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[flake8] | ||
# 127 is width of the Github code viewer, | ||
# black default is 88 so this will only warn about comments >127 | ||
max-line-length = 127 | ||
# Ignore errors due to incompatibility with black | ||
#https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html | ||
extend-ignore = E203,E701 |
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name: dimension_reduction_pca | ||
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on: | ||
push: | ||
branches: [ main ] | ||
pull_request: | ||
branches: [ main ] | ||
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jobs: | ||
test: | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- uses: actions/checkout@v4 | ||
- name: Set up Python 3.9 | ||
uses: actions/setup-python@v5 | ||
with: | ||
python-version: 3.9 | ||
cache: 'pip' | ||
- name: Install dependencies | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install . | ||
pip install .[dev] | ||
- name: Lint with flake8 | ||
run: | | ||
# stop the build if there are Python syntax errors or undefined names | ||
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | ||
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | ||
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | ||
- name: Test with pytest | ||
run: | | ||
pytest |
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*~ | ||
data/output/ | ||
data/upload/ | ||
.file_manager_vars | ||
data/upload/ | ||
build/ | ||
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.DS_Store | ||
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# Byte-compiled / optimized / DLL files | ||
__pycache__/ | ||
data/output/ | ||
data/upload/ | ||
*.py[cod] | ||
*$py.class | ||
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# C extensions | ||
*.so | ||
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# Distribution / packaging | ||
.Python | ||
build/ | ||
develop-eggs/ | ||
dist/ | ||
downloads/ | ||
eggs/ | ||
.eggs/ | ||
lib/ | ||
lib64/ | ||
parts/ | ||
sdist/ | ||
var/ | ||
wheels/ | ||
share/python-wheels/ | ||
*.egg-info/ | ||
.installed.cfg | ||
*.egg | ||
MANIFEST | ||
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# PyInstaller | ||
# Usually these files are written by a python script from a template | ||
# before PyInstaller builds the exe, so as to inject date/other infos into it. | ||
*.manifest | ||
*.spec | ||
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# Installer logs | ||
pip-log.txt | ||
pip-delete-this-directory.txt | ||
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# Unit test / coverage reports | ||
htmlcov/ | ||
.tox/ | ||
.nox/ | ||
.coverage | ||
.coverage.* | ||
.cache | ||
nosetests.xml | ||
coverage.xml | ||
*.cover | ||
*.py,cover | ||
.hypothesis/ | ||
.pytest_cache/ | ||
cover/ | ||
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# Translations | ||
*.mo | ||
*.pot | ||
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# Django stuff: | ||
*.log | ||
local_settings.py | ||
db.sqlite3 | ||
db.sqlite3-journal | ||
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# Flask stuff: | ||
instance/ | ||
.webassets-cache | ||
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# Scrapy stuff: | ||
.scrapy | ||
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# Sphinx documentation | ||
docs/_build/ | ||
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# PyBuilder | ||
.pybuilder/ | ||
target/ | ||
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# Jupyter Notebook | ||
.ipynb_checkpoints | ||
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# IPython | ||
profile_default/ | ||
ipython_config.py | ||
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# pyenv | ||
# For a library or package, you might want to ignore these files since the code is | ||
# intended to run in multiple environments; otherwise, check them in: | ||
# .python-version | ||
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# pipenv | ||
# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. | ||
# However, in case of collaboration, if having platform-specific dependencies or dependencies | ||
# having no cross-platform support, pipenv may install dependencies that don't work, or not | ||
# install all needed dependencies. | ||
#Pipfile.lock | ||
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# poetry | ||
# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. | ||
# This is especially recommended for binary packages to ensure reproducibility, and is more | ||
# commonly ignored for libraries. | ||
# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control | ||
#poetry.lock | ||
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# pdm | ||
# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. | ||
#pdm.lock | ||
# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it | ||
# in version control. | ||
# https://pdm.fming.dev/#use-with-ide | ||
.pdm.toml | ||
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm | ||
__pypackages__/ | ||
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# Celery stuff | ||
celerybeat-schedule | ||
celerybeat.pid | ||
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# SageMath parsed files | ||
*.sage.py | ||
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# Environments | ||
.env | ||
.venv | ||
env/ | ||
venv/ | ||
ENV/ | ||
env.bak/ | ||
venv.bak/ | ||
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# Spyder project settings | ||
.spyderproject | ||
.spyproject | ||
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# Rope project settings | ||
.ropeproject | ||
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# mkdocs documentation | ||
/site | ||
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# mypy | ||
.mypy_cache/ | ||
.dmypy.json | ||
dmypy.json | ||
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# Pyre type checker | ||
.pyre/ | ||
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# pytype static type analyzer | ||
.pytype/ | ||
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# Cython debug symbols | ||
cython_debug/ | ||
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# PyCharm | ||
# JetBrains specific template is maintained in a separate JetBrains.gitignore that can | ||
# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore | ||
# and can be added to the global gitignore or merged into this file. For a more nuclear | ||
# option (not recommended) you can uncomment the following to ignore the entire idea folder. | ||
#.idea/ | ||
EC-lab | ||
lab book | ||
LTspice files | ||
TRS | ||
proc | ||
ESpectrum Stream 00012.bin | ||
Frame Stream 00012.bin | ||
Metadata 00012.json | ||
test.zarr | ||
misc | ||
test_fast.zarr | ||
zarr_utils.py | ||
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data/ | ||
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.vscode/ |
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default_language_version: | ||
python: python3 | ||
repos: | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v4.5.0 | ||
hooks: | ||
- id: trailing-whitespace | ||
- id: end-of-file-fixer | ||
- id: check-ast | ||
- id: check-case-conflict | ||
- id: check-merge-conflict | ||
- id: check-symlinks | ||
- id: check-yaml | ||
- id: debug-statements | ||
- repo: https://github.com/gitguardian/ggshield | ||
rev: v1.25.0 | ||
hooks: | ||
- id: ggshield | ||
language_version: python3 | ||
stages: [commit] | ||
# Using this mirror lets us use mypyc-compiled black, which is about 2x faster | ||
- repo: https://github.com/psf/black-pre-commit-mirror | ||
rev: 24.2.0 | ||
hooks: | ||
- id: black | ||
- repo: https://github.com/pycqa/flake8 | ||
rev: 7.0.0 | ||
hooks: | ||
- id: flake8 | ||
- repo: https://github.com/pycqa/isort | ||
rev: 5.13.2 | ||
hooks: | ||
- id: isort | ||
args: ["--profile", "black"] |
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FROM python:3.9 | ||
LABEL maintainer="THE MLEXCHANGE TEAM" | ||
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RUN apt-get update | ||
RUN pip3 install --upgrade pip &&\ | ||
pip3 install . | ||
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WORKDIR /app/work | ||
ENV HOME /app/work | ||
ENV PYTHONUNBUFFERED=1 | ||
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COPY umap_run.py umap_run.py | ||
COPY src src | ||
CMD ["echo", "running umap"] |
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# Example for parameters to excecute | ||
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# I/O | ||
io_parameters: | ||
uid_retrieve: # uid for feature vectors from autoencoder | ||
data_type: 'file' # either "file" or "tiled" | ||
root_uri: https://tiled-seg.als.lbl.gov/api/v1/metadata/reconstruction/rec20190524_085542_clay_testZMQ_8bit | ||
data_uris: ['20190524_085542_clay_testZMQ_'] | ||
data_tiled_api_key: | ||
result_tiled_uri: http://localhost:8888 | ||
result_tiled_api_key: | ||
uid_save: | ||
output_dir: 'data/output' | ||
load_model_path: | ||
save_model_path: | ||
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model_parameters: | ||
n_components: 2 | ||
min_dist: 0.1 | ||
n_neighbors: 5 |
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