LCNE-patchseq-analysis 0.2.0__tar.gz → 0.4.0__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 (46) hide show
  1. lcne_patchseq_analysis-0.4.0/.codeocean/datasets.json +9 -0
  2. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.gitignore +2 -1
  3. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/PKG-INFO +4 -2
  4. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/README.md +1 -1
  5. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/environment/Dockerfile +6 -6
  6. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/environment/postInstall +1 -0
  7. lcne_patchseq_analysis-0.4.0/notebook/playground.ipynb +1453 -0
  8. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/pyproject.toml +4 -1
  9. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/__init__.py +5 -0
  10. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/data_util/__init__.py +1 -0
  11. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/data_util/metadata.py +63 -0
  12. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/data_util/nwb.py +70 -0
  13. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/panel_nwb_viz.py +149 -0
  14. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/pipeline_util/__init__.py +1 -0
  15. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/pipeline_util/ephys.py +123 -0
  16. {lcne_patchseq_analysis-0.2.0/src/LCNE_patchseq_analysis/data_util → lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/pipeline_util}/lims.py +12 -5
  17. lcne_patchseq_analysis-0.4.0/src/LCNE_patchseq_analysis/pipeline_util/metadata.py +183 -0
  18. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/src/LCNE_patchseq_analysis.egg-info/PKG-INFO +4 -2
  19. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/src/LCNE_patchseq_analysis.egg-info/SOURCES.txt +8 -3
  20. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/src/LCNE_patchseq_analysis.egg-info/requires.txt +2 -0
  21. lcne_patchseq_analysis-0.2.0/notebook/demo.ipynb +0 -291
  22. lcne_patchseq_analysis-0.2.0/src/LCNE_patchseq_analysis/__init__.py +0 -2
  23. lcne_patchseq_analysis-0.2.0/src/LCNE_patchseq_analysis/data_util/__init__.py +0 -1
  24. lcne_patchseq_analysis-0.2.0/src/LCNE_patchseq_analysis/data_util/ephys.py +0 -1
  25. lcne_patchseq_analysis-0.2.0/src/LCNE_patchseq_analysis/data_util/metadata.py +0 -129
  26. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.flake8 +0 -0
  27. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.github/ISSUE_TEMPLATE/bug_report.md +0 -0
  28. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.github/ISSUE_TEMPLATE/feature_request.md +0 -0
  29. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.github/ISSUE_TEMPLATE/user-story.md +0 -0
  30. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.github/workflows/init.yml +0 -0
  31. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.github/workflows/tag_and_publish.yml +0 -0
  32. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.github/workflows/test_and_lint.yml +0 -0
  33. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/LICENSE +0 -0
  34. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/Makefile +0 -0
  35. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/make.bat +0 -0
  36. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/source/_static/dark-logo.svg +0 -0
  37. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/source/_static/favicon.ico +0 -0
  38. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/source/_static/light-logo.svg +0 -0
  39. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/source/conf.py +0 -0
  40. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/docs/source/index.rst +0 -0
  41. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/setup.cfg +0 -0
  42. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/setup.py +0 -0
  43. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/src/LCNE_patchseq_analysis.egg-info/dependency_links.txt +0 -0
  44. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/src/LCNE_patchseq_analysis.egg-info/top_level.txt +0 -0
  45. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/tests/__init__.py +0 -0
  46. {lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/tests/test_example.py +0 -0
lcne_patchseq_analysis-0.4.0/.codeocean/datasets.json ADDED
@@ -0,0 +1,9 @@
1
+ {
2
+ "version": 1,
3
+ "attached_datasets": [
4
+ {
5
+ "id": "64d1d93f-16ab-4ded-92c7-ed66c852cf78",
6
+ "mount": "LCNE-patchseq-ephys-raw"
7
+ }
8
+ ]
9
+ }
{lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/.gitignore RENAMED
@@ -140,4 +140,5 @@ dmypy.json
140
140
 
141
141
  .vscode
142
142
  metadata.yml
143
- data
143
+ data
144
+ LIMS_credentials.json
{lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
2
2
  Name: LCNE-patchseq-analysis
3
- Version: 0.2.0
3
+ Version: 0.4.0
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>
@@ -12,6 +12,8 @@ License-File: LICENSE
12
12
  Requires-Dist: numpy
13
13
  Requires-Dist: pandas
14
14
  Requires-Dist: matplotlib
15
+ Requires-Dist: panel
16
+ Requires-Dist: jupyter_bokeh
15
17
  Provides-Extra: dev
16
18
  Requires-Dist: black; extra == "dev"
17
19
  Requires-Dist: coverage; extra == "dev"
@@ -36,7 +38,7 @@ Requires-Dist: pg8000; extra == "pipeline"
36
38
  [![License](https://img.shields.io/badge/license-MIT-brightgreen)](LICENSE)
37
39
  ![Code Style](https://img.shields.io/badge/code%20style-black-black)
38
40
  [![semantic-release: angular](https://img.shields.io/badge/semantic--release-angular-e10079?logo=semantic-release)](https://github.com/semantic-release/semantic-release)
39
- ![Interrogate](https://img.shields.io/badge/interrogate-81.2%25-yellow)
41
+ ![Interrogate](https://img.shields.io/badge/interrogate-92.1%25-brightgreen)
40
42
  ![Coverage](https://img.shields.io/badge/coverage-100%25-brightgreen?logo=codecov)
41
43
  ![Python](https://img.shields.io/badge/python->=3.9-blue?logo=python)
42
44
 
{lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/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-81.2%25-yellow)
6
+ ![Interrogate](https://img.shields.io/badge/interrogate-92.1%25-brightgreen)
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-0.2.0 → lcne_patchseq_analysis-0.4.0}/environment/Dockerfile RENAMED
@@ -1,13 +1,9 @@
1
- # hash:sha256:4381990f759d87b4e81e36c74374fc4954659b3ccf18d32d432653272a4faa93
1
+ # hash:sha256:7dbb41516855b7a4c5c2a305cc83a36b2ceee9b1e4f83644fbeaffd8054316cf
2
2
  ARG REGISTRY_HOST
3
- FROM $REGISTRY_HOST/codeocean/jupyterlab:3.6.1-miniconda4.12.0-python3.9-ubuntu20.04
3
+ FROM $REGISTRY_HOST/codeocean/mambaforge3:23.1.0-4-python3.10.12-ubuntu22.04
4
4
 
5
5
  ARG DEBIAN_FRONTEND=noninteractive
6
6
 
7
- ARG GIT_ASKPASS
8
- ARG GIT_ACCESS_TOKEN
9
- COPY git-askpass /
10
-
11
7
  ADD "https://github.com/coder/code-server/releases/download/v4.95.3/code-server-4.95.3-linux-amd64.tar.gz" /.code-server/code-server.tar.gz
12
8
 
13
9
  RUN cd /.code-server \
@@ -15,5 +11,9 @@ RUN cd /.code-server \
15
11
  && rm code-server.tar.gz \
16
12
  && ln -s /.code-server/code-server-4.95.3-linux-amd64/bin/code-server /usr/bin/code-server
17
13
 
14
+ ARG GIT_ASKPASS
15
+ ARG GIT_ACCESS_TOKEN
16
+ COPY git-askpass /
17
+
18
18
  COPY postInstall /
19
19
  RUN /postInstall
{lcne_patchseq_analysis-0.2.0 → lcne_patchseq_analysis-0.4.0}/environment/postInstall RENAMED
@@ -16,6 +16,7 @@ if code-server --disable-telemetry --version; then
16
16
  code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension mhutchie.git-graph
17
17
  code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension zhuangtongfa.material-theme
18
18
  code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension ms-python.black-formatter
19
+ code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension randomfractalsinc.vscode-data-preview
19
20
  # code-server --disable-telemetry --extensions-dir=/.vscode/extensions --install-extension ryanluker.vscode-coverage-gutters
20
21
 
21
22
  curl -L -o copilot_1.161.zip https://github.com/user-attachments/files/16859733/copilot_1.161.zip