#357 monai-full PR version

vscentrum · Nov 29, 2024 · 8894c21 · 8894c21
1 parent 6a6fcd6
commit 8894c21
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diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/NiBabel-2023b.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/NiBabel-2023b.eb
@@ -33,8 +33,6 @@ exts_list = [
     }),
 ]
 
-# fix_python_shebang_for = ['bin/*']
-
 sanity_check_paths = {
     'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'],
     'dirs': ['lib/python%(pyshortver)s/site-packages'],

diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/clearml-2023b.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/clearml-2023b.eb
@@ -9,26 +9,6 @@ Experiment Management, Data Management, Pipeline, Orchestration, Scheduling & Se
 
 toolchain = {'name': 'foss', 'version': '2023b'}
 
-#DEPS:
-    # OK attrs>=18.0
-    # ok furl>=2.0.0
-    # OK jsonschema>=2.6.0
-    # OK numpy>=1.10
-    # OK pathlib2>=2.3.0
-    # OK Pillow>=4.1.1
-    # OK psutil>=3.4.2
-    # OK pyparsing>=2.0.3
-    # OK python-dateutil>=2.6.1
-    # ok pyjwt>=2.4.0,<2.9.0 ; python_version > '3.5'
-    # OK PyYAML>=3.12
-    # ok referencing<0.40 ; python_version >= '3.8'
-    # OK requests>=2.20.0
-    # OK six>=1.16.0
-    # OK urllib3>=1.21.1
-    # ok referencing 0.35.1 requires rpds-py, which is not installed.
-    # ok furl 2.1.3 requires orderedmultidict, which is not installed.
-
-
 builddependencies = [
     ('hatchling', '1.18.0'),
     ('maturin', '1.3.1'),
@@ -40,10 +20,6 @@ dependencies = [
     ('SciPy-bundle', '2023.11'),
     ('PyYAML', '6.0.1'),
     ('Pillow', '10.2.0'),
-#     ('networkx', '3.2.1'),
-#     ('dask', '2024.5.1'),
-#     ('imageio', '2.34.1'),
-#     ('scikit-learn', '1.3.2'),
 ]
 
 use_pip = True

diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/mlflow-2023b.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/mlflow-2023b.eb
@@ -9,38 +9,6 @@ packaging code into reproducible runs, and sharing and deploying models."""
 
 toolchain = {'name': 'gfbf', 'version': '2023b'}
 
-#DEPS:
-    # ok alembic<2,!=1.10.0
-    # ok docker<8,>=4.0.0
-    # OK Flask<4
-    # OK numpy<3
-    # OK scipy<2
-    # OK pandas<3
-    # OK sqlalchemy<3,>=1.4.0
-    # ok gunicorn<24; platform_system != 'Windows'
-    # OK scikit-learn<2
-    # OK pyarrow<19,>=4.0.0
-    # OK markdown<4,>=3.3
-    # OK Jinja2<4,>=2.11; platform_system != 'Windows'
-    # OK matplotlib<4
-    # ok graphene<4
-    # ok mlflow 2.18.0 requires mlflow-skinny, which is not installed.
-    # ok graphene 3.4.1 requires graphql-core, which is not installed.
-    # ok graphene 3.4.1 requires graphql-relay, which is not installed.
-    # ok mlflow-skinny 2.18.0 requires cachetools, which is not installed.
-    # ok mlflow-skinny 2.18.0 requires databricks-sdk, which is not installed.
-    # ok mlflow-skinny 2.18.0 requires opentelemetry-api, which is not installed.
-    # ok mlflow-skinny 2.18.0 requires opentelemetry-sdk, which is not installed.
-    # OK mlflow-skinny 2.18.0 requires protobuf, which is not installed.
-    # OK mlflow-skinny 2.18.0 requires pyyaml, which is not installed.
-    # ok mlflow-skinny 2.18.0 requires sqlparse, which is not installed.
-    # ok opentelemetry-sdk 1.27.0 requires opentelemetry-semantic-conventions, which is not installed.
-    # ok databricks-sdk 0.36.0 requires google-auth, which is not installed.
-    # OK opentelemetry-api 1.27.0 requires deprecated, which is not installed.
-    # ok google-auth 2.35.0 requires pyasn1-modules, which is not installed.
-    # ok google-auth 2.35.0 requires rsa, which is not installed.
-
-
 builddependencies = [
     ('binutils', '2.40'),
     ('hatchling', '1.18.0'),
@@ -59,7 +27,7 @@ dependencies = [
     ('Flask', '3.0.0'),
     ('Arrow', '16.1.0'),
     ('Markdown', '3.6'),
-    ('Deprecated', '1.2.14'), # not merged yet (Spyder)
+    ('Deprecated', '1.2.14'),
 ]
 
 sanity_pip_check = True

diff --git a/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/monai-2023b-full.eb b/357_Synthcity/2023b_v0.2.11_new/monai-2023b-full/monai-2023b-full.eb
@@ -13,107 +13,15 @@ toolchain = {'name': 'foss', 'version': '2023b'}
 
 github_account = 'Project-MONAI'
 
-# DEPS:
-    # setup_requires =
-    #     OK torch
-    #     OK ninja
-    # install_requires =
-    #     OK torch>=1.9
-    #     OK numpy>=1.20
-    # extras =
-        # ok pytorch-ignite==0.4.11 -> add to exts - pin to 0.4.11 version + fix from monai
-        # ok gdown>=4.7.3
-        # OK? scipy>=1.12.0; python_version >= '3.9' -> no, I have 1.11.4 -> unpin? - seems I do not have to unpin - no pip check errors
-        # OK CREATED itk>=5.2 - ctreated ITK-5.4.0
-        # OK CREATED nibabel
-        # OK pillow!=8.3.0  # https://github.com/python-pillow/Pillow/issues/5571
-        # OK tensorboard>=2.12.0  # https://github.com/Project-MONAI/MONAI/issues/7434
-        # OK CREATED scikit-image>=0.19.0
-        # OK tqdm>=4.47.0
-        # ok lmdb
-        # OK ninja
-        # OK torchvision
-        # OK psutil - v5.9.6 in pypi bundle
-        # X cucim-cu12; platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10"
-        # OK CREATED openslide-python + CREATED OpenSlide-4.0.0
-        # OK CREATED imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
-        # OK tifffile; platform_system == "Linux" or platform_system == "Darwin" in scikit-image
-        # OK pandas
-        # OK requests
-        # OK CREATED einops
-        # OK transformers>=4.36.0, <4.41.0; python_version <= '3.10'
-        # OK CREATED mlflow>=2.12.2
-        # OK CREATED clearml>=1.10.0rc0
-        # OK matplotlib>=3.6.3
-        # OK tensorboardX
-        # OK pyyaml
-        # ok fire
-        # OK jsonschema - v4.17.3 in pypi bundle
-        # ok pynrrd
-        # OK CREATED pydicom - in NiBabel
-        # OK h5py
-        # ok nni==2.10.1; platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine
-        # OK optuna
-        # git+https://github.com/Project-MONAI/MetricsReloaded@monai-support#egg=MetricsReloaded
-        # OK CREATED onnx>=1.13.0
-        # ok typeguard  # https://github.com/microsoft/nni/issues/5457
-        # ok filelock<3.12.0  # https://github.com/microsoft/nni/issues/5523
-        # OK CREATED zarr
-        # ok lpips==0.1.4
-        # X nvidia-ml-py
-        # ok huggingface_hub
-        # CREATE pyamg>=5.0.0
-        # git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588
-    # ok fire 0.7.0 requires termcolor, which is not installed.
-    # OK gdown 5.2.0 requires beautifulsoup4, which is not installed.
-    # OK gdown 5.2.0 requires tqdm, which is not installed.
-
-# Optional deps from import monai; monai.config.print_config():
-    # Optional dependencies:
-    # Pytorch Ignite version: 0.4.11
-    # ITK version: 5.3.0
-    # Nibabel version: 5.3.2
-    # scikit-image version: 0.24.0
-    # scipy version: 1.11.4
-    # Pillow version: 10.4.0
-    # Tensorboard version: 2.18.0
-    # gdown version: 5.2.0
-    # TorchVision version: 0.17.0
-    # tqdm version: 4.66.2
-    # lmdb version: 1.5.1
-    # psutil version: 5.9.6
-    # pandas version: 2.1.3
-    # einops version: 0.8.0
-    # transformers version: 4.44.0
-    # mlflow version: 2.18.0
-    # pynrrd version: NOT INSTALLED or UNKNOWN VERSION.
-    # clearml version: 1.16.5
-
-
-# extras: not in local_pip_extras now
-    # [ 
-    # cucim, (some cuda stuff)
-    # pynvml, (NVIDIA mng lib)
-    # onnxruntime, (not needed?)
-    # ]
-
-# ORIGINAL from 5.3.0
-# local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel,pydicom,"
-# local_pip_extras += "openslide,pandas,pillow,psutil,pyyaml,scipy,"
-# local_pip_extras += "skimage,tensorboard,torchvision,tqdm"
-
-local_pip_extras = "einops,fire,gdown,ignite,scipy,tqdm,itk,jsonschema,lmdb,nibabel,pydicom,ninja,h5py,optuna,"
-# local_pip_extras += "openslide,pandas,pillow,psutil,pyyaml,skimage,tensorboard,torchvision,_hubhuggingface,nni,"
-# local_pip_extras += "transformers,mlflow,clearml,matplotlib,tensorboardX,tifffile,imagecodecs,onnx,zarr,lpips,pynrrd"
-
-# local_pip_extras = "all"
+local_pip_extras = "einops,fire,gdown,ignite,scipy,tqdm,itk,jsonschema,lmdb,nibabel,pydicom,ninja,h5py,optuna,pyamg,"
+local_pip_extras += "openslide,pandas,pillow,psutil,pyyaml,skimage,tensorboard,torchvision,huggingface_hub,"
+local_pip_extras += "transformers,mlflow,clearml,matplotlib,tensorboardX,tifffile,imagecodecs,onnx,zarr,lpips,pynrrd"
 
 builddependencies = [
     ('hatchling', '1.18.0'),
     ('Ninja', '1.11.1'),
 ]
 
-# dep_list.txt for details
 dependencies = [
     ('Python', '3.11.5'),
     ('Python-bundle-PyPI', '2023.10'),
@@ -126,16 +34,16 @@ dependencies = [
     ('pydicom', '3.0.1'),
     ('NiBabel', '5.3.2'),
     ('openslide-python', '1.4.1'),
-    ('Pillow-SIMD', '10.4.0'), # not merged yet
+    ('Pillow-SIMD', '10.4.0'),
     ('PyYAML', '6.0.1'),
     ('scikit-image', '0.24.0'),
-    ('tensorboard', '2.18.0'), # not merged yet
-    ('torchvision', '0.17.0'), # not merged yet
+    ('tensorboard', '2.18.0'),
+    ('torchvision', '0.17.0'),
     ('Transformers', '4.44.0'),
     ('MLflow', '2.18.0'),
     ('matplotlib', '3.8.2'),
     ('clearml', '1.16.5'),
-    ('tensorboardX', '2.6.2.2'), # not merged yet
+    ('tensorboardX', '2.6.2.2'),
     ('imagecodecs', '2024.6.1'),
     ('h5py', '3.11.0'),
     ('Optuna', '3.6.1'),
@@ -147,23 +55,19 @@ dependencies = [
 use_pip = True
 
 exts_list = [
+    ('nptyping', '2.5.0', {
+        'checksums': ['e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a'],
+    }),
     ('pynrrd', '1.0.0', {
         'modulename': 'nrrd',
         'checksums': ['4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2'],
     }),
     ('lpips', '0.1.4', {
         'checksums': ['3846331df6c69688aec3d300a5eeef6c529435bc8460bd58201c3d62e56188fa'],
     }),
-    ('filelock', '3.11.0', {
-        'checksums': ['3618c0da67adcc0506b015fd11ef7faf1b493f0b40d87728e19986b536890c37'],
-    }),
     ('typeguard', '4.1.2', {
         'checksums': ['3be187945f9ef5a9f6d7a926dfe54babb7dfd807085ce05f9a5e8735f2487990'],
     }),
-    ('nni', '3.0', {
-        'source_tmpl': '%(name)s-%(version)s-py3-none-manylinux1_x86_64.whl',
-        'checksums': ['176456f8275c096655b6f178dc0589a7642afbb37ecbcce7afe6ad9949592088'],
-    }),
     ('huggingface-hub', '0.26.2', {
         'sources': ['huggingface_hub-%(version)s.tar.gz'],
         'checksums': ['b100d853465d965733964d123939ba287da60a547087783ddff8a323f340332b'],
@@ -196,13 +100,6 @@ exts_list = [
     }),
 ]
 
-    # (name, version, {
-    #     'preinstallopts': 'BUILD_MONAI=1',
-    #     'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'],
-    #     'sources': ['%(version)s.tar.gz'],
-    #     'checksums': ['3ed592c7a760f5c3084021da5585cd1ba5e52a969b85a62e1f15495cb71ae26e'],
-    # }),
-
 sanity_pip_check = True
 
 sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"]