appletree 0.5.1

Description:

appletree 0.5.1

Appletree
A high-Performance Program simuLatEs and fiTs REsponse of xEnon.







Installation and Set-Up
Regular installation:
With cpu support:
pip install appletree[cpu]

With CUDA Toolkit 11.2 support:
pip install appletree[cuda112] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

With CUDA Toolkit 12.1 support:
pip install appletree[cuda121] -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Developer setup:
Clone the repository:
git clone https://github.com/XENONnT/appletree
cd appletree

To install the package and requirements in your environment, replace pip install appletree[*] to python3 -m pip install .[*] --user in the above pip commands.
To install appletree in editable mode, insert --editable argument after install in the above pip install or python3 -m pip install commands.
For example, to install in your environment and in editable mode with CUDA Toolkit 12.1 support:
python3 -m pip install --editable .[cuda121] --user -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html

Then you are now good to go!
Usage
The best way to start with the appletree package is to have a look at the tutorial notebooks.
Contributing
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
Please make sure to update tests as appropriate.
v0.5.1 / 2024-07-31

Fix S1 bias coordinate by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/174
Modified truncate_normal with jax.random.truncated_normal by @mhliu0001 in https://github.com/XENONnT/appletree/pull/175
Revert "Modified truncate_normal with jax.random.truncated_normal" by @mhliu0001 in https://github.com/XENONnT/appletree/pull/176
Change eps added to histogram to mean(eff) by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/177
Add lineage hash for all levels: Config, Plugin, Component, and Context by @dachengx in https://github.com/XENONnT/appletree/pull/178
Separate and save lineage for all levels by @dachengx in https://github.com/XENONnT/appletree/pull/179
Allow component lineage with no binning by @dachengx in https://github.com/XENONnT/appletree/pull/180

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.5.0...v0.5.1
v0.5.0 / 2024-06-30

Nestv2 parameter by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/167
Nearest neighbor interpolator by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/168
Add 1D nearest neighbour and linear interpolator by @dachengx in https://github.com/XENONnT/appletree/pull/170
Fix software versions in tests by @dachengx in https://github.com/XENONnT/appletree/pull/171

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.4.0...v0.5.0
v0.4.0 / 2024-05-27

Try using jax.random.binomial by @dachengx in https://github.com/XENONnT/appletree/pull/148
Turn off add_eps_to_hist in NR and ER by @FaroutYLq in https://github.com/XENONnT/appletree/pull/152
Debug when bins_type is not set by @dachengx in https://github.com/XENONnT/appletree/pull/153
Specifically install lxml_html_clean by @dachengx in https://github.com/XENONnT/appletree/pull/157
Initialize context from backend by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/156
Add parameter_alias to translate parameters in par_config by @dachengx in https://github.com/XENONnT/appletree/pull/160
Allow user to aggressively use memory by @dachengx in https://github.com/XENONnT/appletree/pull/164
Fix a bug of plotter which contains inf by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/165

New Contributors

@FaroutYLq made their first contribution in https://github.com/XENONnT/appletree/pull/152

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.3.2...v0.4.0
v0.3.2 / 2024-03-06

Remove scikit-learn version requirement by @dachengx in https://github.com/XENONnT/appletree/pull/131
Use trusted publisher because username/password authentication is no longer supported by @dachengx in https://github.com/XENONnT/appletree/pull/132
Be compatible with JAX_ENABLE_X64=1 by @dachengx in https://github.com/XENONnT/appletree/pull/134
Raise more information when file can not be found by @dachengx in https://github.com/XENONnT/appletree/pull/135
Preserve dtype of results in multiple_simulations by @dachengx in https://github.com/XENONnT/appletree/pull/137
Copy memory from GPU to CPU by @dachengx in https://github.com/XENONnT/appletree/pull/139
Bug fix when using force_no_eff with tuple data_names by @dachengx in https://github.com/XENONnT/appletree/pull/141
Add Gamma, Negative Binomial, and Generalized Poisson Distribution by @dachengx in https://github.com/XENONnT/appletree/pull/145
Add support for 1D fitting by @dachengx in https://github.com/XENONnT/appletree/pull/144
Correct the sigmas in TwoHalfNorm by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/143
Plotter for MCMC diagnostics by @zihaoxu98 in https://github.com/XENONnT/appletree/pull/146

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.3.1...v0.3.2
v0.3.1 / 2024-01-12

Smarter SigmaMap handling and needed_parameters by @xzh19980906 in https://github.com/XENONnT/appletree/pull/116
Move messages of used parameter in SigmaMap.build by @dachengx in https://github.com/XENONnT/appletree/pull/117
Set required_parameter as method of Config by @dachengx in https://github.com/XENONnT/appletree/pull/119
Optional applying efficiency in multiple_simulations by @dachengx in https://github.com/XENONnT/appletree/pull/123
Fix S1/S2 correction and gas gain when simulating S1/S2PE by @mhliu0001 in https://github.com/XENONnT/appletree/pull/122
Prevent already cached functions from being changed by @dachengx in https://github.com/XENONnT/appletree/pull/125
Update docstring to google style by @dachengx in https://github.com/XENONnT/appletree/pull/126
Update conf, add napoleon by @dachengx in https://github.com/XENONnT/appletree/pull/127
Small bug fix when no llh_name is used by @dachengx in https://github.com/XENONnT/appletree/pull/129

New Contributors

@mhliu0001 made their first contribution in https://github.com/XENONnT/appletree/pull/122

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.3.0...v0.3.1
v0.3.0 / 2023-08-31

Fix function name to simulate_weighted_data, nothing else changed by @dachengx in https://github.com/XENONnT/appletree/pull/99
Stop jax from preallocating memory by @dachengx in https://github.com/XENONnT/appletree/pull/100
fix meshgrid binning by @hoetzsch in https://github.com/XENONnT/appletree/pull/101
Binning is not required by Component by @dachengx in https://github.com/XENONnT/appletree/pull/103
Upper clipping on binomial randgen in normal approx by @xzh19980906 in https://github.com/XENONnT/appletree/pull/107
Rename fake maps by @xzh19980906 in https://github.com/XENONnT/appletree/pull/106
Update fake maps filenames by @dachengx in https://github.com/XENONnT/appletree/pull/108
Skip mongo DB when finding files by @xzh19980906 in https://github.com/XENONnT/appletree/pull/111
Raise error if file does not exist by @xzh19980906 in https://github.com/XENONnT/appletree/pull/110
Rename lce to correction by @dachengx in https://github.com/XENONnT/appletree/pull/109
Add function to check the usage of configs, check_unused_configs by @dachengx in https://github.com/XENONnT/appletree/pull/112
Proposal to use pre-commit for continuous integration by @dachengx in https://github.com/XENONnT/appletree/pull/113

New Contributors

@hoetzsch made their first contribution in https://github.com/XENONnT/appletree/pull/101

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.2.3...v0.3.0
v0.2.3 / 2023-05-29

Add pip install user by @dachengx in https://github.com/XENONnT/appletree/pull/96
Installation with various extras_requires for different CUDA support by @dachengx in https://github.com/XENONnT/appletree/pull/97

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.2.2...v0.2.3
v0.2.2 / 2023-05-25

Stop using MANIFEST.in, move to a modern way of file system configuration by @dachengx in https://github.com/XENONnT/appletree/pull/94

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.2.1...v0.2.2
v0.2.1 / 2023-05-22

Change variables s1 s2 to s1_area s2_area by @dachengx in https://github.com/XENONnT/appletree/pull/86
Remove duplicated import pd by @xzh19980906 in https://github.com/XENONnT/appletree/pull/87
Generate number of events in the defined ROI by @dachengx in https://github.com/XENONnT/appletree/pull/88
Update DOI link by @dachengx in https://github.com/XENONnT/appletree/pull/89
Loosen requirement after beta phase and specify jax find-links by @dachengx in https://github.com/XENONnT/appletree/pull/90
Update notebooks by @dachengx in https://github.com/XENONnT/appletree/pull/91
Add more tests by @dachengx in https://github.com/XENONnT/appletree/pull/92

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.2.0...v0.2.1
v0.2.0 / 2023-03-15

Add NESTv2 yields parameterization and literature constrain by @dachengx in https://github.com/XENONnT/appletree/pull/82
Add uncertainty on electron lifetime by @dachengx in https://github.com/XENONnT/appletree/pull/83
Add NESTv2 NR parameters of quanta distribution's width by @dachengx in https://github.com/XENONnT/appletree/pull/85

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.1.0...v0.2.0
v0.1.0 / 2023-02-12

Add corner as dependency by @dachengx in https://github.com/XENONnT/appletree/pull/55
Add .h5 backend to store MCMC results by @dachengx in https://github.com/XENONnT/appletree/pull/57
Add document by @xzh19980906 in https://github.com/XENONnT/appletree/pull/61
More docs by @xzh19980906 in https://github.com/XENONnT/appletree/pull/62
Deduce and compile codes to generate Ly & Qy curve by @dachengx in https://github.com/XENONnT/appletree/pull/60
Convert PDF spectrum to CDF by default by @xzh19980906 in https://github.com/XENONnT/appletree/pull/72
Add R dimension for template generation by @xzh19980906 in https://github.com/XENONnT/appletree/pull/74
Use specific config for certain llh by @dachengx in https://github.com/XENONnT/appletree/pull/78
Config can read map and assign itself a mapping function by @dachengx in https://github.com/XENONnT/appletree/pull/79
Stricter needed parameters check and save meta data to samples by @dachengx in https://github.com/XENONnT/appletree/pull/80
Irregular binning option in likelihood by @xzh19980906 in https://github.com/XENONnT/appletree/pull/81

Full Changelog: https://github.com/XENONnT/appletree/compare/v0.0.0...v0.1.0
v0.0.0 / 2022-10-13

Add more notebooks by @dachengx in https://github.com/XENONnT/appletree/pull/52
Introduce numpyro as dependency by @dachengx in https://github.com/XENONnT/appletree/pull/53
Try upload to pypi by @dachengx in https://github.com/XENONnT/appletree/pull/54

Full Changelog: https://github.com/XENONnT/appletree/commits/v0.0.0