Bugfix 249 warnings (#281)

* Delete requirements_36.txt Python 3.6 no longer supported * #249 Add test_future_warnings test * #249 additional sample data * Bugfix Issue #249 Future Warnings- replace append with pd.concat * Bugfix issue #249 add the test for future warnings * Bugfix #249 additional data * Bugfix Issue #249 additional data that wasn't previously committed * Bugfix #249 add sum stat import * Bugfix #249 added workflow to check for Python package vulnerabilities * Updated requirements.txt for nco and all others * issue #249 add imports to pandas and warning * Bugfix 249 future warnings (#280) * Bump pillow from 8.3.2 to 9.3.0 (#260) Bumps [pillow](https://github.com/python-pillow/Pillow) from 8.3.2 to 9.3.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@8.3.2...9.3.0) --- updated-dependencies: - dependency-name: pillow dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bugfix 251 test scorecard (#256) * Replace Python versions 3.8.6 and 3.8.12 with 3.8 * Bugfix #251 replace SettingWithCopyWarning with Warning. SettingWithCopyWarning no longer available for this check * Adding double asterisks to end bolding on mulitple lines Co-authored-by: Julie Prestopnik <[email protected]> * bugfix_249_warnings (#261) * Update unit_tests.yml replace 3.8.6 and 3.8.12 with 3.8 for Python because latest version of ubuntu does not have support for python 3.8.6 * Feature 251 test scorecard (#253) * Issue #251 In Pandas 1.3 and above, the SettingWithCopy Warning category has been removed. Replace the check for category=SettingWithCopyWarning with Warning, since SettingWithCopyWarning is a subclass of Warning * Added ending asterisks for end bold to fix these warnings: WARNING: Inline strong start-string without end-string. Co-authored-by: Julie Prestopnik <[email protected]> * Feature 250 test event equalize (#252) * Remove Python 3.8.6 and 3.8.12 and use Python 3.8 instead. The latest version of ubuntu no longer has python 3.8.6 available. * Issue #250 fix the test_equalize_axis_data_no_fcst_var fixture * Added ending asterisks for end bold to fix these warnings: WARNING: Inline strong start-string without end-string. * #251 allow test to run check on numpy types regardless of numpy version * Update unit_tests.yml add python 3.10 to testing to evaluate package compatibility * Update unit_tests.yml remove Python 3.10 there are issues with HDF5 Co-authored-by: Julie Prestopnik <[email protected]> * Delete requirements_36.txt Python 3.6 no longer supported * #249 Add test_future_warnings test * #249 additional sample data * Update requirements.txt https://github.com/dtcenter/METcalcpy/security/dependabot/22 * Update requirements.txt https://github.com/dtcenter/METcalcpy/security/dependabot/20 * #249 replacing pd.append with pd.concat and adding tests and data * #249 added tests * #249 Additional test data * Revert "Merge branch 'develop' of https://github.com/dtcenter/METcalcpy into bugfix_249_warnings" This reverts commit 7f203bf, reversing changes made to dd87d77. Co-authored-by: Julie Prestopnik <[email protected]> * Adding file based on testing on Acorn for NCO (#265) * Per #267, updating modulefiles * Adding script for testing on WCOSS2 * Correcting filename * Bugfix release (#272) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Hank Fisher <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Julie Prestopnik <[email protected]> Co-authored-by: Hank Fisher <[email protected]>
dtcenter · Feb 23, 2023 · 93cc002 · 93cc002
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diff --git a/.github/workflows/vulnerabilities.yaml b/.github/workflows/vulnerabilities.yaml
@@ -0,0 +1,38 @@
+# This workflow will check third-party Python packages for vulnerabilities using pip-audit.
+# pip-audit finds vulnerabilities from packages that are dependencies of
+# the packages in the requirements.txt file. A summary is generated at the end of the action.
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-githu
+
+name: Python vulnerability check
+
+on:
+  push:
+    branches:
+      - develop
+      - develop-ref
+      - feature_*
+      - main_*
+      - bugfix_*
+      - test_*
+      - issue_*
+  pull_request:
+    types: [opened, reopened, synchronize]
+
+jobs:
+  selftest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: install
+        run: |
+          python -m venv env/
+          source env/bin/activate
+          python -m pip install .
+      - uses: pypa/[email protected]
+        with:
+          inputs: requirements.txt
+          virtual-environment: env/
+          local: true
+          summary: true
+
+
diff --git a/metcalcpy/agg_stat_bootstrap.py b/metcalcpy/agg_stat_bootstrap.py
@@ -294,7 +294,7 @@ def calculate_values(self):
             # get results for axis1
             out_frame = self._proceed_with_axis("1")
             if self.params['series_val_2']:
-                out_frame = out_frame.append(self._proceed_with_axis("2"))
+                out_frame = pd.concat([out_frame, self._proceed_with_axis("2")])
 
         else:
             out_frame = pd.DataFrame()

diff --git a/metcalcpy/sum_stat.py b/metcalcpy/sum_stat.py
@@ -37,6 +37,8 @@
 import time
 import logging
 import yaml
+import pandas as pd
+import warnings
 from inspect import signature
 
 from metcalcpy import GROUP_SEPARATOR
@@ -182,6 +184,7 @@ def aggregate_special_fields(self, axis='1'):
         Args:
             axis - y1 or y1 axis
         """
+        warnings.filterwarnings('error')
 
         # check if indy_vals have a field that need to be aggregated - the field with ';'
         has_agg_indy_field = any(any(GROUP_SEPARATOR in i for i in item) for item in self.params['indy_vals'])
@@ -235,7 +238,7 @@ def aggregate_special_fields(self, axis='1'):
                                                             point_data,
                                                             self.params['line_type'])
 
-                    aggregated_values = aggregated_values.append(point_data)
+                    aggregated_values = pd.concat([aggregated_values, point_data])
             self.input_data = aggregated_values
             self.input_data.reset_index(inplace=True, drop=True)
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,49 +1,13 @@
-attrs==21.4.0
-certifi==2021.10.8
-cffi==1.15.0
-cftime==1.5.1.1
-charset-normalizer==2.0.12
-cloudpickle==2.0.0
-cryptography==39.0.1
-cycler==0.11.0
-cytoolz==0.11.0
-dask==2022.3.0
-fsspec==2022.2.0
-idna==3.3
-imagecodecs-lite==2019.12.3
 imageio==2.6.1
-importlib-metadata==4.11.3
 imutils==0.5.4
-iniconfig==1.1.1
-locket==0.2.0
-metpy==1.1.0
-netCDF4==1.5.7
-networkx==2.7.1
+metpy==1.3.1
+netCDF4==1.6.2
 numpy==1.22.3
 opencv-python>=4.5.3
-packaging==21.3
-pandas==1.2.3
-partd==1.2.0
-pint==0.18
-Pillow>=9.2.0
-pluggy==1.0.0
-pooch==1.6.0
-py==1.11.0
-pycparser==2.21
-pyOpenSSL==22.0.0
-pyparsing==3.0.7
+pandas==1.5.1
+pint==0.19
 pytest==7.2.0
-pytz==2022.1
-PyWavelets==1.1.1
-PyYAML==5.4.1
-requests==2.27.1
+PyYAML==6.0
 scikit-image==0.18.1
-scipy==1.8.0
-six==1.16.0
-tifffile==2019.7.26.2
-tomli==2.0.1
-toolz==0.11.2
-typing_extensions==4.1.1
-urllib3==1.26.9
-xarray==2022.3.0
-zipp==3.7.0
+scipy==1.8.1
+xarray==2022.3.0
diff --git a/test/data/agg_stat_and_boot_output.data b/test/data/agg_stat_and_boot_output.data