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.

I added hatch to handle dynamic versioning:
https://github.com/pypa/hatch/tree/master/backend

it has support for uv. Let me know what you think!

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.

This file was moved to the notebooks. It likely got cached when I ported the helper functions into the utils. Preprocessing is not part of buscar.

There was a lot of moving parts when decoupling the notebooks and the buscar package. I am sorry.

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?

These were remnants of Buscar's initial Poetry setup, but I have since migrated to using uv. All should be supported by uv

Sounds good, thanks for the clarification!

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.

I still show tests are not passing. I followed the directions in the contributing file. Did I miss a step? If not, are additional changes needed to ensure this is working?

user@machine buscar: uv sync --frozen --group dev Audited 64 packages in 7ms user@machine buscar: uv run --frozen pytest ============================================================================================================ test session starts ============================================================================================================= platform darwin -- Python 3.13.5, pytest-9.0.3, pluggy-1.6.0 rootdir: /Users/buntend/Documents/work/buscar configfile: pyproject.toml testpaths: tests plugins: cov-7.1.0 collected 0 items / 3 errors =================================================================================================================== ERRORS =================================================================================================================== ___________________________________________________________________________________________________ ERROR collecting tests/test_checks.py ____________________________________________________________________________________________________ ImportError while importing test module '/Users/buntend/Documents/work/buscar/tests/test_checks.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../../.local/share/uv/python/cpython-3.13.5-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_checks.py:5: in <module> from buscar.checks import check_for_nans src/buscar/__init__.py:9: in <module> from buscar._data_utils import add_cell_id_hash as add_cell_id_hash E ModuleNotFoundError: No module named 'buscar._data_utils' ___________________________________________________________________________________________________ ERROR collecting tests/test_metrics.py ___________________________________________________________________________________________________ ImportError while importing test module '/Users/buntend/Documents/work/buscar/tests/test_metrics.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../../.local/share/uv/python/cpython-3.13.5-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_metrics.py:4: in <module> from buscar.metrics import calculate_buscar_scores, compute_earth_movers_distance src/buscar/__init__.py:9: in <module> from buscar._data_utils import add_cell_id_hash as add_cell_id_hash E ModuleNotFoundError: No module named 'buscar._data_utils' _________________________________________________________________________________________________ ERROR collecting tests/test_signatures.py __________________________________________________________________________________________________ ImportError while importing test module '/Users/buntend/Documents/work/buscar/tests/test_signatures.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../../.local/share/uv/python/cpython-3.13.5-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_signatures.py:4: in <module> from buscar.signatures import identify_signatures src/buscar/__init__.py:9: in <module> from buscar._data_utils import add_cell_id_hash as add_cell_id_hash E ModuleNotFoundError: No module named 'buscar._data_utils' ========================================================================================================== short test summary info =========================================================================================================== ERROR tests/test_checks.py ERROR tests/test_metrics.py ERROR tests/test_signatures.py !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!

Co-authored-by: Dave Bunten <ekgto445@gmail.com>

axiomcura · 2026-05-06T17:52:10Z

Hey @d33bs Thank you for your thorough review. It's ready for a second round. Hopefully I was able to answer and catch all your comments.

d33bs

Thanks for addressing some of the comments @axiomcura ! I am requesting changes again due to tests (CI within the context of this PR and local test failures) and a strong recommendation to include trusted publishing as part of the work in this PR (instead of a suggestion to manually upload builds).

d33bs · 2026-05-06T18:08:03Z

+Publish to PyPI after configuring a PyPI token:

 ```bash
-poetry install
+uv publish


I strongly urge removing this manual procedure from any guidance. It has has implicit security risks and generally might convey that the project is less mature or professional than it is. Trusted publishing is the recommended path for production-grade Python software and I highly recommend following this approach within the context of this PR (you're not far away from it). Concretely, this means adding another CI job definition following the guide here https://docs.pypi.org/trusted-publishers/using-a-publisher/ and configuring your PyPI account to receive the release on trigger from GitHub. Alongside this, you might consider adding more than one maintainer or the Way Lab group for access to the entry on PyPI (providing redundancy for access to the PyPI releases and avoiding a potential blocked future state).

d33bs · 2026-05-06T18:18:05Z

I still show tests are not passing. I followed the directions in the contributing file. Did I miss a step? If not, are additional changes needed to ensure this is working?

user@machine buscar: uv sync --frozen --group dev Audited 64 packages in 7ms user@machine buscar: uv run --frozen pytest ============================================================================================================ test session starts ============================================================================================================= platform darwin -- Python 3.13.5, pytest-9.0.3, pluggy-1.6.0 rootdir: /Users/buntend/Documents/work/buscar configfile: pyproject.toml testpaths: tests plugins: cov-7.1.0 collected 0 items / 3 errors =================================================================================================================== ERRORS =================================================================================================================== ___________________________________________________________________________________________________ ERROR collecting tests/test_checks.py ____________________________________________________________________________________________________ ImportError while importing test module '/Users/buntend/Documents/work/buscar/tests/test_checks.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../../.local/share/uv/python/cpython-3.13.5-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_checks.py:5: in <module> from buscar.checks import check_for_nans src/buscar/__init__.py:9: in <module> from buscar._data_utils import add_cell_id_hash as add_cell_id_hash E ModuleNotFoundError: No module named 'buscar._data_utils' ___________________________________________________________________________________________________ ERROR collecting tests/test_metrics.py ___________________________________________________________________________________________________ ImportError while importing test module '/Users/buntend/Documents/work/buscar/tests/test_metrics.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../../.local/share/uv/python/cpython-3.13.5-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_metrics.py:4: in <module> from buscar.metrics import calculate_buscar_scores, compute_earth_movers_distance src/buscar/__init__.py:9: in <module> from buscar._data_utils import add_cell_id_hash as add_cell_id_hash E ModuleNotFoundError: No module named 'buscar._data_utils' _________________________________________________________________________________________________ ERROR collecting tests/test_signatures.py __________________________________________________________________________________________________ ImportError while importing test module '/Users/buntend/Documents/work/buscar/tests/test_signatures.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: ../../../.local/share/uv/python/cpython-3.13.5-macos-aarch64-none/lib/python3.13/importlib/__init__.py:88: in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_signatures.py:4: in <module> from buscar.signatures import identify_signatures src/buscar/__init__.py:9: in <module> from buscar._data_utils import add_cell_id_hash as add_cell_id_hash E ModuleNotFoundError: No module named 'buscar._data_utils' ========================================================================================================== short test summary info =========================================================================================================== ERROR tests/test_checks.py ERROR tests/test_metrics.py ERROR tests/test_signatures.py !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 3 errors during collection !!!!

d33bs · 2026-05-06T18:38:15Z

+on:
+  push:
+    branches: [main]
+  pull_request:


This doesn't seem to be triggering for this PR. I'd expect tests to show as passing for this PR based on the implied configuration here. Consider adding the main branch here as a specifier to help encourage the execution within the context of this PR.

d33bs · 2026-05-06T18:56:36Z

+      - name: Set up uv
+        uses: astral-sh/setup-uv@v8.1.0
+
+      - name: Install dependencies
+        run: uv sync --group dev --frozen
+
+      - name: Run pre-commit (required)
+        run: uv run --frozen pre-commit run --all-files --show-diff-on-failure


Instead of using the dev environment for this could you leverage pre-commit-action to install pre-commit and run the checks? This might also free up the dependency within the pyproject.toml file.

d33bs · 2026-05-06T18:58:19Z

+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4


This and other actions are out of date (checkout is for example at v6). Consider setting up a dependabot configuration to help keep this updated automatically. See here for an example of what this might look like.

d33bs · 2026-05-06T19:00:29Z

+      - name: Upload coverage artifact
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+
+      - name: Upload HTML coverage artifact
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-html
+          path: htmlcov


What purpose do these files serve (do you need them)? If you don't need them, consider ditching these steps. Otherwise, consider indicating within the contributing guide what they're to be used for. You could also consider a service like Codecov to help track and communicate code coverage as you move forward on a PR to PR basis.

d33bs · 2026-05-06T19:07:33Z

-[tool.poetry]
+[dependency-groups]
+dev = [
+  "pre-commit>=4.2.0",


Rebumping this comment. Please see the comments in the CI yml configuration as well.

d33bs · 2026-05-06T19:09:00Z

Sounds good, thanks for the clarification!

d33bs · 2026-05-06T19:15:35Z

+        shell: bash
+        run: |
+          uv pip install --force-reinstall dist/*.whl
+          uv run --frozen python -c "import buscar; print(buscar.__name__)"


After this point in this job you could add additional steps to upload the package to PyPI automatically using trusted publishing.

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

View reviewed changes

axiomcura and others added 2 commits May 6, 2026 09:27

Update README.md

28a5238

Co-authored-by: Dave Bunten <ekgto445@gmail.com>

Update LICENSE

47489fe

Co-authored-by: Dave Bunten <ekgto445@gmail.com>

axiomcura mentioned this pull request May 6, 2026

Use trusted publishing instead of uv publishing #96

Open

axiomcura added 7 commits May 6, 2026 11:50

removed poetry deps and updated to uv

db4c396

updated docs and tests

5b97042

removed data_utils.py file

048a866

removed meta yaml file.

1ab6a47

removed test_data_utils.py file

ab6ca59

updated license

b45bf1f

added contributing md

83a554d

axiomcura added 4 commits May 6, 2026 11:51

updated readme and contributing

219e25c

updated license in pyproject.toml file

7ebedf0

updated ci

80d461d

added versioning

9f01593

d33bs requested changes May 6, 2026

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axiomcura commented May 6, 2026

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axiomcura commented Mar 22, 2026 •

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