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Merge pull request #668 from benjeffery/py3.10
Test and build wheels on 3.10
2 parents 28f0b25 + bddd327 commit 10d7274

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‎.github/workflows/docker/shared.env‎

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PYTHON_VERSIONS=(
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cp310-cp310
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cp39-cp39
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cp38-cp38
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cp37-cp37m

‎.github/workflows/tests.yml‎

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@@ -28,7 +28,7 @@ jobs:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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python: [ 3.7, 3.9 ]
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python: [ 3.7, "3.10" ]
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os: [ macos-latest, ubuntu-latest, windows-latest ]
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defaults:
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run:
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/usr/share/miniconda/envs/anaconda-client-env
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~/osx-conda
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~/.profile
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key: ${{ runner.os }}-${{ matrix.python}}-conda-v10-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
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key: ${{ runner.os }}-${{ matrix.python}}-conda-v11-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
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- name: Install Conda
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uses: conda-incubator/setup-miniconda@v2
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run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
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- name: Install pip deps
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if: steps.cache.outputs.cache-hit != 'true'
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if: steps.cache.outputs.cache-hit != 'true' && matrix.python != 3.7
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shell: bash -l {0}
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run: pip install -r requirements/CI-tests-pip/requirements.txt
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- name: Fix pandas on 3.7
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if: steps.cache.outputs.cache-hit != 'true' && matrix.python == 3.7
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shell: bash -l {0}
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run: pip install -r requirements/CI-tests-pip/requirements3.7.txt
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- name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms
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if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest'
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run: |

‎.github/workflows/wheels.yml‎

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runs-on: macos-latest
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strategy:
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matrix:
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python: [3.7, 3.8, 3.9]
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python: [3.7, 3.8, 3.9, "3.10"]
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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# runs-on: windows-latest
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# strategy:
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# matrix:
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# python: [3.7, 3.8, 3.9]
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# python: [3.7, 3.8, 3.9, "3.10"]
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# wordsize: [64]
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# steps:
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# - name: Checkout
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runs-on: macos-latest
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strategy:
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matrix:
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python: [3.7, 3.8, 3.9]
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python: [3.7, 3.8, 3.9, "3.10"]
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steps:
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- name: Download wheels
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uses: actions/download-artifact@v2
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# runs-on: windows-latest
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# strategy:
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# matrix:
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# python: [3.7, 3.8, 3.9]
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# python: [3.7, 3.8, 3.9, "3.10"]
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# wordsize: [64]
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# steps:
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# - name: Download wheels
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needs: ['manylinux']
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strategy:
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matrix:
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python: [3.7, 3.8, 3.9]
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python: [3.7, 3.8, 3.9, "3.10"]
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steps:
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- name: Download wheels
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uses: actions/download-artifact@v2

‎.mergify.yml‎

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@@ -5,11 +5,11 @@ queue_rules:
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- "#changes-requested-reviews-by=0"
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- status-success=Lint
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- status-success=Python (3.7, macos-latest)
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- status-success=Python (3.9, macos-latest)
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- status-success=Python (3.10, macos-latest)
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- status-success=Python (3.7, ubuntu-latest)
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- status-success=Python (3.9, ubuntu-latest)
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- status-success=Python (3.10, ubuntu-latest)
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- status-success=Python (3.7, windows-latest)
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- status-success=Python (3.9, windows-latest)
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- status-success=Python (3.10, windows-latest)
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- "status-success=ci/circleci: build"
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pull_request_rules:
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- label=AUTOMERGE-REQUESTED
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- status-success=Lint
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- status-success=Python (3.7, macos-latest)
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- status-success=Python (3.9, macos-latest)
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- status-success=Python (3.10, macos-latest)
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- status-success=Python (3.7, ubuntu-latest)
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- status-success=Python (3.9, ubuntu-latest)
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- status-success=Python (3.10, ubuntu-latest)
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- status-success=Python (3.7, windows-latest)
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- status-success=Python (3.9, windows-latest)
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- status-success=Python (3.10, windows-latest)
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- "status-success=ci/circleci: build"
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actions:
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queue:

‎evaluation.py‎

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@@ -1484,7 +1484,8 @@ def run_ancestor_quality(args):
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c="Frequency",
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cmap="brg",
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s=2,
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norm=NormalizeBandWidths(band_widths=freq_bins),
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# FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
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# norm=NormalizeBandWidths(band_widths=freq_bins),
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)
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ax.errorbar(
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x=data[x_col],
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c="Inferred time inaccuracy",
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cmap="BrBG",
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s=data.n_mismatches.values,
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norm=MidpointNormalize(midpoint=0),
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# FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
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# norm=MidpointNormalize(midpoint=0),
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)
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ax.set(**ax_params)
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ax.legend(handles=legend_elements, title="# bad sites\nper ancestor")
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with warnings.catch_warnings():
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# matplotlib warns for nans in error bars
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warnings.simplefilter("ignore")
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plt.errorbar(
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g.sem().index,
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g.mean().values,
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yerr=g.sem().values,
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marker="o",
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ls="none",
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ecolor="0.6",
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)
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# FIXME #669 error in matplotlib here
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# plt.errorbar(
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# g.sem().index,
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# g.mean().values,
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# yerr=g.sem().values,
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# marker="o",
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# ls="none",
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# ecolor="0.6",
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# )
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plt.ylabel(Inaccuracy_label)
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plt.xlabel("Frequency")
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plt.ylim(None, args.diff_y_lim)
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c="Frequency",
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cmap="brg",
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s=2,
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norm=NormalizeBandWidths(band_widths=freq_bins),
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# FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
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# norm=NormalizeBandWidths(band_widths=freq_bins),
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)
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data = data.sort_values(by="Known time order")
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ax.errorbar(
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c="Frequency",
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cmap="brg",
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s=2,
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norm=NormalizeBandWidths(band_widths=freq_bins),
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# FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
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# norm=NormalizeBandWidths(band_widths=freq_bins),
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)
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ax.set(ylabel=Inaccuracy_label, xscale="log", ylim=(-0.01, 1), xlim=(1))
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save_figure(name_format.format(name))

‎requirements/CI-tests-complete/requirements.txt‎

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attrs==20.3.0
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codecov==2.1.10
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attrs==21.4.0
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codecov==2.1.12
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colorama==0.4.4
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daiquiri==3.0.0
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h5py==3.2.1
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humanize==3.5.0
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lmdb==1.1.1
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daiquiri==3.0.1
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h5py==3.6.0
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humanize==4.1.0
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lmdb==1.3.0
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matplotlib==3.4.1
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meson==0.56 # FIXME pinning meson for now, https://github.com/tskit-dev/tsinfer/issues/471
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msprime==1.0.1
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numpy==1.20.2
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pandas==1.2.4
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pytest==6.2.4
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pytest-cov==2.10.1
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pytest-xdist==2.2.1
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seaborn==0.11.1
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sortedcontainers==2.3.0
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tqdm==4.60.0
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msprime==1.1.1
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numpy==1.21.6
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pandas==1.2.5
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pytest==7.1.2
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pytest-cov==3.0.0
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pytest-xdist==2.5.0
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seaborn==0.11.2
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sortedcontainers==2.4.0
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tqdm==4.64.0
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tskit==0.4.1
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zarr==2.11.3

‎requirements/CI-tests-conda/requirements.txt‎

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lmdb==0.9.24
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msprime==1.0.2
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python-lmdb==0.96
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zarr==2.11.3
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h5py<3.4
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h5py==3.6.0
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lmdb==0.9.29
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msprime==1.1.1
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numcodecs==0.9.1
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python-lmdb==1.3.0

‎requirements/CI-tests-pip/requirements.txt‎

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attrs==21.2.0
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attrs==21.4.0
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colorama==0.4.4
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daiquiri==3.0.1
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humanize==3.12.0
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matplotlib==3.5.0
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numpy==1.21.4
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pandas==1.2.5
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pytest==6.2.5
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pytest-xdist==2.4.0
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humanize==4.1.0
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matplotlib==3.5.2
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numpy==1.21.6
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pandas==1.4.2
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pytest==7.1.2
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pytest-xdist==2.5.0
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seaborn==0.11.2
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sortedcontainers==2.4.0
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tqdm==4.62.3
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tqdm==4.64.0
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tskit==0.4.1
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zarr==2.11.3

‎requirements/CI-tests-pip/requirements3.7.txt‎

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attrs==21.4.0
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colorama==0.4.4
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daiquiri==3.0.1
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humanize==4.1.0
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matplotlib==3.5.2
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numpy==1.21.6
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pandas==1.3.5
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pytest==7.1.2
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pytest-xdist==2.5.0
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seaborn==0.11.2
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sortedcontainers==2.4.0
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tqdm==4.64.0
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tskit==0.4.1
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zarr==2.11.3

‎setup.py‎

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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3 :: Only",
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"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
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"Development Status :: 3 - Alpha",

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