bmtool 0.7.0.6.4__py3-none-any.whl → 0.7.1.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (30) hide show
  1. bmtool/SLURM.py +162 -109
  2. bmtool/__init__.py +1 -1
  3. bmtool/__main__.py +8 -7
  4. bmtool/analysis/entrainment.py +290 -147
  5. bmtool/analysis/lfp.py +279 -134
  6. bmtool/analysis/netcon_reports.py +41 -44
  7. bmtool/analysis/spikes.py +114 -73
  8. bmtool/bmplot/connections.py +658 -325
  9. bmtool/bmplot/entrainment.py +17 -18
  10. bmtool/bmplot/lfp.py +24 -17
  11. bmtool/bmplot/netcon_reports.py +0 -4
  12. bmtool/bmplot/spikes.py +97 -48
  13. bmtool/connectors.py +394 -251
  14. bmtool/debug/commands.py +13 -7
  15. bmtool/debug/debug.py +2 -2
  16. bmtool/graphs.py +26 -19
  17. bmtool/manage.py +6 -11
  18. bmtool/plot_commands.py +350 -151
  19. bmtool/singlecell.py +357 -195
  20. bmtool/synapses.py +564 -470
  21. bmtool/util/commands.py +1079 -627
  22. bmtool/util/neuron/celltuner.py +989 -609
  23. bmtool/util/util.py +992 -588
  24. {bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/METADATA +40 -2
  25. bmtool-0.7.1.1.dist-info/RECORD +34 -0
  26. {bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/WHEEL +1 -1
  27. bmtool-0.7.0.6.4.dist-info/RECORD +0 -34
  28. {bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/entry_points.txt +0 -0
  29. {bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/licenses/LICENSE +0 -0
  30. {bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/top_level.txt +0 -0
{bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: bmtool
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- Version: 0.7.0.6.4
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+ Version: 0.7.1.1
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  Summary: BMTool
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  Home-page: https://github.com/cyneuro/bmtool
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  Download-URL:
@@ -16,6 +16,7 @@ Classifier: Programming Language :: Python :: 3.6
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  Classifier: Topic :: Software Development :: Libraries
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  Classifier: Topic :: Software Development :: Libraries :: Python Modules
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  Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.8
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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  Requires-Dist: neuron==8.2.4
@@ -35,6 +36,11 @@ Requires-Dist: requests
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  Requires-Dist: pyyaml
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  Requires-Dist: PyWavelets
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  Requires-Dist: numba
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+ Provides-Extra: dev
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+ Requires-Dist: ruff>=0.1.0; extra == "dev"
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+ Requires-Dist: pyright>=1.1.0; extra == "dev"
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+ Requires-Dist: pytest>=7.0.0; extra == "dev"
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+ Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
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  Dynamic: author
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  Dynamic: author-email
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  Dynamic: classifier
@@ -49,7 +55,7 @@ Dynamic: summary
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  # bmtool
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  A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
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- [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cyneuro/bmtool/blob/master/LICENSE)
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+ [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cyneuro/bmtool/blob/master/LICENSE)
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  ## In depth documentation and examples can be found [here](https://cyneuro.github.io/bmtool/)
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@@ -78,3 +84,35 @@ BMTool provides several modules to simplify the development of computational neu
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  - **Visualization**: Plot connection matrices, network positions, and more
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  - **Simulation Management**: Run simulations on SLURM clusters with parameter sweeps
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  - **Analysis**: Process simulation results efficiently
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+
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+ ## Development
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+
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+ ### Code Quality Tools
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+
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+ BMTool now uses modern Python code quality tools to maintain high standards:
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+ - **Ruff**: A fast Python linter for code style and error checking
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+ - **Pyright**: Static type checker to catch type-related bugs early
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+
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+ To install development dependencies in your conda environment:
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+
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+ ```bash
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+ # Activate your conda environment
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+ conda activate bmtk
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+
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+ # Install development dependencies
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+ pip install -e ".[dev]"
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+ ```
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+
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+ To run the tools:
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+
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+ ```bash
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+ # Run Ruff linter
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+ ruff check bmtool/
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+
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+ # Run Ruff with auto-fix
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+ ruff check --fix bmtool/
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+
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+ # Run Pyright type checker
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+ pyright
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+ ```
bmtool-0.7.1.1.dist-info/RECORD ADDED
@@ -0,0 +1,34 @@
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+ bmtool/SLURM.py,sha256=UBfITY1MtYo95nyKglgGSqAC9Ds8PBvlHczsiNMFxvc,20573
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+ bmtool/__init__.py,sha256=r_8fXc-2uj1DndCdhB4jME51r1pn6ESTD5zRc355BrU,134
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+ bmtool/__main__.py,sha256=uCEqPwRxIuNRUASKhsvh4S8Nkp4dqnvfXTMUv-wWWRU,665
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+ bmtool/connectors.py,sha256=4SJRqBXM145_-nFycGrnlfjSyaoarOr0QkHl00jWq4I,74384
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+ bmtool/graphs.py,sha256=gBTzI6c2BBK49dWGcfWh9c56TAooyn-KaiEy0Im1HcI,6717
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+ bmtool/manage.py,sha256=lsgRejp02P-x6QpA7SXcyXdalPhRmypoviIA2uAitQs,608
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+ bmtool/plot_commands.py,sha256=Dxm_RaT4CtHnfsltTtUopJ4KVbfhxtktEB_b7bFEXII,12716
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+ bmtool/singlecell.py,sha256=I2yolbAnNC8qpnRkNdnDCLidNW7CktmBuRrcowMZJ3A,45041
9
+ bmtool/synapses.py,sha256=wlRY7IixefPzafqG6k2sPIK4s6PLG9Kct-oCaVR29wA,64269
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+ bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
11
+ bmtool/analysis/entrainment.py,sha256=Nzrt1pKHEDzrx9TYnsE0sbevxl4iht1fymA29khq8Pg,26841
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+ bmtool/analysis/lfp.py,sha256=S2JvxkjcK3-EH93wCrhqNSFY6cX7fOq74pz64ibHKrc,26556
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+ bmtool/analysis/netcon_reports.py,sha256=VnPZNKPaQA7oh1q9cIatsqQudm4cOtzNtbGPXoiDCD0,2909
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+ bmtool/analysis/spikes.py,sha256=ScP4EeX2QuEd_FXyj3W0WWgZKvZwwneuWuKFe3xwaCY,15115
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+ bmtool/bmplot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
16
+ bmtool/bmplot/connections.py,sha256=P1JBG4xCbLVq4sfQuUE6c3dO949qajrjdQcrazdmDS4,53861
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+ bmtool/bmplot/entrainment.py,sha256=TC2qJV0Z6YiK5X7bEpiEyf7nZiWU__466Uhq0kbrhIY,1611
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+ bmtool/bmplot/lfp.py,sha256=SNpbWGOUnYEgnkeBw5S--aPN5mIGD22Gw2Pwus0_lvY,2034
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+ bmtool/bmplot/netcon_reports.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
20
+ bmtool/bmplot/spikes.py,sha256=Lg8V3ynYCqk-QJvq-BOInjZMHYHrxHgXjtDOX67df-A,11148
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+ bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
22
+ bmtool/debug/commands.py,sha256=VV00f6q5gzZI503vUPeG40ABLLen0bw_k4-EX-H5WZE,580
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+ bmtool/debug/debug.py,sha256=9yUFvA4_Bl-x9s29quIEG3pY-S8hNJF3RKBfRBHCl28,208
24
+ bmtool/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
25
+ bmtool/util/commands.py,sha256=Nn-R-4e9g8ZhSPZvTkr38xeKRPfEMANB9Lugppj82UI,68564
26
+ bmtool/util/util.py,sha256=owce5BEusZO_8T5x05N2_B583G26vWAy7QX29V0Pj0Y,62818
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+ bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ bmtool/util/neuron/celltuner.py,sha256=lokRLUM1rsdSYBYrNbLBBo39j14mm8TBNVNRnSlhHCk,94868
29
+ bmtool-0.7.1.1.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
30
+ bmtool-0.7.1.1.dist-info/METADATA,sha256=ONMkDOU2sGv2xzC9jbP5z9HdGFI2HGO_2fwS6cIBj3w,3623
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+ bmtool-0.7.1.1.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
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+ bmtool-0.7.1.1.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
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+ bmtool-0.7.1.1.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
34
+ bmtool-0.7.1.1.dist-info/RECORD,,
{bmtool-0.7.0.6.4.dist-info → bmtool-0.7.1.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (80.3.1)
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+ Generator: setuptools (80.4.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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bmtool-0.7.0.6.4.dist-info/RECORD DELETED
@@ -1,34 +0,0 @@
1
- bmtool/SLURM.py,sha256=PST_jOD5ZmwbJj15Tgq3UIvdq4FYN4EkPuDt66P8OXU,20136
2
- bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
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- bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
4
- bmtool/connectors.py,sha256=uLhZIjur0_jWOtSZ9w6-PHftB9Xj6FFXWL5tndEMDYY,73570
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- bmtool/graphs.py,sha256=ShBgJr1iZrM3ugU2wT6hbhmBAkc3mmf7yZQfPuPEqPM,6691
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- bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
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- bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
8
- bmtool/singlecell.py,sha256=imcdxIzvYVkaOLSGDxYp8WGGssGwXXBCRhzhlqVp7hA,44267
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- bmtool/synapses.py,sha256=Ow2fZavA_3_5BYCjcgPjW0YsyVOetn1wvLxL7hQvbZo,64556
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- bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
11
- bmtool/analysis/entrainment.py,sha256=7lFlGMApL_2snwdvIPDLFW1KKPdyiuCnZ5ADa7ujx5o,24439
12
- bmtool/analysis/lfp.py,sha256=6u9cHnac-5Fzpk9ecQew7MmXBAolzKZakRsnPn3-C2U,24109
13
- bmtool/analysis/netcon_reports.py,sha256=7moyoUC45Cl1_6sGqwZ5aKphK_8i4AimroePXcgUnIo,3057
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- bmtool/analysis/spikes.py,sha256=kcJZQsvPVzQgcuiO-El_4OODW57hwNwdok_RsFMITCg,15097
15
- bmtool/bmplot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
16
- bmtool/bmplot/connections.py,sha256=re6QZX_NfQnIaWayGt3EhMINhCeMMSQ6rFR2sJbFeWk,51385
17
- bmtool/bmplot/entrainment.py,sha256=3IBD6tfW7lvkuB6DTan7rAVAeznOOzmHLr1qA2rgtCY,1671
18
- bmtool/bmplot/lfp.py,sha256=bfjUGt6al0t5mWTcSIyl03usLIqoQVXfmsvpZl4lol4,2023
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- bmtool/bmplot/netcon_reports.py,sha256=VFw4sJIt4Zc0-__eYnksN8Ku9qMhbPpHJEkXMWUiD30,4
20
- bmtool/bmplot/spikes.py,sha256=sy8u6Ng-EVHdIa70uE0_CAsrxT8pBmcmQ-7S2RLxg5Y,10770
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- bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
22
- bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
23
- bmtool/debug/debug.py,sha256=xqnkzLiH3s-tS26Y5lZZL62qR2evJdi46Gud-HzxEN4,207
24
- bmtool/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
25
- bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
26
- bmtool/util/util.py,sha256=XR0qZnv_Q47jMBKQpFzCSkCuKe9u8L3YSGJAOpP2zT0,57630
27
- bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
28
- bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
29
- bmtool-0.7.0.6.4.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
30
- bmtool-0.7.0.6.4.dist-info/METADATA,sha256=aVJLw_Ix9HpHlV4PxKWVj58JkYeOoLoLbt5FNPYZTVs,2799
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- bmtool-0.7.0.6.4.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
32
- bmtool-0.7.0.6.4.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
33
- bmtool-0.7.0.6.4.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
34
- bmtool-0.7.0.6.4.dist-info/RECORD,,