Merge branch 'main' of https://github.com/MouseLand/suite2p into refactor

Author: chriski777

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,60 @@
+name: Bug report
+description: Report a bug.
+title: "BUG: <Please write a comprehensive title after the 'BUG: ' prefix>"
+
+body:
+- type: markdown
+  attributes:
+    value: >
+      Thank you for taking the time to file a bug report. Before creating a new
+      issue, please make sure to take a few minutes to check if this issue has been 
+      brought up before.
+    
+- type: textarea
+  attributes: 
+    label: "Describe the issue:"
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Reproduce the code example:"
+    description: >
+      A short code example that reproduces the problem/missing feature. It
+      should be self-contained, i.e., can be copy-pasted into the Python
+      interpreter or run as-is via `python myproblem.py`. Please include as much 
+      detail you can about the ops.npy that was used.
+    placeholder: |
+      import suite2p
+      << your code here >>
+    render: python
+  validations:
+    required: true
+  
+- type: textarea
+  attributes:
+    label: "Error message:"
+    description: >
+      Please include full error message, if any.
+    placeholder: |
+      << Full traceback starting from `Traceback: ...` >>
+    render: shell
+
+- type: textarea
+  attributes:
+    label: "Version information:"
+    description: >
+      Output from running `suite2p --version` in your command line.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Context for the issue:"
+    description: |
+      Please explain how this issue affects your work or why it should be prioritized.
+    placeholder: |
+      << your explanation here >>
+  validations:
+    required: false
+

.github/ISSUE_TEMPLATE/documentation_issue.yml

@@ -0,0 +1,22 @@
+name: Documentation
+description: Report an issue related to suite2p documentation.
+title: "DOC: <Please write a comprehensive title after the 'DOC: ' prefix>"
+
+body:
+- type: textarea
+  attributes: 
+    label: "Issue with current documentation:"
+    description: >
+      Please make sure to leave a reference to the document/code you're
+      referring to. Please report where in https://suite2p.readthedocs.io/ you see this issue. 
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Idea or request for content:"
+    description: >
+      Please describe as clearly as possible what topics you think are missing
+      from the current documentation. Make sure to check
+      https://colab.research.google.com/github/MouseLand/suite2p/blob/main/jupyter/run_suite2p_colab_2021.ipynb 
+      and see if this documentation should be added there.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,27 @@
+name: Feature request
+description: Suggest an additional feature you'd like to see in suite2p.
+title: "FEATURE: <Please write a comprehensive title after the 'FEATURE: ' prefix>"
+
+body:
+- type: textarea
+  attributes: 
+    label: "Feature you'd like to see:"
+    description: >
+        Provide a clear and concise description of what problem you'd like this feature to address. 
+        Then, provide a clear description of the solution you'd like to see.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Attempted alternative approaches:"
+    description: >
+       Provide a description of alternative approaches you've tried. 
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Additional Context"
+    description: >
+        Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/installation_issue.yml

@@ -0,0 +1,22 @@
+name: Installation issue
+description: Report an issue with installation for suite2p.
+title: "<Please write a comprehensive title.>"
+
+body:
+    
+- type: textarea
+  attributes: 
+    label: "Describe the issue:"
+    description: >
+      Let us know what issues you are having with installation.
+  validations:
+    required: true
+
+- type: textarea
+  attributes:
+    label: "Provide environment info:"
+    description: >
+      Please run `conda info` in your suite2p environment in your terminal/anaconda prompt to let us know the versions of your packages.
+  validations:
+    required: true
+  

.readthedocs.yml

@@ -18,7 +18,7 @@ formats:
 
 # specify dependencies
 python:
-   version: 3.7
+   version: 3.8
    install:
       - method: pip
         path: .

setup.py

@@ -5,7 +5,7 @@
         'rastermap>0.1.0',
         'tifffile',
         'scanimage-tiff-reader>=1.4.1',
-        'torch==1.11.0',
+        'torch==1.13.1',
         'paramiko',
         'numpy>=1.16',
         'numba>=0.43.1',