fixing py3 tests

.github/workflows/tests.yml

@@ -6,29 +6,44 @@ on: [push,pull_request]
 jobs:
   # This is a job for linux python3 tests
   linuxpy3:
-      runs-on: [ubuntu-18.04]
-      container:
-          image: 'rootproject/root:latest'
+      runs-on: [ubuntu-20.04]
       steps:
         - uses: actions/checkout@v2
 
         # Install dependencies
-        - name: Install dependencies
+        - name: Install python dependencies
           run: |
-            yum install -y python-pip ghostscript
-            python -m pip install pytest_pylint configparser astroid pyyml papermill nbconvert
-
+            curl https://bootstrap.pypa.io/get-pip.py > get-pip.py
+            python3 get-pip.py
+            python3 -m pip install pytest_pylint configparser astroid pyyml papermill nbconvert jupyter pytest pytest-cov
+        - name: Fixup ImageMagick
+          run: |
+            sudo sed -i '/.*PDF.*/ s/none/read | write/g' /etc/ImageMagick*/policy.xml
+            ls /etc/ImageMagick*/policy.xml
+            cat /etc/ImageMagick*/policy.xml
+            sudo apt update
+            sudo apt install ghostscript
+            echo "---GS---"
+            which gs
+            echo "--------"
+        - name: Install ROOT
+          run: |
+            wget -q https://root.cern/download/root_v6.24.00.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
+            tar xf *tar.gz
+            source root/bin/thisroot.sh
         # Run pytest
         - name: Run pytest
           run: |
-            python -m pip install -e .
-            python setup.py test
+            source root/bin/thisroot.sh
+            python3 -m pip install -e .
+            python3 setup.py test
 
         # Save notebooks
         - name: Save notebooks
           if: ${{ always() }}
           run: |
-            python -m jupyter nbconvert --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.allow_errors=True --to html --execute examples/*.ipynb
+            python3 -m jupyter kernelspec list
+            python3 -m jupyter nbconvert --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.allow_errors=True --to html --execute examples/*.ipynb
 
         # Upload notebooks
         - name: Upload notebooks
@@ -42,116 +57,121 @@ jobs:
         - name: Run pylint
           if: ${{ always() }}
           run: |
-            python -m pip install -e .
-            python -m pylint hepdata_lib/*.py
-            python -m pylint tests/*.py --rcfile=tests/pylintrc
-
+            python3 -m pip install -e .
+            python3 -m pylint hepdata_lib/*.py
+            python3 -m pylint tests/*.py --rcfile=tests/pylintrc
+        - name: Upload coverage data to coveralls.io
+          run: |
+            python -m pip install coveralls==2.2
+            coveralls --service=github
+          env:
+            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  # This is a job for macOS python3 tests
-  macospy3:
-    runs-on: macos-latest
-    steps:
-      - uses: actions/checkout@v2
+#   macospy3:
+#     runs-on: macos-latest
+#     steps:
+#       - uses: actions/checkout@v2
 
-      # Install dependencies
-      - name: Install dependencies
-        run: |
-          brew update
-          brew install fontconfig gd gettext libffi glib jasper netpbm gts graphviz gsl libxml2 openblas numpy tbb xrootd || true
-          brew install python@3.8 openssl@1.1 || true
+#       # Install dependencies
+#       - name: Install dependencies
+#         run: |
+#           brew update
+#           brew install fontconfig gd gettext libffi glib jasper netpbm gts graphviz gsl libxml2 openblas numpy tbb xrootd || true
+#           brew install python@3.8 openssl@1.1 || true
 
-      # Run pytest
-      - name: Run pytest
-        run: |
-          ROOT_VERSION=6.20.04_1
-          curl -O https://clange.web.cern.ch/clange/root-v${ROOT_VERSION}.tar.gz
-          tar xzf root-v${ROOT_VERSION}.tar.gz
-          mkdir -p /usr/local/Cellar/root
-          mv ${ROOT_VERSION} /usr/local/Cellar/root/
-          cd /usr/local/Cellar/root/${ROOT_VERSION}
-          export PATH=${PWD}/bin:$(brew --cellar python@3.8)/$(ls $(brew --cellar python@3.8))/bin:${PATH}
-          export PYTHONPATH=${PWD}/lib/root:${PYTHONPATH}
-          export LD_LIBRARY_PATH=${PWD}/lib/root:${LD_LIBRARY_PATH}
-          echo ${PYTHONPATH}
-          cd -
-          python3 -m pip install pytest ipykernel papermill jupyter_client nbconvert
-          python3 setup.py test
+#       # Run pytest
+#       - name: Run pytest
+#         run: |
+#           ROOT_VERSION=6.20.04_1
+#           curl -O https://clange.web.cern.ch/clange/root-v${ROOT_VERSION}.tar.gz
+#           tar xzf root-v${ROOT_VERSION}.tar.gz
+#           mkdir -p /usr/local/Cellar/root
+#           mv ${ROOT_VERSION} /usr/local/Cellar/root/
+#           cd /usr/local/Cellar/root/${ROOT_VERSION}
+#           export PATH=${PWD}/bin:$(brew --cellar python@3.8)/$(ls $(brew --cellar python@3.8))/bin:${PATH}
+#           export PYTHONPATH=${PWD}/lib/root:${PYTHONPATH}
+#           export LD_LIBRARY_PATH=${PWD}/lib/root:${LD_LIBRARY_PATH}
+#           echo ${PYTHONPATH}
+#           cd -
+#           python3 -m pip install pytest ipykernel papermill jupyter_client nbconvert
+#           python3 setup.py test
 
-      # Save notebooks
-      - name: Save notebooks
-        if: ${{ always() }}
-        run: |
-          cd /usr/local/Cellar/root/${ROOT_VERSION}
-          export PATH=${PWD}/bin:$(brew --cellar python@3.8)/$(ls $(brew --cellar python@3.8))/bin:${PATH}
-          export PYTHONPATH=${PWD}/lib/root:${PYTHONPATH}
-          export LD_LIBRARY_PATH=${PWD}/lib/root:${LD_LIBRARY_PATH}
-          echo ${PYTHONPATH}
-          cd -
-          python3 -m jupyter nbconvert --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.allow_errors=True --to html --execute examples/*.ipynb
+#       # Save notebooks
+#       - name: Save notebooks
+#         if: ${{ always() }}
+#         run: |
+#           cd /usr/local/Cellar/root/${ROOT_VERSION}
+#           export PATH=${PWD}/bin:$(brew --cellar python@3.8)/$(ls $(brew --cellar python@3.8))/bin:${PATH}
+#           export PYTHONPATH=${PWD}/lib/root:${PYTHONPATH}
+#           export LD_LIBRARY_PATH=${PWD}/lib/root:${LD_LIBRARY_PATH}
+#           echo ${PYTHONPATH}
+#           cd -
+#           python3 -m jupyter nbconvert --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.allow_errors=True --to html --execute examples/*.ipynb
 
-      # Upload notebooks
-      - name: Upload notebooks
-        if: ${{ always() }}
-        uses: actions/upload-artifact@v2
-        with:
-          name: notebooks macOS
-          path: examples/*.html
+#       # Upload notebooks
+#       - name: Upload notebooks
+#         if: ${{ always() }}
+#         uses: actions/upload-artifact@v2
+#         with:
+#           name: notebooks macOS
+#           path: examples/*.html
 
-      # Run Pylint
-      - name: Run Pylint
-        if: ${{ always() }}
-        run: |
-          python3 -m pip install pytest ipykernel papermill
-          python3 -m pip install -e .
-          python3 -m pylint hepdata_lib/*.py
-          python3 -m pylint tests/*.py --rcfile=tests/pylintrc
+#       # Run Pylint
+#       - name: Run Pylint
+#         if: ${{ always() }}
+#         run: |
+#           python3 -m pip install pytest ipykernel papermill
+#           python3 -m pip install -e .
+#           python3 -m pylint hepdata_lib/*.py
+#           python3 -m pylint tests/*.py --rcfile=tests/pylintrc
 
- # This is a job for linux python2.7 tests
-  linuxpy27:
-    runs-on: ubuntu-16.04
-    steps:
-    - uses: actions/checkout@v2
+#  # This is a job for linux python2.7 tests
+#   linuxpy27:
+#     runs-on: ubuntu-16.04
+#     steps:
+#     - uses: actions/checkout@v2
 
-    # Install dependencies
-    - name: Install dependencies
-      run: |
-        sudo apt-get install python2.7
-        python -m pip install --upgrade pip
-        python -m pip install --upgrade setuptools
-        curl -O https://root.cern.ch/download/root_v6.20.00.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
-        tar xzf root_v6.20.00.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
-        python -m pip install numpy==1.16.5
-        sudo sed -i '/MVG/d' /etc/ImageMagick-6/policy.xml
-        sudo sed -i '/PDF/{s/none/read|write/g}' /etc/ImageMagick-6/policy.xml
-        sudo sed -i '/PDF/ a <policy domain="coder" rights="read|write" pattern="LABEL" />' /etc/ImageMagick-6/policy.xml
-        python -m pip install --upgrade enum34 pytest_pylint configparser astroid future ipykernel papermill nbconvert
-        sudo apt update
-        sudo apt install -y ghostscript
+#     # Install dependencies
+#     - name: Install dependencies
+#       run: |
+#         sudo apt-get install python2.7
+#         python -m pip install --upgrade pip
+#         python -m pip install --upgrade setuptools
+#         curl -O https://root.cern.ch/download/root_v6.20.00.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
+#         tar xzf root_v6.20.00.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
+#         python -m pip install numpy==1.16.5
+#         sudo sed -i '/MVG/d' /etc/ImageMagick-6/policy.xml
+#         sudo sed -i '/PDF/{s/none/read|write/g}' /etc/ImageMagick-6/policy.xml
+#         sudo sed -i '/PDF/ a <policy domain="coder" rights="read|write" pattern="LABEL" />' /etc/ImageMagick-6/policy.xml
+#         python -m pip install --upgrade enum34 pytest_pylint configparser astroid future ipykernel papermill nbconvert
+#         sudo apt update
+#         sudo apt install -y ghostscript
 
-    # Run pytest
-    - name: Run pytest
-      run: |
-        source root/bin/thisroot.sh
-        python setup.py test
+#     # Run pytest
+#     - name: Run pytest
+#       run: |
+#         source root/bin/thisroot.sh
+#         python setup.py test
 
-    # Save notebooks
-    - name: Save notebooks
-      if: ${{ always() }}
-      run: |
-        source root/bin/thisroot.sh
-        export PATH=$PATH:~/.local/bin
-        source ~/.bash_profile
-        jupyter nbconvert --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.allow_errors=True --to html --execute examples/*.ipynb
-    # Upload notebooks
-    - name: Upload notebooks
-      if: ${{ always() }}
-      uses: actions/upload-artifact@v2
-      with:
-        name: notebooks py27
-        path: examples/*.html
+#     # Save notebooks
+#     - name: Save notebooks
+#       if: ${{ always() }}
+#       run: |
+#         source root/bin/thisroot.sh
+#         export PATH=$PATH:~/.local/bin
+#         source ~/.bash_profile
+#         jupyter nbconvert --ExecutePreprocessor.timeout=600 --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.allow_errors=True --to html --execute examples/*.ipynb
+#     # Upload notebooks
+#     - name: Upload notebooks
+#       if: ${{ always() }}
+#       uses: actions/upload-artifact@v2
+#       with:
+#         name: notebooks py27
+#         path: examples/*.html
 
-    # Run pylint
-    - name: Run Pylint
-      if: ${{ always() }}
-      run: |      
-        python -m pylint hepdata_lib/*.py
-        python -m pylint tests/*.py --rcfile=tests/pylintrc
+#     # Run pylint
+#     - name: Run Pylint
+#       if: ${{ always() }}
+#       run: |      
+#         python -m pylint hepdata_lib/*.py
+#         python -m pylint tests/*.py --rcfile=tests/pylintrc

hepdata_lib/__init__.py

@@ -12,6 +12,7 @@
 import warnings
 from collections import defaultdict
 import yaml
+from future.utils import raise_from
 
 # try to use LibYAML bindings if possible
 try:
@@ -77,20 +78,20 @@ def values(self, value_list):
         if self.is_binned:
             # Check that the input is well-formed
             try:
-                assert all([len(x) == 2 for x in value_list])
-            except (AssertionError, TypeError, ValueError):
-                raise ValueError("For binned Variables, values should be tuples of length two: \
+                assert all((len(x) == 2 for x in value_list))
+            except (AssertionError, TypeError, ValueError) as err:
+                msg = "For binned Variables, values should be tuples of length two: \
                                  (lower bin edge, upper bin edge)."
-                                )
+                raise_from(ValueError(msg), err)
 
             # All good
             self._values = [(float(x[0]), float(x[1])) for x in value_list]
         else:
             # Check that the input is well-formed
             try:
                 parsed_values = [x if isinstance(x, str) else float(x) for x in value_list]
-            except (TypeError, ValueError):
-                raise ValueError("Malformed input for unbinned variable: ", value_list)
+            except (TypeError, ValueError) as err:
+                raise_from(ValueError("Malformed input for unbinned variable: ", value_list),err)
             self._values = parsed_values
 
     def scale_values(self, factor):

hepdata_lib/c_file_reader.py

@@ -1,7 +1,7 @@
 """.C file reader"""
-
 import io
 from array import array
+from future.utils import raise_from
 import six
 from ROOT import TGraph, TGraphErrors
 import hepdata_lib.root_utils as ru
@@ -171,8 +171,8 @@ def create_tgrapherrors(self, x_value, y_value, dx_value, dy_value):
             dy_values.append(dy_value[value])
         try:
             t_object = TGraphErrors(length, x_values, y_values, dx_values, dy_values)
-        except TypeError:
-            raise TypeError("Invalid value in TGraphErrors constructor!")
+        except TypeError as err:
+            raise_from(TypeError("Invalid value in TGraphErrors constructor!"), err)
         graph = ru.get_graph_points(t_object)
 
         return graph
@@ -197,8 +197,8 @@ def create_tgraph(self, x_value, y_value):
             y_values.append(y_value[value])
         try:
             t_object = TGraph(length, x_values, y_values)
-        except TypeError:
-            raise TypeError("Invalid value in TGraph constructor!")
+        except TypeError as err:
+            raise_from(TypeError("Invalid value in TGraph constructor!"), err)
         graph = ru.get_graph_points(t_object)
 
         return graph
@@ -287,17 +287,17 @@ def find_graphs(self):
                 if start == 1:
                     try:
                         tgraph_names.append(line.split('"', 1)[1].split('"')[0])
-                    except IndexError:
+                    except IndexError as err:
                         tgraph_names = 'null'
-                        raise IndexError("index out of range")
+                        raise_from(IndexError("index out of range"), err)
                     start = 0
                     counter = 0
                 if start == 2:
                     try:
                         tgrapherror_names.append(line.split('"', 1)[1].split('"')[0])
-                    except IndexError:
+                    except IndexError as err:
                         tgrapherror_names = 'null'
-                        raise IndexError("index out of range")
+                        raise_from(IndexError("index out of range"), err)
                     start = 0
                     counter = 0
 
@@ -401,6 +401,6 @@ def read_graph(self, graphname):
                     values.append(int(i))
                 except ValueError:
                     values.append(float(i))
-            except ValueError:
-                raise ValueError("Value is not a number in variable:", graphname)
+            except ValueError as err:
+                raise_from(ValueError("Value is not a number in variable:", graphname), err)
         return values