LCNE-patchseq-analysis 0.32.2__tar.gz → 0.32.4__tar.gz

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 (79) hide show
  1. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.codeocean/datasets.json +4 -0
  2. lcne_patchseq_analysis-0.32.4/.gitattributes +0 -0
  3. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/PKG-INFO +4 -2
  4. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/README.md +1 -1
  5. lcne_patchseq_analysis-0.32.4/assets/fonts/Helvetica.ttf +0 -0
  6. lcne_patchseq_analysis-0.32.4/code/run +5 -0
  7. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/environment/Dockerfile +2 -2
  8. lcne_patchseq_analysis-0.32.4/environment/postInstall +17 -0
  9. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/notebook/demo_raw_spike_waveforms.ipynb +81 -168
  10. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/pyproject.toml +3 -1
  11. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/__init__.py +1 -1
  12. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/core.py +9 -15
  13. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/pipeline.py +10 -24
  14. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/plot.py +21 -57
  15. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/population.py +28 -70
  16. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/figures/__init__.py +17 -2
  17. lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached/__init__.py +1 -0
  18. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/asymmetry_index_from_eFEL.py +5 -7
  19. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/asymmetry_index_from_waveform.py +25 -57
  20. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/fig_3a.py +11 -2
  21. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/fig_3c.py +26 -6
  22. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/main_figure.py +8 -5
  23. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/sup_figures.py +2 -2
  24. lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/main_pca_tau.py +639 -0
  25. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/figures/util.py +23 -5
  26. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/pipeline_util/s3.py +3 -9
  27. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis.egg-info/PKG-INFO +4 -2
  28. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis.egg-info/SOURCES.txt +11 -9
  29. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis.egg-info/requires.txt +2 -0
  30. lcne_patchseq_analysis-0.32.2/.gitattributes +0 -1
  31. lcne_patchseq_analysis-0.32.2/environment/postInstall +0 -29
  32. lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures/asymmetry_index_from_eFEL.ipynb +0 -3
  33. lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures/asymmetry_index_from_waveform.ipynb +0 -3
  34. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.codeocean/resources.json +0 -0
  35. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.flake8 +0 -0
  36. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.github/ISSUE_TEMPLATE/bug_report.md +0 -0
  37. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.github/ISSUE_TEMPLATE/feature_request.md +0 -0
  38. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.github/ISSUE_TEMPLATE/user-story.md +0 -0
  39. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.github/workflows/init.yml +0 -0
  40. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.github/workflows/tag_and_publish.yml +0 -0
  41. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.github/workflows/test_and_lint.yml +0 -0
  42. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.gitignore +0 -0
  43. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/LICENSE +0 -0
  44. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/docs/Makefile +0 -0
  45. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/docs/make.bat +0 -0
  46. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/docs/source/_static/dark-logo.svg +0 -0
  47. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/docs/source/_static/light-logo.svg +0 -0
  48. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/docs/source/conf.py +0 -0
  49. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/docs/source/index.rst +0 -0
  50. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/notebook/efel.ipynb +0 -0
  51. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/notebook/figures.ipynb +0 -0
  52. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/notebook/morphology.ipynb +0 -0
  53. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/notebook/playground.ipynb +0 -0
  54. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/notebook/population_analysis.ipynb +0 -0
  55. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/setup.cfg +0 -0
  56. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/setup.py +0 -0
  57. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/data_util/__init__.py +0 -0
  58. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/data_util/mesh.py +0 -0
  59. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/data_util/metadata.py +0 -0
  60. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/data_util/nwb.py +0 -0
  61. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/__init__.py +0 -0
  62. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/efel_per_spike_features.json +0 -0
  63. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/io.py +0 -0
  64. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/efel/util.py +0 -0
  65. {lcne_patchseq_analysis-0.32.2/src/LCNE_patchseq_analysis/figures → lcne_patchseq_analysis-0.32.4/src/LCNE_patchseq_analysis/figures/cached}/fig_3b.py +0 -0
  66. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/pipeline_util/__init__.py +0 -0
  67. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/pipeline_util/ephys.py +0 -0
  68. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/pipeline_util/lims.py +0 -0
  69. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/pipeline_util/metadata.py +0 -0
  70. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/pipeline_util/sequencing.py +0 -0
  71. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/plot_util/swc.py +0 -0
  72. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/population_analysis/__init__.py +0 -0
  73. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/population_analysis/anova.py +0 -0
  74. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/population_analysis/filters.py +0 -0
  75. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis/population_analysis/spikes.py +0 -0
  76. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis.egg-info/dependency_links.txt +0 -0
  77. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/src/LCNE_patchseq_analysis.egg-info/top_level.txt +0 -0
  78. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/tests/__init__.py +0 -0
  79. {lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/tests/test_example.py +0 -0
{lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/.codeocean/datasets.json RENAMED
@@ -4,6 +4,10 @@
4
4
  {
5
5
  "id": "68ef27d7-9d95-40ce-9e40-7de93dccf5f8",
6
6
  "mount": "LCNE-patchseq-ephys"
7
+ },
8
+ {
9
+ "id": "c5d5e922-1863-4869-99ff-fdce3e10edc7",
10
+ "mount": "fonts"
7
11
  }
8
12
  ]
9
13
  }
lcne_patchseq_analysis-0.32.4/.gitattributes ADDED
File without changes
{lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: LCNE-patchseq-analysis
3
- Version: 0.32.2
3
+ Version: 0.32.4
4
4
  Summary: Generated from aind-library-template
5
5
  Author: Allen Institute for Neural Dynamics
6
6
  Author-email: Han Hou <han.hou@alleninstitute.org>
@@ -19,6 +19,8 @@ Requires-Dist: requests
19
19
  Requires-Dist: trimesh
20
20
  Requires-Dist: statsmodels
21
21
  Requires-Dist: matplotlib_venn
22
+ Requires-Dist: scipy
23
+ Requires-Dist: scikit-learn
22
24
  Provides-Extra: dev
23
25
  Requires-Dist: black; extra == "dev"
24
26
  Requires-Dist: coverage; extra == "dev"
@@ -72,7 +74,7 @@ Dynamic: license-file
72
74
  [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
73
75
  ![Code Style](https://img.shields.io/badge/code%20style-black-black)
74
76
  [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
75
- ![Interrogate](https://img.shields.io/badge/interrogate-85.8%25-yellow)
77
+ ![Interrogate](https://img.shields.io/badge/interrogate-86.3%25-yellow)
76
78
  ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
77
79
  ![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
78
80
 
{lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/README.md RENAMED
@@ -3,7 +3,7 @@
3
3
  [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
4
4
  ![Code Style](https://img.shields.io/badge/code%20style-black-black)
5
5
  [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
6
- ![Interrogate](https://img.shields.io/badge/interrogate-85.8%25-yellow)
6
+ ![Interrogate](https://img.shields.io/badge/interrogate-86.3%25-yellow)
7
7
  ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
8
8
  ![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
9
9
 
lcne_patchseq_analysis-0.32.4/code/run ADDED
@@ -0,0 +1,5 @@
1
+ #!/usr/bin/env bash
2
+ set -ex
3
+
4
+ # This is the master script for the capsule. When you click "Reproducible Run", the code in this file will execute.
5
+ python -m LCNE_patchseq_analysis.figures.main_pca_tau
{lcne_patchseq_analysis-0.32.2 → lcne_patchseq_analysis-0.32.4}/environment/Dockerfile RENAMED
@@ -15,8 +15,8 @@ ARG GIT_ASKPASS
15
15
  ARG GIT_ACCESS_TOKEN
16
16
  COPY git-askpass /
17
17
 
18
- RUN pip install --no-cache-dir "git+https://github.com/AllenNeuralDynamics/LCNE-patchseq-analysis.git@main#egg=LCNE-patchseq-analysis[panel]"
19
-
18
+ RUN pip install -U --no-cache-dir \
19
+ "git+https://github.com/AllenNeuralDynamics/LCNE-patchseq-analysis.git@b8c709294e970e35beda633757255b00d579f832#egg=LCNE-patchseq-analysis"
20
20
 
21
21
  COPY postInstall /
22
22
  RUN /postInstall
lcne_patchseq_analysis-0.32.4/environment/postInstall ADDED
@@ -0,0 +1,17 @@
1
+ #!/usr/bin/env bash
2
+ set -e
3
+
4
+ HOME_DIR="${HOME:-/root}"
5
+ BASHRC="${HOME_DIR}/.bashrc"
6
+
7
+ cat >> "$BASHRC" <<'EOF'
8
+
9
+ # LCNE editable install (runs once on first login, src/ only available at runtime)
10
+ if [ ! -f "$HOME/.lcne_editable_setup_done" ]; then
11
+ echo "Installing local package in editable mode from /root/capsule..."
12
+ pip install -e /root/capsule
13
+ echo "Editable install complete"
14
+
15
+ touch "$HOME/.lcne_editable_setup_done"
16
+ fi
17
+ EOF