Merge pull request #13 from MouseLand/main

pull from upstream

Author: ttngu207

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -30,6 +30,16 @@ body:
     render: python
   validations:
     required: true
+
+- type: textarea
+  attributes:
+    label: "Example input dataset used to reproduce the issue:"
+    description: >
+      Please provide a link to a minimal example dataset that can be 
+      used to reproduce the bug. For developers to quickly fix your issue, it's important 
+      that they can reproduce your problem locally.
+    placeholder: |
+      << Dropbox/Google Drive, etc., some link to the dataset >>
   
 - type: textarea
   attributes:

.github/workflows/test_and_deploy.yml

@@ -66,15 +66,22 @@ jobs:
       # ONLY UNCOMMENT SECTION BELOW FOR DEBUGGING PURPOSES: allows one to ssh into host machine. 
       # Follow instructions in  https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account 
       # to add your ssh keys.
-#      - name: Job failed. Activating debugging mode via up-term.
-#        if: ${{ failure() }}
-#        uses: lhotari/action-upterm@v1
-#        with:
-#           ## limits ssh access and adds the ssh public key for the user which triggered the workflow
-#            limit-access-to-actor: true
-#           ## limits ssh access and adds the ssh public keys of the listed GitHub users
-#            limit-access-to-users: chriski777, carsen-stringera
-            
+      # - name: Job failed. Activating debugging mode via up-term.
+      #   if: ${{ failure() }}
+      #   # As of Dec. 2024, The following action does NOT work for MACOS (https://github.com/lhotari/action-upterm/issues/24)
+      #   # uses: lhotari/action-upterm@v1
+      #   # with:
+      #   #   ## limits ssh access and adds the ssh public key for the user which triggered the workflow
+      #   #    limit-access-to-actor: true
+      #   #   ## limits ssh access and adds the ssh public keys of the listed GitHub users
+      #   #    limit-access-to-users: chriski777 #, carsen-stringera
+        
+      #   # As of Dec. 2024, use the following for debugging the GitHub Action runners for MacOS
+      #   uses: owenthereal/action-upterm@v1
+      #   with:
+      #      limit-access-to-actor: true
+      #      limit-access-to-users: chriski777   
+           
       - name: Coverage
         # Only run coverage once
         if: runner.os == 'Linux'

README.md

@@ -9,7 +9,6 @@
 [![Python version](https://img.shields.io/pypi/pyversions/suite2p)](https://pypistats.org/packages/suite2p)
 [![Licence: GPL v3](https://img.shields.io/github/license/MouseLand/suite2p)](https://github.com/MouseLand/suite2p/blob/main/LICENSE)
 [![Contributors](https://img.shields.io/github/contributors-anon/MouseLand/suite2p)](https://github.com/MouseLand/suite2p/graphs/contributors)
-[![website](https://img.shields.io/website?url=https%3A%2F%2Fwww.suite2p.org)](https://www.suite2p.org)
 [![repo size](https://img.shields.io/github/repo-size/MouseLand/suite2p)](https://github.com/MouseLand/suite2p/)
 [![GitHub stars](https://img.shields.io/github/stars/MouseLand/suite2p?style=social)](https://github.com/MouseLand/suite2p/)
 [![GitHub forks](https://img.shields.io/github/forks/MouseLand/suite2p?style=social)](https://github.com/MouseLand/suite2p/)
@@ -95,7 +94,7 @@ If you want to download and edit the code, and use that version,
 2. Run `conda create --name suite2p python=3.9`
 3. To activate this new environment, run `conda activate suite2p` (you will have to activate every time you want to run suite2p)
 4. Install the local version of suite2p into this environment in develop mode with the command `pip install -e .[all]`
-5. Run tests: `python setup.py test` or `pytest -vs`, this will automatically download the test data into your `suite2p` folder. The test data is split into two parts: test inputs and expected test outputs which will be downloaded in `data/test_inputs` and `data/test_outputs` respectively. The .zip files for these two parts can be downloaded from these links: [test_inputs](https://www.suite2p.org/static/test_data/test_inputs.zip) and [test_outputs](https://www.suite2p.org/static/test_data/test_outputs.zip).
+5. Run tests: `python setup.py test` or `pytest -vs`, this will automatically download the test data into your `suite2p` folder. The test data is split into two parts: test inputs and expected test outputs which will be downloaded in `data/test_inputs` and `data/test_outputs` respectively. The .zip files for these two parts can be downloaded from these links: [test_inputs](https://osf.io/download/67f0087b1ec6658af9b25a70/) and [test_outputs](https://osf.io/download/67f007dba7eb86d7808b8832/).
 
 ## Examples
 
@@ -123,7 +122,7 @@ Then:
 
 ### Using the GUI
 
-<img src="https://www.suite2p.org/static/images/multiselect.gif" width="800" alt="selecting multiple ROIs in suite2p with Ctrl"/>
+<img src="https://github.com/MouseLand/MouseLand.github.io/releases/download/v0.1/multiselect.gif" width="800" alt="selecting multiple ROIs in suite2p with Ctrl"/>
 
 
 The suite2p output goes to a folder called "suite2p" inside your save_path, which by default is the same as the data_path. If you ran suite2p in the GUI, it loads the results automatically. Otherwise, you can load the results with File -> Load results or by dragging and dropping the stat.npy file into the GUI.

conftest.py

@@ -18,7 +18,7 @@ def data_dir():
     data_path.mkdir(exist_ok=True)
     download_cached_inputs(data_path)
     cached_outputs = data_path.joinpath('test_outputs')
-    cached_outputs_url = 'https://www.suite2p.org/static/test_data/test_outputs.zip'
+    cached_outputs_url = 'https://osf.io/download/67f007dba7eb86d7808b8832/'
     if not os.path.exists(cached_outputs):
         extract_zip(data_path.joinpath('test_outputs.zip'), cached_outputs_url, data_path)
     return data_path
@@ -32,7 +32,7 @@ def test_ops(tmpdir, data_dir):
 def download_cached_inputs(data_path):
     """ Downloads test_input data if not present on machine. This function was created so it can also be used by scripts/generate_test_data.py."""
     cached_inputs = data_path.joinpath('test_inputs')
-    cached_inputs_url = 'https://www.suite2p.org/static/test_data/test_inputs.zip'
+    cached_inputs_url = 'https://osf.io/download/67f0087b1ec6658af9b25a70/'
     if not os.path.exists(cached_inputs):
         extract_zip(data_path.joinpath('test_inputs.zip'), cached_inputs_url, data_path)