| # Dependencies for the dataset readers, the analysis code, and reproducing the figures/tables |
| # (reproduce.py). This is NOT the inference stack: `pip install magnet-nmr` and the Option B checkout |
| # pull torch from magnet/pyproject.toml and magnet/requirements.txt instead, so nothing here reaches |
| # an inference-only install. |
| # Loose floors so a future release can't silently break CI; tests also need pytest. |
| # numpy + h5py cover the sigma readers; the delta22 reader additionally uses |
| # pandas (DataFrame assembly), openpyxl (reads the experimental .xlsx), and tqdm. |
| numpy>=1.20 |
| h5py>=3.0 |
| pandas>=1.3 |
| openpyxl>=3.0 |
| tqdm>=4.0 |
| # the leveling-effect analysis (analysis/code/leveling.py) and its tests use scikit-learn |
| # for the principal-components step. matplotlib + adjustText are needed only to redraw its |
| # figures, not to run the tests, so they are not listed here. |
| scikit-learn>=1.0 |
| # the applications analysis (analysis/code/applications.py) fits the composite linear model with |
| # statsmodels. Its figure notebooks also draw boxplots with matplotlib + seaborn; those are needed |
| # only to redraw the figures (not to run the readers or the tests), and seaborn pulls matplotlib in |
| # as a dependency. |
| statsmodels>=0.13 |
| seaborn>=0.12 |
| # the DFT8K functional-group analysis (analysis/code/dft8k_residuals.py's |
| # functional_group_errors/find_extreme_residual, used by fig5b_dft8k.ipynb) parses each molecule's |
| # SMILES and matches functional-group substructures with RDKit. Not needed for the rest of the |
| # repo's readers or tests. |
| rdkit>=2023.9 |
|
|
| # Reproducing the figures and tables (reproduce.py) executes the analysis notebooks, which draw with |
| # matplotlib (adjustText places the leveling-figure labels) and use scipy directly. matplotlib and |
| # scipy already arrive transitively via seaborn and scikit-learn; they are listed explicitly because |
| # the notebooks import them. nbconvert + ipykernel are the headless notebook-execution stack |
| # reproduce.py drives; they are the only reason a plain reader/test run does not need them. |
| matplotlib>=3.5 |
| scipy>=1.7 |
| adjustText>=1.0 |
| nbconvert>=7.0 |
| ipykernel>=6.0 |
|
|
