Fix tests (#210)

* Fix tests

* Pin cython

* Type gooder

* Install cython earlier

* back back baaaaack

* Update setup.py

* Install centrosome branch

* Update test_cellpose.yml

* Update test_stardist.yml

Author: bethac07

.github/workflows/test.yml

@@ -46,10 +46,9 @@ jobs:
           pip install wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
           pip install --upgrade pip setuptools wheel
           pip install numpy
+          pip install git+https://github.com/CellProfiler/centrosome.git@cython3
 
-  test_basic_plugins:
-    needs: build_cellprofiler
-      - name: Install basic CellProfiler plugins (require )
+      - name: Install basic CellProfiler plugins require 
         run: |
           pip install -e .
       - name: Run basic plugin pipeline
@@ -62,19 +61,3 @@ jobs:
           sh ./tests/headless_test/test_run.sh "module histogrammatching" logfile
           sh ./tests/headless_test/test_run.sh "module pixelshuffle" logfile
 
-  test_cellpose_plugin:
-    needs: build_cellprofiler
-      - name: Run cellpose plugin pipeline
-        run: |
-          pip install -e .[cellpose]
-          python -m cellprofiler -c -r -p ./tests/headless_test/4.2.5_plugins_test_pipeline_CELLPOSE.cppipe -i ./tests/headless_test/test_pipeline_img -o . --plugins-directory=./active_plugins --log-level=DEBUG 2>&1 | tee logfile
-          sh ./tests/headless_test/test_run.sh "module runcellpose" logfile
-          
-  test_stardist_plugin:
-    needs: build_cellprofiler
-      - name: Run stardist plugin pipeline
-        run: |
-          pip uninstall -y cellpose torch
-          pip install -e .[stardist]
-          python -m cellprofiler -c -r -p ./tests/headless_test/4.2.5_plugins_test_pipeline_STARDIST.cppipe -i ./tests/headless_test/test_pipeline_img -o . --plugins-directory=./active_plugins --log-level=DEBUG 2>&1 | tee logfile
-          sh ./tests/headless_test/test_run.sh "module runstardist" logfile

.github/workflows/test_cellpose.yml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   build_cellprofiler:
-    name: Build CellProfiler
+    name: Test CellProfiler-Cellpose
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -46,10 +46,8 @@ jobs:
           pip install wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
           pip install --upgrade pip setuptools wheel
           pip install numpy
+          pip install git+https://github.com/CellProfiler/centrosome.git@cython3
 
-
-  test_cellpose_plugin:
-    needs: build_cellprofiler
       - name: Run cellpose plugin pipeline
         run: |
           pip install -e .[cellpose]

.github/workflows/test_stardist.yml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   build_cellprofiler:
-    name: Build CellProfiler
+    name: Test CellProfiler-Stardist
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
@@ -46,12 +46,10 @@ jobs:
           pip install wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
           pip install --upgrade pip setuptools wheel
           pip install numpy
+          pip install git+https://github.com/CellProfiler/centrosome.git@cython3
           
-  test_stardist_plugin:
-    needs: build_cellprofiler
       - name: Run stardist plugin pipeline
         run: |
-          pip uninstall -y cellpose torch
           pip install -e .[stardist]
           python -m cellprofiler -c -r -p ./tests/headless_test/4.2.5_plugins_test_pipeline_STARDIST.cppipe -i ./tests/headless_test/test_pipeline_img -o . --plugins-directory=./active_plugins --log-level=DEBUG 2>&1 | tee logfile
           sh ./tests/headless_test/test_run.sh "module runstardist" logfile