Prepare Buscar for pip and conda packaging by axiomcura · Pull Request #87 · WayScience/buscar

axiomcura · 2026-03-22T16:44:37Z

This PR prepares Buscar for distribution through standard Python packaging workflows, with updates aimed at making the project ready for both pip/PyPI installation and conda-based installation through the existing recipe/meta.yaml recipe. It also refreshes the project documentation so users and contributors can clearly see package status, supported Python versions, test status, and coverage outputs.

In this PR:

Updated packaging metadata in pyproject.toml for pip-installable distribution.
Added and refreshed uv.lock for reproducible uv-managed environments.
Removed the old Poetry lockfile in favor of uv-based dependency locking.
Updated recipe/meta.yaml so the conda recipe matches the package dependencies and supported Python range.
Added README badges for DOI, tests, supported Python versions, and coverage artifacts.
Documented local development and coverage commands using uv.
Updated CI coverage reporting to generate XML and HTML reports.
Added CI artifact uploads for coverage reports.
Verified that the package builds into a source distribution and wheel.
Verified package metadata with twine check

This closes #78 and #88

review-notebook-app · 2026-03-22T16:44:43Z

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* removed cluster refinement module * removed heterogeneity * updated metrics * created buscar module (separated notebook utils and buscar software) * updated test module * updated imports to reflect module changs * ignore vscode cached files * updated metrics * Update notebooks/2.cfret-analysis/nbconverted/1.cfret-pilot-buscar-analysis.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/nbconverted/1.cfret-pilot-buscar-analysis.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update buscar/metrics.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/4.cpjump1-analysis/nbconverted/4.run_buscar_rankings_base_on_moa.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/nbconverted/1.cfret-pilot-buscar-analysis.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update buscar/metrics.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/1.compound-prioritization/nbconverted/4.measure-phenotypic-activity.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/4.cpjump1-analysis/nbconverted/3.calculate-on-off-scores.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * applied copilot's changes * update processing module * reran buscar on cfret data * reran nbconvert * removed pdf * update cpjump1 analysis module * updates * added mitocheck analysis module * added label shuffling method * mitocheck buscar ranking analysis * removed cpjump analysis folder, this should be in another PR * fixed bugs * fix bugs and updates * updated plots * fixes and updates --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* updated all plots * updated plots * name changes on axis update * update * Update notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/plots/nbconverted/3.cfret-signature-effect-size-vs-sig-plot.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/plots/nbconverted/1.on-and-off-pca-and-umap-plots.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update notebooks/2.cfret-analysis/plots/nbconverted/4.cfret-compound-scores-plot.r Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update r_buscar_env.yaml Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * updated plots and comments * update --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

d33bs

Great job! I left a few comments. I'm requesting changes because I'm concerned mostly about the environment management and how you're planning to publish to PyPI. Please don't hesitate to let me know if you have any questions.

d33bs · 2026-05-05T22:18:52Z

I suggest a follow up PR which focuses on the conda universe, abiding a separation of concerns. There could be, for instance, completely different needs with this.

d33bs · 2026-05-05T22:20:33Z

+
+[project]
 name = "buscar"
 version = "0.1.0"


Consider using a dynamic version so you don't need to use static references. This would free you up to use git tags for the versioning, making for a more flexible release process. Reference this file for an example of how to do this with poetry.

d33bs · 2026-05-05T22:21:09Z

+__all__ = [
+    "add_cell_id_hash",
+    "compute_earth_movers_distance",
+    "identify_signatures",
+    "score_compounds",
+]


Do you really need this block? Consider removing it.

d33bs · 2026-05-05T22:21:55Z

This looks like it's related to a change outside of just pip and conda. Consider moving this to another PR.

d33bs · 2026-05-05T22:27:05Z

+      - name: Run tests
+        if: matrix.os != 'ubuntu-latest' || matrix.python-version != '3.12'
+        run: poetry run pytest


Consider splitting tests from the build process, which is distinct from software testing. You could make the build a separate job which depends on the tests to succeed.

d33bs · 2026-05-05T22:35:11Z

This file looks important. What happened to it? Consider keeping it in place and focusing on only pip + conda installation for this PR.

d33bs · 2026-05-05T22:37:12Z

+
+about:
+  home: https://github.com/WayScience/buscar
+  summary: A framework for prioritizing compounds in high-content imaging screens using single-cell profiles.


This differs from the description in the pyproject file. Consider keeping this in alignment. Also, consider keeping this description in the github description for the repo (and keeping all 3 in alignment).

d33bs · 2026-05-05T22:39:07Z

This and other changes don't directly pertain to the pip and conda packaging focus, distracting from the goals. I suggest avoiding this pattern in the future, it complicates review, maintenance, and history for the project.

d33bs · 2026-05-05T22:42:43Z

Should this be a poetry lockfile instead of uv?

d33bs · 2026-05-05T22:44:03Z

When I checked out the code in this PR, installed, and ran tests I found there were failures: ERROR collecting tests/test_checks.py. I specifically used poetry, abiding the current pyproject.toml designations.

axiomcura added 6 commits March 6, 2026 15:00

init python packaging

ef546c3

file updates

89e106a

added code coverage

17ae544

updated packaging files

50e0f89

updated deps

413f05f

update deps

09cf3f5

axiomcura and others added 5 commits March 31, 2026 14:03

removed unwanted files/notebooks and updated tests.

fdeeb38

Merge remote-tracking branch 'origin/main' into buscar-pip-packaging

5e35efd

added uv and conda packaging

e74c9c0

axiomcura mentioned this pull request May 5, 2026

Parameters variable names for measure_phenotypic_activity() is very confusing #77

Closed

updated packaging and readme

c21f786

axiomcura marked this pull request as ready for review May 5, 2026 20:05

axiomcura requested review from d33bs May 5, 2026 20:18

axiomcura changed the title ~~Buscar pip packaging~~ Prepare Buscar for pip and conda packaging May 5, 2026

d33bs requested changes May 5, 2026

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Prepare Buscar for pip and conda packaging#87

Prepare Buscar for pip and conda packaging#87
axiomcura wants to merge 12 commits intoWayScience:mainfrom
axiomcura:buscar-pip-packaging

axiomcura commented Mar 22, 2026 •

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axiomcura commented Mar 22, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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axiomcura commented Mar 22, 2026 •

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