From cd97b0746044cbf54b4888fa8cc4a4439ee9d34d Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 12:39:28 +0200 Subject: [PATCH 1/9] Modify requirements_base.txt for package updates Updated requirements by adding and commenting out several packages. --- requirements_base.txt | 38 ++++++++++++++++++++++++-------------- 1 file changed, 24 insertions(+), 14 deletions(-) diff --git a/requirements_base.txt b/requirements_base.txt index 6cd91a8..4ba66f5 100644 --- a/requirements_base.txt +++ b/requirements_base.txt @@ -18,6 +18,7 @@ pyarrow jupysql duckdb duckdb-engine +ibis # Visualization plotly matplotlib @@ -30,29 +31,31 @@ igraph netcbs # ML and interpretability scikit-learn -catboost -xgboost -lime +#catboost +#lime eli5 shap -imbalanced-learn -interpret +captum +#imbalanced-learn +#interpret optuna #ray[tune] # Strongly recommend the nightly build on torchtune so we can use all the custom functionality we've been building # pip install --pre torchtune --extra-index-url https://download.pytorch.org/whl/nightly/cpu -torchtune -peft +#torchtune +#peft hydra-core +#hydra-optuna-sweeper jupyterlab-optuna -# Synthetic data // +# Synthetic data metasyn metasyn-disclosure # Statistics statsmodels #pymc3 (pymc3 is at the current version not playing nicely with the other packages in pip) +lifelines # survival analysis # Deep learning -torch==2.8 +torch>=2.8 #tensorflow (nit does not play nicely with pip) torch-geometric # PyG CPU wheels for torch 2.8 (win_amd64, linux, macOS universal2; cp39-cp313) @@ -66,15 +69,22 @@ torch-spline-conv #intel-extension-for-pytorch #not yet available for windows #keras #dgl -splink gensim -pytorch-lightning +#pytorch-lightning transformers -hf-transfer umap-learn -inspect-ai +#inspect-ai torchao wandb +#mlflow tensorboard -json5 +flash-attn #attention-based learning faster +accelerate #annoy +# Configuration files +json5 +PyYAML +## Testing +pytest +ruff +pre-commit From 790c6c2ab213df24864c45d20d680e74176629ad Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 13:32:25 +0200 Subject: [PATCH 2/9] delete unnecessary files --- environment0000.txt | 304 ------------------------------------------ main.py | 6 - requirements_base.txt | 90 ------------- 3 files changed, 400 deletions(-) delete mode 100644 environment0000.txt delete mode 100644 main.py delete mode 100644 requirements_base.txt diff --git a/environment0000.txt b/environment0000.txt deleted file mode 100644 index bc8456a..0000000 --- a/environment0000.txt +++ /dev/null @@ -1,304 +0,0 @@ -absl-py==2.3.1 -accelerate==1.8.1 -aiobotocore==2.23.0 -aiohappyeyeballs==2.6.1 -aiohttp==3.12.13 -aioitertools==0.12.0 -aiosignal==1.3.2 -alembic==1.16.2 -altair==5.5.0 -annotated-types==0.7.0 -antlr4-python3-runtime==4.9.3 -anyio==4.9.0 -aplr==10.9.0 -argon2-cffi==25.1.0 -argon2-cffi-bindings==21.2.0 -arrow==1.3.0 -asttokens==3.0.0 -async-lru==2.0.5 -attrs==25.3.0 -babel==2.17.0 -backoff==2.2.1 -beautifulsoup4==4.13.4 -bleach==6.2.0 -blinker==1.9.0 -blobfile==3.0.0 -bokeh==3.7.3 -botocore==1.38.27 -bottle==0.13.4 -catboost==1.2.8 -certifi==2025.6.15 -cffi==1.17.1 -charset-normalizer==3.4.2 -choreographer==1.0.9 -click==8.1.8 -cloudpickle==3.1.1 -colorama==0.4.6 -colorcet==3.1.0 -colorlog==6.9.0 -comm==0.2.2 -contourpy==1.3.2 -cycler==0.12.1 -dash==2.18.2 -dash-core-components==2.0.0 -dash-html-components==2.0.0 -dash-table==5.0.0 -dash_cytoscape==1.0.2 -dask==2025.5.1 -datasets==3.6.0 -debugpy==1.8.14 -decorator==5.2.1 -defusedxml==0.7.1 -dill==0.3.8 -distro==1.9.0 -docstring_parser==0.16 -duckdb==1.3.1 -duckdb_engine==0.17.0 -eli5==0.16.0 -et_xmlfile==2.0.0 -executing==2.2.0 -Faker==37.4.0 -fastjsonschema==2.21.1 -filelock==3.18.0 -Flask==3.0.3 -fonttools==4.58.5 -fqdn==1.5.1 -frozenlist==1.7.0 -fsspec==2025.3.0 -gensim==4.3.3 -gevent==25.5.1 -gitdb==4.0.12 -GitPython==3.1.44 -graphviz==0.21 -greenlet==3.2.3 -grpcio==1.73.1 -h11==0.16.0 -h5py==3.14.0 -hf_transfer==0.1.9 -holoviews==1.21.0 -httpcore==1.0.9 -httpx==0.28.1 -huggingface-hub==0.33.2 -hvplot==0.11.3 -hydra-core==1.3.2 -idna==3.10 -igraph==0.11.9 -ijson==3.4.0 -imageio==2.37.0 -imbalanced-learn==0.13.0 -importlib_metadata==8.7.0 -inspect_ai==0.3.112 -interpret==0.6.13 -interpret-core==0.6.13 -ipykernel==6.29.5 -ipython==9.4.0 -ipython-genutils==0.2.0 -ipython_pygments_lexers==1.1.1 -ipywidgets==8.1.7 -isoduration==20.11.0 -itsdangerous==2.2.0 -jax==0.6.2 -jaxlib==0.6.2 -jedi==0.19.2 -Jinja2==3.1.6 -jmespath==1.0.1 -joblib==1.5.1 -json5==0.12.0 -jsonlines==4.0.0 -jsonpatch==1.33 -jsonpath-ng==1.7.0 -jsonpointer==3.0.0 -jsonref==1.1.0 -jsonschema==4.24.0 -jsonschema-specifications==2025.4.1 -jupysql==0.11.1 -jupysql-plugin==0.4.5 -jupyter==1.1.1 -jupyter-console==6.6.3 -jupyter-events==0.12.0 -jupyter-lsp==2.2.5 -jupyter_client==8.6.3 -jupyter_core==5.8.1 -jupyter_server==2.16.0 -jupyter_server_terminals==0.5.3 -jupyterlab==4.4.4 -jupyterlab-optuna==0.2.2 -jupyterlab_pygments==0.3.0 -jupyterlab_server==2.27.3 -jupyterlab_widgets==3.0.15 -kagglehub==0.3.12 -kaleido==1.0.0 -kiwisolver==1.4.8 -lazy_loader==0.4 -lightning-utilities==0.14.3 -lime==0.2.0.1 -lingua-language-detector==2.1.1 -linkify-it-py==2.0.3 -llvmlite==0.44.0 -locket==1.0.0 -logistro==1.1.0 -lxml==6.0.0 -Mako==1.3.10 -Markdown==3.8.2 -markdown-it-py==3.0.0 -MarkupSafe==3.0.2 -matplotlib==3.10.3 -matplotlib-inline==0.1.7 -mdit-py-plugins==0.4.2 -mdurl==0.1.2 -metasyn==1.1.0 -mistune==3.1.3 -ml_dtypes==0.5.1 -mmh3==5.1.0 -mpmath==1.3.0 -multidict==6.6.3 -multiprocess==0.70.16 -narwhals==1.45.0 -nbclient==0.10.2 -nbconvert==7.16.6 -nbformat==5.10.4 -nest-asyncio==1.6.0 -netCBS==0.3.1 -networkx==3.5 -notebook==7.4.4 -notebook_shim==0.2.4 -numba==0.61.2 -numpy==1.26.4 -omegaconf==2.3.0 -openpyxl==3.1.5 -opt_einsum==3.4.0 -optuna==4.4.0 -orjson==3.10.18 -overrides==7.7.0 -packaging==25.0 -pandas==2.3.0 -pandocfilters==1.5.1 -panel==1.7.2 -param==2.2.1 -parso==0.8.4 -partd==1.4.2 -patsy==1.0.1 -peft==0.16.0 -pillow==11.3.0 -platformdirs==4.3.8 -ploomber-core==0.2.26 -plotly==6.2.0 -ply==3.11 -polars==1.31.0 -posthog==6.0.2 -prettytable==3.16.0 -prometheus_client==0.22.1 -prompt_toolkit==3.0.51 -propcache==0.3.2 -protobuf==6.31.1 -psutil==7.0.0 -pure_eval==0.2.3 -pyarrow==20.0.0 -pycparser==2.22 -pycryptodomex==3.23.0 -pydantic==2.11.7 -pydantic_core==2.33.2 -pyg-lib==0.4.0+pt27cpu -Pygments==2.19.2 -pynndescent==0.5.13 -pyparsing==3.2.3 -pyreadstat==1.3.0 -python-dateutil==2.9.0.post0 -python-dotenv==1.1.1 -python-json-logger==3.3.0 -pytorch-lightning==2.5.2 -pytz==2025.2 -pyviz_comms==3.0.6 -pywin32==310 -pywinpty==2.0.15 -PyYAML==6.0.2 -pyzmq==27.0.0 -referencing==0.36.2 -regex==2024.11.6 -regexmodel==0.3.5 -requests==2.32.4 -retrying==1.4.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -rich==13.9.4 -rpds-py==0.26.0 -s3fs==2025.3.0 -safetensors==0.5.3 -SALib==1.5.1 -scikit-image==0.25.2 -scikit-learn==1.6.1 -scipy==1.13.1 -seaborn==0.13.2 -semver==3.0.4 -Send2Trash==1.8.3 -sentencepiece==0.2.0 -sentry-sdk==2.32.0 -shap==0.48.0 -shortuuid==1.0.13 -simplejson==3.20.1 -six==1.17.0 -sklearn-compat==0.1.3 -slicer==0.0.8 -smart_open==7.3.0.post1 -smmap==5.0.2 -sniffio==1.3.1 -soupsieve==2.7 -splink==4.0.8 -SQLAlchemy==2.0.41 -sqlglot==26.33.0 -sqlparse==0.5.3 -stack-data==0.6.3 -statsmodels==0.14.4 -sympy==1.14.0 -tabulate==0.9.0 -tenacity==9.1.2 -tensorboard==2.19.0 -tensorboard-data-server==0.7.2 -terminado==0.18.1 -texttable==1.7.0 -textual==2.1.2 -threadpoolctl==3.6.0 -tifffile==2025.6.11 -tiktoken==0.9.0 -tinycss2==1.4.0 -tokenizers==0.21.2 -toolz==1.0.0 -torch==2.7.1 -torch-geometric==2.6.1 -torch_cluster==1.6.3+pt27cpu -torch_scatter==2.1.2+pt27cpu -torch_sparse==0.6.18+pt27cpu -torch_spline_conv==1.2.2+pt27cpu -torchao==0.11.0 -torchdata==0.11.0 -torchmetrics==1.7.3 -torchtune==0.6.1 -tornado==6.5.1 -tqdm==4.67.1 -traitlets==5.14.3 -transformers==4.53.0 -types-python-dateutil==2.9.0.20250516 -typing-inspection==0.4.1 -typing_extensions==4.14.0 -tzdata==2025.2 -uc-micro-py==1.0.3 -umap-learn==0.5.9.post2 -uri-template==1.3.0 -urllib3==2.5.0 -wandb==0.21.0 -wcwidth==0.2.13 -webcolors==24.11.1 -webencodings==0.5.1 -websocket-client==1.8.0 -Werkzeug==3.0.6 -widgetsnbextension==4.0.14 -wrapt==1.17.2 -xgboost==3.0.2 -xxhash==3.5.0 -xyzservices==2025.4.0 -yarl==1.20.1 -zipp==3.23.0 -zope.event==5.1 -zope.interface==7.2 --f https://data.pyg.org/whl/torch-2.7.0+cpu.html - diff --git a/main.py b/main.py deleted file mode 100644 index 5fed753..0000000 --- a/main.py +++ /dev/null @@ -1,6 +0,0 @@ -def main(): - print("Hello from cbs-python!") - - -if __name__ == "__main__": - main() diff --git a/requirements_base.txt b/requirements_base.txt deleted file mode 100644 index 4ba66f5..0000000 --- a/requirements_base.txt +++ /dev/null @@ -1,90 +0,0 @@ -# Notebooks and ipython -jupyterlab -notebook -ipython -jupyter -# Data handling -dask -h5py -openpyxl -scipy -pandas -pyreadstat -numpy -numba -jax -polars -pyarrow -jupysql -duckdb -duckdb-engine -ibis -# Visualization -plotly -matplotlib -seaborn -hvplot -kaleido -# Networks -networkx -igraph -netcbs -# ML and interpretability -scikit-learn -#catboost -#lime -eli5 -shap -captum -#imbalanced-learn -#interpret -optuna -#ray[tune] -# Strongly recommend the nightly build on torchtune so we can use all the custom functionality we've been building -# pip install --pre torchtune --extra-index-url https://download.pytorch.org/whl/nightly/cpu -#torchtune -#peft -hydra-core -#hydra-optuna-sweeper -jupyterlab-optuna -# Synthetic data -metasyn -metasyn-disclosure -# Statistics -statsmodels -#pymc3 (pymc3 is at the current version not playing nicely with the other packages in pip) -lifelines # survival analysis -# Deep learning -torch>=2.8 -#tensorflow (nit does not play nicely with pip) -torch-geometric -# PyG CPU wheels for torch 2.8 (win_amd64, linux, macOS universal2; cp39-cp313) ---find-links https://data.pyg.org/whl/torch-2.8.0+cpu.html -pyg-lib # has win_amd64 + linux + macOS universal2 wheels on this index -torch-sparse -torch-scatter -torch-cluster -torch-spline-conv -#torch-quiver #not yet available for windows -#intel-extension-for-pytorch #not yet available for windows -#keras -#dgl -gensim -#pytorch-lightning -transformers -umap-learn -#inspect-ai -torchao -wandb -#mlflow -tensorboard -flash-attn #attention-based learning faster -accelerate -#annoy -# Configuration files -json5 -PyYAML -## Testing -pytest -ruff -pre-commit From fca3a8b8a420df238fa8c10997c090714232bb7d Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 13:36:06 +0200 Subject: [PATCH 3/9] add uv support --- test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test.py b/test.py index af26c26..8d512b6 100644 --- a/test.py +++ b/test.py @@ -1,6 +1,6 @@ """Quick smoke test that pyg-lib imports and is usable. -Run with: python test.py +Run with: uv run python test.py (pyg-lib's import name is `pyg_lib`, with an underscore.) """ From 3fdc9ad64e7609828d72efb2add1b30ee7f643d2 Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 13:56:55 +0200 Subject: [PATCH 4/9] update env --- environment0000.txt | 266 +++ pyproject.toml | 55 +- requirements.in | 92 ++ uv.lock | 3786 ++++++++++++++----------------------------- 4 files changed, 1626 insertions(+), 2573 deletions(-) create mode 100644 environment0000.txt create mode 100644 requirements.in diff --git a/environment0000.txt b/environment0000.txt new file mode 100644 index 0000000..78af7d1 --- /dev/null +++ b/environment0000.txt @@ -0,0 +1,266 @@ +--find-links https://data.pyg.org/whl/torch-2.9.0+cpu.html + +absl-py==2.4.0 +accelerate==1.14.0 +aiohappyeyeballs==2.6.2 +aiohttp==3.14.1 +aiosignal==1.4.0 +alembic==1.18.5 +annotated-doc==0.0.4 +annotated-types==0.7.0 +antlr4-python3-runtime==4.9.3 +anyio==4.14.1 +argon2-cffi==25.1.0 +argon2-cffi-bindings==25.1.0 +arrow==1.4.0 +asttokens==3.0.1 +async-lru==2.3.0 +attrs==26.1.0 +autograd==1.9.0 +autograd-gamma==0.5.0 +babel==2.18.0 +backoff==2.2.1 +beautifulsoup4==4.15.0 +bleach==6.4.0 +bokeh==3.9.1 +bottle==0.13.4 +captum==0.9.0 +certifi==2026.6.17 +cffi==2.0.0 +cfgv==3.5.0 +charset-normalizer==3.4.7 +choreographer==1.3.0 +click==8.4.2 +cloudpickle==3.1.2 +colorama==0.4.6 +colorcet==3.2.1 +colorlog==6.10.1 +comm==0.2.3 +contourpy==1.3.3 +cycler==0.12.1 +dask==2026.6.0 +debugpy==1.8.21 +decorator==5.3.1 +defusedxml==0.7.1 +distlib==0.4.3 +distro==1.9.0 +duckdb==1.5.4 +duckdb-engine==0.17.0 +eli5==0.16.0 +et-xmlfile==2.0.0 +executing==2.2.1 +faker==40.23.0 +fastjsonschema==2.21.2 +filelock==3.29.4 +fonttools==4.63.0 +formulaic==1.2.2 +fqdn==1.5.1 +frozenlist==1.8.0 +fsspec==2026.6.0 +gensim==4.4.0 +gitdb==4.0.12 +gitpython==3.1.50 +graphviz==0.21 +greenlet==3.5.3 +grpcio==1.81.1 +h11==0.16.0 +h5py==3.16.0 +hf-xet==1.5.1 +holoviews==1.23.0 +httpcore==1.0.9 +httpx==0.28.1 +huggingface-hub==1.21.0 +hvplot==0.12.2 +hydra-core==1.3.3 +ibis==3.3.0 +identify==2.6.19 +idna==3.18 +igraph==1.0.0 +iniconfig==2.3.0 +interface-meta==2.0.1 +ipykernel==7.3.0 +ipython==9.15.0 +ipython-genutils==0.2.0 +ipython-pygments-lexers==1.1.1 +ipywidgets==8.1.8 +isoduration==20.11.0 +jax==0.10.2 +jaxlib==0.10.2 +jedi==0.20.0 +jinja2==3.1.6 +joblib==1.5.3 +json5==0.15.0 +jsonpointer==3.1.1 +jsonschema==4.26.0 +jsonschema-specifications==2025.9.1 +jupysql==0.11.1 +jupysql-plugin==0.4.5 +jupyter==1.1.1 +jupyter-builder==1.0.2 +jupyter-client==8.9.1 +jupyter-console==6.6.3 +jupyter-core==5.9.1 +jupyter-events==0.12.1 +jupyter-lsp==2.3.1 +jupyter-server==2.20.0 +jupyter-server-terminals==0.5.4 +jupyterlab==4.6.0 +jupyterlab-optuna==0.3.0 +jupyterlab-pygments==0.3.0 +jupyterlab-server==2.28.0 +jupyterlab-widgets==3.0.16 +kaleido==1.3.0 +kiwisolver==1.5.0 +lark==1.3.1 +lifelines==0.30.3 +lingua-language-detector==2.2.0 +linkify-it-py==2.1.0 +llvmlite==0.47.0 +locket==1.0.0 +logistro==2.0.1 +mako==1.3.12 +markdown==3.10.2 +markdown-it-py==4.2.0 +markupsafe==3.0.3 +matplotlib==3.11.0 +matplotlib-inline==0.2.2 +mdit-py-plugins==0.6.1 +mdurl==0.1.2 +metasyn==2.1.0 +metasyn-disclosure==0.3.1 +mistune==3.3.2 +ml-dtypes==0.5.4 +mpmath==1.3.0 +multidict==6.7.1 +narwhals==2.22.1 +nbclient==0.11.0 +nbconvert==7.17.1 +nbformat==5.10.4 +nest-asyncio2==1.7.2 +netcbs==0.3.1 +networkx==3.6.1 +nh3==0.3.6 +nodeenv==1.10.0 +notebook==7.6.0 +notebook-shim==0.2.4 +numba==0.65.1 +numpy==2.4.6 +omegaconf==2.3.1 +openpyxl==3.1.5 +opt-einsum==3.4.0 +optuna==4.9.0 +orjson==3.11.9 +packaging==26.2 +pandas==2.3.3 +pandocfilters==1.5.1 +panel==1.9.3 +panel-material-ui==0.12.0 +param==2.4.1 +parso==0.8.7 +partd==1.4.2 +patsy==1.0.2 +pillow==12.2.0 +platformdirs==4.10.0 +ploomber-core==0.2.27 +plotly==6.8.0 +pluggy==1.6.0 +polars==1.42.0 +polars-runtime-32==1.42.0 +posthog==7.21.1 +pre-commit==4.6.0 +prettytable==3.18.0 +prometheus-client==0.25.0 +prompt-toolkit==3.0.52 +propcache==0.5.2 +protobuf==7.35.1 +psutil==7.2.2 +pure-eval==0.2.3 +pyarrow==24.0.0 +pycparser==3.0 +pydantic==2.13.4 +pydantic-core==2.46.4 +pyg-lib==0.7.0+pt29cpu +pygments==2.20.0 +pynndescent==0.6.0 +pyparsing==3.3.2 +pyreadstat==1.3.5 +pytest==9.1.1 +python-dateutil==2.9.0.post0 +python-discovery==1.4.2 +python-json-logger==4.1.0 +pytz==2026.2 +pyviz-comms==3.0.6 +pywinpty==3.0.5 +pyyaml==6.0.3 +pyzmq==27.1.0 +referencing==0.37.0 +regex==2026.6.28 +regexmodel==0.3.5 +requests==2.34.2 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rfc3987-syntax==1.1.0 +rich==15.0.0 +rpds-py==2026.5.1 +ruff==0.15.20 +safetensors==0.8.0 +scikit-learn==1.9.0 +scipy==1.18.0 +seaborn==0.13.2 +send2trash==2.1.0 +sentry-sdk==2.63.0 +setuptools==81.0.0 +shap==0.49.1 +shellingham==1.5.4 +simplejson==4.1.1 +six==1.17.0 +slicer==0.0.8 +smart-open==8.0.0 +smmap==5.0.3 +soupsieve==2.8.4 +sqlalchemy==2.0.51 +sqlglot==30.12.0 +sqlparse==0.5.5 +stack-data==0.6.3 +statsmodels==0.14.6 +sympy==1.14.0 +tabulate==0.10.0 +tensorboard==2.20.0 +tensorboard-data-server==0.7.2 +terminado==0.18.1 +texttable==1.7.0 +threadpoolctl==3.6.0 +tinycss2==1.5.1 +tokenizers==0.22.2 +toolz==1.1.0 +torch==2.12.1 +torch-cluster==1.6.3+pt29cpu +torch-geometric==2.8.0 +torch-scatter==2.1.2+pt29cpu +torch-sparse==0.6.18+pt29cpu +torch-spline-conv==1.2.2+pt29cpu +torchao==0.17.0 +tornado==6.5.7 +tqdm==4.68.3 +traitlets==5.15.1 +transformers==5.12.1 +typer==0.25.1 +typing-extensions==4.15.0 +typing-inspection==0.4.2 +tzdata==2026.2 +uc-micro-py==2.0.0 +umap-learn==0.5.12 +uri-template==1.3.0 +urllib3==2.7.0 +virtualenv==21.5.1 +wandb==0.28.0 +wcwidth==0.8.1 +webcolors==25.10.0 +webencodings==0.5.1 +websocket-client==1.9.0 +werkzeug==3.1.8 +widgetsnbextension==4.0.15 +wrapt==2.2.2 +xxhash==3.8.0 +xyzservices==2026.3.0 +yarl==1.24.2 diff --git a/pyproject.toml b/pyproject.toml index 08d743e..b734953 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,20 +5,19 @@ description = "Add your description here" readme = "README.md" requires-python = ">=3.12" dependencies = [ - "catboost==1.2.10", + "accelerate==1.14.0", + "captum==0.9.0", "dask==2026.6.0", "duckdb==1.5.4", "duckdb-engine==0.17.0", "eli5==0.16.0", + "flash-attn==2.8.3.post1 ; sys_platform == 'linux'", "gensim==4.4.0", "h5py==3.16.0", - "hf-transfer==0.1.9", "hvplot==0.12.2", "hydra-core==1.3.3", + "ibis==3.3.0", "igraph==1.0.0", - "imbalanced-learn==0.14.2", - "inspect-ai==0.3.241", - "interpret==0.7.8", "ipython==9.15.0", "jax==0.10.2", "json5==0.15.0", @@ -27,7 +26,7 @@ dependencies = [ "jupyterlab==4.6.0", "jupyterlab-optuna==0.3.0", "kaleido==1.3.0", - "lime==0.2.0.1", + "lifelines==0.30.3", "matplotlib==3.11.0", "metasyn==2.1.0", "metasyn-disclosure==0.3.1", @@ -38,56 +37,34 @@ dependencies = [ "numpy==2.4.6", "openpyxl==3.1.5", "optuna==4.9.0", - "pandas==3.0.4", - "peft==0.19.1", + "pandas==2.3.3", "plotly==6.8.0", "polars==1.42.0", + "pre-commit==4.6.0", "pyarrow==24.0.0", - "pyg-lib==0.6.0", + "pyg-lib==0.7.0 ; platform_machine != 'arm64' or sys_platform != 'darwin'", "pyreadstat==1.3.5", - "pytorch-lightning==2.6.5", + "pytest==9.1.1", + "pyyaml==6.0.3", + "ruff==0.15.20", "scikit-learn==1.9.0", "scipy==1.18.0", "seaborn==0.13.2", - "shap==0.52.0", - "splink==4.0.16", + "shap==0.49.1", "statsmodels==0.14.6", "tensorboard==2.20.0", - "torch==2.8", + "torch==2.12.1", "torch-cluster==1.6.3", "torch-geometric==2.8.0", "torch-scatter==2.1.2", "torch-sparse==0.6.18", "torch-spline-conv==1.2.2", "torchao==0.17.0", - "torchtune==0.6.1", "transformers==5.12.1", "umap-learn==0.5.12", "wandb==0.28.0", - "xgboost==3.3.0", ] -[tool.uv] -environments = [ - "sys_platform == 'win32'", - "sys_platform == 'linux'", - "sys_platform == 'darwin' and platform_machine == 'arm64'", -] - -# PyG CPU wheels (built for torch 2.8) come from the PyG flat (find-links) -# index, not PyPI. Persisted here so every uv add/lock/sync/export can find -# them without a --find-links flag. -[[tool.uv.index]] -name = "pyg-cpu" -url = "https://data.pyg.org/whl/torch-2.8.0+cpu.html" -format = "flat" -explicit = true - -# Route the five PyG binary packages to that index (explicit = true means it's -# used ONLY for these, never for general PyPI resolution). -[tool.uv.sources] -pyg-lib = { index = "pyg-cpu" } -torch-scatter = { index = "pyg-cpu" } -torch-sparse = { index = "pyg-cpu" } -torch-cluster = { index = "pyg-cpu" } -torch-spline-conv = { index = "pyg-cpu" } +[tool.uv.pip] +find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] +emit-find-links = true diff --git a/requirements.in b/requirements.in new file mode 100644 index 0000000..5972673 --- /dev/null +++ b/requirements.in @@ -0,0 +1,92 @@ +# Keep always these for CBS +jupyterlab # notebook IDE +notebook # classic Jupyter notebook interface +ipython # interactive Python shell +jupyter # Jupyter meta-package +openpyxl # read/write Excel files +pyreadstat # read SPSS/SAS/Stata files +pandas # dataframes +numpy # arrays and numerical computing +scipy # scientific computing +polars # fast dataframes +duckdb # in-process SQL database +duckdb-engine # SQLAlchemy driver for duckdb +ibis # dataframe API over SQL backends +matplotlib # plotting +seaborn # statistical plotting +networkx # graph analysis +igraph # fast graph analysis +netcbs # CBS-specific helpers +scikit-learn # classic ML +metasyn # synthetic data generation +metasyn-disclosure # disclosure control for synthetic data +PyYAML # YAML parsing + +## Optional packages, specific for 9424 +# Data handling +dask # parallel/out-of-core dataframes +h5py # HDF5 file format +numba # JIT compilation for numerical code +jax # array computing with autodiff/JIT +pyarrow # Arrow/Parquet file format +jupysql # run SQL in notebooks + +# Visualization +plotly # interactive plots +hvplot # high-level plotting on top of holoviews +kaleido # static image export for plotly + +# ML and interpretability +#catboost +#lime +eli5 # model inspection/explanation +shap # SHAP value model explanations +captum # PyTorch model interpretability +#imbalanced-learn +#interpret +optuna # hyperparameter optimization +#ray[tune] +# Strongly recommend the nightly build on torchtune so we can use all the custom functionality we've been building +# pip install --pre torchtune --extra-index-url https://download.pytorch.org/whl/nightly/cpu +#torchtune +#peft +hydra-core # config management +#hydra-optuna-sweeper +jupyterlab-optuna # Optuna dashboard in JupyterLab +# Statistics +statsmodels # statistical models +#pymc3 (pymc3 is at the current version not playing nicely with the other packages in pip) +lifelines # survival analysis +# Deep learning +torch # deep learning framework +#tensorflow (nit does not play nicely with pip) +torch-geometric # graph neural networks +# PyG CPU wheels for torch 2.9 (win_amd64, linux, macOS universal2; cp39-cp313) +# see [tool.uv.pip] find-links in pyproject.toml for the wheel index URL +pyg-lib; sys_platform != "darwin" or platform_machine != "arm64" # no macOS arm64 wheel for this torch build on data.pyg.org # PyG acceleration library +torch-sparse # sparse tensor ops for PyG +torch-scatter # scatter ops for PyG +torch-cluster # clustering ops for PyG +torch-spline-conv # spline-based conv ops for PyG +#torch-quiver #not yet available for windows +#intel-extension-for-pytorch #not yet available for windows +#keras +#dgl +gensim # topic modeling/word embeddings +#pytorch-lightning +transformers # pretrained NLP/LLM models +umap-learn # dimensionality reduction +#inspect-ai +torchao # PyTorch quantization/optimization +wandb # experiment tracking +#mlflow +tensorboard # training visualization +flash-attn; sys_platform == "linux" #attention-based learning faster; CUDA build, no official wheels for macOS/Windows +accelerate # multi-GPU/mixed-precision training helper +#annoy +# Configuration files +json5 # JSON5 parsing +## Testing +pytest # testing framework +ruff # linter/formatter +pre-commit # git hook manager diff --git a/uv.lock b/uv.lock index b37aba9..9b051af 100644 --- a/uv.lock +++ b/uv.lock @@ -2,20 +2,12 @@ version = 1 revision = 3 requires-python = ">=3.12" resolution-markers = [ - "python_full_version >= '3.14' and sys_platform == 'win32'", - "python_full_version == '3.13.*' and sys_platform == 'win32'", - "python_full_version < '3.13' and sys_platform == 'win32'", - "python_full_version >= '3.14' and sys_platform == 'linux'", - "python_full_version == '3.13.*' and sys_platform == 'linux'", - "python_full_version < '3.13' and sys_platform == 'linux'", - "python_full_version >= '3.14' and platform_machine == 'arm64' and sys_platform == 'darwin'", - "python_full_version == '3.13.*' and platform_machine == 'arm64' and sys_platform == 'darwin'", - "python_full_version < '3.13' and platform_machine == 'arm64' and sys_platform == 'darwin'", -] -supported-markers = [ - 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diff --git a/.gitignore b/.gitignore index b694934..4083cc5 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ -.venv \ No newline at end of file +.venv +.DS_Store \ No newline at end of file From 8975ce4cab41ea6902d61ccdb6ee80de17668bf7 Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 13:57:21 +0200 Subject: [PATCH 6/9] update README with full instructions --- README.md | 150 +++++++++++++++++++++++++++++++----------------------- 1 file changed, 86 insertions(+), 64 deletions(-) diff --git a/README.md b/README.md index 7609567..b61151b 100644 --- a/README.md +++ b/README.md @@ -1,106 +1,128 @@ -## Configuring Python in CBS Remote Access (RA) +## What this is for -**Python is not installed by default at CBS RA (yet).** To activate Python, contact the CBS microdata team at [`microdata@cbs.nl`](mailto:microdata@cbs.nl). +CBS Remote Access (RA) only lets you use Python packages that CBS has approved and +installed in advance. To get a package approved, you submit a file listing exactly +which packages (and versions) you need, and CBS installs them for you. -### Default Python Packages +This repository helps you build that file correctly, without needing to understand +Python packaging in depth. You will: -By default, some packages are available in Python at CBS RA, such as `pandas`, `pyreadstat` or `matplotlib` +1. Write down which packages you want, in a simple text file (`requirements.in`). +2. Run two commands that figure out the exact versions that work together. +3. Get a ready-to-send file (`environment0000.txt`) to email to CBS. +4. Use the same setup on your own computer, outside of CBS RA, while you work. -If you require additional packages or specific versions, follow the steps below to create and submit your own Python environment. +You only need to follow these steps once per project (and again whenever you want +to add a new package). --- -### Creating a Custom Python Environment +### Step 0: Install `uv` -Follow these instructions to set up and submit a customized Python environment. You need to use a **Windows** computer. +`uv` is the tool that does the heavy lifting (figuring out compatible package +versions). Install it once, following the official instructions: +https://docs.astral.sh/uv/getting-started/installation/ -#### Step 1: Check Existing Environment +If you've never used a terminal before: a terminal is just a window where you +type commands instead of clicking buttons. On Windows, open "PowerShell" or +"Command Prompt"; on Mac, open "Terminal" (both are pre-installed). The +installation instructions above include a single command to paste in and run. -- Check if `environment0000.txt` (replace `0000` with your actual project number) already contains the required packages and suitable versions. -- **If yes:** Send this file directly to CBS. -- **If no:** Continue to Step 2. +### Step 1: Download this repository to your computer -#### Step 2: Create the Environment (Windows + Conda) +Important: save it to a normal folder on your computer's hard drive — **not** a +folder that syncs to the cloud (OneDrive, pCloud Drive, Dropbox, Google Drive, etc). +Cloud-sync folders can silently break the setup in step 3. -Install conda locally (only needed if you do not already have Conda installed): -- Follow the official Conda installation instructions [here](https://conda.io/projects/conda/en/latest/user-guide/install/index.html#regular-installation). -- If you're unfamiliar with command-line tools, consider installing [Anaconda](https://www.anaconda.com/products/individual) instead. - -On your local Windows machine: - -```sh -conda create -n 0000 python -conda activate 0000 -conda install pip -pip install package_name -``` - -Replace `package_name` with the packages you need (e.g., `pip install numpy`). If you want to install all the packages in the requirements.txt file in this repository, use `pip install -r requirements.txt` - -**Note:** If using Jupyter Notebook or Spyder, install these explicitly, e.g.: +If you're comfortable with git: ```sh -pip install jupyter spyder +git clone +cd cbs_python ``` -#### Step 3: Export the Environment +Otherwise, download the repository as a ZIP from its webpage and unzip it into a +local folder. -Export the environment into a requirements file: +### Step 2: Say which packages you want -```sh -pip freeze > C:\temp\environment0000.txt -``` +Open `requirements.in` in a text editor. It's a plain list of package names, one +per line, already organized into groups (data handling, visualization, etc.), with +a short comment next to each one explaining what it's for. -Check `environment0000.txt` for local paths (`file://`). If found, regenerate using: +- To add a package, add a new line with its name. +- To remove one, delete its line (or put a `#` in front of it to keep it for later). -```sh -pip list --format=freeze > C:\temp\environment0000.txt -``` +You don't need to write version numbers — the next step figures those out for you. -#### Step 4: Verify Environment +### Step 3: Let `uv` work out the exact versions -Validate your environment by removing and recreating it: +Open a terminal in the repository folder and run: ```sh -conda remove -n 0000 --all -conda create -n 0000 -conda activate 0000 -conda install pip -pip install -r C:\temp\environment0000.txt +uv init --bare # only needed the very first time +uv add --bounds exact -r requirements.in ``` -Test thoroughly before submission by running python and importing your packages one by one. +This checks that all the packages you listed actually work together, and writes +the result into two files that you don't need to edit by hand: -#### Step 5: Submit Your Environment +- `pyproject.toml` — the exact version of each package you asked for in + `requirements.in` (e.g. `pandas==2.3.3`), so the choice is recorded and won't + silently change later. +- `uv.lock` — every other package those packages depend on internally, also + pinned to an exact version, so the same complete set can be reproduced + identically on any computer. -Send your verified `environment0000.txt` (replace 0000 by your project number) to CBS via email. +Together they're the "recipe" that `uv run` (step 5) and the CBS export (step 4) +both read from. +**Some packages aren't on the normal package index and need to be installed +from a URL instead** — for example the PyTorch Geometric (PyG) wheels used by +`pyg-lib`, `torch-sparse`, etc. The URL for that is kept in one place, +`pyproject.toml`, instead of in `requirements.in`: +```toml +[tool.uv.pip] +find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] +emit-find-links = true +``` ---- +- `find-links` makes `uv pip compile` (step 4) look at that URL too, so you + don't need to pass `--find-links` again on that command. +- `emit-find-links = true` makes `uv pip compile` write the `--find-links` + line at the top of the generated `environment0000.txt`. That way, whoever + installs that file with plain `pip install -r environment0000.txt` (e.g. + CBS RA) automatically knows where to find these packages too — without it, + `pip` would fail the same way `uv` did before you added this section. -## Using Python at CBS RA +This `[tool.uv.pip]` section only applies to `uv pip compile` (step 4). If you +add a new PyG package and need to run `uv add` or `uv lock` again (step 3), +pass the same URL on the command itself: -We recommend to use Python through Visual Studio Code (VS Code), installed by default: +```sh +uv add --bounds exact -r requirements.in --find-links https://data.pyg.org/whl/torch-2.9.0+cpu.html +``` -- In VS Code, select the Python interpreter in the bottom-right corner of the editor. +### Step 4: Create the file to send to CBS -You could also use Python through Jupyter in RA, for that, open an Anaconda terminal in the RA and run: +CBS RA runs Windows, so generate a Windows-specific version of the package list: ```sh -conda activate 0000 -jupyter notebook --notebook-dir=H: +uv pip compile pyproject.toml --python-version 3.12 --python-platform windows --no-annotate --no-header -o environment0000.txt ``` -This opens Jupyter in your shared directory (`H:`). +Rename `environment0000.txt` so `0000` matches your project number. This file can +be installed with plain `pip` (no `uv` needed), which is what CBS RA will do. +Email it to CBS as described in the "Creating a Custom Python Environment" section +above. ---- +### Step 5: Use the same packages on your own computer -## Contact - -This documentation is maintained by the [ODISSEI Social Data Science (SoDa)](https://odissei-data.nl/nl/soda/) team. - -For technical questions or suggestions: +```sh +uv run jupyterlab +``` -- File an issue in the project's issue tracker, or -- Contact [Javier Garcia-Bernardo](https://github.com/jgarciab). +`uv run ` runs any command (Jupyter, a script, etc.) using exactly the +packages you listed, installing anything missing automatically. This way, what you +test on your own computer matches what you'll have access to in CBS RA. From 0b438a54b2e54fdff254fc954c0ebc1faaf9b968 Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 13:58:06 +0200 Subject: [PATCH 7/9] remove older files --- README-test-uv.md | 134 ----------------------------------- sane/environment.yml | 95 ------------------------- sane/environment_precise.yml | 37 ---------- sane/export_manual_env.py | 72 ------------------- 4 files changed, 338 deletions(-) delete mode 100644 README-test-uv.md delete mode 100644 sane/environment.yml delete mode 100644 sane/environment_precise.yml delete mode 100644 sane/export_manual_env.py diff --git a/README-test-uv.md b/README-test-uv.md deleted file mode 100644 index 704e387..0000000 --- a/README-test-uv.md +++ /dev/null @@ -1,134 +0,0 @@ -## Configuring Python in CBS Remote Access (RA) - -**Python is not installed by default at CBS RA (yet).** To activate Python, contact the CBS microdata team at [`microdata@cbs.nl`](mailto:microdata@cbs.nl). - -### Default Python Packages - -By default, some packages are available in Python at CBS RA, such as `pandas`, `pyreadstat` or `matplotlib` - -If you require additional packages or specific versions, follow the steps below to create and submit your own Python environment. UV is able to create a library of dependencies that can run on multiple OS. However, to install dependencies specifically for Windows follow the next steps. - ---- - -### Creating a Custom Python Environment - -Follow these instructions to set up and submit a customized Python environment. You need to use a **Windows** computer. - -#### Step 1: Check Existing Environment - -- Check if `environment0000.txt` (replace `0000` with your actual project number) already contains the required packages and suitable versions. -- **If yes:** Send this file directly to CBS. -- **If no:** Continue to Step 2. - -#### Step 2: Create the Environment (Windows + UV) - -Install UV locally (only needed if you do not already have UV installed): -- Follow the official UV installation instructions [here](https://docs.astral.sh/uv/getting-started/installation/). - - -On your local Terminal machine: - -If the project has not been initialized with uv then write the -next command in your machine terminal: - -```sh -uv init --python python_version -``` - -If the project requires to run the code outside the RA environment then it is possible to select on which OS the code should run. - -in the pyproject.toml file insert the following lines: - -[tool.uv] -environments = [ - "sys_platform == 'win32'", - "sys_platform == 'darwin' and platform_machine == 'arm64'", -] - -It is possible to add more OS system - -[tool.uv] -environments = [ - "sys_platform == 'win32'", - "sys_platform == 'linux'", - "sys_platform == 'darwin' and platform_machine == 'arm64'", -] - - -To add a package -```sh -uv add package_name -``` - - -Aternatively If you want to install all the packages in the requirements.txt file in this repository, use `uv add --bounds exact -r requirements_base.txt` this command will pin the exact dependency version - -**(to be updated with uv)Note:** If using Jupyter Notebook or Spyder, install these explicitly, e.g.: - -```sh -pip install jupyter spyder -``` - -#### Step 4: Export the Environment (Windows + UV) - -Export the environment into a requirements file: - -```sh -uv pip compile requirements_base.txt --python-version 3.12 --python-platform windows --no-annotate --no-header -o environment0000.txt -``` - -Aternatively If you want to export a requirement.txt that contains dependencies for different platforms use -```sh -uv export --format requirements-txt --no-hashes --no-header --no-annotate --no-emit-project --python 3.12 | - ForEach-Object { ($_ -split ';')[0].TrimEnd() } | - Set-Content -Encoding ascii environment_9424.txt -``` - - -#### (update with UV)Step 4: Verify Environment - -Validate your environment by removing and recreating it: - -```sh -conda remove -n 0000 --all -conda create -n 0000 -conda activate 0000 -conda install pip -pip install -r C:\temp\environment0000.txt -``` - -Test thoroughly before submission by running python and importing your packages one by one. - -#### Step 5: Submit Your Environment - -Send your verified `environment0000.txt` (replace 0000 by your project number) to CBS via email. - - - ---- - -## (update with UV) Using Python at CBS RA - -We recommend to use Python through Visual Studio Code (VS Code), installed by default: - -- In VS Code, select the Python interpreter in the bottom-right corner of the editor. - -You could also use Python through Jupyter in RA, for that, open an Anaconda terminal in the RA and run: - -```sh -conda activate 0000 -jupyter notebook --notebook-dir=H: -``` - -This opens Jupyter in your shared directory (`H:`). - ---- - -## Contact - -This documentation is maintained by the [ODISSEI Social Data Science (SoDa)](https://odissei-data.nl/nl/soda/) team. - -For technical questions or suggestions: - -- File an issue in the project's issue tracker, or -- Contact [Javier Garcia-Bernardo](https://github.com/jgarciab). diff --git a/sane/environment.yml b/sane/environment.yml deleted file mode 100644 index 0436465..0000000 --- a/sane/environment.yml +++ /dev/null @@ -1,95 +0,0 @@ -name: sane -channels: - - conda-forge - -dependencies: - - python=3.12 - - # Notebooks and IPython - - jupyterlab - - notebook - - ipython - - jupyter - - # Data handling - - dask - - openpyxl - - scipy - - pandas - - pyreadstat - - numpy - - polars - - pyarrow - - jupysql - - duckdb - - duckdb-engine - - arrow - - python-dateutil - - # Visualization - - plotly - - matplotlib - - geopandas - - shapely - - fiona - - cartopy - - folium - - gdal - - geojson - - pyproj - - seaborn - - hvplot - - bokeh - - altair - - panel - - python-kaleido - - # Networks - - networkx - - igraph - - # ML and interpretability - - scikit-learn - - lime - - eli5 - - shap - - imbalanced-learn - - interpret - - optuna - - xgboost - - lightgbm - - catboost - - joblib - - mlflow - - dowhy - - causalml - - causal-learn - - pgmpy - - pymc - - numpyro - - blackjax - - nutpie - - # NLP and text - - nltk - - spacy - - # SQL / DB Interface - - sqlalchemy - - # Data validation and config - - pandera - - pydantic - - # Parallel / performance - - multiprocess - - threadpoolctl - - # File/HTML/PDF parsing - - beautifulsoup4 - - lxml - - # Pip-only packages - - pip - - pip: - - metasyn # synthetic data diff --git a/sane/environment_precise.yml b/sane/environment_precise.yml deleted file mode 100644 index 23a89bc..0000000 --- a/sane/environment_precise.yml +++ /dev/null @@ -1,37 +0,0 @@ -name: sane -channels: -- conda-forge -dependencies: -- dask=2025.3.0 -- duckdb-engine=0.15.0 -- duckdb=1.2.1 -- eli5=0.13.0 -- hvplot=0.11.2 -- python-igraph=0.11.8 -- imbalanced-learn=0.13.0 -- interpret=0.6.10 -- ipython=9.1.0 -- jupysql=0.11.1 -- jupyter=1.1.1 -- jupyterlab=4.4.0 -- lime=0.2.0.1 -- matplotlib=3.10.1 -- networkx=3.4.2 -- notebook=7.4.0 -- numpy=2.2.4 -- openpyxl=3.1.5 -- optuna=4.2.1 -- pandas=2.2.3 -- pip=25.0.1 -- plotly=6.0.1 -- polars=1.27.1 -- pyarrow=19.0.1 -- pyreadstat=1.2.8 -- python=3.12.10 -- scikit-learn=1.6.1 -- scipy=1.15.2 -- seaborn=0.13.2 -- shap=0.47.1 -- statsmodels=0.14.4 -- pip: - - metasyn==1.1.0 diff --git a/sane/export_manual_env.py b/sane/export_manual_env.py deleted file mode 100644 index 6ad2785..0000000 --- a/sane/export_manual_env.py +++ /dev/null @@ -1,72 +0,0 @@ -import yaml -import subprocess -import json -from pathlib import Path - -# === Step 1: Load packages from original environment.yml === -with open("environment.yml", "r") as f: - env_data = yaml.safe_load(f) - -original_packages = set() -for dep in env_data.get("dependencies", []): - if isinstance(dep, str): - pkg_name = dep.split("=")[0].strip().lower() - original_packages.add(pkg_name) - elif isinstance(dep, dict) and "pip" in dep: - for pip_pkg in dep["pip"]: - pip_name = pip_pkg.split("==")[0].strip().lower() - original_packages.add(pip_name) - -# === Step 2: Get installed packages from current environment === -installed = subprocess.check_output(['conda', 'list', '--json']) -installed = json.loads(installed) - -installed_versions = { - pkg['name'].lower(): f"{pkg['name']}={pkg['version']}" - for pkg in installed if pkg['channel'] != 'pypi' -} - -installed_versions_pip = { - pkg['name'].lower(): f"{pkg['name']}={pkg['version']}" - for pkg in installed if pkg['channel'] == 'pypi' -} - -# === Step 3: Match and build new list with pinned versions === -conda_pkgs = [] -pip_pkgs = [] - -for name in original_packages: - if name in installed_versions: - conda_pkgs.append(installed_versions[name]) - elif name in installed_versions_pip: - # Try to find pip-installed version - try: - version = subprocess.check_output( - ['pip', 'show', name] - ).decode() - for line in version.splitlines(): - if line.startswith("Version:"): - pip_version = line.split(":")[1].strip() - pip_pkgs.append(f"{name}=={pip_version}") - break - except subprocess.CalledProcessError: - print(f"⚠️ Package not found via conda or pip: {name}") - else: - print(f"⚠️ Package not found via conda or pip: {name}") -# === Step 4: Write new environment.yml with pinned versions === -precise_env = { - "name": env_data.get("name", "precise_env"), - "channels": env_data.get("channels", ["conda-forge"]), - "dependencies": sorted(conda_pkgs) -} - -# Ensure pip section is a dictionary under dependencies -if pip_pkgs: - precise_env["dependencies"].append({"pip": sorted(pip_pkgs)}) - -# Save the file -output_path = Path("environment_precise.yml") -with output_path.open("w") as f: - yaml.dump(precise_env, f, sort_keys=False) - -print(f"✅ Saved precise environment to: {output_path.resolve()}") From 299d42a129a759ea9885425ce1a03e8a294e8e24 Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 16:30:33 +0200 Subject: [PATCH 8/9] fix mac issues --- README.md | 101 +++++++++++++++++++++++++++++--------------- environment0000.txt | 3 +- pyproject.toml | 13 ++++-- requirements.in | 3 -- uv.lock | 21 ++------- 5 files changed, 82 insertions(+), 59 deletions(-) diff --git a/README.md b/README.md index b61151b..4c31034 100644 --- a/README.md +++ b/README.md @@ -1,22 +1,20 @@ ## What this is for -CBS Remote Access (RA) only lets you use Python packages that CBS has approved and -installed in advance. To get a package approved, you submit a file listing exactly -which packages (and versions) you need, and CBS installs them for you. +CBS Remote Access (RA) only lets you use Python packages that CBS has approved and installed in advance. To get a package approved, you submit a file pip requirements.txt file listing exactly which packages (and versions) you need, and CBS installs them for you. -This repository helps you build that file correctly, without needing to understand -Python packaging in depth. You will: +This repository helps you build that file correctly, without needing to understand Python packaging in depth. You will: 1. Write down which packages you want, in a simple text file (`requirements.in`). 2. Run two commands that figure out the exact versions that work together. 3. Get a ready-to-send file (`environment0000.txt`) to email to CBS. 4. Use the same setup on your own computer, outside of CBS RA, while you work. -You only need to follow these steps once per project (and again whenever you want -to add a new package). +You only need to follow these steps once per project (and again whenever you want to add a new package). --- +## Basic configuration + ### Step 0: Install `uv` `uv` is the tool that does the heavy lifting (figuring out compatible package @@ -77,32 +75,9 @@ the result into two files that you don't need to edit by hand: Together they're the "recipe" that `uv run` (step 5) and the CBS export (step 4) both read from. -**Some packages aren't on the normal package index and need to be installed -from a URL instead** — for example the PyTorch Geometric (PyG) wheels used by -`pyg-lib`, `torch-sparse`, etc. The URL for that is kept in one place, -`pyproject.toml`, instead of in `requirements.in`: - -```toml -[tool.uv.pip] -find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] -emit-find-links = true -``` - -- `find-links` makes `uv pip compile` (step 4) look at that URL too, so you - don't need to pass `--find-links` again on that command. -- `emit-find-links = true` makes `uv pip compile` write the `--find-links` - line at the top of the generated `environment0000.txt`. That way, whoever - installs that file with plain `pip install -r environment0000.txt` (e.g. - CBS RA) automatically knows where to find these packages too — without it, - `pip` would fail the same way `uv` did before you added this section. - -This `[tool.uv.pip]` section only applies to `uv pip compile` (step 4). If you -add a new PyG package and need to run `uv add` or `uv lock` again (step 3), -pass the same URL on the command itself: - -```sh -uv add --bounds exact -r requirements.in --find-links https://data.pyg.org/whl/torch-2.9.0+cpu.html -``` +If this command fails with an error, see "Advanced configuration" below — most +failures come from specific packages (PyTorch Geometric, flash-attn, etc.) that +need a bit of extra setup in `pyproject.toml`. ### Step 4: Create the file to send to CBS @@ -126,3 +101,63 @@ uv run jupyterlab `uv run ` runs any command (Jupyter, a script, etc.) using exactly the packages you listed, installing anything missing automatically. This way, what you test on your own computer matches what you'll have access to in CBS RA. + +--- + +## Advanced configuration + +A few packages need extra settings in `pyproject.toml`, added by hand, before +`uv add` / `uv lock` / `uv pip compile` will work. These settings only need to +be added once — after that, steps 3 and 4 above work normally. + +### Packages installed from a URL instead of the normal package index + +Some packages aren't on the normal package index and need to be installed from +a URL instead — for example the PyTorch Geometric (PyG) wheels used by +`pyg-lib`, `torch-sparse`, etc. Add the URL under `[tool.uv]` (used by `uv add` +and `uv lock`) and under `[tool.uv.pip]` (used by `uv pip compile`): + +```toml +[tool.uv] +find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] + +[tool.uv.pip] +find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] +emit-find-links = true +``` + +- `[tool.uv] find-links` makes `uv add`/`uv lock` (step 3) look at that URL. +- `[tool.uv.pip] find-links` makes `uv pip compile` (step 4) look at that URL. + Both are needed — they're read by different commands. +- `emit-find-links = true` makes `uv pip compile` write the `--find-links` + line at the top of the generated `environment0000.txt`. That way, whoever + installs that file with plain `pip install -r environment0000.txt` (e.g. + CBS RA) automatically knows where to find these packages too — without it, + `pip` would fail to find them. + +If you don't add this, `uv` may report that no matching version exists for a +package, even though it's listed correctly in `requirements.in`. + +### Packages that fail to build with "ModuleNotFoundError: No module named 'torch'" + +Some packages (e.g. `torch-cluster`, `torch-scatter`, `torch-sparse`, +`torch-spline-conv`, `flash-attn`) are compiled from source, and their build +script imports `torch` without declaring it as something it needs in order to +build — so `uv` builds them in a clean environment that doesn't have `torch` +yet, and the build fails with `ModuleNotFoundError: No module named 'torch'`. + +The error message includes the fix. Add the affected package(s) under +`[tool.uv.extra-build-dependencies]` in `pyproject.toml`: + +```toml +[tool.uv.extra-build-dependencies] +flash-attn = ["torch"] +torch-sparse = ["torch"] +torch-scatter = ["torch"] +torch-cluster = ["torch"] +torch-spline-conv = ["torch"] +``` + +This tells `uv` to install `torch` into the temporary build environment first, +so the package's build script can find it. Without this, both `uv add` and +`uv pip compile` fail with the same error. diff --git a/environment0000.txt b/environment0000.txt index 78af7d1..fc173e3 100644 --- a/environment0000.txt +++ b/environment0000.txt @@ -104,7 +104,7 @@ jupyter-events==0.12.1 jupyter-lsp==2.3.1 jupyter-server==2.20.0 jupyter-server-terminals==0.5.4 -jupyterlab==4.6.0 +jupyterlab==4.6.1 jupyterlab-optuna==0.3.0 jupyterlab-pygments==0.3.0 jupyterlab-server==2.28.0 @@ -179,7 +179,6 @@ pyarrow==24.0.0 pycparser==3.0 pydantic==2.13.4 pydantic-core==2.46.4 -pyg-lib==0.7.0+pt29cpu pygments==2.20.0 pynndescent==0.6.0 pyparsing==3.3.2 diff --git a/pyproject.toml b/pyproject.toml index b734953..47af242 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,6 @@ [project] name = "cbs-python" version = "0.1.0" -description = "Add your description here" -readme = "README.md" requires-python = ">=3.12" dependencies = [ "accelerate==1.14.0", @@ -23,7 +21,7 @@ dependencies = [ "json5==0.15.0", "jupysql==0.11.1", "jupyter==1.1.1", - "jupyterlab==4.6.0", + "jupyterlab==4.6.1", "jupyterlab-optuna==0.3.0", "kaleido==1.3.0", "lifelines==0.30.3", @@ -42,7 +40,6 @@ dependencies = [ "polars==1.42.0", "pre-commit==4.6.0", "pyarrow==24.0.0", - "pyg-lib==0.7.0 ; platform_machine != 'arm64' or sys_platform != 'darwin'", "pyreadstat==1.3.5", "pytest==9.1.1", "pyyaml==6.0.3", @@ -65,6 +62,14 @@ dependencies = [ "wandb==0.28.0", ] + [tool.uv.pip] find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] emit-find-links = true + +[tool.uv.extra-build-dependencies] +flash-attn = ["torch"] +torch-sparse = ["torch"] +torch-scatter = ["torch"] +torch-cluster = ["torch"] +torch-spline-conv = ["torch"] diff --git a/requirements.in b/requirements.in index 5972673..01cea16 100644 --- a/requirements.in +++ b/requirements.in @@ -61,9 +61,6 @@ lifelines # survival analysis torch # deep learning framework #tensorflow (nit does not play nicely with pip) torch-geometric # graph neural networks -# PyG CPU wheels for torch 2.9 (win_amd64, linux, macOS universal2; cp39-cp313) -# see [tool.uv.pip] find-links in pyproject.toml for the wheel index URL -pyg-lib; sys_platform != "darwin" or platform_machine != "arm64" # no macOS arm64 wheel for this torch build on data.pyg.org # PyG acceleration library torch-sparse # sparse tensor ops for PyG torch-scatter # scatter ops for PyG torch-cluster # clustering ops for PyG diff --git a/uv.lock b/uv.lock index 9b051af..d4d563c 100644 --- a/uv.lock +++ b/uv.lock @@ -459,7 +459,6 @@ dependencies = [ { name = "polars" }, { name = "pre-commit" }, { name = "pyarrow" }, - { name = "pyg-lib", marker = "platform_machine != 'arm64' or sys_platform != 'darwin'" }, { name = "pyreadstat" }, { name = "pytest" }, { name = "pyyaml" }, @@ -502,7 +501,7 @@ requires-dist = [ { name = "json5", specifier = "==0.15.0" }, { name = "jupysql", specifier = "==0.11.1" }, { name = "jupyter", specifier = "==1.1.1" }, - { name = "jupyterlab", specifier = "==4.6.0" }, + { name = "jupyterlab", specifier = "==4.6.1" }, { name = "jupyterlab-optuna", specifier = "==0.3.0" }, { name = "kaleido", specifier = "==1.3.0" }, { name = "lifelines", specifier = "==0.30.3" }, @@ -521,7 +520,6 @@ requires-dist = [ { name = "polars", specifier = "==1.42.0" }, { name = "pre-commit", specifier = "==4.6.0" }, { name = "pyarrow", specifier = "==24.0.0" }, - { name = "pyg-lib", marker = "platform_machine != 'arm64' or sys_platform != 'darwin'", specifier = "==0.7.0" }, { name = "pyreadstat", specifier = "==1.3.5" }, { name = "pytest", specifier = "==9.1.1" }, { name = "pyyaml", specifier = "==6.0.3" }, @@ -2096,7 +2094,7 @@ wheels = [ [[package]] name = "jupyterlab" -version = "4.6.0" +version = "4.6.1" source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "async-lru" }, @@ -2113,9 +2111,9 @@ dependencies = [ { name = "tornado" }, { name = "traitlets" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/f8/3c/1ebd737b860cdbe61eed71536d06aab4e1781fbdcf07ecd5a1afe05b8adf/jupyterlab-4.6.0.tar.gz", hash = "sha256:6a8b88f2aae7ed4d012c634fc957c1a27f3aa217c32f0ced0175fac9ee17f9e5", size = 28181861, upload-time = "2026-06-18T13:52:56.039Z" } +sdist = { url = "https://files.pythonhosted.org/packages/bc/2a/d6af53bfd45a43a5bfe7e40ba47ee7a8921a807daf4bb708e3a295bbb54d/jupyterlab-4.6.1.tar.gz", hash = "sha256:75315982ed28427edaa62bb85eadb5105e4043a757643c910efd787fe6ed0837", size = 28179125, upload-time = "2026-06-29T12:48:45.402Z" } wheels = [ - { url = "https://files.pythonhosted.org/packages/0a/eb/aa48075d0aa3d0188db34ba2704f53791757743c0bb02e18c4eef989b6de/jupyterlab-4.6.0-py3-none-any.whl", hash = "sha256:b6938cb8a1ef3d43860ff4745a680c62cc0a9385f9672295bb56cd2e7cfeebe2", size = 17143447, upload-time = "2026-06-18T13:52:51.42Z" }, + { url = "https://files.pythonhosted.org/packages/5a/81/90ac6cc31d248e83a0d1eab343a5e6e68bc783d3f74fbe61640f42a61da4/jupyterlab-4.6.1-py3-none-any.whl", hash = "sha256:85a58546c831f3dce6cf919468c26874c9065e99c42279fb4abb8e1b552a98bb", size = 17164660, upload-time = "2026-06-29T12:48:41.21Z" }, ] [[package]] @@ -3930,17 +3928,6 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/fa/c3/7c8b240552251faf6b3a957db200fcfbbcec36763c050428b601e0c9b83b/pydantic_core-2.46.4-graalpy312-graalpy250_312_native-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:00c603d540afdd6b80eb39f078f33ebd46211f02f33e34a32d9f053bba711de0", size = 2147590, upload-time = "2026-05-06T13:39:29.883Z" }, ] -[[package]] -name = "pyg-lib" -version = "0.7.0+pt29cpu" -source = { registry = "https://data.pyg.org/whl/torch-2.9.0+cpu.html" } -wheels = [ - { url = "https://data.pyg.org/whl/torch-2.9.0%2Bcpu/pyg_lib-0.7.0%2Bpt29cpu-cp312-cp312-win_amd64.whl" }, - { url = "https://data.pyg.org/whl/torch-2.9.0%2Bcpu/pyg_lib-0.7.0%2Bpt29cpu-cp313-cp313-win_amd64.whl" }, - { url = "https://data.pyg.org/whl/torch-2.9.0%2Bcpu/pyg_lib-0.7.0%2Bpt29cpu-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl" }, - { url = "https://data.pyg.org/whl/torch-2.9.0%2Bcpu/pyg_lib-0.7.0%2Bpt29cpu-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl" }, -] - [[package]] name = "pygments" version = "2.20.0" From 9539c1ebcc4bc6c06de98c468dffc5c2ff5490de Mon Sep 17 00:00:00 2001 From: Javier Garcia-Bernardo Date: Mon, 29 Jun 2026 16:31:14 +0200 Subject: [PATCH 9/9] remove unneded library instructions --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 4c31034..d891921 100644 --- a/README.md +++ b/README.md @@ -118,9 +118,6 @@ a URL instead — for example the PyTorch Geometric (PyG) wheels used by and `uv lock`) and under `[tool.uv.pip]` (used by `uv pip compile`): ```toml -[tool.uv] -find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] - [tool.uv.pip] find-links = ["https://data.pyg.org/whl/torch-2.9.0+cpu.html"] emit-find-links = true