Caching and test for GP

.github/workflows/continous_integration.yml

@@ -1,18 +1,51 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Unit Test nmma
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
+  workflow_dispatch:
 
 jobs:
+
+  download-files:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout branch being tested
+        uses: actions/checkout@v3
+
+      - name: Cache svdmodels directory
+        uses: actions/cache@v3
+        with:
+          path: svdmodels
+          key: svdmodels-${{ runner.os }}-${{ hashFiles('**/LICENSE') }}
+          restore-keys: svdmodels-${{ runner.os }}-
+
+      - name: Check if SVD models exist
+        id: check-artifact-download
+        run: |
+          if [ -d "svdmodels" ]; then
+            echo "Artifacts exist, skipping download."
+            echo "::set-output name=exists::true"
+          else
+            echo "Artifacts do not exist, will download."
+            echo "::set-output name=exists::false"
+          fi
+      - name: Download SVD models
+        if: steps.check-artifact-download.outputs.exists == 'false'
+        run: |
+          wget --show-progress -O svdmodels.tar https://enlil.gw.physik.uni-potsdam.de/~jhawar/svdmodels/svdmodels.tar
+          mkdir -p svdmodels
+          tar -xvf svdmodels.tar -C svdmodels/
+          rm svdmodels.tar
+        working-directory: ${{ github.workspace }}
+
   build:
 
     runs-on: ubuntu-latest
+    needs: download-files
     strategy:
       fail-fast: false
       matrix:
@@ -26,28 +59,34 @@ jobs:
           POSTGRES_PASSWORD: anything
         ports:
           - 5432:5432
-        # needed because the postgres container does not provide a
-        # healthcheck
         options: >-
           --health-cmd pg_isready
           --health-interval 10s
           --health-timeout 5s
           --health-retries 5
-
     steps:
     - name: Checkout branch being tested
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+
+    - name: Restore SVD models from cache
+      uses: actions/cache@v3
+      with:
+        path: svdmodels
+        key: svdmodels-${{ runner.os }}-${{ hashFiles('**/LICENSE') }}
+        restore-keys: svdmodels-${{ runner.os }}-
+
     - name: Get pip cache dir
       id: pip-cache
       run: |
         python -m pip install --upgrade pip setuptools wheel
         echo "::set-output name=dir::$(pip cache dir)"
     - name: pip cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ runner.os }}-pip-2-${{ hashFiles('**/setup.py', '**/requirements.txt') }}
@@ -77,7 +116,7 @@ jobs:
         psql -U nmma -h localhost -c "GRANT ALL PRIVILEGES ON DATABASE nmma TO nmma;" nmma
     - name: Test with pytest
       run: |
-        python -m coverage run --source nmma -m pytest nmma/tests/*
+        python -m coverage run --source nmma -m pytest nmma/tests/*.py
       env:
         LD_LIBRARY_PATH: .:/home/runner/work/nmma/nmma/MultiNest/lib # for Linux
     - name: Run Coveralls

.github/workflows/delete-branch-cache.yml

@@ -0,0 +1,33 @@
+name: Cleanup cache for PR
+on:
+  pull_request:
+    types:
+      - closed
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v3
+
+      - name: Cleanup
+        run: |
+          gh extension install actions/gh-actions-cache
+
+          REPO=${{ github.repository }}
+          BRANCH="refs/pull/${{ github.event.pull_request.number }}/merge"
+
+          echo "Fetching list of cache key"
+          cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 )
+
+          ## Setting this to not fail the workflow while deleting cache keys. 
+          set +e
+          echo "Deleting caches..."
+          for cacheKey in $cacheKeysForPR
+          do
+              gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
+          done
+          echo "Done"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

nmma/em/utils.py

@@ -4,7 +4,7 @@
 import numpy as np
 import os
 import pandas as pd
-from scipy.interpolate import interpolate as interp
+import scipy.interpolate as interp
 import scipy.signal
 import scipy.constants
 import scipy.stats

nmma/tests/analysis.py

@@ -3,22 +3,24 @@
 
 from ..em import analysis
 
-
 def test_analysis():
 
-    dataDir = f"{os.path.dirname(__file__)}/data"
+    workingDir=os.path.dirname(__file__)
+
+    dataDir = os.path.join(workingDir, 'data')
+    svdmodels=os.path.join(workingDir, '../../svdmodels/')
 
     args = Namespace(
-        model="Me2017",
+        model="Bu2019lm",
         interpolation_type="sklearn_gp",
-        svd_path="svdmodels",
+        svd_path=svdmodels,
         outdir="outdir",
         label="injection",
         trigger_time=None,
         data=None,
-        prior="priors/Me2017.prior",
+        prior="priors/Bu2019lm.prior",
         tmin=0.1,
-        tmax=20.0,
+        tmax=10.0,
         dt=0.5,
         log_space_time=False,
         photometric_error_budget=0.1,
@@ -30,13 +32,13 @@ def test_analysis():
         Ebv_max=0.0,
         grb_resolution=5,
         jet_type=0,
-        error_budget="1",
+        error_budget="0",
         sampler="pymultinest",
         cpus=1,
-        nlive=512,
+        nlive=64,
         reactive_sampling=False,
         seed=42,
-        injection=f"{dataDir}/injection.json",
+        injection=f"{dataDir}/Bu2019lm_injection.json",
         injection_num=0,
         injection_detection_limit=None,
         injection_outfile="outdir/lc.csv",
@@ -66,6 +68,7 @@ def test_analysis():
         sample_over_Hubble=False,
         sampler_kwargs="{}",
         verbose=False,
+        local_only=True
     )
 
-    analysis.main(args)
+    analysis.main(args)