Update requirements

Author: benjeffery

.github/workflows/tests.yml

@@ -53,7 +53,7 @@ jobs:
             /usr/share/miniconda/envs/anaconda-client-env
             ~/osx-conda
             ~/.profile
-          key: ${{ runner.os }}-${{ matrix.python}}-conda-v10-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
+          key: ${{ runner.os }}-${{ matrix.python}}-conda-v11-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
 
       - name: Install Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -97,10 +97,15 @@ jobs:
         run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
 
       - name: Install pip deps
-        if: steps.cache.outputs.cache-hit != 'true'
+        if: steps.cache.outputs.cache-hit != 'true' && matrix.python != 3.7
         shell: bash -l {0}
         run: pip install -r requirements/CI-tests-pip/requirements.txt
 
+      - name: Fix pandas on 3.7
+        if: steps.cache.outputs.cache-hit != 'true' && matrix.python == 3.7
+        shell: bash -l {0}
+        run: pip install -r requirements/CI-tests-pip/requirements3.7.txt
+
       - name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms
         if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest'
         run: |

evaluation.py

@@ -1484,7 +1484,8 @@ def run_ancestor_quality(args):
         c="Frequency",
         cmap="brg",
         s=2,
-        norm=NormalizeBandWidths(band_widths=freq_bins),
+        # FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
+        # norm=NormalizeBandWidths(band_widths=freq_bins),
     )
     ax.errorbar(
         x=data[x_col],
@@ -1577,7 +1578,8 @@ def run_ancestor_quality(args):
         c="Inferred time inaccuracy",
         cmap="BrBG",
         s=data.n_mismatches.values,
-        norm=MidpointNormalize(midpoint=0),
+        # FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
+        # norm=MidpointNormalize(midpoint=0),
     )
     ax.set(**ax_params)
     ax.legend(handles=legend_elements, title="# bad sites\nper ancestor")
@@ -1630,14 +1632,15 @@ def run_ancestor_quality(args):
     with warnings.catch_warnings():
         # matplotlib warns for nans in error bars
         warnings.simplefilter("ignore")
-        plt.errorbar(
-            g.sem().index,
-            g.mean().values,
-            yerr=g.sem().values,
-            marker="o",
-            ls="none",
-            ecolor="0.6",
-        )
+        # FIXME #669 error in matplotlib here
+        # plt.errorbar(
+        #     g.sem().index,
+        #     g.mean().values,
+        #     yerr=g.sem().values,
+        #     marker="o",
+        #     ls="none",
+        #     ecolor="0.6",
+        # )
     plt.ylabel(Inaccuracy_label)
     plt.xlabel("Frequency")
     plt.ylim(None, args.diff_y_lim)
@@ -1650,7 +1653,8 @@ def run_ancestor_quality(args):
         c="Frequency",
         cmap="brg",
         s=2,
-        norm=NormalizeBandWidths(band_widths=freq_bins),
+        # FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
+        # norm=NormalizeBandWidths(band_widths=freq_bins),
     )
     data = data.sort_values(by="Known time order")
     ax.errorbar(
@@ -1678,7 +1682,8 @@ def run_ancestor_quality(args):
         c="Frequency",
         cmap="brg",
         s=2,
-        norm=NormalizeBandWidths(band_widths=freq_bins),
+        # FIXME #669 pandas no longer (as of 1.3.0) supports passing "norm"
+        # norm=NormalizeBandWidths(band_widths=freq_bins),
     )
     ax.set(ylabel=Inaccuracy_label, xscale="log", ylim=(-0.01, 1), xlim=(1))
     save_figure(name_format.format(name))

requirements/CI-tests-complete/requirements.txt

@@ -1,20 +1,20 @@
-attrs==20.3.0
-codecov==2.1.10
+attrs==21.4.0
+codecov==2.1.12
 colorama==0.4.4
-daiquiri==3.0.0
-h5py==3.2.1
-humanize==3.5.0
-lmdb==1.1.1
+daiquiri==3.0.1
+h5py==3.6.0
+humanize==4.1.0
+lmdb==1.3.0
 matplotlib==3.4.1
 meson==0.56 # FIXME pinning meson for now, https://github.com/tskit-dev/tsinfer/issues/471
-msprime==1.0.1
-numpy==1.20.2
-pandas==1.2.4
-pytest==6.2.4
-pytest-cov==2.10.1
-pytest-xdist==2.2.1
-seaborn==0.11.1
-sortedcontainers==2.3.0
-tqdm==4.60.0
+msprime==1.1.1
+numpy==1.21.6
+pandas==1.2.5
+pytest==7.1.2
+pytest-cov==3.0.0
+pytest-xdist==2.5.0
+seaborn==0.11.2
+sortedcontainers==2.4.0
+tqdm==4.64.0
 tskit==0.4.1
 zarr==2.11.3

requirements/CI-tests-conda/requirements.txt

@@ -1,5 +1,5 @@
-lmdb==0.9.24
-msprime==1.0.2
-python-lmdb==0.96
-zarr==2.11.3
-h5py<3.4
+h5py==3.6.0
+lmdb==0.9.29
+msprime==1.1.1
+numcodecs==0.9.1
+python-lmdb==1.3.0

requirements/CI-tests-pip/requirements.txt

@@ -1,13 +1,14 @@
-attrs==21.2.0
+attrs==21.4.0
 colorama==0.4.4
 daiquiri==3.0.1
-humanize==3.12.0
-matplotlib==3.5.0
-numpy==1.21.4
-pandas==1.2.5
-pytest==6.2.5
-pytest-xdist==2.4.0
+humanize==4.1.0
+matplotlib==3.5.2
+numpy==1.21.6
+pandas==1.4.2
+pytest==7.1.2
+pytest-xdist==2.5.0
 seaborn==0.11.2
 sortedcontainers==2.4.0
-tqdm==4.62.3
+tqdm==4.64.0
 tskit==0.4.1
+zarr==2.11.3

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

@@ -0,0 +1,14 @@
+attrs==21.4.0
+colorama==0.4.4
+daiquiri==3.0.1
+humanize==4.1.0
+matplotlib==3.5.2
+numpy==1.21.6
+pandas==1.3.5
+pytest==7.1.2
+pytest-xdist==2.5.0
+seaborn==0.11.2
+sortedcontainers==2.4.0
+tqdm==4.64.0
+tskit==0.4.1
+zarr==2.11.3