Create tests.yml #1
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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) |