Merge pull request #24 from jburel/gha

Gha

Author: joshmoore

.env-gha

@@ -0,0 +1,19 @@
+AWS_ACCESS_KEY_ID=minioadmin
+AWS_SECRET_ACCESS_KEY=minioadmin
+BUCKET=ngff-latency-benchmark
+HOST=nginx
+
+XY=32
+Z=1
+C=1
+T=1
+XC=1
+ZC=1
+ROOT=/tmp
+NAME=${XY}-Z-${Z}-T-${T}-C-${C}-XYC-${XC}-ZC-${ZC}
+DIR=${ROOT}/${NAME}
+BASE=IMS_XY-${NAME}
+ROUNDS=20
+TEST_REPEATS=1
+
+S3ARGS={"anon": true, "client_kwargs": {"endpoint_url": "http://${HOST}:9000"}}

.github/workflows/main.yml

@@ -0,0 +1,28 @@
+---
+name: Build
+
+on: 
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 0 * * 0'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set env
+        run: |
+          rm .env
+          mv .env-gha .env
+      - name: Build
+        run: |
+          docker-compose pull && docker-compose build
+      - name: Generate
+        run: ./generate.sh
+      - name: Start Upload and Run benchmark
+        run: ./test.sh
+      - name: Check logs
+        run: docker-compose logs
+        if: ${{ failure() }}

benchmark/Dockerfile

@@ -2,6 +2,7 @@ FROM continuumio/miniconda3
 COPY environment.yml /tmp/environment.yml
 RUN conda update -n base -c defaults conda
 RUN conda env create -n benchmark -f /tmp/environment.yml
+RUN conda list -n benchmark
 
 # Note: docker-compose.yml mounts this file on each run
 #       to prevent stale copies.

benchmark/benchmark.py

@@ -183,7 +183,7 @@ def run(self, chunk_index):
                     try:
                         group = zarr.group(store=store)
                         data = group["0"]
-                    except KeyError:
+                    except (KeyError, ValueError):
                         # This likely happens due to dim
                         data = zarr.open(store, mode="r")
                     chunks = data.chunks

test.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+set -eu
+
+# start
+docker-compose up -d
+# upload
+docker-compose run --rm upload
+# run benchmark
+docker-compose run --rm benchmark -sv