From 0cd0ec841d8abda06cb88cdbb169084e8700f034 Mon Sep 17 00:00:00 2001 From: Robbi Bishop-Taylor Date: Tue, 19 Dec 2023 23:29:15 +0000 Subject: [PATCH] Revert coverage copy, use pre-gen requirements.txt --- Dockerfile | 19 +- requirements-testing.txt | 717 +++++++++++++++++++++++++++++++++++++++ tests/run_tests | 6 +- 3 files changed, 732 insertions(+), 10 deletions(-) create mode 100644 requirements-testing.txt diff --git a/Dockerfile b/Dockerfile index 63e43c2..3358c0e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,14 +20,23 @@ RUN apt-get update && \ apt-get autoremove && \ rm -rf /var/lib/{apt,dpkg,cache,log} -# Install pip-tools -RUN pip install pip-tools +# # Install pip-tools +# RUN pip install pip-tools + +# # Pip installation +# RUN mkdir -p /conf +# COPY requirements.in /conf/ +# RUN pip-compile --extra-index-url=https://packages.dea.ga.gov.au/ --output-file=/conf/requirements.txt /conf/requirements.in +# RUN pip install -r /conf/requirements.txt + +#### TEMPORARY TEST # Pip installation RUN mkdir -p /conf -COPY requirements.in /conf/ -RUN pip-compile --extra-index-url=https://packages.dea.ga.gov.au/ --output-file=/conf/requirements.txt /conf/requirements.in -RUN pip install -r /conf/requirements.txt +COPY requirements-testing.txt /conf/ +RUN pip install -r /conf/requirements-testing.txt + +#### TEMPORARY TEST # Copy source code and install it RUN mkdir -p /code diff --git a/requirements-testing.txt b/requirements-testing.txt new file mode 100644 index 0000000..7ed9dee --- /dev/null +++ b/requirements-testing.txt @@ -0,0 +1,717 @@ +# +# This file is autogenerated by pip-compile with Python 3.10 +# by the following command: +# +# pip-compile --extra-index-url=https://packages.dea.ga.gov.au/ --output-file=requirements.txt requirements.in +# +--extra-index-url https://packages.dea.ga.gov.au/ + +affine==2.4.0 + # via + # datacube + # datacube-ows + # odc-algo + # odc-geo + # odc-stac + # rasterio + # rasterstats +aiohttp==3.9.1 + # via + # -r requirements.in + # dea-tools +aiosignal==1.3.1 + # via aiohttp +annotated-types==0.6.0 + # via pydantic +asttokens==2.4.1 + # via stack-data +async-timeout==4.0.3 + # via aiohttp +attrs==23.1.0 + # via + # aiohttp + # datacube + # fiona + # jsonschema + # rasterio + # referencing +babel==2.14.0 + # via + # datacube-ows + # flask-babel +blinker==1.7.0 + # via flask +boto3==1.34.4 + # via + # datacube + # dea-tools +botocore==1.34.4 + # via + # -r requirements.in + # boto3 + # datacube + # dea-tools + # s3transfer +bottleneck==1.3.7 + # via + # datacube + # xskillscore +branca==0.7.0 + # via + # dea-tools + # folium + # ipyleaflet +cachetools==5.3.2 + # via + # datacube + # odc-geo +certifi==2023.11.17 + # via + # fiona + # netcdf4 + # pyproj + # rasterio + # requests +cffi==1.16.0 + # via timezonefinder +cftime==1.6.3 + # via + # netcdf4 + # xskillscore +charset-normalizer==3.3.2 + # via requests +ciso8601==2.3.1 + # via + # datacube + # dea-tools +click==8.1.3 + # via + # -r requirements.in + # click-plugins + # cligj + # dask + # datacube + # datacube-ows + # distributed + # fiona + # flask + # planetary-computer + # rasterio + # rasterstats +click-plugins==1.1.1 + # via + # fiona + # rasterio +cligj==0.7.2 + # via + # fiona + # rasterio + # rasterstats +cloudpickle==3.0.0 + # via + # dask + # dask-glm + # datacube + # distributed +colour==0.1.5 + # via datacube-ows +comm==0.2.0 + # via ipywidgets +contourpy==1.2.0 + # via matplotlib +coverage[toml]==7.3.3 + # via + # coverage + # pytest-cov +cycler==0.12.1 + # via matplotlib +dask[array,dataframe]==2023.12.1 + # via + # dask-glm + # dask-image + # dask-ml + # datacube + # dea-tools + # distributed + # odc-algo + # odc-stac + # xhistogram + # xskillscore +dask-glm==0.3.2 + # via dask-ml +dask-image==2023.3.0 + # via odc-algo +dask-ml==2023.3.24 + # via dea-tools +datacube[performance,s3]==1.8.13 + # via + # -r requirements.in + # datacube + # datacube-ows + # dea-tools + # odc-algo + # odc-ui +datacube-ows==1.8.36 + # via dea-tools +dea-tools==0.3.1.dev5 + # via -r requirements.in +decorator==5.1.1 + # via ipython +deepdiff==6.7.1 + # via datacube-ows +distributed==2023.12.1 + # via + # dask-glm + # dask-ml + # datacube + # odc-algo +exceptiongroup==1.2.0 + # via + # ipython + # pytest +executing==2.0.1 + # via stack-data +fiona==1.9.5 + # via + # dea-tools + # geopandas + # rasterstats +flask==3.0.0 + # via + # datacube-ows + # flask-babel + # prometheus-flask-exporter +flask-babel==4.0.0 + # via datacube-ows +folium==0.15.1 + # via dea-tools +fonttools==4.47.0 + # via matplotlib +frozenlist==1.4.1 + # via + # aiohttp + # aiosignal +fsspec==2023.12.2 + # via + # dask + # datacube-ows +geoalchemy2==0.14.2 + # via + # datacube + # datacube-ows +geographiclib==2.0 + # via geopy +geopandas==0.13.2 + # via + # -r requirements.in + # dea-tools +geopy==2.4.1 + # via dea-tools +greenlet==3.0.2 + # via sqlalchemy +h3==3.7.6 + # via timezonefinder +hdstats==0.2.1 + # via dea-tools +idna==3.6 + # via + # requests + # yarl +imageio==2.33.1 + # via + # pims + # scikit-image +importlib-metadata==7.0.0 + # via dask +iniconfig==2.0.0 + # via pytest +ipyleaflet==0.18.1 + # via odc-ui +ipython==8.18.1 + # via + # ipywidgets + # jupyter-ui-poll + # odc-ui +ipywidgets==8.1.1 + # via + # ipyleaflet + # odc-ui +iso8601==2.1.0 + # via pyows +itsdangerous==2.1.2 + # via flask +jedi==0.19.1 + # via ipython +jinja2==3.1.2 + # via + # branca + # distributed + # flask + # flask-babel + # folium +jmespath==1.0.1 + # via + # boto3 + # botocore +joblib==1.3.2 + # via + # dea-tools + # scikit-learn +jsonschema==4.20.0 + # via + # datacube + # pystac +jsonschema-specifications==2023.11.2 + # via jsonschema +jupyter-ui-poll==0.2.2 + # via odc-ui +jupyterlab-widgets==3.0.9 + # via ipywidgets +kiwisolver==1.4.5 + # via matplotlib +lark==1.1.8 + # via + # datacube + # datacube-ows +llvmlite==0.41.1 + # via numba +locket==1.0.0 + # via + # distributed + # partd +lxml==4.9.4 + # via + # datacube-ows + # dea-tools + # owslib + # pyows + # pytmd +markupsafe==2.1.3 + # via + # jinja2 + # werkzeug +matplotlib==3.7.1 + # via + # -r requirements.in + # datacube-ows + # dea-tools + # odc-ui + # seaborn +matplotlib-inline==0.1.6 + # via ipython +msgpack==1.0.7 + # via distributed +multidict==6.0.4 + # via + # aiohttp + # yarl +multipledispatch==1.0.0 + # via + # dask-glm + # dask-ml +netcdf4==1.6.5 + # via + # datacube + # pytmd +networkx==3.2.1 + # via scikit-image +numba==0.58.1 + # via + # dask-ml + # sparse + # xskillscore +numexpr==2.8.8 + # via odc-algo +numpy==1.24.3 + # via + # -r requirements.in + # bottleneck + # cftime + # contourpy + # dask + # dask-image + # dask-ml + # datacube + # datacube-ows + # dea-tools + # folium + # hdstats + # imageio + # matplotlib + # netcdf4 + # numba + # numexpr + # odc-algo + # odc-geo + # odc-stac + # odc-ui + # pandas + # pims + # properscoring + # pygeos + # pytmd + # pywavelets + # rasterio + # rasterstats + # scikit-image + # scikit-learn + # scipy + # seaborn + # shapely + # snuggs + # sparse + # tifffile + # timezonefinder + # xarray + # xhistogram + # xskillscore +odc-algo==0.2.3 + # via + # -r requirements.in + # odc-ui +odc-geo==0.4.0 + # via + # -r requirements.in + # dea-tools + # odc-stac +odc-stac==0.3.8 + # via dea-tools +odc-ui==0.2.1 + # via + # -r requirements.in + # dea-tools +ordered-set==4.1.0 + # via deepdiff +owslib==0.29.3 + # via dea-tools +packaging==23.2 + # via + # dask + # dask-ml + # datacube + # dea-tools + # distributed + # geoalchemy2 + # geopandas + # matplotlib + # planetary-computer + # pytest + # scikit-image + # setuptools-scm + # xarray +pandas==1.5.3 + # via + # -r requirements.in + # dask + # dask-ml + # datacube + # dea-tools + # geopandas + # odc-stac + # odc-ui + # seaborn + # sunriset + # xarray +parso==0.8.3 + # via jedi +partd==1.4.1 + # via dask +pexpect==4.9.0 + # via ipython +pillow==10.1.0 + # via + # datacube-ows + # imageio + # matplotlib + # scikit-image +pims==0.6.1 + # via dask-image +planetary-computer==1.0.0 + # via dea-tools +pluggy==1.3.0 + # via pytest +prometheus-client==0.19.0 + # via prometheus-flask-exporter +prometheus-flask-exporter==0.23.0 + # via datacube-ows +prompt-toolkit==3.0.43 + # via ipython +properscoring==0.1 + # via xskillscore +psutil==5.9.7 + # via distributed +psycopg2==2.9.9 + # via + # datacube + # datacube-ows +ptyprocess==0.7.0 + # via pexpect +pure-eval==0.2.2 + # via stack-data +pycparser==2.21 + # via cffi +pydantic==2.5.2 + # via planetary-computer +pydantic-core==2.14.5 + # via pydantic +pygeos==0.14 + # via -r requirements.in +pygments==2.17.2 + # via ipython +pyows==0.2.7 + # via datacube-ows +pyparsing==3.1.1 + # via + # datacube-ows + # matplotlib + # snuggs +pyproj==3.4.1 + # via + # -r requirements.in + # datacube + # dea-tools + # geopandas + # odc-geo + # pytmd +pystac[validation]==1.9.0 + # via + # odc-stac + # planetary-computer + # pystac-client +pystac-client==0.7.5 + # via + # dea-tools + # planetary-computer +pytest==7.4.3 + # via + # -r requirements.in + # pytest-cov + # pytest-dependency +pytest-cov==4.1.0 + # via -r requirements.in +pytest-dependency==0.5.1 + # via -r requirements.in +python-dateutil==2.8.2 + # via + # botocore + # datacube + # datacube-ows + # dea-tools + # matplotlib + # owslib + # pandas + # pystac + # pystac-client + # pytmd +python-dotenv==1.0.0 + # via planetary-computer +python-slugify==8.0.1 + # via datacube-ows +pytmd==2.0.5 + # via + # -r requirements.in + # dea-tools +pytz==2023.3 + # via + # -r requirements.in + # datacube-ows + # dea-tools + # flask-babel + # owslib + # pandas + # planetary-computer + # sunriset +pywavelets==1.5.0 + # via scikit-image +pyyaml==6.0.1 + # via + # dask + # datacube + # distributed + # owslib + # pytmd +rasterio==1.3.4 + # via + # -r requirements.in + # datacube + # datacube-ows + # dea-tools + # odc-algo + # odc-stac + # odc-ui + # rasterstats +rasterstats==0.19.0 + # via dea-tools +referencing==0.32.0 + # via + # jsonschema + # jsonschema-specifications +regex==2023.10.3 + # via datacube-ows +requests==2.31.0 + # via + # datacube-ows + # dea-tools + # folium + # owslib + # planetary-computer + # pystac-client +rpds-py==0.15.2 + # via + # jsonschema + # referencing +ruamel-yaml==0.18.5 + # via datacube +ruamel-yaml-clib==0.2.8 + # via ruamel-yaml +s3transfer==0.9.0 + # via boto3 +scikit-image==0.19.3 + # via + # -r requirements.in + # dea-tools + # odc-algo +scikit-learn==1.2.2 + # via + # -r requirements.in + # dask-glm + # dask-ml + # dea-tools + # xskillscore +scipy==1.10.1 + # via + # -r requirements.in + # dask-glm + # dask-image + # dask-ml + # datacube-ows + # dea-tools + # hdstats + # properscoring + # pytmd + # scikit-image + # scikit-learn + # sparse + # xskillscore +seaborn==0.13.0 + # via -r requirements.in +setuptools-scm==8.0.4 + # via + # datacube-ows + # pytmd +shapely==2.0.1 + # via + # -r requirements.in + # datacube + # dea-tools + # geopandas + # odc-geo + # rasterstats +simplejson==3.19.2 + # via rasterstats +six==1.16.0 + # via + # asttokens + # fiona + # python-dateutil +slicerator==1.1.0 + # via pims +snuggs==1.4.7 + # via rasterio +sortedcontainers==2.4.0 + # via distributed +sparse==0.14.0 + # via dask-glm +sqlalchemy==1.4.50 + # via + # datacube + # geoalchemy2 +stack-data==0.6.3 + # via ipython +sunriset==1.0 + # via -r requirements.in +tblib==3.0.0 + # via distributed +text-unidecode==1.3 + # via python-slugify +threadpoolctl==3.2.0 + # via scikit-learn +tifffile==2023.12.9 + # via + # dask-image + # scikit-image +timezonefinder==6.2.0 + # via datacube-ows +tomli==2.0.1 + # via + # coverage + # pytest + # setuptools-scm +toolz==0.12.0 + # via + # dask + # datacube + # distributed + # odc-algo + # odc-stac + # partd + # xskillscore +tornado==6.4 + # via distributed +tqdm==4.65.0 + # via + # -r requirements.in + # dea-tools +traitlets==5.14.0 + # via + # comm + # ipython + # ipywidgets + # matplotlib-inline + # traittypes +traittypes==0.2.1 + # via ipyleaflet +typing-extensions==4.9.0 + # via + # pydantic + # pydantic-core + # setuptools-scm +urllib3==2.0.7 + # via + # botocore + # distributed + # requests +wcwidth==0.2.12 + # via prompt-toolkit +werkzeug==3.0.1 + # via flask +widgetsnbextension==4.0.9 + # via ipywidgets +xarray==2023.1.0 + # via + # -r requirements.in + # datacube + # datacube-ows + # dea-tools + # odc-algo + # odc-stac + # odc-ui + # xhistogram + # xskillscore +xhistogram==0.3.2 + # via xskillscore +xskillscore==0.0.24 + # via -r requirements.in +xyzservices==2023.10.1 + # via + # folium + # ipyleaflet +yarl==1.9.4 + # via aiohttp +zict==3.0.0 + # via distributed +zipp==3.17.0 + # via importlib-metadata + +# The following packages are considered to be unsafe in a requirements file: +# setuptools diff --git a/tests/run_tests b/tests/run_tests index e68afe4..a8652d4 100644 --- a/tests/run_tests +++ b/tests/run_tests @@ -1,8 +1,4 @@ #!/bin/sh # Run integration tests and generate code coverage -pytest --cov=intertidal --cov-report=xml tests/integration - -# Copy code coverage to artifacts directory so they are -# accessible outside docker container via mounted volume -cp coverage.xml /mnt/artifacts/ +pytest --cov=intertidal --cov-report=xml tests/integration \ No newline at end of file