pinned tests are nice for reproducibility (#197)

* pinned tests are nice for reproducibility

* Update pytest.yml

* Update setup.py

* less cmt in test

* Revert "less cmt in test"

This reverts commit f6dbb82.

Co-authored-by: Tianyu Zhu <tz2263@columbia.edu>

.github/dependabot.yml

@@ -0,0 +1,23 @@
+# Set update schedule for GitHub Actions to check they are up to date
+# If one of the github actions is out of date, dependabot will open a
+# PR to update the version of that action
+
+version: 2
+updates:
+  # Maintain the requirements in the github actiuons
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "monthly"
+    assignees:
+      - jorana
+  # Maintain the requirements requirements folder
+  - package-ecosystem: "pip"
+    directory: "/extra_requirements"
+    schedule:
+      # Check for updates to requirements every week
+      interval: "monthly"
+    open-pull-requests-limit: 10
+    assignees:
+      - jorana

.github/workflows/pytest.yml

@@ -0,0 +1,101 @@
+# Test straxen on each PR.
+# We run three types of tests:
+#  - Pytest -> these are the "normal" tests and should be run for all
+#    python versions
+#  - Coveralls -> this is to see if we are coverering all our lines of
+#    code with our tests. The results get uploaded to
+#    coveralls.io/github/XENONnT/straxen
+#  - pytest_no_database -> we want to make sure we can run the tests even
+#    if we don't have access to our datebase since this will e.g. happen
+#    when someone is pushing a PR from their own fork as we don't
+#    propagate our secrets there.
+
+name: Test package
+
+# Trigger this code when a new release is published
+on:
+  workflow_dispatch:
+  release:
+    types: [created]
+  pull_request:
+    branches:
+      - master
+      - stable
+  push:
+    branches:
+      - master
+
+jobs:
+  update:
+    name: "${{ matrix.test }}_py${{ matrix.python-version }}"
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: True
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+        test: ['coveralls', 'pytest', 'pytest_no_database']
+        # Only run coverage / no_database on py3.8
+        exclude:
+          - python-version: 3.7
+            test: coveralls
+          - python-version: 3.9
+            test: coveralls
+          - python-version: 3.7
+            test: pytest_no_database
+          - python-version: 3.9
+            test: pytest_no_database
+    steps:
+      # Setup and installation
+      - name: Setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - name: Install requirements for tests and latest strax
+        run: |
+            pip install -r extra_requirements/requirements-tests.txt
+      # Secrets and required files
+      - name: patch utilix file
+        # Patch this file if we want to have access to the database
+        if:  matrix.test != 'pytest_no_database'
+        run: bash .github/scripts/create_readonly_utilix_config.sh
+        env:
+          # RunDB
+          RUNDB_API_URL: ${{ secrets.RUNDB_API_URL }}
+          RUNDB_API_USER_READONLY: ${{ secrets.RUNDB_API_USER_READONLY }}
+          RUNDB_API_PASSWORD_READONLY: ${{ secrets.RUNDB_API_PASSWORD_READONLY}}
+          PYMONGO_URL: ${{ secrets.PYMONGO_URL }}
+          PYMONGO_USER: ${{ secrets.PYMONGO_USER }}
+          PYMONGO_PASSWORD: ${{ secrets.PYMONGO_PASSWORD }}
+          PYMONGO_DATABASE: ${{ secrets.PYMONGO_DATABASE }}
+          # SCADA
+          SCADA_URL: ${{ secrets.SCADA_URL }}
+          SCADA_VALUE_URL: ${{ secrets.SCADA_VALUE_URL }}
+          SCADA_USER: ${{ secrets.SCADA_USER }}
+          SCADA_LOGIN_URL: ${{ secrets.SCADA_LOGIN_URL }}
+          SCADA_PWD: ${{ secrets.SCADA_PWD }}
+
+      # Run tests
+      - name: Test package
+        # This is running a normal test
+        if: matrix.test == 'pytest_no_database' || matrix.test == 'pytest'
+        run: |
+          python setup.py test -v
+      - name: Coveralls
+        # Make the coverage report and upload
+        env:
+          NUMBA_DISABLE_JIT: 1
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # We need to check if we had access to the secrets, otherwise coveralls
+          # will yield a low coverage because of the lack of interfacing with the
+          # database.
+          HAVE_ACCESS_TO_SECTETS: ${{ secrets.RUNDB_API_URL }}
+        if: matrix.test == 'coveralls' && env.HAVE_ACCESS_TO_SECTETS != null
+        run: |
+          coverage run --source=wfsim setup.py test -v
+          coveralls --service=github
+
+      # Done
+      - name: goodbye
+        run: echo "tests done, bye bye"

extra_requirements/requirements-tests.txt

@@ -0,0 +1,35 @@
+# Test compatibility with these most often:
+strax==0.16.1
+straxen==0.19.3
+
+# File for the requirements of straxen with the automated tests
+blosc==1.10.4                                   # Strax dependency
+boltons==21.0.0
+datashader==0.13.0
+dask==2021.7.2
+dill==0.3.4                                     # Strax dependency
+coveralls==3.2.0
+commentjson==0.9.0
+coverage==5.5
+flake8==3.9.2
+holoviews==1.14.5
+ipywidgets==7.6.3
+hypothesis==6.14.5
+jupyter-client==6.1.12                          # for ipywidgets
+matplotlib==3.4.2
+multihist==0.6.4
+npshmex==0.2.1                                  # Strax dependency
+numba==0.53.1                                   # Strax dependency
+numpy==1.19.5
+pandas==1.2.5                                   # Strax dependency
+psutil==5.8.0                                   # Strax dependency
+pytest==6.2.4
+pytest-cov==2.12.1
+scikit-learn==0.24.2
+scipy==1.7.0                                    # Strax dependency
+tensorflow==2.5.1
+tqdm==4.62.0
+xarray==0.19.0
+utilix==0.6.1
+zstd==1.5.0.2                                   # Strax dependency
+uproot==4.0.0

setup.py

@@ -36,7 +36,10 @@
             'graphviz']},
     packages=['wfsim',
               'wfsim.core',
-              'wfsim.pax_datastructure',],
+              'wfsim.pax_datastructure',
+              'extra_requirements'],
+    package_dir={'extra_requirements': 'extra_requirements'},
+    package_data={'extra_requirements': ['requirements-tests.txt']},
     classifiers=[
         'Development Status :: 4 - Beta',
         'License :: OSI Approved :: BSD License',