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tests.yml
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name: Run tests
on:
push:
branches: [ "dev" ]
pull_request:
branches: [ "dev" ]
permissions:
contents: read
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
build:
runs-on: ubuntu-latest
continue-on-error: true
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10"]
steps:
- uses: actions/checkout@v3
- name: Set up Python 3
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Sanity check that the py4DSTEM module imports
id: install
run: |
pip install .
python -c "import py4DSTEM; print(py4DSTEM.__version__)"
cache:
needs: build
runs-on: ubuntu-latest
continue-on-error: true
strategy:
fail-fast: false
matrix:
python-version: ["3.8"]
steps:
- uses: actions/checkout@v3
- name: Set up Python 3
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Checkout latest from tutorials
uses: actions/checkout@v3
with:
repository: py4DSTEM/py4DSTEM_tutorials
path: './py4DSTEM_tutorials'
- name: Install download dependencies
run: |
python -m pip install gdown jupyter
- name: Cache data files
id: cache-data
uses: actions/cache@v3
env:
cache-name: cache-data
with:
path: data
key: ${{ env.cache-name }}-${{ hashFiles('./py4DSTEM_tutorials/**/.ipynb') }}
- if: ${{ steps.cache-data.outputs.cache-hit != 'true' }}
name: Download tutorial data
uses: jannekem/run-python-script-action@v1
continue-on-error: true
with:
script: |
import json
import os
import shutil
import gdown
from nbconvert.preprocessors import ExecutePreprocessor, CellExecutionError
import nbformat
data_dir = os.path.abspath("data")
if not os.path.exists(data_dir):
os.makedirs(data_dir)
notebooks_dir = os.path.abspath("./py4DSTEM_tutorials/notebooks/")
google_url = 'https://drive.google.com'
downloads = {}
notebooks = sorted([p.name for p in os.scandir(notebooks_dir) if '.ipynb' in p.name and p.is_file()])
failures = 0
for nb_file in notebooks:
downloads[nb_file] = []
print("\tChecking for downloads and hardcoded paths in {}".format(nb_file))
with open(os.path.join(notebooks_dir, nb_file), 'r') as f:
nb = nbformat.read(f, as_version=4)
for i in range(len(nb['cells'])):
text = nb['cells'][i]['source']
if google_url in text:
lines = text.split()
urls = [x.strip() for x in lines if google_url in x]
# download file
print("\tDownloading input files for {}".format(nb_file))
for u in urls:
download_url = u.split('(')[1][:-1]
name = gdown.download(url=download_url, fuzzy=True)
if name is not None:
destination = os.path.join(data_dir, name)
shutil.move(name, destination)
downloads[nb_file].append(destination)
else:
print("Unable to download {}".format(download_url))
failures += 1
with open(os.path.join(data_dir, 'download_files.json'), 'w') as f:
json.dump(downloads, f)
print(json.dumps(downloads))
print("{}: {}".format(data_dir, os.listdir(data_dir)))
if failures > 0:
import sys
sys.exit(1)
test:
needs: [build, cache]
runs-on: ubuntu-latest
continue-on-error: true
strategy:
fail-fast: false
matrix:
python-version: ["3.8", "3.9", "3.10"]
steps:
- uses: actions/checkout@v3
- name: Set up Python 3
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
- name: Checkout tutorials
uses: actions/checkout@v3
with:
repository: py4DSTEM/py4DSTEM_tutorials
path: './py4DSTEM_tutorials'
- name: Install tutorial dependencies
run: |
python -m pip install .
python -m pip install "jedi==0.17.2" "dask[complete]" pymatgen gdown jupyter
- name: Get cached data files
uses: actions/cache@v3
env:
cache-name: cache-data
with:
path: data
key: ${{ env.cache-name }}-${{ hashFiles('./py4DSTEM_tutorials/**/.ipynb') }}
- name: Run tutorial notebooks
uses: jannekem/run-python-script-action@v1
with:
script: |
import json
import os
import re
import traceback
from nbconvert.preprocessors import ExecutePreprocessor, CellExecutionError
import nbformat
data_dir = os.path.abspath("data")
print("{}: {}".format(data_dir, os.listdir(data_dir)))
notebooks_dir = os.path.abspath("./py4DSTEM_tutorials/notebooks/")
os.chdir(notebooks_dir)
google_url = 'https://drive.google.com'
with open(os.path.join(data_dir, 'download_files.json'), 'r') as f:
downloads = json.load(f)
print(downloads)
notebooks = sorted([p.name for p in os.scandir(notebooks_dir) if '.ipynb' in p.name and p.is_file()])
failed = []
succeeded = []
for nb_file in notebooks:
print("Testing {}".format(nb_file))
print("{} in downloads: {}, {}".format(nb_file, nb_file in downloads, downloads[nb_file]))
changed = False
print("\tChecking for downloads and hardcoded paths in {}".format(nb_file))
with open(nb_file, 'r') as f:
nb = nbformat.read(f, as_version=4)
for i in range(len(nb['cells'])):
text = nb['cells'][i]['source']
replaced_text = ""
if 'file_' in text:
results = [m for m in re.finditer(r'file_\w+\s*=\s*[r]?[\'\"](.*)[\'\"]', text)]
for r in results:
name_matches = 0
for fpath in downloads[nb_file]:
fname = os.path.split(fpath)[-1]
if fname in r.group():
parts = r.group().split('=')
replacement = "{} = '{}'".format(parts[0], fpath)
name_matches += 1
text = text.replace(r.group(), replacement)
changed = True
break
nb['cells'][i]['source'] = text
if changed:
print("\tWriting path updates back to {}".format(nb_file))
with open(nb_file, 'w', encoding='utf-8') as f:
nbformat.write(nb, f)
print("\tExecuting {}".format(nb_file))
try:
ep = ExecutePreprocessor(timeout=600, kernel_name='python3')
ep.preprocess(nb, {'metadata': {'path': notebooks_dir}})
succeeded.append(nb_file)
except Exception as e:
failed.append(nb_file)
tb = "\n".join(["\t{}".format(line) for line in traceback.format_exc().splitlines()])
print("\n\t{0} {1} {0}\n\n{2}\n\t{0} {1} {0}\n".format("*"*20, nb_file, tb))
print("{} Notebooks ran without errors.".format(len(succeeded)))
print("{} Notebooks failed with errors".format(len(failed)))
if len(failed) > 0:
import sys
sys.exit(1)