Skip to content

Commit

Permalink
Fix benchmarks and pandas compat (#1100)
Browse files Browse the repository at this point in the history
  • Loading branch information
flying-sheep authored Aug 21, 2023
1 parent 79e144f commit b19a5ea
Show file tree
Hide file tree
Showing 4 changed files with 24 additions and 15 deletions.
23 changes: 11 additions & 12 deletions .github/workflows/benchmark.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@ jobs:
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -e {0} # -e to fail on error
shell: bash -el {0} # -e to fail on error, -l for mamba

strategy:
fail-fast: false
matrix:
python: ["3.10"]
python: ["3.11"]
os: [ubuntu-latest]

env:
Expand All @@ -33,12 +33,15 @@ jobs:
if: ${{ github.ref_name != 'main' }}
# Errors on main branch

- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v4
- uses: mamba-org/setup-micromamba@v1
with:
python-version: ${{ matrix.python }}
cache: "pip"
cache-dependency-path: "**/pyproject.toml"
environment-name: asv
cache-environment: true
create-args: >-
python=3.11
asv
mamba
packaging
- name: Cache datasets
uses: actions/cache@v3
Expand All @@ -47,12 +50,8 @@ jobs:
~/.cache
key: benchmark-state-${{ hashFiles('benchmarks/**') }}

- name: Install dependencies
run: |
pip install asv
- name: Quick benchmark run
working-directory: ${{ env.ASV_DIR }}
run: |
asv machine --yes
asv run -qev --strict
asv run --quick --show-stderr --verbose
8 changes: 8 additions & 0 deletions anndata/tests/test_views.py
Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,14 @@ def test_views():
assert adata_subset.obs["foo"].tolist() == list(range(2))


def test_view_subset_shapes():
adata = gen_adata((20, 10), **GEN_ADATA_DASK_ARGS)

view = adata[:, ::2]
assert view.var.shape == (5, 8)
assert {k: v.shape[0] for k, v in view.varm.items()} == {k: 5 for k in view.varm}


def test_modify_view_component(matrix_type, mapping_name):
adata = ad.AnnData(
np.zeros((10, 10)),
Expand Down
4 changes: 2 additions & 2 deletions benchmarks/asv.conf.json
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
// If missing or the empty string, the tool will be automatically
// determined by looking for tools on the PATH environment
// variable.
"environment_type": "conda",
"environment_type": "mamba",

// timeout in seconds for installing any dependencies in environment
// defaults to 10 min
Expand Down Expand Up @@ -117,7 +117,7 @@
// // additional env for python2.7
// {"python": "2.7", "numpy": "1.8"},
// // additional env if run on windows+conda
// {"platform": "win32", "environment_type": "conda", "python": "2.7", "libpython": ""},
// {"platform": "win32", "environment_type": "mamba", "python": "2.7", "libpython": ""},
// ],

// The directory (relative to the current directory) that benchmarks are
Expand Down
4 changes: 3 additions & 1 deletion pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,9 @@ classifiers = [
"Topic :: Scientific/Engineering :: Visualization",
]
dependencies = [
"pandas>=1.1.1", # pandas <1.1.1 has pandas/issues/35446
# pandas <1.1.1 has pandas/issues/35446
# pandas 2.1.0rc0 has pandas/issues/54622
"pandas >=1.1.1, !=2.1.0rc0",
"numpy>=1.16.5", # required by pandas 1.x
"scipy>1.4",
"h5py>=3",
Expand Down

0 comments on commit b19a5ea

Please sign in to comment.