A high-Performance Program simuLatEs and fiTs REsponse of xEnon.
Project description
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
, andContext
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 inpar_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 tupledata_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_require
s 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
tos1_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
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