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docs: compare gene selection among model configurations #596

Merged
merged 133 commits into from
Aug 8, 2024
Merged

docs: compare gene selection among model configurations #596

merged 133 commits into from
Aug 8, 2024
+2,437 −863

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@cameronraysmith cameronraysmith commented Jul 30, 2024 •
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@cameronraysmith
deps(pyproject): reenable expression
d46ec34 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(poetry): sync lock
654c1de 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(requirements): sync
a7fdbe1 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(conda): sync
376af9c 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith cameronraysmith self-assigned this Jul 30, 2024
@cameronraysmith cameronraysmith added the documentation Improvements or additions to documentation label Jul 30, 2024
@cameronraysmith cameronraysmith added this to the 0.3.x milestone Jul 30, 2024
@cameronraysmith
fix(nbs): use subdirectory for pancreas tutorial
94427a8 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): add gitignore
b87f977 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
feat(nbs): initialize downsampled pancreas tutorial
f7a0006 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): sync freeze
76fba9a 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(io): allow specification of a download filename prefix
d0d5439 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
feat(io): add cluster module
b98ca30 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
feat(nbs): add support for model comparison to pancreas notebook
7cb5f77 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): sync freeze
6d05f85 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
test(io): add test for cluster module
88796a8 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(io): add doctest for get_remote_task_results
f4d8e7f 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(nix): add workflows to check groups
be3645e 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(src): lint
96365ee 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(nbs): separate references to preprocessing and results
afc6bc9 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(nbs): add stub for preprocessing notebook
cf23251 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
refactor(nbs): migrate results notebook to subdir
f48ab6c 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
refactor(tests): mirror package folder structure
ca44535 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(bazel): update test module paths
675955c 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): sync freeze
87b1bab 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(make): run slow tests with test-cov-xml target
bc58fed 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(tasks): download_dataset accepts Path type
846d5a7 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
test(tasks): add package fixtures
78c70a7 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(tasks): declare skip preprocess doctest once
49be02f 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
test(tasks): add slow call to preprocess function
057333f 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(workflows): bump summarize cache to 2024.8.5.2
a674c7a 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(plots): ensure data is a dense array before flattening
feaa936 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
docs(tutorials): add more detailed gene selection data
bf8304f 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): sync freeze
8909cc3 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
feat(plots): add option to plot log spliced data to rainbow plot
6226003 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(plots): default to highest and lowest shared time correlation gen…
d5aae5c 
…es in summary plot

Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(plots): use cividis in plot posterior time
68c90ef 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(workflows): bump summarize cache to 2024.8.5.3
f01c6dc 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(nbs): add parameter posterior estimates to pancreas results
65246de 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): sync freeze
ca3751e 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(plots): enable offset parameters in posterior distribution plots
fe25b4c 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(tasks): remove unused t0 from model1 posterior samples
583f786 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(workflows): bump summarize cache to 2024.8.5.4
1750a74 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(plots): make parameter names an argument of posterior plot function
c2c35f5 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
fix(tasks): remove ad hoc modification of posterior samples
7738f5c 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith
chore(nbs): sync freeze
fb7b840 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith cameronraysmith added skip-ci Skip CI workflow and removed execute-workflow Control workflow execution on PRs dev-mode Do not rebuild images and use branch name instead of git short SHA for image tags labels Aug 8, 2024
@cameronraysmith
chore(version): 0.3.0b2
bcc26ac 
Signed-off-by: Cameron Smith <[email protected]>
@cameronraysmith cameronraysmith removed the skip-ci Skip CI workflow label Aug 8, 2024
@cameronraysmith cameronraysmith marked this pull request as ready for review August 8, 2024 18:13
@cameronraysmith cameronraysmith requested a review from a team as a code owner August 8, 2024 18:13
@cameronraysmith cameronraysmith merged commit bcc26ac into beta Aug 8, 2024
22 checks passed
@cameronraysmith cameronraysmith deleted the 595-gsmc branch August 8, 2024 18:25
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