• Move tetracycline gene FC to flat

  thalassemia

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  c476fa1

• Fix publishDir substitution

  thalassemia

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  ff6db2e

• Activate Python virtual environment in Singularity containers

  thalassemia

  committed
  9426bc8

• Clarify C compilers

  thalassemia

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  19ea32b

• Force uv to install in container venv

  thalassemia

  committed
  c268a23

Commits on Dec 8, 2024

• Unique indices should be unique between molecule types as well

  thalassemia

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  b766b20

• Add temporary flag to GHA jobs while waiting for stochastic-arrow release

  thalassemia

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  2b95c00

• Add dev dependencies for QA tests

  thalassemia

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  5226b8b

• Remove redundant data

  thalassemia

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  2308bdf

• Fix CI tests

  thalassemia

  committed
  e28883a

• Use cast to fix type check

  thalassemia

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  053d03c

• Set writable flag after converting to MetadataArray

  thalassemia

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  7c2ff81

• Handle unique molecules with zero count

  thalassemia

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  e759f3d

• Use official uv GitHub action

  thalassemia

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  daf8283

Commits on Dec 9, 2024

• Fix pytests

  thalassemia

  committed
  01d3620

Commits on Dec 12, 2024

• Regenerate unique indices after merging partial and full mRNA arrays

  thalassemia

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  158711a

• Update to latest stochastic-arrow

  thalassemia

  committed
  563235c