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Adding testing on windows and osx #6

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Adding testing on windows and osx #6

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c2e33bd
Adding testing on windows and osx
blowekamp Apr 6, 2021
b5b9591
Use URI format for output of precomputed-pyramid
blowekamp Apr 6, 2021
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44 changes: 44 additions & 0 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,50 @@ jobs:
- name: Run trufflehog3 detector
run: |
trufflehog3 -v -c trufflehog3.yml . && echo "tufflehog3 OK"
test:
needs: linting_test
strategy:
matrix:
os: [ubuntu-latest, macos-latest, windows-latest]
python-version: [3.6, 3.7, 3.8]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Create LFS file list
run: |
git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
- name: Restore LFS cache
uses: actions/cache@v2
id: lfs-cache
with:
path: .git/lfs
key: lfs-v1-${{ hashFiles('.lfs-assets-id') }}
restore-keys:
lfs-v1-
- name: Git LFS Pull
run: |
git lfs pull
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements-dev.txt
pip install -e .
- name: Test with pytest
run: |
python -m pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml
- name: Upload pytest test results
uses: actions/upload-artifact@v1
with:
name: pytest-results-${{ matrix.python-version }}
path: junit/test-results-${{ matrix.python-version }}.xml
# Use always() to always run this step to publish test results when there are test failures
if: ${{ always() }}

test_package:
needs: linting_test
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3 changes: 2 additions & 1 deletion pytools/ng/mrc2ngpc.py
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Expand Up @@ -18,6 +18,7 @@
import os.path
import sys
import logging
from pathlib import Path


@click.command()
Expand Down Expand Up @@ -74,7 +75,7 @@ def main(input_image, output_precompute, flat, gzip):
if not gzip:
cmd_opts.append("--no-gzip")

cmd = ["volume-to-precomputed-pyramid"] + cmd_opts + [nifti_filename, output_precompute]
cmd = ["volume-to-precomputed-pyramid"] + cmd_opts + [nifti_filename, Path(output_precompute).as_uri()]

logger.info("Executing conversion of NIFTI to Neruoglancer precompute pyramid...")
logger.debug(f"Executing: {cmd}")
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