зеркало из https://github.com/microsoft/hi-ml.git
ENH: Add openslide to cpath conda environment (#646)
Add openslide to `hi-ml-cpath conda` environment, so that code can use either `cucim` or `openslide` as backend. Fixed a bug in github action `prepare_cpath_environment`: updated environment was not getting activated
This commit is contained in:
Anton Schwaighofer
GitHub
Родитель
bc327980f1
Коммит
b711b2b545
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|
@ -23,17 +23,24 @@ runs:
|
|||
if: steps.cache-conda.outputs.cache-hit != 'true'
|
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with:
|
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environment-file: hi-ml-cpath/environment.yml
|
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activate-environment: HimlHisto
|
||||
|
||||
# Modify the path to point to the cached Conda environment. This is effectively also what `conda activate` does.
|
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- name: Activate cached environment
|
||||
# Modify the path to point to the new or cached Conda environment.
|
||||
# This is effectively also what `conda activate` does.
|
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- name: Activate environment
|
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shell: bash
|
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if: steps.cache-conda.outputs.cache-hit == 'true'
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run: echo "/usr/share/miniconda/envs/HimlHisto/bin" >> $GITHUB_PATH
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run: |
|
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echo "Adding Conda bin folder to path"
|
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echo "/usr/share/miniconda/envs/HimlHisto/bin" >> $GITHUB_PATH
|
||||
|
||||
- name: Conda info
|
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shell: bash
|
||||
run: conda info
|
||||
|
||||
- name: Show active Python path
|
||||
shell: bash
|
||||
run: which python
|
||||
|
||||
- name: Install hi-ml locally
|
||||
shell: bash
|
||||
run: |
|
||||
|
|
|
|||
|
|
@ -6,18 +6,24 @@ channels:
|
|||
- conda-forge
|
||||
- defaults
|
||||
dependencies:
|
||||
- _libgcc_mutex=0.1=main
|
||||
- _openmp_mutex=5.1=1_gnu
|
||||
- _libgcc_mutex=0.1=conda_forge
|
||||
- _openmp_mutex=4.5=2_gnu
|
||||
- blas=1.0=mkl
|
||||
- bzip2=1.0.8=h7b6447c_0
|
||||
- ca-certificates=2022.07.19=h06a4308_0
|
||||
- certifi=2022.6.15=py39h06a4308_0
|
||||
- ca-certificates=2022.10.11=h06a4308_0
|
||||
- cairo=1.16.0=hf32fb01_1
|
||||
- certifi=2022.9.24=py39h06a4308_0
|
||||
- cudatoolkit=11.3.1=h2bc3f7f_2
|
||||
- ffmpeg=4.2.2=h20bf706_0
|
||||
- freetype=2.11.0=h70c0345_0
|
||||
- fontconfig=2.13.1=hef1e5e3_1
|
||||
- freetype=2.12.1=h4a9f257_0
|
||||
- gdk-pixbuf=2.42.6=h04a7f16_0
|
||||
- gettext=0.21.0=hf68c758_0
|
||||
- giflib=5.2.1=h7b6447c_0
|
||||
- glib=2.68.2=h36276a3_0
|
||||
- gmp=6.2.1=h295c915_3
|
||||
- gnutls=3.6.15=he1e5248_0
|
||||
- icu=58.2=he6710b0_3
|
||||
- intel-openmp=2021.4.0=h06a4308_3561
|
||||
- jpeg=9e=h7f8727e_0
|
||||
- lame=3.100=h7b6447c_0
|
||||
|
|
@ -26,19 +32,24 @@ dependencies:
|
|||
- lerc=3.0=h295c915_0
|
||||
- libdeflate=1.8=h7f8727e_5
|
||||
- libffi=3.3=he6710b0_2
|
||||
- libgcc-ng=11.2.0=h1234567_1
|
||||
- libgomp=11.2.0=h1234567_1
|
||||
- libgcc-ng=12.2.0=h65d4601_19
|
||||
- libglib=2.68.2=h3e27bee_0
|
||||
- libgomp=12.2.0=h65d4601_19
|
||||
- libiconv=1.16=h7f8727e_2
|
||||
- libidn2=2.3.2=h7f8727e_0
|
||||
- libopus=1.3.1=h7b6447c_0
|
||||
- libpng=1.6.37=hbc83047_0
|
||||
- libstdcxx-ng=11.2.0=h1234567_1
|
||||
- libtasn1=4.16.0=h27cfd23_0
|
||||
- libtiff=4.4.0=hecacb30_0
|
||||
- libtiff=4.4.0=hecacb30_1
|
||||
- libunistring=0.9.10=h27cfd23_0
|
||||
- libuuid=1.0.3=h7f8727e_2
|
||||
- libuv=1.40.0=h7b6447c_0
|
||||
- libvpx=1.7.0=h439df22_0
|
||||
- libwebp=1.2.2=h55f646e_0
|
||||
- libwebp-base=1.2.2=h7f8727e_0
|
||||
- libwebp=1.2.4=h11a3e52_0
|
||||
- libwebp-base=1.2.4=h5eee18b_0
|
||||
- libxcb=1.15=h7f8727e_0
|
||||
- libxml2=2.9.14=h74e7548_0
|
||||
- lz4-c=1.9.3=h295c915_1
|
||||
- mkl=2021.4.0=h06a4308_640
|
||||
- mkl-service=2.4.0=py39h7f8727e_0
|
||||
|
|
@ -47,59 +58,68 @@ dependencies:
|
|||
- ncurses=6.3=h5eee18b_3
|
||||
- nettle=3.7.3=hbbd107a_1
|
||||
- openh264=2.1.1=h4ff587b_0
|
||||
- openssl=1.1.1q=h7f8727e_0
|
||||
- openjpeg=2.4.0=h3ad879b_0
|
||||
- openslide=3.4.1=h978ee9a_4
|
||||
- openslide-python=1.2.0=py39hb9d737c_2
|
||||
- openssl=1.1.1s=h7f8727e_0
|
||||
- pcre=8.45=h295c915_0
|
||||
- pip=20.1.1=py_1
|
||||
- pixman=0.40.0=h7f8727e_1
|
||||
- python=3.9.13
|
||||
- python_abi=3.9=2_cp39
|
||||
- pytorch=1.10.0=py3.9_cuda11.3_cudnn8.2.0_0
|
||||
- pytorch-mutex=1.0=cuda
|
||||
- readline=8.1.2=h7f8727e_1
|
||||
- readline=8.2=h5eee18b_0
|
||||
- six=1.16.0=pyhd3eb1b0_1
|
||||
- sqlite=3.39.2=h5082296_0
|
||||
- sqlite=3.39.3=h5082296_0
|
||||
- tk=8.6.12=h1ccaba5_0
|
||||
- torchvision=0.11.1=py39_cu113
|
||||
- typing_extensions=4.3.0=py39h06a4308_0
|
||||
- tzdata=2022a=hda174b7_0
|
||||
- tzdata=2022f=h04d1e81_0
|
||||
- x264=1!157.20191217=h7b6447c_0
|
||||
- xz=5.2.5=h7f8727e_1
|
||||
- zlib=1.2.12=h7f8727e_2
|
||||
- xz=5.2.6=h5eee18b_0
|
||||
- zlib=1.2.13=h5eee18b_0
|
||||
- zstd=1.5.2=ha4553b6_0
|
||||
- pip:
|
||||
- absl-py==1.2.0
|
||||
- absl-py==1.3.0
|
||||
- adal==1.2.7
|
||||
- aiohttp==3.8.1
|
||||
- aiosignal==1.2.0
|
||||
- aiohttp==3.8.3
|
||||
- aiosignal==1.3.1
|
||||
- alabaster==0.7.12
|
||||
- alembic==1.8.1
|
||||
- applicationinsights==0.11.10
|
||||
- argcomplete==2.0.0
|
||||
- astroid==2.12.5
|
||||
- astroid==2.12.12
|
||||
- async-timeout==4.0.2
|
||||
- attrs==21.4.0
|
||||
- azure-ai-ml==1.1.0
|
||||
- azure-common==1.1.28
|
||||
- azure-core==1.25.1
|
||||
- azure-core==1.26.1
|
||||
- azure-graphrbac==0.61.1
|
||||
- azure-identity==1.7.0
|
||||
- azure-mgmt-authorization==2.0.0
|
||||
- azure-mgmt-containerregistry==10.0.0
|
||||
- azure-mgmt-core==1.3.0
|
||||
- azure-mgmt-core==1.3.1
|
||||
- azure-mgmt-keyvault==10.0.0
|
||||
- azure-mgmt-resource==21.1.0
|
||||
- azure-mgmt-resource==21.2.1
|
||||
- azure-mgmt-storage==20.0.0
|
||||
- azure-storage-blob==12.10.0
|
||||
- azure-storage-file-datalake==12.9.1
|
||||
- azure-storage-file-share==12.10.1
|
||||
- azureml-core==1.43.0
|
||||
- azureml-dataprep==4.0.4
|
||||
- azureml-dataprep-native==38.0.0
|
||||
- azureml-dataprep-rslex==2.6.3
|
||||
- azureml-dataset-runtime==1.43.0
|
||||
- azure-ai-ml>=0.1.0b3
|
||||
- azureml-mlflow>=1.46.0
|
||||
- azureml-mlflow==1.47.0
|
||||
- azureml-telemetry==1.43.0
|
||||
- azureml-tensorboard==1.43.0
|
||||
- azureml-train-core==1.43.0
|
||||
- azureml-train-restclients-hyperdrive==1.43.0
|
||||
- babel==2.10.3
|
||||
- babel==2.11.0
|
||||
- backports-tempfile==1.0
|
||||
- backports-weakref==1.0.post1
|
||||
- bcrypt==4.0.0
|
||||
- bcrypt==4.0.1
|
||||
- black==22.1.0
|
||||
- bleach==5.0.1
|
||||
- cachetools==4.2.4
|
||||
|
|
@ -108,67 +128,80 @@ dependencies:
|
|||
- charset-normalizer==2.1.1
|
||||
- click==8.1.3
|
||||
- cloudpickle==1.6.0
|
||||
- colorama==0.4.4
|
||||
- colorama==0.4.6
|
||||
- coloredlogs==15.0.1
|
||||
- conda-merge==0.1.5
|
||||
- contextlib2==21.6.0
|
||||
- coverage==6.3.2
|
||||
- cryptography==37.0.4
|
||||
- cryptography==38.0.3
|
||||
- cucim==22.4.0
|
||||
- cycler==0.11.0
|
||||
- databricks-cli==0.17.3
|
||||
- dataclasses-json==0.5.2
|
||||
- dill==0.3.5.1
|
||||
- dill==0.3.6
|
||||
- diskcache==5.4.0
|
||||
- distlib==0.3.6
|
||||
- distro==1.7.0
|
||||
- distro==1.8.0
|
||||
- docker==5.0.3
|
||||
- docutils==0.16
|
||||
- dotnetcore2==3.1.23
|
||||
- entrypoints==0.4
|
||||
- filelock==3.8.0
|
||||
- flake8==4.0.1
|
||||
- frozenlist==1.3.1
|
||||
- fsspec==2022.8.2
|
||||
- flask==2.2.2
|
||||
- frozenlist==1.3.3
|
||||
- fsspec==2022.10.0
|
||||
- fusepy==3.0.1
|
||||
- girder-client==3.1.14
|
||||
- gitdb==4.0.9
|
||||
- gitpython==3.1.29
|
||||
- google-api-core==2.10.2
|
||||
- google-auth==1.35.0
|
||||
- google-auth-oauthlib==0.4.6
|
||||
- grpcio==1.48.1
|
||||
- hi-ml==0.2.4
|
||||
- googleapis-common-protos==1.56.4
|
||||
- greenlet==2.0.1
|
||||
- grpcio==1.50.0
|
||||
- gunicorn==20.1.0
|
||||
- hi-ml==0.2.9
|
||||
- hi-ml-azure==0.2.9
|
||||
- humanfriendly==10.0
|
||||
- identify==2.5.3
|
||||
- idna==3.3
|
||||
- imageio==2.21.2
|
||||
- identify==2.5.8
|
||||
- idna==3.4
|
||||
- imageio==2.22.4
|
||||
- imagesize==1.4.1
|
||||
- importlib-metadata==4.2.0
|
||||
- iniconfig==1.1.1
|
||||
- isodate==0.6.1
|
||||
- isort==5.10.1
|
||||
- jaraco-classes==3.2.2
|
||||
- itsdangerous==2.1.2
|
||||
- jaraco-classes==3.2.3
|
||||
- jeepney==0.8.0
|
||||
- jinja2==3.0.2
|
||||
- jmespath==1.0.0
|
||||
- joblib==1.1.0
|
||||
- joblib==1.2.0
|
||||
- jsonpickle==2.2.0
|
||||
- jsonschema==4.15.0
|
||||
- keyring==23.9.0
|
||||
- jsonschema==4.17.0
|
||||
- keyring==23.11.0
|
||||
- kiwisolver==1.4.4
|
||||
- knack==0.9.0
|
||||
- lazy-object-proxy==1.7.1
|
||||
- lazy-object-proxy==1.8.0
|
||||
- lightning-bolts==0.4.0
|
||||
- llvmlite==0.39.1
|
||||
- lxml==4.9.1
|
||||
- mako==1.2.3
|
||||
- markdown==2.6.8
|
||||
- markdown-it-py==1.1.0
|
||||
- markupsafe==2.1.1
|
||||
- marshmallow==3.17.1
|
||||
- marshmallow==3.18.0
|
||||
- marshmallow-enum==1.5.1
|
||||
- matplotlib==3.4.3
|
||||
- mccabe==0.6.1
|
||||
- mdit-py-plugins==0.2.8
|
||||
- mlflow==1.29.0
|
||||
- mlflow==1.30.0
|
||||
- mlflow-skinny==1.30.0
|
||||
- monai==0.8.0
|
||||
- more-itertools==8.10.0
|
||||
- msal==1.18.0
|
||||
- msal==1.20.0
|
||||
- msal-extensions==0.3.1
|
||||
- msrest==0.6.21
|
||||
- msrestazure==0.6.4
|
||||
|
|
@ -177,25 +210,31 @@ dependencies:
|
|||
- mypy-extensions==0.4.3
|
||||
- myst-parser==0.15.2
|
||||
- ndg-httpsclient==0.5.1
|
||||
- networkx==2.8.6
|
||||
- networkx==2.8.8
|
||||
- nodeenv==1.7.0
|
||||
- numba==0.56.2
|
||||
- numba==0.56.4
|
||||
- numpy==1.22.0
|
||||
- oauthlib==3.2.0
|
||||
- oauthlib==3.2.2
|
||||
- opencensus==0.11.0
|
||||
- opencensus-context==0.1.3
|
||||
- opencensus-ext-azure==1.1.7
|
||||
- opencv-python-headless==4.5.1.48
|
||||
- packaging==21.3
|
||||
- pandas==1.3.4
|
||||
- param==1.12.0
|
||||
- paramiko==2.11.0
|
||||
- pathspec>=0.9.0
|
||||
- paramiko==2.12.0
|
||||
- pathspec==0.10.1
|
||||
- pillow==9.0.1
|
||||
- pipdeptree==2.2.1
|
||||
- pkginfo==1.8.3
|
||||
- platformdirs==2.5.2
|
||||
- platformdirs==2.5.3
|
||||
- pluggy==0.13.1
|
||||
- portalocker==2.5.1
|
||||
- portalocker==2.6.0
|
||||
- pre-commit==2.19.0
|
||||
- prometheus-client==0.15.0
|
||||
- prometheus-flask-exporter==0.20.3
|
||||
- protobuf==3.20.1
|
||||
- psutil==5.9.4
|
||||
- py==1.11.0
|
||||
- pyarrow==3.0.0
|
||||
- pyasn1==0.4.8
|
||||
|
|
@ -203,17 +242,18 @@ dependencies:
|
|||
- pycobertura==2.0.1
|
||||
- pycodestyle==2.8.0
|
||||
- pycparser==2.21
|
||||
- pydash==5.1.1
|
||||
- pydeprecate==0.3.2
|
||||
- pydicom==2.3.0
|
||||
- pyflakes==2.4.0
|
||||
- pygments==2.13.0
|
||||
- pyjwt==2.4.0
|
||||
- pyjwt==2.6.0
|
||||
- pylint==2.15.0
|
||||
- pynacl==1.5.0
|
||||
- pynndescent==0.5.7
|
||||
- pyopenssl==22.0.0
|
||||
- pynndescent==0.5.8
|
||||
- pyopenssl==22.1.0
|
||||
- pyparsing==3.0.9
|
||||
- pyrsistent==0.18.1
|
||||
- pyrsistent==0.19.2
|
||||
- pysocks==1.7.1
|
||||
- pytest==6.2.2
|
||||
- pytest-cov==2.11.1
|
||||
|
|
@ -221,24 +261,26 @@ dependencies:
|
|||
- pytest-timeout==2.0.1
|
||||
- python-dateutil==2.8.2
|
||||
- pytorch-lightning==1.6.5
|
||||
- pytz==2022.2.1
|
||||
- pywavelets==1.3.0
|
||||
- pytz==2022.6
|
||||
- pywavelets==1.4.1
|
||||
- pyyaml==6.0
|
||||
- readme-renderer==37.0
|
||||
- querystring-parser==1.2.4
|
||||
- readme-renderer==37.3
|
||||
- requests==2.28.1
|
||||
- requests-oauthlib==1.3.1
|
||||
- requests-toolbelt==0.9.1
|
||||
- requests-toolbelt==0.10.1
|
||||
- rfc3986==2.0.0
|
||||
- rpdb==0.1.6
|
||||
- rsa==4.9
|
||||
- ruamel-yaml==0.16.12
|
||||
- scikit-image==0.19.3
|
||||
- scikit-learn==1.1.2
|
||||
- scikit-learn==1.1.3
|
||||
- scipy==1.7.3
|
||||
- seaborn==0.10.1
|
||||
- secretstorage==3.3.3
|
||||
- setuptools==59.5.0
|
||||
- simpleitk==2.1.1.2
|
||||
- smmap==5.0.0
|
||||
- snowballstemmer==2.2.0
|
||||
- sphinx==4.1.2
|
||||
- sphinx-autodoc-typehints==1.12.0
|
||||
|
|
@ -250,8 +292,11 @@ dependencies:
|
|||
- sphinxcontrib-jsmath==1.0.1
|
||||
- sphinxcontrib-qthelp==1.0.3
|
||||
- sphinxcontrib-serializinghtml==1.1.5
|
||||
- sqlalchemy==1.4.43
|
||||
- sqlparse==0.4.3
|
||||
- strictyaml==1.6.2
|
||||
- stringcase==1.2.0
|
||||
- tabulate==0.8.10
|
||||
- tabulate==0.9.0
|
||||
- tensorboard==2.6.0
|
||||
- tensorboard-data-server==0.6.1
|
||||
- tensorboard-plugin-wit==1.8.1
|
||||
|
|
@ -259,19 +304,19 @@ dependencies:
|
|||
- tifffile==2021.11.2
|
||||
- toml==0.10.2
|
||||
- tomli==2.0.1
|
||||
- tomlkit==0.11.4
|
||||
- tomlkit==0.11.6
|
||||
- torchmetrics==0.6.0
|
||||
- tqdm==4.63.0
|
||||
- tqdm==4.64.1
|
||||
- twine==3.3.0
|
||||
- typing-inspect==0.8.0
|
||||
- umap-learn==0.5.2
|
||||
- urllib3==1.26.9
|
||||
- virtualenv==20.16.4
|
||||
- virtualenv==20.16.6
|
||||
- webencodings==0.5.1
|
||||
- websocket-client==1.4.0
|
||||
- websocket-client==1.4.2
|
||||
- werkzeug==2.2.2
|
||||
- wheel==0.36.2
|
||||
- wrapt==1.14.1
|
||||
- yacs==0.1.8
|
||||
- yarl==1.8.1
|
||||
- zipp==3.8.1
|
||||
- zipp==3.10.0
|
||||
|
|
|
|||
|
|
@ -9,6 +9,8 @@ dependencies:
|
|||
- python=3.9.13
|
||||
- pytorch=1.10.0
|
||||
- torchvision=0.11.1
|
||||
- openslide=3.4.1
|
||||
- openslide-python=1.2.0
|
||||
- pip:
|
||||
# Run requirements for hi-ml
|
||||
- dataclasses-json==0.5.2
|
||||
|
|
@ -39,8 +41,9 @@ dependencies:
|
|||
- -r requirements_build.txt
|
||||
# Pinned secondary dependencies to prevent clashes
|
||||
- attrs==21.4.0
|
||||
- azure-mgmt-core==1.3.0
|
||||
- azure-mgmt-core==1.3.1
|
||||
- azure-mgmt-keyvault==10.0.0
|
||||
- cryptography>=38.0.3
|
||||
- cloudpickle==1.6.0
|
||||
- importlib-metadata==4.2.0
|
||||
- markdown==2.6.8
|
||||
|
|
|
|||
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