pin pandas version to less than 3, add missing required packages, temporarily remove sorting of index in boxplot (llnl#271)

* pin pandas version to less than 3

* separate codecov workflow in CI, add python 3.12, 3.13

* fix if check

* fix wheel package name

* add missing more-itertools to list of requirements

more-itertools is in setup.py

* add missing tqdm

* temporarily remove sorting of index in boxplot, so tests pass

Pandas error trying to sort columns, most are tuples, but one is a slice.
TypeError: '<' not supported between instances of 'tuple' and 'slice'

Author: slabasan

.github/workflows/coverage.yaml

@@ -0,0 +1,70 @@
+name: unit tests to collect code coverage
+
+on:
+  push:
+    branches: [ develop ]
+    secrets:
+      THICKET_CODECOV_TOKEN:
+        required: true
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12", "3.13"]
+        exclude:
+          - os: macos-latest
+            python-version: [3.5, 3.6]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Python Dependencies for 3.12 and later
+      if: ${{ matrix.python-version >= '3.12' }}
+      run: |
+        python -m pip install --upgrade pip pytest setuptools wheel
+        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: Standard Install Python3 Dependencies
+      run: |
+        python -m pip install --upgrade pip pytest
+        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 coverage tools
+      run: |
+        pip install codecov
+        pip install pytest-cov
+
+    - name: Basic Test with pytest
+      run: |
+        PYTHONPATH=. $(which pytest) --cov=./ --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.THICKET_CODECOV_TOKEN }}
+      with:
+        directory: ./coverage/reports
+        env_vars: OS,PYTHON
+        files: /home/runner/work/hatchet/hatchet/coverage.xml
+        flags: unittests
+        verbose: true
+        fail_ci_if_error: true

.github/workflows/unit-tests.yaml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         # TODO: add macos-latest
         os: [ubuntu-latest]
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12", "3.13"]
         exclude:
           - os: macos-latest
             python-version: [3.5, 3.6]
@@ -33,7 +33,17 @@ jobs:
         # Obtain the latest cached version of npm (either local cache or action cache)
         node-version: node
 
-    - name: Install Python3 dependencies
+    - name: Install Python3 dependencies for 3.12 and later
+      if: ${{ matrix.python-version >= '3.12' }}
+      run: |
+        python -m pip install --upgrade pip pytest setuptools wheel
+        pip install -r requirements.txt
+        python -m pip install --upgrade --force-reinstall git+https://github.com/LLNL/hatchet.git@develop
+        python setup.py install
+        python setup.py build_ext --inplace
+        python -m pip list
+
+    - name: Standard Install Python3 Dependencies
       run: |
         python -m pip install --upgrade pip pytest
         pip install -r requirements.txt
@@ -65,23 +75,6 @@ jobs:
       run: |
         pip install extrap
 
-    - name: Install coverage tools
-      run: |
-        pip install codecov
-        pip install pytest-cov
-
     - name: Basic Test with pytest
       run: |
-        PYTHONPATH=. $(which pytest) --cov=./ --cov-report=xml
-
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v4
-      env:
-        CODECOV_TOKEN: ${{ secrets.THICKET_CODECOV_TOKEN }}
-      with:
-        directory: ./coverage/reports/
-        env_vars: OS,PYTHON
-        files: /home/runner/work/thicket/thicket/coverage.xml
-        flags: unittests
-        verbose: true
-        fail_ci_if_error: true
+        PYTHONPATH=. $(which pytest)

requirements.txt

@@ -1,7 +1,9 @@
 scipy
 numpy
-pandas>=1.1
+pandas>=1.1,<3
 llnl-hatchet
 matplotlib
 seaborn
 beautifulsoup4
+more-itertools
+tqdm

setup.py

@@ -44,7 +44,7 @@ def readme():
     install_requires=[
         "scipy",
         "numpy",
-        "pandas >= 1.1",
+        "pandas >= 1.1,<3",
         "llnl-hatchet",
         "tqdm",
         "more-itertools",

thicket/stats/calc_boxplot_statistics.py

@@ -177,6 +177,6 @@ def calc_boxplot_statistics(thicket, columns=[], quartiles=[0.25, 0.5, 0.75], **
             thicket.statsframe.dataframe = thicket.statsframe.dataframe.join(df_box)
 
         # sort columns in index
-        thicket.statsframe.dataframe = thicket.statsframe.dataframe.sort_index(axis=1)
+        # thicket.statsframe.dataframe = thicket.statsframe.dataframe.sort_index(axis=1)
 
     return output_column_names