Deprecate Python2 CI coverage, fix Python3 CI

.github/workflows/build_and_upload_wheels.yaml

@@ -34,23 +34,6 @@ jobs:
         with:
           path: ./wheelhouse/*.whl
 
-  build_wheels_linux_27:
-    name: Build wheels for Python 2.7 on Linux
-    runs-on: ubuntu-20.04
-    steps:
-      - uses: actions/checkout@v3
-
-      # Neeed to use cibuildwheel 1 for Python 2.7
-      - uses: pypa/[email protected]
-        env:
-          CIBW_SKIP: pp*
-          CIBW_ARCHS_LINUX: auto
-          CIBW_PROJECT_REQUIRES_PYTHON: "~=2.7"
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: ./wheelhouse/*.whl
-
   # TODO: uncomment if/when we decide to build wheels for macOS
   # build_wheels_macos_36_37:
   #   name: Build wheels for Python 3.6 and 3.7 on macOS
@@ -84,22 +67,6 @@ jobs:
   #       with:
   #         path: ./wheelhouse/*.whl
 
-  # build_wheels_macos_27:
-  #   name: Build wheels for Python 2.7 on macOS
-  #   runs-on: macos-12
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     # Neeed to use cibuildwheel 1 for Python 2.7
-  #     - uses: pypa/[email protected]
-  #       env:
-  #         CIBW_SKIP: pp*
-  #         CIBW_BUILD: cp27-macosx_x86_64
-
-  #     - uses: actions/upload-artifact@v3
-  #       with:
-  #         path: ./wheelhouse/*.whl
-
   build_sdist:
     name: Build sdist
     runs-on: ubuntu-20.04
@@ -122,7 +89,6 @@ jobs:
       - build_wheels_linux_27
         # - build_wheels_macos_36_37
         # - build_wheels_macos_38_plus
-        # - build_wheels_macos_27
       - build_sdist
     runs-on: ubuntu-20.04
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
@@ -144,7 +110,6 @@ jobs:
       - build_wheels_linux_27
         # - build_wheels_macos_36_37
         # - build_wheels_macos_38_plus
-        # - build_wheels_macos_27
       - build_sdist
     runs-on: ubuntu-20.04
     if: github.event_name == 'release' && github.event.action == 'published'

.github/workflows/pip-install-tester.yaml

@@ -38,7 +38,6 @@ jobs:
         python -m pip install --upgrade pip pytest
 
     - name: Build Python 3 dependencies
-      if: ${{ matrix.python-version != 2.7 }}
       run: |
         python -m pip install tables
 

.github/workflows/unit-tests.yaml

@@ -17,7 +17,7 @@ jobs:
         #       https://github.com/actions/setup-python/issues/162
         os: [ubuntu-20.04]
         # TODO: add pypy2, pypy3
-        python-version: [2.7, 3.5, 3.6, 3.7, 3.8]
+        python-version: [3.5, 3.6, 3.7, 3.8]
         exclude:
           - os: macos-latest
             python-version: [3.5, 3.6]
@@ -30,19 +30,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install Python2.7 dependencies
-      if: ${{ matrix.python-version == 2.7 }}
-      run: |
-        python -m pip install --upgrade pytest numexpr==2.7.3
-        pip install -r requirements.txt
-        # Optional Dependency for HDF Checkpointing
-        pip install tables
-        python setup.py install
-        python setup.py build_ext --inplace
-        python -m pip list
-
     - name: Install Python3 dependencies
-      if: ${{ matrix.python-version != 2.7 }}
       run: |
         python -m pip install --upgrade pip pytest
         pip install -r requirements.txt
@@ -101,8 +89,8 @@ jobs:
         echo -e "PWD:${PWD}"
         which cali-query
 
-    - name: Build Timemory
-      if: ${{ matrix.python-version >= 3.6 }}
+    - name: Build Timemory for Python 3.6
+      if: ${{ matrix.python-version == 3.6 }}
       run: |
         python -m pip install --upgrade scikit-build
         # python -m pip install --upgrade --no-cache-dir --no-deps -v --pre timemory --install-option=--disable-{c,gotcha,tools}
@@ -114,6 +102,7 @@ jobs:
 
     - name: "Upload coverage to Codecov"
       uses: codecov/codecov-action@d9f34f8cd5cb3b3eb79b3e4b5dae3a16df499a70 # @v2.1.0
+      if: ${{ matrix.python-version >= 3.7 }}
       with:
         fail_ci_if_error: true
         verbose: true

hatchet/readers/caliper_native_reader.py

@@ -5,6 +5,7 @@
 
 
 import pandas as pd
+import numpy as np
 import os
 
 import caliperreader as cr
@@ -349,6 +350,7 @@ def read(self):
                 default_metric_dict[list(self.record_data_cols)[idx]] = 0
             else:
                 default_metric_dict[list(self.record_data_cols)[idx]] = None
+        default_metric_dict["nid"] = np.nan
 
         # create a list of dicts, one dict for each missing row
         missing_nodes = []
@@ -440,6 +442,7 @@ def read(self):
         with self.timer.phase("data frame"):
             # merge the metrics and node dataframes on the nid column
             dataframe = pd.merge(df_metrics, self.df_nodes, on="nid")
+            dataframe["nid"] = dataframe["nid"].astype(pd.Int64Dtype())
 
             # set the index to be a MultiIndex
             indices = ["node"]

hatchet/tests/caliper.py

@@ -5,6 +5,7 @@
 
 import subprocess
 import numpy as np
+import pandas as pd
 
 import pytest
 import sys
@@ -224,7 +225,7 @@ def test_graphframe_native_lulesh_from_file(lulesh_caliper_cali):
         if col in ("time (inc)", "time"):
             assert gf.dataframe[col].dtype == np.float64
         elif col in ("nid", "rank"):
-            assert gf.dataframe[col].dtype == np.int64
+            assert gf.dataframe[col].dtype == pd.Int64Dtype()
         elif col in ("name", "node"):
             assert gf.dataframe[col].dtype == object
 
@@ -250,7 +251,7 @@ def test_graphframe_native_lulesh_from_caliperreader(lulesh_caliper_cali):
         if col in ("time (inc)", "time"):
             assert gf.dataframe[col].dtype == np.float64
         elif col in ("nid", "rank"):
-            assert gf.dataframe[col].dtype == np.int64
+            assert gf.dataframe[col].dtype == pd.Int64Dtype()
         elif col in ("name", "node"):
             assert gf.dataframe[col].dtype == object
 

setup.py

@@ -94,7 +94,7 @@
         "License :: OSI Approved :: MIT License",
     ],
     keywords="",
-    python_requires=">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*",
+    python_requires=">=3.5",
     packages=[
         "hatchet",
         "hatchet.readers",