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add tests for reading of legacy files (closes #92) (#168)
* add tests for reading of legacy files (closes #92) Reference files are generated with src/mudata/tests/reference.py. This is based on the mudata fixture in tests/conftest.py, but it had to be modified, since NumPy does not guarantee stability of its random number generator across versions, so this needs to be completely deterministic. * add GitHub action to automatically generate test files for each release
1 parent bbb98fe commit 44cd0e3

19 files changed

Lines changed: 581 additions & 3 deletions

‎.github/workflows/release.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -6,8 +6,14 @@ on:
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- "v?[0-9]+.[0-9]+.[0-9]+**"
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workflow_dispatch:
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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permissions:
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contents: read
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env:
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ref_name: ${{ github.ref_name }}
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jobs:
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# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
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release:
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name: Upload release to PyPI
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runs-on: ubuntu-latest
@@ -30,3 +36,89 @@ jobs:
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run: uv build
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- name: Publish package distributions to PyPI
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uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b # v1.14.0
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is-prerelease:
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name: Check if this is a pre-release
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runs-on: ubuntu-slim
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outputs:
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is_prerelease: ${{ steps.check_prerelease.outputs.is_prerelease }}
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steps:
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- name: Check if this is a pre-release
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id: check_prerelease
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run: |
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PRE=$(echo "$ref_name" | sed -E 's/^v[0-9]+\.[0-9]+\.[0-9]+(.+?)$/\1/' | wc -w)
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if [ $PRE = 0 ] ; then
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PRE=false
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else
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PRE=true
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fi
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echo "is_prerelease=$PRE" | tee $GITHUB_OUTPUT
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generate-test-data:
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name: Generate test files for backwards compatibility testing
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needs: is-prerelease
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if: ${{ needs.is-prerelease.outputs.is_prerelease == 'false' && github.event_name == 'push' && github.event.created && github.ref_type == 'tag' }}
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runs-on: ubuntu-slim
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env:
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data_path: ./tests/data/archives/${{ github.ref_name }}
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default_branch: ${{ github.event.repository.default_branch }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
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with:
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filter: blob:none
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fetch-depth: 0
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persist-credentials: true
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- name: Install uv
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uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
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with:
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enable-cache: false
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- name: Get environment
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# get the test environment with the oldest Python
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id: get-env
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run: |
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ENV=$(uvx hatch env show --json | jq -r '[to_entries[] | select(.key | startswith("hatch-test") and (contains("pre") | not))]
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| sort_by(.value.python)[0].key')
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echo "hatch_env=${ENV}" | tee $GITHUB_ENV
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- name: create hatch environment
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run: uvx hatch env create "$hatch_env"
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- name: generate output directory
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run: mkdir -p "$data_path"
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- name: generate files
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working-directory: ${{ env.data_path }}
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run: |
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uvx hatch run "$hatch_env":../../../../src/mudata/tests/reference.py
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uvx hatch run "$hatch_env":sh -c "uv pip freeze | uv pip compile - -o pylock.toml"
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- name: configure git
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run: |
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git config user.name github-actions
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git config user.email github-actions@github.com
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BRANCH=$(git branch --show-current)
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if [ ! "$BRANCH" ] ; then
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BRANCH=$(git branch -a --contains "$ref_name" | tail -n 1 | sed 's/^\s*remotes\/origin\///')
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fi
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echo branch=${BRANCH} | tee $GITHUB_ENV
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- name: commit and push
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if: ${{ env.branch != '' }}
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working-directory: ${{ env.data_path }}
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run: |
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git checkout "$branch"
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git add .
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git commit -m "add backwards compat test files for $ref_name"
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git push
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if [ "$branch" != "$default_branch" ] ; then
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git checkout "$default_branch"
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git pull
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git cherry-pick -x "$branch"
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git push
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fi
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- name: commit and push
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if: ${{ env.branch == '' }}
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working-directory: ${{ env.data_path }}
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run: |
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git checkout "$default_branch"
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git pull
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git add .
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git commit -m "add backwards compat test files for $ref_name"
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git push

‎pyproject.toml‎

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,15 @@ dev = [
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"pre-commit",
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"twine>=4.0.2",
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]
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test = [ "coverage>=7.10", "jsonschema", "mudata[io]", "packaging", "pytest", "referencing" ]
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test = [
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"coverage>=7.10",
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"fast-array-utils>=1.2.3", # for anndata.tests.helpers
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"jsonschema",
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"mudata[io]",
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"packaging",
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"pytest",
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"referencing"
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]
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doc = [
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"anndata>=0.13",
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"docutils>=0.8,!=0.18.*,!=0.19.*",
@@ -139,6 +147,10 @@ filterwarnings = [
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"ignore:Writing zarr v2 data will no longer be the default",
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"ignore::scipy.sparse.SparseEfficiencyWarning",
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]
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markers = [
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"array_api: required to import anndata.tests.helpers.assert_equal",
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"gpu: required to import anndata.tests.helpers.assert_equal",
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]
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strict = true
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testpaths = [ "tests" ]
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‎src/mudata/_core/utils.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -123,7 +123,7 @@ def try_convert_series_to_numpy_dtype(col: pd.Series) -> pd.Series:
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col = col.astype(bool)
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case pd.core.arrays.integer.IntegerDtype(type=dtype) | pd.core.arrays.floating.FloatingDtype(type=dtype):
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col = col.astype(dtype)
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case pd.StringDtype():
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case pd.StringDtype() if pd.__version__ < "3":
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col = col.astype(object)
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return col
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‎src/mudata/tests/__init__.py‎

Whitespace-only changes.

‎src/mudata/tests/reference.py‎

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#!/usr/bin/env python3
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from typing import Literal
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import numpy as np
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import pandas as pd
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import zarr
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from anndata import AnnData
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from mudata import MuData, write_h5mu, write_zarr
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def generate_reference(axis: Literal[0, 1]) -> MuData:
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"""Generate a reference MuData object to test backwards compatibility."""
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mod1 = AnnData(
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np.arange(0, 200, 0.1, dtype=np.float32).reshape(-1, 20), obs=pd.DataFrame(index=[str(i) for i in range(100)])
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)
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mod2 = AnnData(
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np.arange(101, 3101, 1, dtype=np.float32).reshape(-1, 30),
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obs=pd.DataFrame(index=[str(i) for i in range(99, -1, -1)]),
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)
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mod1.var["assert-bool"] = True
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mod2.var["assert-bool"] = False
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mod1.var["assert-boolean-1"] = True
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mod2.var["assert-boolean-2"] = False
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mod1.raw = mod1[:, :10].copy()
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mods = {"mod2": mod2, "mod1": mod1}
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attr = "obs" if axis == 0 else "var"
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oattr = "var" if axis == 0 else "obs"
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for modname, mod in mods.items():
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mod.var["feature_type"] = modname
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setattr(mod, f"{attr}_names", [f"{attr}_{i}" for i in range(mod.shape[axis])])
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setattr(mod, f"{oattr}_names", [f"{modname}_{oattr}_{i}" for i in range(mod.shape[1 - axis])])
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mod1.obs.index.name = "fizz"
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mod2.var.index.name = "buzz"
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mdata = MuData(mods, axis=axis)
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mdata.obs["arange"] = np.arange(mdata.n_obs)
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return mdata
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if __name__ == "__main__":
44+
for axis in (0, 1):
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mdata = generate_reference(axis)
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write_h5mu(f"mdata_axis{axis}.h5mu", mdata, compression="gzip", compression_opts=9)
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write_zarr(zarr.storage.ZipStore(f"mdata_axis{axis}.zarr.zip", mode="w"), mdata)

‎tests/data/archives/v0.1.2/mdata_axis0.h5mu‎

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‎tests/data/archives/v0.1.2/mdata_axis0.zarr.zip‎

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‎tests/data/archives/v0.1.2/pylock.toml‎

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@@ -0,0 +1,112 @@
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‎tests/data/archives/v0.2.4/mdata_axis0.h5mu‎

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‎tests/data/archives/v0.2.4/mdata_axis0.zarr.zip‎

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