#357 working 2023b version no test - todo tests deps

357_Synthcity/2023b_v0.2.11_new/DEPS-0.2.11.txt

@@ -6,11 +6,11 @@ aiohappyeyeballs             2.4.3 -> HAVE 2.3.2
 aiohttp                      3.10.10 -> HAVE 3.9.5
 aiosignal                    1.3.1 OK
 alembic                      1.13.3 -> HAVE 1.13.1
-arfpy                        0.1.1 OK
+arfpy                        0.1.1 OK exts
 attrs                        24.2.0 -> HAVE 23.1.0
 autograd                     1.7.0 OK
 autograd-gamma               0.5.0 OK
-be_great                     0.0.8 OK
+be_great                     0.0.8 OK exts
 blis                         0.7.11 OK
 Brotli                       1.1.0 OK
 cachetools                   5.5.0 OK
@@ -32,14 +32,14 @@ fastai                       2.7.18 OK
 fastcore                     1.7.19 OK
 fastdownload                 0.0.7 OK
 fastprogress                 1.0.3 OK
-feather-format               0.4.1 
-fflows                       0.0.3
-filelock                     3.16.1
-fonttools                    4.54.1
+feather-format               0.4.1 OK exts
+fflows                       0.0.3 OK exts
+filelock                     3.16.1 -> HAVE 3.13.0
+fonttools                    4.54.1 ? -> HAVE 4.53.1
 formulaic                    1.0.2 OK
-frozenlist                   1.5.0
-fsspec                       2024.9.0
-geomloss                     0.2.6
+frozenlist                   1.5.0 ?
+fsspec                       2024.9.0 -> HAVE 2023.10.0
+geomloss                     0.2.6 OK exts
 google-ai-generativelanguage 0.6.10
 google-api-core              2.22.0
 google-api-python-client     2.151.0
@@ -49,42 +49,42 @@ google-generativeai          0.8.3
 googleapis-common-protos     1.65.0
 greenlet                     3.1.1 -> HAVE 3.0.3
 grpcio                       1.67.1 OK
-grpcio-status                1.67.1
+grpcio-status                1.67.1 ?
 h5py                         3.12.1 -> HAVE 3.11.0
-httplib2                     0.22.0
+httplib2                     0.22.0 ?
 huggingface-hub              0.26.2 OK
-idna                         3.10
-imbalanced-learn             0.12.4
-importlib_metadata           8.5.0
-inflate64                    1.0.0
+idna                         3.10 ?
+imbalanced-learn             0.12.4 OK
+importlib_metadata           8.5.0 -> HAVE 6.8.0
+inflate64                    1.0.0 OK exts
 interface-meta               1.3.0 OK
-Jinja2                       3.1.4
-joblib                       1.4.2
-keopscore                    2.2.3
-kiwisolver                   1.4.7
+Jinja2                       3.1.4 -> HAVE 3.1.2
+joblib                       1.4.2 -> HAVE 1.3.2
+keopscore                    2.2.3 OK exts
+kiwisolver                   1.4.7 -> HAVE 1.4.5
 langcodes                    3.4.1 OK
 language_data                1.2.0 OK
 lifelines                    0.29.0 OK
-lightning-utilities          0.11.8
+lightning-utilities          0.11.8 OK
 llvmlite                     0.43.0 OK
 loguru                       0.7.2 OK
 Mako                         1.3.6 -> HAVE 1.2.4
-marisa-trie                  1.2.1
-Markdown                     3.7 OK
-markdown-it-py               3.0.0
-MarkupSafe                   3.0.2
+marisa-trie                  1.2.1 OK
+Markdown                     3.7 -> HAVE 3.6
+markdown-it-py               3.0.0 OK
+MarkupSafe                   3.0.2 -> HAVE 2.1.3
 matplotlib                   3.9.2 -> HAVE 3.8.2
-mdurl                        0.1.2
+mdurl                        0.1.2 OK
 monai                        1.4.0 OK (without extras)
-mpmath                       1.3.0
-multidict                    6.1.0
+mpmath                       1.3.0 OK
+multidict                    6.1.0 -> HAVE 6.0.5
 multiprocess                 0.70.16 OK
-multivolumefile              0.2.3
+multivolumefile              0.2.3 OK exts
 murmurhash                   1.0.10 OK
 networkx                     2.8.8 OK
-nflows                       0.14
+nflows                       0.14 OK exts
 numba                        0.60.0 OK
-numpy                        1.26.4
+numpy                        1.26.4 -> HAVE 1.26.2
 nvidia-cublas-cu12           12.1.3.1
 nvidia-cuda-cupti-cu12       12.1.105
 nvidia-cuda-nvrtc-cu12       12.1.105
@@ -97,47 +97,47 @@ nvidia-cusparse-cu12         12.1.0.106
 nvidia-nccl-cu12             2.19.3
 nvidia-nvjitlink-cu12        12.6.77
 nvidia-nvtx-cu12             12.1.105
-opacus                       1.5.2
-opt_einsum                   3.4.0
-optuna                       4.0.0 -> AVE 3.6.1
-packaging                    24.1
-pandas                       2.2.3
-patsy                        0.5.6
-pgmpy                        0.1.26
-pillow                       11.0.0
-pip                          24.0
+opacus                       1.5.2 OK exts
+opt_einsum                   3.4.0 OK exts
+optuna                       4.0.0 -> HAVE 3.6.1
+packaging                    24.1 -> HAVE 23.2
+pandas                       2.2.3 -> HAVE 2.1.3
+patsy                        0.5.6 OK
+pgmpy                        0.1.26 OK exts
+pillow                       11.0.0 -> maybe not needed - have pillow-simd
+pip                          24.0 X
 preshed                      3.0.9 OK
-propcache                    0.2.0
-proto-plus                   1.25.0
+propcache                    0.2.0 X
+proto-plus                   1.25.0 ?
 protobuf                     5.28.3 -> HAVE 4.25.3
-psutil                       6.1.0
-py7zr                        0.22.0
+psutil                       6.1.0 -> HAVE 5.9.6
+py7zr                        0.22.0 OK exts
 pyarrow                      18.0.0 -> HAVE 16.0.1
-pyasn1                       0.6.1
+pyasn1                       0.6.1 ?
 pyasn1_modules               0.4.1 OK
-pybcj                        1.0.2
-pybind11                     2.13.6
-pycox                        0.3.0
-pycryptodomex                3.21.0
-pydantic                     1.10.18
-Pygments                     2.18.0
-pykeops                      2.2.3
-pyparsing                    3.2.0
-pyppmd                       1.1.0
-python-dateutil              2.9.0.post0
+pybcj                        1.0.2 OK exts
+pybind11                     2.13.6 -> HAVE 2.11.1
+pycox                        0.3.0 OK exts
+pycryptodomex                3.21.0 OK exts
+pydantic                     1.10.18 OK
+Pygments                     2.18.0 ?
+pykeops                      2.2.3 OK exts
+pyparsing                    3.2.0 -> HAVE 3.1.1
+pyppmd                       1.1.0 OK exts
+python-dateutil              2.9.0.post0 -> HAVE 2.8.2
 pytorch-lightning            1.9.5 OK
-pyts                         0.13.0
-pytz                         2024.2
+pyts                         0.13.0 OK (tsai)
+pytz                         2024.2 -> HAVE 2023.3.post1
 PyYAML                       6.0.2 -> HAVE 6.0.1
-pyzstd                       0.16.2
+pyzstd                       0.16.2 OK exts
 redis                        5.2.0 -> HAVE 7.2.4
-regex                        2024.9.11
-requests                     2.32.3
-rich                         13.9.3
+regex                        2024.9.11 -> HAVE 2023.10.3
+requests                     2.32.3 -> HAVE 2.31.0
+rich                         13.9.3 -> HAVE 13.6.0
 rsa                          4.9 OK
 safetensors                  0.4.5 -> HAVE 0.4.4
 scikit-learn                 1.5.2 -> HAVE 1.4.0
-scipy                        1.14.1
+scipy                        1.14.1 -> HAVE 1.11.4
 setuptools                   75.3.0
 shap                         0.46.0 OK
 shellingham                  1.5.4
@@ -155,31 +155,31 @@ synthcity                    0.2.11
 tenacity                     9.0.0
 tensorboard                  2.18.0
 tensorboard-data-server      0.7.2 OK
-texttable                    1.7.0
+texttable                    1.7.0 OK exts
 thinc                        8.2.5 OK
 threadpoolctl                3.5.0
 tokenizers                   0.20.1 -> HAVE 0.19.1
 torch                        2.2.0 -> HAVE 2.1.2
 torchdata                    0.7.1 OK
 torchmetrics                 1.5.1
 torchtext                    0.16.2 OK
-torchtuples                  0.2.2
+torchtuples                  0.2.2 OK
 torchvision                  0.17.0 OK
 tqdm                         4.66.6 -> HAVE 4.66.2
 transformers                 4.46.1 -> HAVE 4.44.0
 triton                       2.2.0
 tsai                         0.3.9 OK
 typer                        0.12.5 -> USE 0.10.0 - has no pdm dep - no pdm for 2023b
-typing_extensions            4.12.2
-tzdata                       2024.2
-uritemplate                  4.1.1
-urllib3                      2.2.3
+typing_extensions            4.12.2 -> HAVE 4.10.0
+tzdata                       2024.2 -> HAVE 2023.3
+uritemplate                  4.1.1 ?
+urllib3                      2.2.3 -> HAVE 2.0.7
 wasabi                       1.1.3 OK
 weasel                       0.4.1 OK
 Werkzeug                     3.1.0 OK
 wrapt                        1.16.0 OK
 xgboost                      2.1.2 -> HAVE 2.1.1
-xgbse                        0.3.3
+xgbse                        0.3.3 !!! 
 xxhash                       3.5.0 -> HAVE 3.4.1
-yarl                         1.17.1
-zipp                         3.20.2
+yarl                         1.17.1 -> HAVE 1.9.4
+zipp                         3.20.2 -> HAVE 3.17.0

357_Synthcity/2023b_v0.2.11_new/accelerate-2023b.eb

@@ -1,7 +1,7 @@
 easyblock = 'PythonBundle'
 
 name = 'accelerate'
-version = '0.33.0'
+version = '1.0.1'
 
 homepage = 'https://github.com/huggingface/accelerate'
 description = """A simple way to launch, train, and use PyTorch models on almost any device and 
@@ -14,9 +14,10 @@ dependencies = [
     ('Python', '3.11.5'),
     ('Python-bundle-PyPI', '2023.10'),
     ('SciPy-bundle', '2023.11'),
-    ('PyTorch-bundle', '2.1.2'),
+    ('PyTorch', '2.1.2'),
     ('PyYAML', '6.0.1'),
     ('Safetensors', '0.4.4'),
+    ('tqdm', '4.66.2'),
 ]
 
 sanity_pip_check = True
@@ -25,10 +26,10 @@ use_pip = True
 exts_list = [
     ('huggingface-hub', '0.26.2', {
         'sources': ['huggingface_hub-%(version)s.tar.gz'],
-        'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'],
+        'checksums': ['b100d853465d965733964d123939ba287da60a547087783ddff8a323f340332b'],
     }),
     (name, version, {
-        'checksums': ['11ba481ed6ea09191775df55ce464aeeba67a024bd0261a44b77b30fb439e26a'],
+        'checksums': ['e8f95fc2db14915dc0a9182edfcf3068e5ddb2fa310b583717ad44e5c442399c'],
     }),
 ]
 

357_Synthcity/2023b_v0.2.11_new/fastai-2023b.eb

@@ -10,6 +10,22 @@ toolchain = {'name': 'foss', 'version': '2023b'}
 
 use_pip = True
 
+# DEPS:
+    # OK fastdownload>=0.0.5,<2 
+    # OK fastcore>=1.5.29,<1.8 
+    # OK torchvision>=0.11 
+    # OK matplotlib 
+    # OK pandas 
+    # OK requests 
+    # OK pyyaml 
+    # OK fastprogress>=0.2.4 
+    # OK pillow>=9.0.0 
+    # OK scikit-learn 
+    # OK scipy 
+    # OK spacy<4 
+    # OK packaging
+    # OK torch>=1.10,<2.6
+
 dependencies = [
     ('Python', '3.11.5'),
     ('PyTorch', '2.1.2'),
@@ -27,13 +43,13 @@ exts_list = [
         'checksums': ['20507edb8e89406a1fbd7775e6e2a3d81a4dd633dd506b0e9cf0e1613e831d6a'],
     }),
     ('fastcore', '1.7.19', {
-        'checksums': ['3f23dfadd77428be99558fdad66bf04c79a9c626e694c7404ede816ed8372987'],
+        'checksums': ['72ac75cf3f7a591966e24aa37a4283512a097a098b4794c944ce707f71ba0f02'],
     }),
     ('fastprogress', '1.0.3', {
         'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'],
     }),
     (name, version, {
-        'checksums': ['f2cc20fd18cdf5ec738cc56d29d54de75887d48ad15f9d35cf50c38d3a856923'],
+        'checksums': ['b20593dbcae7522f1d77a8f5163d1fd60314f292640496804dc356e41cb36454'],
     }),
 ]
 

357_Synthcity/2023b_v0.2.11_new/grpcio-1.67.1_use-ebroot.patch

@@ -0,0 +1,52 @@
+Author: yqshao (Yunqi Shao), Update: Pavel Tománek (Inuits)
+Update setup.py to use dependencies from EB
+--- setup.py.orig	2024-11-04 12:15:44.508837000 +0100
++++ setup.py	2024-11-04 12:20:12.717679000 +0100
+@@ -298,29 +298,33 @@
+     CORE_C_FILES = filter(lambda x: "third_party/cares" not in x, CORE_C_FILES)
+
+ if BUILD_WITH_SYSTEM_OPENSSL:
++    EBROOTOPENSSL = os.environ.get('EBROOTOPENSSL')
+     CORE_C_FILES = filter(
+         lambda x: "third_party/boringssl" not in x, CORE_C_FILES
+     )
+     CORE_C_FILES = filter(lambda x: "src/boringssl" not in x, CORE_C_FILES)
+-    SSL_INCLUDE = (os.path.join("/usr", "include", "openssl"),)
++    SSL_INCLUDE = (os.path.join(EBROOTOPENSSL, "include", "openssl"),)
+
+ if BUILD_WITH_SYSTEM_ZLIB:
++    EBROOTZLIB = os.environ.get('EBROOTZLIB')
+     CORE_C_FILES = filter(lambda x: "third_party/zlib" not in x, CORE_C_FILES)
+-    ZLIB_INCLUDE = (os.path.join("/usr", "include"),)
++    ZLIB_INCLUDE = (os.path.join(EBROOTZLIB, "include"),)
+
+ if BUILD_WITH_SYSTEM_CARES:
+     CORE_C_FILES = filter(lambda x: "third_party/cares" not in x, CORE_C_FILES)
+     CARES_INCLUDE = (os.path.join("/usr", "include"),)
+
+ if BUILD_WITH_SYSTEM_RE2:
++    EBROOTRE2 = os.environ.get('EBROOTRE2')
+     CORE_C_FILES = filter(lambda x: "third_party/re2" not in x, CORE_C_FILES)
+-    RE2_INCLUDE = (os.path.join("/usr", "include", "re2"),)
++    RE2_INCLUDE = (os.path.join(EBROOTRE2, "include", "re2"),)
+
+ if BUILD_WITH_SYSTEM_ABSL:
++    EBROOTABSEIL = os.environ.get('EBROOTABSEIL')
+     CORE_C_FILES = filter(
+         lambda x: "third_party/abseil-cpp" not in x, CORE_C_FILES
+     )
+-    ABSL_INCLUDE = (os.path.join("/usr", "include"),)
++    ABSL_INCLUDE = (os.path.join(EBROOTABSEIL, "include"),)
+
+ EXTENSION_INCLUDE_DIRECTORIES = (
+     (PYTHON_STEM,)
+@@ -363,8 +367,7 @@
+     EXTENSION_LIBRARIES += ("re2",)
+ if BUILD_WITH_SYSTEM_ABSL:
+     EXTENSION_LIBRARIES += tuple(
+-        lib.stem[3:]
+-        for lib in sorted(pathlib.Path("/usr").glob("lib*/libabsl_*.so"))
++        lib.stem[3:] for lib in pathlib.Path(EBROOTABSEIL).glob("lib*/libabsl_*.so")
+     )
+
+ DEFINE_MACROS = (("_WIN32_WINNT", 0x600),)

357_Synthcity/2023b_v0.2.11_new/grpcio-2023b.eb

@@ -41,12 +41,10 @@ exts_list = [
             "GRPC_PYTHON_BUILD_SYSTEM_RE2=True "
             "GRPC_PYTHON_BUILD_SYSTEM_ABSL=True "
         ),
-        'patches': ['grpcio-1.57.0_use-ebroot.patch'],
+        'patches': ['grpcio-1.67.1_use-ebroot.patch'],
         'checksums': [
-            {'grpcio-1.62.3.tar.gz':
-             '4439bbd759636e37b66841117a66444b454937e27f0125205d2d117d7827c643'},
-            {'grpcio-1.57.0_use-ebroot.patch':
-             '5faf822cd817b723ae9361e43656d0ecc7b3333a166bbab2df80b43ae588e510'},
+            {'grpcio-1.67.1.tar.gz': '3dc2ed4cabea4dc14d5e708c2b426205956077cc5de419b4d4079315017e9732'},
+            {'grpcio-1.67.1_use-ebroot.patch': '8606002b8689d9ffde1c7aa097f0fd430430b42f2230ea427b73525de69c568b'},
         ],
     }),
 ]

357_Synthcity/2023b_v0.2.11_new/imbalanced-learn-2023b.eb

@@ -20,7 +20,7 @@ use_pip = True
 exts_list = [
     (name, version, {
         'modulename': 'imblearn',
-        'checksums': ['5b00796a01419e9102bd425e27c319d58d1f6cf2dfa751e02ed7f4edf67c3c1b'],
+        'checksums': ['8153ba385d296b07d97e0901a2624a86c06b48c94c2f92da3a5354827697b7a3'],
     }),
 ]
 

357_Synthcity/2023b_v0.2.11_new/monai-2023b.eb

@@ -84,4 +84,6 @@ exts_list = [
 
 sanity_pip_check = True
 
+sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"]
+
 moduleclass = 'vis'