Update deps and fix evaluation.py for new pandas

Author: benjeffery

.github/workflows/tests.yml

@@ -65,7 +65,6 @@ jobs:
           channels: conda-forge
           channel-priority: strict
           auto-update-conda: true
-          use-only-tar-bz2: true
 
       - name: Fix windows .profile
         if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'

evaluation.py

@@ -270,7 +270,7 @@ def run_edges_performance(args):
 
     df = pd.DataFrame(results)
     df.length /= MB
-    dfg = df.groupby(df.length).mean()
+    dfg = df.groupby(df.length).mean(numeric_only=True)
     # print(dfg.estimated_anc_edges.describe())
     print(dfg)
 
@@ -595,7 +595,7 @@ def run_ancestor_properties(args):
     progress.close()
 
     df = pd.DataFrame(results)
-    dfg = df.groupby(df.length).mean()
+    dfg = df.groupby(df.length).mean(numeric_only=True)
     print(dfg)
 
     name_format = os.path.join(
@@ -1736,15 +1736,18 @@ def run_node_degree(args):
             path_compression=path_compression,
         )
         degree, depth = get_node_degree_by_depth(estimated_ancestors_ts)
-        df = df.append(
-            pd.DataFrame(
-                {
-                    "degree": degree,
-                    "depth": depth,
-                    "type": "estimated",
-                    "path_compression": path_compression,
-                }
-            )
+        df = pd.concat(
+            [
+                df,
+                pd.DataFrame(
+                    {
+                        "degree": degree,
+                        "depth": depth,
+                        "type": "estimated",
+                        "path_compression": path_compression,
+                    }
+                ),
+            ]
         )
         exact_ancestors_ts = run_infer(
             smc_ts,
@@ -1753,15 +1756,18 @@ def run_node_degree(args):
             path_compression=path_compression,
         )
         degree, depth = get_node_degree_by_depth(exact_ancestors_ts)
-        df = df.append(
-            pd.DataFrame(
-                {
-                    "degree": degree,
-                    "depth": depth,
-                    "type": "exact",
-                    "path_compression": path_compression,
-                }
-            )
+        df = pd.concat(
+            [
+                df,
+                pd.DataFrame(
+                    {
+                        "degree": degree,
+                        "depth": depth,
+                        "type": "exact",
+                        "path_compression": path_compression,
+                    }
+                ),
+            ]
         )
 
     name_format = os.path.join(

requirements/CI-tests-complete/requirements.txt

@@ -1,23 +1,15 @@
-attrs==21.4.0
-build==0.8.0
-codecov==2.1.12
-colorama==0.4.4
-daiquiri==3.0.1
-h5py==3.6.0
-humanize==4.1.0
-lmdb==1.3.0
-matplotlib==3.4.1
-meson==0.62.0 
-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
-setuptools==65.4.1
-sortedcontainers==2.4.0
-tqdm==4.64.0
-tskit==0.5.3
-twine==4.0.1
-zarr==2.11.3
+build==1.2.1
+colorama==0.4.6
+daiquiri==3.2.5.1
+humanize==4.10.0
+lmdb==1.5.1
+matplotlib==3.9.1
+meson==1.5.0
+msprime==1.3.2
+pytest==8.2.2
+pytest-cov==5.0.0
+seaborn==0.13.2
+sgkit[vcf]==0.9.0
+tskit==0.5.8
+tqdm==4.66.4
+twine==5.1.1

requirements/CI-tests-conda/requirements.txt

@@ -1,5 +1,10 @@
-h5py==3.6.0
-lmdb==0.9.29
-msprime==1.1.1
-numcodecs==0.9.1
-python-lmdb==1.3.0
+pytest==8.2.2
+msprime==1.3.2
+humanize==4.10.0
+python-lmdb==1.4.1
+tqdm==4.66.4
+daiquiri==3.0.0
+matplotlib==3.9.1
+seaborn==0.13.2
+colorama==0.4.6
+tskit==0.5.8