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Add cluster_resolution_finder and cluster_decision_tree for help deciding the proper resolution #3532

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b37477c
Add cluster_decision_tree and cluster_resolution_finder with tests
joe-jhou2 Mar 27, 2025
88306f6
Fix formatting issue
joe-jhou2 Mar 27, 2025
4cd3134
igraph install
joe-jhou2 Mar 27, 2025
0b2f126
formatting fix
joe-jhou2 Mar 27, 2025
6126013
Restructure cluster_resolution_finder and cluster_decision_tree to fo…
joe-jhou2 Mar 28, 2025
12cf89d
Register mpl_image_compare marker in pyproject.toml for pytest-mpl
joe-jhou2 Mar 28, 2025
25569b2
Merge branch 'main' into feature-cluster-decision-tree
joe-jhou2 Mar 28, 2025
1aadcc4
comment out one test
joe-jhou2 Mar 28, 2025
69b16c7
suppress print statements during testing
joe-jhou2 Mar 28, 2025
70dea35
suppress print statements during testing
joe-jhou2 Mar 28, 2025
8e25dfc
Merge branch 'main' into feature-cluster-decision-tree
joe-jhou2 Apr 2, 2025
c74cd1a
Fix the check-milestone workflow
joe-jhou2 Apr 3, 2025
a91e9f1
Fix the check-milestone workflow
joe-jhou2 Apr 3, 2025
bc5dd9f
restore check-milestone workflow
joe-jhou2 Apr 3, 2025
f595f5d
Merge branch 'main' into feature-cluster-decision-tree
flying-sheep Apr 11, 2025
e422ad1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 11, 2025
5932717
WIP: save changes before pulling
joe-jhou2 Apr 14, 2025
d6d4e72
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 15, 2025
ce51530
fix ruff error
joe-jhou2 Apr 15, 2025
c084342
fix ruff error
joe-jhou2 Apr 15, 2025
9d6dd21
Merge branch 'main' into feature-cluster-decision-tree
joe-jhou2 Apr 15, 2025
6e19de7
refactror main function to class
joe-jhou2 Apr 17, 2025
3eb806a
Merge branch 'feature-cluster-decision-tree' of https://github.com/jo…
joe-jhou2 Apr 17, 2025
da8f6f4
Merge branch 'main' into feature-cluster-decision-tree
joe-jhou2 Apr 17, 2025
ac54dfd
refactror main function to class
joe-jhou2 Apr 17, 2025
0cffc68
refactror main function to class
joe-jhou2 Apr 17, 2025
44cc72f
Defer networkx import
flying-sheep Apr 22, 2025
34d9f1c
Merge branch 'main' into feature-cluster-decision-tree
joe-jhou2 Apr 22, 2025
e171c8c
Skip TC004 warning for now
joe-jhou2 Apr 22, 2025
a0ff151
Skip TC004 warning for now
joe-jhou2 Apr 22, 2025
202280e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 22, 2025
00e10c8
Skip TC004 warning for now
joe-jhou2 Apr 22, 2025
2d60321
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 22, 2025
01a1e87
modify seaborn import
joe-jhou2 Apr 22, 2025
20bf0a8
modify seaborn import
joe-jhou2 Apr 22, 2025
2644a42
Merge branch 'scverse:main' into feature-cluster-decision-tree
joe-jhou2 Apr 26, 2025
1f4c098
add verbose to find_cluster_resolution
joe-jhou2 Apr 26, 2025
e460214
Merge branch 'scverse:main' into feature-cluster-decision-tree
joe-jhou2 May 6, 2025
7ee7bac
Merge branch 'main' into feature-cluster-decision-tree
joe-jhou2 May 15, 2025
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8 changes: 4 additions & 4 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -64,19 +64,19 @@ jobs:

- name: Install dependencies
if: matrix.dependencies-version == null
run: uv pip install --system --compile "scanpy[dev,test-full] @ ."
run: uv pip install --system --compile "scanpy[dev,test-full,leiden] @ ."
- name: Install dependencies (no optional features)
if: matrix.dependencies-version == 'min-optional'
run: uv pip install --system --compile "scanpy[dev,test-min] @ ."
run: uv pip install --system --compile "scanpy[dev,test-min,leiden] @ ."
- name: Install dependencies (minimum versions)
if: matrix.dependencies-version == 'minimum'
run: |
uv pip install --system --compile tomli packaging
deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extra dev test)
deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extra dev test leiden)
uv pip install --system --compile $deps "scanpy @ ."
- name: Install dependencies (pre-release versions)
if: matrix.dependencies-version == 'pre-release'
run: uv pip install -v --system --compile --pre "scanpy[dev,test-full] @ ." "anndata[dev,test] @ git+https://github.com/scverse/anndata.git"
run: uv pip install -v --system --compile --pre "scanpy[dev,test-full,leiden] @ ." "anndata[dev,test] @ git+https://github.com/scverse/anndata.git"

- name: Run pytest
if: matrix.test-type == null
Expand Down
6 changes: 6 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,10 @@
/docs/api/generated
/docs/external/generated
/docs/jupyter_execute
cluster tree demo figure.pptx
mytest.py
_cluster_tree_standelone.py
expected.png

# tests
/*cache/
Expand Down Expand Up @@ -45,3 +49,5 @@ Thumbs.db
# asv benchmark files
/benchmarks/.asv
/benchmarks/data/
myenv/
test.py
1 change: 1 addition & 0 deletions .readthedocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,3 +23,4 @@ python:
- doc
- dev # for towncrier
- leiden
- pytest-mpl # image comparison
2 changes: 2 additions & 0 deletions src/scanpy/plotting/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
tracksplot,
violin,
)
from ._cluster_tree import cluster_decision_tree
from ._dotplot import DotPlot, dotplot
from ._matrixplot import MatrixPlot, matrixplot
from ._preprocessing import filter_genes_dispersion, highly_variable_genes
Expand Down Expand Up @@ -58,6 +59,7 @@
"DotPlot",
"MatrixPlot",
"StackedViolin",
"cluster_decision_tree",
"clustermap",
"correlation_matrix",
"dendrogram",
Expand Down
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