Merge pull request #27 from nel-lab/ci-new

update CI pipelines

.github/workflows/black.yml

@@ -1,6 +1,6 @@
 name: Lint
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   lint:

.github/workflows/python-app.yml

@@ -4,8 +4,6 @@
 name: Python application
 
 on:
-  push:
-    branches: [ master ]
   pull_request:
     branches: [ master ]
 
@@ -33,9 +31,8 @@ jobs:
     - name: install caiman
       run: |
         cd ..
-        git clone https://github.com/kushalkolar/CaImAn.git
+        git clone https://github.com/flatironinstitute/CaImAn.git
         cd CaImAn
-        git checkout mcorr-basename-prefix
         pip install -r requirements.txt
         pip install .
         caimanmanager.py install
@@ -53,3 +50,4 @@ jobs:
     - name: Test with pytest
       run: |
         pytest .
+

.github/workflows/python-package-conda.yml

@@ -1,6 +1,8 @@
 name: Python Package using Conda
 
-on: [push]
+on:
+  pull_request:
+    branches: [ master ]
 
 jobs:
   build-linux:
@@ -10,10 +12,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python '3.9'
+    - name: Set up Python '3.10'
       uses: actions/setup-python@v3
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory
@@ -24,15 +26,18 @@ jobs:
         conda install -c conda-forge mamba
         conda clean -a
         
-    - name: install caiman
-      run: |
-        mamba install -c conda-forge caiman
+        #   - name: install caiman
+        #     run: |
+        #       mamba install -c conda-forge caiman
         
     - name: install mesmerize-core
       run: |
+        mamba env update -n base --file environment.yml
+        caimanmanager.py install
         pip install .
         
     - name: Test with pytest
       run: |
         mamba install pytest
         pytest
+

environment.yml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+dependencies:
+  - caiman >= 1.9.10
+  - pandas
+  - requests
+  - qtpy
+  - pyqt
+  - click
+

mesmerize_core/algorithms/mcorr.py

@@ -116,7 +116,7 @@ def main(batch_path, uuid, data_path: str = None):
 
         # filename to move the output back to data dir
         mcorr_memmap = Path(input_movie_path).parent.joinpath(
-            f"{uuid}_{output_path.stem}.mmap"
+            f"{uuid}-{output_path.stem}.mmap"
         )
 
         # move the output file