bmtool 0.7.0.6.2__py3-none-any.whl → 0.7.1__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 +250 -143
  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-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/METADATA +41 -3
  25. bmtool-0.7.1.dist-info/RECORD +34 -0
  26. {bmtool-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/WHEEL +1 -1
  27. bmtool-0.7.0.6.2.dist-info/RECORD +0 -34
  28. {bmtool-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/entry_points.txt +0 -0
  29. {bmtool-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/licenses/LICENSE +0 -0
  30. {bmtool-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/top_level.txt +0 -0
{bmtool-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: bmtool
3
- Version: 0.7.0.6.2
3
+ Version: 0.7.1
4
4
  Summary: BMTool
5
5
  Home-page: https://github.com/cyneuro/bmtool
6
6
  Download-URL:
@@ -16,8 +16,10 @@ Classifier: Programming Language :: Python :: 3.6
16
16
  Classifier: Topic :: Software Development :: Libraries
17
17
  Classifier: Topic :: Software Development :: Libraries :: Python Modules
18
18
  Classifier: Operating System :: OS Independent
19
+ Requires-Python: >=3.8
19
20
  Description-Content-Type: text/markdown
20
21
  License-File: LICENSE
22
+ Requires-Dist: neuron==8.2.4
21
23
  Requires-Dist: bmtk
22
24
  Requires-Dist: click
23
25
  Requires-Dist: clint
@@ -34,7 +36,11 @@ Requires-Dist: requests
34
36
  Requires-Dist: pyyaml
35
37
  Requires-Dist: PyWavelets
36
38
  Requires-Dist: numba
37
- Requires-Dist: neuron
39
+ Provides-Extra: dev
40
+ Requires-Dist: ruff>=0.1.0; extra == "dev"
41
+ Requires-Dist: pyright>=1.1.0; extra == "dev"
42
+ Requires-Dist: pytest>=7.0.0; extra == "dev"
43
+ Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
38
44
  Dynamic: author
39
45
  Dynamic: author-email
40
46
  Dynamic: classifier
@@ -49,7 +55,7 @@ Dynamic: summary
49
55
  # bmtool
50
56
  A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.
51
57
 
52
- [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cyneuro/bmtool/blob/master/LICENSE)
58
+ [![license](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cyneuro/bmtool/blob/master/LICENSE)
53
59
 
54
60
  ## In depth documentation and examples can be found [here](https://cyneuro.github.io/bmtool/)
55
61
 
@@ -78,3 +84,35 @@ BMTool provides several modules to simplify the development of computational neu
78
84
  - **Visualization**: Plot connection matrices, network positions, and more
79
85
  - **Simulation Management**: Run simulations on SLURM clusters with parameter sweeps
80
86
  - **Analysis**: Process simulation results efficiently
87
+
88
+ ## Development
89
+
90
+ ### Code Quality Tools
91
+
92
+ BMTool now uses modern Python code quality tools to maintain high standards:
93
+
94
+ - **Ruff**: A fast Python linter for code style and error checking
95
+ - **Pyright**: Static type checker to catch type-related bugs early
96
+
97
+ To install development dependencies in your conda environment:
98
+
99
+ ```bash
100
+ # Activate your conda environment
101
+ conda activate bmtk
102
+
103
+ # Install development dependencies
104
+ pip install -e ".[dev]"
105
+ ```
106
+
107
+ To run the tools:
108
+
109
+ ```bash
110
+ # Run Ruff linter
111
+ ruff check bmtool/
112
+
113
+ # Run Ruff with auto-fix
114
+ ruff check --fix bmtool/
115
+
116
+ # Run Pyright type checker
117
+ pyright
118
+ ```
bmtool-0.7.1.dist-info/RECORD ADDED
@@ -0,0 +1,34 @@
1
+ bmtool/SLURM.py,sha256=UBfITY1MtYo95nyKglgGSqAC9Ds8PBvlHczsiNMFxvc,20573
2
+ bmtool/__init__.py,sha256=r_8fXc-2uj1DndCdhB4jME51r1pn6ESTD5zRc355BrU,134
3
+ bmtool/__main__.py,sha256=uCEqPwRxIuNRUASKhsvh4S8Nkp4dqnvfXTMUv-wWWRU,665
4
+ bmtool/connectors.py,sha256=4SJRqBXM145_-nFycGrnlfjSyaoarOr0QkHl00jWq4I,74384
5
+ bmtool/graphs.py,sha256=gBTzI6c2BBK49dWGcfWh9c56TAooyn-KaiEy0Im1HcI,6717
6
+ bmtool/manage.py,sha256=lsgRejp02P-x6QpA7SXcyXdalPhRmypoviIA2uAitQs,608
7
+ bmtool/plot_commands.py,sha256=Dxm_RaT4CtHnfsltTtUopJ4KVbfhxtktEB_b7bFEXII,12716
8
+ bmtool/singlecell.py,sha256=I2yolbAnNC8qpnRkNdnDCLidNW7CktmBuRrcowMZJ3A,45041
9
+ bmtool/synapses.py,sha256=wlRY7IixefPzafqG6k2sPIK4s6PLG9Kct-oCaVR29wA,64269
10
+ bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
11
+ bmtool/analysis/entrainment.py,sha256=UVYhakyFGmH56UZ2jlshOH86rIKc9hSI-U2-kK2yp7o,25190
12
+ bmtool/analysis/lfp.py,sha256=S2JvxkjcK3-EH93wCrhqNSFY6cX7fOq74pz64ibHKrc,26556
13
+ bmtool/analysis/netcon_reports.py,sha256=VnPZNKPaQA7oh1q9cIatsqQudm4cOtzNtbGPXoiDCD0,2909
14
+ bmtool/analysis/spikes.py,sha256=ScP4EeX2QuEd_FXyj3W0WWgZKvZwwneuWuKFe3xwaCY,15115
15
+ bmtool/bmplot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
16
+ bmtool/bmplot/connections.py,sha256=P1JBG4xCbLVq4sfQuUE6c3dO949qajrjdQcrazdmDS4,53861
17
+ bmtool/bmplot/entrainment.py,sha256=TC2qJV0Z6YiK5X7bEpiEyf7nZiWU__466Uhq0kbrhIY,1611
18
+ bmtool/bmplot/lfp.py,sha256=SNpbWGOUnYEgnkeBw5S--aPN5mIGD22Gw2Pwus0_lvY,2034
19
+ bmtool/bmplot/netcon_reports.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
20
+ bmtool/bmplot/spikes.py,sha256=Lg8V3ynYCqk-QJvq-BOInjZMHYHrxHgXjtDOX67df-A,11148
21
+ bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
22
+ bmtool/debug/commands.py,sha256=VV00f6q5gzZI503vUPeG40ABLLen0bw_k4-EX-H5WZE,580
23
+ 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
27
+ bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
28
+ bmtool/util/neuron/celltuner.py,sha256=lokRLUM1rsdSYBYrNbLBBo39j14mm8TBNVNRnSlhHCk,94868
29
+ bmtool-0.7.1.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
30
+ bmtool-0.7.1.dist-info/METADATA,sha256=qVCMtNEx1YXI0KlMV3hLlhTSdEbbv5xrj2V1ZFWY0ho,3621
31
+ bmtool-0.7.1.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
32
+ bmtool-0.7.1.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
33
+ bmtool-0.7.1.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
34
+ bmtool-0.7.1.dist-info/RECORD,,
{bmtool-0.7.0.6.2.dist-info → bmtool-0.7.1.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (80.3.1)
2
+ Generator: setuptools (80.4.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
5
 
bmtool-0.7.0.6.2.dist-info/RECORD DELETED
@@ -1,34 +0,0 @@
1
- bmtool/SLURM.py,sha256=PST_jOD5ZmwbJj15Tgq3UIvdq4FYN4EkPuDt66P8OXU,20136
2
- bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
3
- bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
4
- bmtool/connectors.py,sha256=uLhZIjur0_jWOtSZ9w6-PHftB9Xj6FFXWL5tndEMDYY,73570
5
- bmtool/graphs.py,sha256=ShBgJr1iZrM3ugU2wT6hbhmBAkc3mmf7yZQfPuPEqPM,6691
6
- bmtool/manage.py,sha256=_lCU0qBQZ4jSxjzAJUd09JEetb--cud7KZgxQFbLGSY,657
7
- bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
8
- bmtool/singlecell.py,sha256=imcdxIzvYVkaOLSGDxYp8WGGssGwXXBCRhzhlqVp7hA,44267
9
- bmtool/synapses.py,sha256=Ow2fZavA_3_5BYCjcgPjW0YsyVOetn1wvLxL7hQvbZo,64556
10
- 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
14
- 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
19
- bmtool/bmplot/netcon_reports.py,sha256=VFw4sJIt4Zc0-__eYnksN8Ku9qMhbPpHJEkXMWUiD30,4
20
- bmtool/bmplot/spikes.py,sha256=sy8u6Ng-EVHdIa70uE0_CAsrxT8pBmcmQ-7S2RLxg5Y,10770
21
- 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-0.7.0.6.2.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
30
- bmtool-0.7.0.6.2.dist-info/METADATA,sha256=4mlswJYoc4CWRzZ8OGfkcPxKIeh7Wt2ZppEeExjKGCU,2792
31
- bmtool-0.7.0.6.2.dist-info/WHEEL,sha256=0CuiUZ_p9E4cD6NyLD6UG80LBXYyiSYZOKDm5lp32xk,91
32
- bmtool-0.7.0.6.2.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
33
- bmtool-0.7.0.6.2.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
34
- bmtool-0.7.0.6.2.dist-info/RECORD,,