Improvements to snakemake containerization - #309

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cailmdaley wants to merge 45 commits into

fix/300-cluster-snakemake-run-fixes

Commits on Aug 27, 2026

Fixes from the snakemake inference run report (#300)

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f1210c2
workflow: profile-driven apptainer containerization (set A)

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workflow: profile-driven apptainer containerization (set B: image_sims)

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workflow: profile-driven apptainer containerization (set C: remaining rules + docs)

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99ca91c
workflow: fix script: directive under the profile-driven container

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workflow: remove last live apptainer-exec shell call + stale sweep-script docs
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profile: add --cleanenv to apptainer-args

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tests: adapt pure-E/B and glass-mock tests to the tomographic API

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54a9c09
docs: sweep comment bloat across the pivot diff

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f9b705b
image_sims: one image, drop dead SLURM env strip, im_mbias_config as script

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aaadd29
covariance: restore cosmocov_process.py as a containerized script: rule

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2176894
tests: container_smoke becomes a real pytest, out of the main workflow

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48c7720
workflow: locate shell-invoked scripts via workflow.source_path

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0ab121d
workflow: use script: for single-process rules, source_path only for MPI

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5b72876
papers/bmodes: delete the unblinding ceremony

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f08aca0
containers: run the CI-published image from one shared path

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c6162c8
deps: ship CosmoSIS in the image, drop the vestigial cosmology pin

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containers: pull the CI image by tag, park the MPI rule

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64e1ac2
tests: drop the glass map-path xfail, its condition is met

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docker: install liblapack-dev, pin MPIFC absolutely

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368153a
docker: point UV_PYTHON at the venv, not the base interpreter

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eb72b7e
workflow: run the launched checkout's sp_validation by default

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8de6ba3
profiles: add a machine-independent default, make candide the machine layer

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236a19a
presentation: containerize the two rules that ran bare python

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78ae806
image_sims: default sif to null and fall back to the workflow's image

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314fda3
containers: give every user their own image, driven by spv-container

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260e2e5
docs: tell the container story once, around the per-user image

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c4e198c
containers: add an opt-in writable sandbox, and one resolution order

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7b47b56
image: build the cosmosis-standard-library fork into the container

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5b9c4b9
docs: prune duplicated and historical comments

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f1325f0
simplify: collapse duplication added by this branch

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bf5722a
simplify: give the sweep drivers one shared preamble; fold a duplicated README section

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cd34415
image: actually build CSL — cosmosis-configure exits 0 under set -u without running make

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ba2fd7c
image: drop set -u in the CSL layer — the configure exports append to unset paths

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image: point limber's Makefile at Debian's GSL (GSL_INC/GSL_LIB)

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rebase onto develop: shed tomography-branch remnants

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docs: make spv-container the install story

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06ec1f3

Commits on Aug 31, 2026

CSL runtime coverage: import-test template modules; patch fork for scipy>=1.15; add fast-pt

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501ba28
ruff autofix (format + safe lint fixes)
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3f60137
Repoint CSL at the UNIONS-WL org fork; trim fast-pt annotation

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88f215e
ruff autofix (format + safe lint fixes)
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7b83dec
Merge remote-tracking branch 'origin/develop' into HEAD
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62e8dcb
lint: noqa E402 on the in-section container-smoke import
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ec5bcfd
Merge remote-tracking branch 'origin/develop' into HEAD
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3ebcaae
Drop CSL scipy workaround after fork merge
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b9993b8