Upgrade to python 3

.github/install.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+if [[ "$INSTALL_METHOD" == "conda" ]]; then
+  echo "Using conda"
+  sudo chown -R "$USER" "$CONDA" # Give CONDA permission to its own files
+  source "$CONDA"/etc/profile.d/conda.sh
+  conda config --set always_yes yes --set changeps1 no
+  conda update -q conda  # get latest conda version
+  # Useful for debugging any issues with conda
+  conda info -a
+
+  sed -i -e "s/- python=.*/- python=$PYTHON_VERSION/g" environment_development.yaml
+  conda install -c conda-forge mamba
+  mamba env create -n CI --file environment_development.yaml
+  conda activate CI
+else
+  echo "Using pip"
+  pip install -U pip setuptools wheel
+  # This installation is not currently supported
+fi

.github/workflows/ci.yml

@@ -8,15 +8,16 @@ on: [push, pull_request]
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   tests:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [2.7]
-        install-method: ["pip"]
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.8]
+        install-method: ["conda"]
     steps:
       - uses: actions/checkout@v2
         with:
-            fetch-depth: 0
+          fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
@@ -28,12 +29,18 @@ jobs:
           INSTALL_METHOD: ${{ matrix.install-method }}
           PYTHON_VERSION: ${{ matrix.python-version }}
         run: |
+          source .github/install.sh
           python --version
-          python -m pip install --upgrade pip
-          python -m pip install pytest
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi 
-          pip install codecov pytest-cov
+          pip install .[all]
           pip freeze
       - name: Tests
-        run: pytest --cov=. --cov-report=xml
+        env:
+          INSTALL_METHOD: ${{ matrix.install-method }}
+        run: |
+          if [[ "$INSTALL_METHOD" == "conda" ]]; then
+            source $CONDA/etc/profile.d/conda.sh
+            conda activate CI
+            conda list
+          fi
+          pytest --cov=protopipe --cov-report=xml
       - uses: codecov/codecov-action@v1

.gitignore

@@ -1,2 +1,86 @@
+# Compiled files
+.pytest_cache
+*.py[co]
 *.pyc
-**/__pycache__
+*.a
+*.o
+*.so
+__pycache__
+
+# Ignore .c files by default to avoid including generated code. If you want to
+# add a non-generated .c extension, use `git add -f filename.c`.
+*.c
+
+# Other generated files
+*/cython_version.py
+htmlcov
+.coverage
+MANIFEST
+
+# ignore version cache file (generated automatically when setup.py is run)
+protopipe_grid_interface/_version_cache.py
+protopipe_grid_interface/_version.py
+
+# Eclipse editor project files
+.project
+.pydevproject
+.settings
+
+# Pycharm editor project files
+.idea
+
+# KDevelop editor project files
+*kdev4
+
+# VSCode
+.vscode
+
+# Packages/installer info
+*.egg
+*.eggs
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+distribute-*.tar.gz
+
+# Other
+.*.swp
+*~
+\#*
+.\#*
+
+# Mac OSX
+.DS_Store
+
+# Rope refactoring data:
+.ropeproject
+
+# ipython notebook checkpoints
+.ipynb_checkpoints
+.cache*
+.cache
+
+*.out
+
+#sonarlint command-line output
+.sonarlint
+
+# output files (should not be stored in git)
+*.log
+*.h5
+*.hdf5
+*.fits
+irf.fits.gz
+table_best_cutoff.fits
+*.pkl.gz
+
+*.pstats
+target
+.mypy_cache

.prospector.yaml

@@ -0,0 +1,8 @@
+pep257:
+  disable:
+    - D104
+    - D201
+    - D202
+    - D203
+    - D211
+    - D213