Merge branch 'main' into chunksize_plots_sizeC_1

Author: joshmoore

.env

@@ -1,14 +1,23 @@
-MINIO_ACCESS_KEY=minioadmin
-MINIO_SECRET_KEY=minioadmin
+AWS_ACCESS_KEY_ID=minioadmin
+AWS_SECRET_ACCESS_KEY=minioadmin
+BUCKET=ngff-latency-benchmark
 HOST=nginx
-XY=32768
-Z=1
-C=32
-T=1
-XC=256
-ZC=1
+
+XY=1024
+Z=1024
+C=1
+T=100
+XC=32
+ZC=32
+ROOT=/var/lib/docker
 ROOT=/uod/idr-scratch/ngff-latency-benchmark
-DIR=${ROOT}/${XY}-Z-${Z}-T-${T}-C-${C}-XYC-${XC}-ZC-${ZC}
-BASE=IMS_XY-${XY}-Z-${Z}-T-${T}-C-${C}-XYC-${XC}-ZC-${ZC}
-ROUNDS=5
-TEST_REPEATS=10
+ROOT=/uod/idr/scratch/idr1-slot2/ngff-latency-benchmark
+ROOT=/home/ubuntu/ngff-latency-benchmark
+
+NAME=${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"}}

.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() }}

.isort.cfg

@@ -1,2 +1,2 @@
 [settings]
-known_third_party = fsspec,h5py,matplotlib,numpy,pandas,pytest,requests,s3fs,seaborn,tifffile,zarr
+known_third_party = fsspec,h5py,matplotlib,numpy,pandas,ptitprince,pytest,requests,s3fs,seaborn,tifffile,zarr

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
     rev: 5.3.2
     hooks:
       - id: isort
+        args: ["--profile", "black"]
 
   - repo: https://github.com/ambv/black
     rev: 20.8b1

README.md

@@ -1,4 +1,6 @@
-# How to use this repository
+[![DOI](https://zenodo.org/badge/329595844.svg)](https://zenodo.org/badge/latestdoi/329595844)
+
+# OME-NGFF: latency benchmark
 
 To get started, clone this repository locally:
 ```
@@ -17,16 +19,6 @@ You will likely want to adjust the parameters in `.env` first, then run:
 which will run several docker-compose commands in a row. This could take
 a substantial amount of time depending on your parameters.
 
-## Or, alternatively download a sample file
-
-```
-mkdir data
-cd data
-../retina.sh
-```
-
-If you choose to use `retina_large`, you will also need to adjust the parameters in `.env`.
-
 
 ## Then, start S3 and upload the data
 

benchmark/Dockerfile

@@ -2,16 +2,17 @@ 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.
 COPY benchmark.sh /benchmark/benchmark.sh
 COPY benchmark.py /benchmark/benchmark.py
-COPY plot_results.py /benchmarks/plot_results.py
+COPY plot_results.py /benchmark/plot_results.py
 
-# see https://github.com/zarr-developers/zarr-python/pull/699
-RUN conda run -n benchmark pip install git+https://github.com/joshmoore/zarr-python@key-sep#egg=zarr
 RUN conda run -n benchmark pip install pytest-profiling
 RUN conda run -n benchmark pip install seaborn
+RUN conda run -n benchmark pip install pytest-csv
+RUN conda run -n benchmark pip install ptitprince
 
 ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "benchmark", "bash", "/benchmark/benchmark.sh"]