Make compatible with TensorFlow >= 2.6

.github/workflows/tests.yml

@@ -17,23 +17,22 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.6, 3.7, 3.8, 3.9]
-        tensorflow: ["tensorflow", "tensorflow<2"]
+        tensorflow: ["tensorflow", "'tensorflow<2' 'keras<2.4'"]
         exclude:
             # https://www.tensorflow.org/install/pip#system-requirements
           - python-version: 3.8
-            tensorflow: "tensorflow<2"
+            tensorflow: "'tensorflow<2' 'keras<2.4'"
           - python-version: 3.9
-            tensorflow: "tensorflow<2"
+            tensorflow: "'tensorflow<2' 'keras<2.4'"
           - os: windows-latest
-            tensorflow: "tensorflow<2"
+            tensorflow: "'tensorflow<2' 'keras<2.4'"
 
     steps:
       - uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - run: python -m pip install --upgrade pip wheel setuptools
-      - run: pip install pytest
-      - run: pip install "${{ matrix.tensorflow }}"
+      - run: pip install ${{ matrix.tensorflow }}
       - uses: actions/checkout@v2
 
       - name: Install edt
@@ -45,13 +44,13 @@ jobs:
         run: |
           brew config
           brew install gcc@9
-          pip install .
+          pip install ".[test]"
         env:
           CC: /usr/local/bin/gcc-9
           CXX: /usr/local/bin/g++-9
 
       - name: Install package (Linux and Windows)
         if: startsWith(matrix.os, 'macos') == false
-        run: pip install .
+        run: pip install ".[test]"
 
       - run: pytest -v --durations=50 -m "not gpu"

.github/workflows/tests_cron.yml

@@ -12,23 +12,22 @@ jobs:
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
         python-version: [3.6, 3.7, 3.8, 3.9]
-        tensorflow: ["tensorflow", "tensorflow<2"]
+        tensorflow: ["tensorflow", "'tensorflow<2' 'keras<2.4'"]
         exclude:
             # https://www.tensorflow.org/install/pip#system-requirements
           - python-version: 3.8
-            tensorflow: "tensorflow<2"
+            tensorflow: "'tensorflow<2' 'keras<2.4'"
           - python-version: 3.9
-            tensorflow: "tensorflow<2"
+            tensorflow: "'tensorflow<2' 'keras<2.4'"
           - os: windows-latest
-            tensorflow: "tensorflow<2"
+            tensorflow: "'tensorflow<2' 'keras<2.4'"
 
     steps:
       - uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
       - run: python -m pip install --upgrade pip wheel setuptools
-      - run: pip install pytest
-      - run: pip install "${{ matrix.tensorflow }}"
+      - run: pip install ${{ matrix.tensorflow }}
       - uses: actions/checkout@v2
 
       - name: Install edt
@@ -40,14 +39,14 @@ jobs:
         run: |
           brew config
           brew install gcc@9
-          pip install --no-binary stardist stardist
+          pip install --no-binary stardist "stardist[test]"
         env:
           CC: /usr/local/bin/gcc-9
           CXX: /usr/local/bin/g++-9
 
       - name: Install package from source (Linux and Windows)
         if: startsWith(matrix.os, 'macos') == false
-        run: pip install --no-binary stardist stardist
+        run: pip install --no-binary stardist "stardist[test]"
 
       # - name: Install package from wheel
       #   run: |

README.md

@@ -54,11 +54,19 @@ compatible with the respective version of TensorFlow. (If you need help and can
 
 2. *StarDist* can then be installed with `pip`:
 
-    `pip install stardist`
+    - If you installed TensorFlow 2 (version *2.x.x*):
+
+          pip install stardist
+
+    - If you installed TensorFlow 1 (version *1.x.x*):
+
+          pip install "stardist[tf1]"
+
 
 #### Notes
 
 - Depending on your Python installation, you may need to use `pip3` instead of `pip`.
+- You can find out which version of TensorFlow is installed via `pip show tensorflow`.
 - We provide pre-compiled binaries ("wheels") that should work for most Linux and Windows platforms, and also recent versions of macOS (Catalina/10.15 or later). If you're having problems, please see the [troubleshooting](#installation-1) section below.
 - *(Optional)* You need to install [gputools](https://github.com/maweigert/gputools) if you want to use OpenCL-based computations on the GPU to speed up training.
 - *(Optional)* You might experience improved performance during training if you additionally install the [Multi-Label Anisotropic 3D Euclidean Distance Transform (MLAEDT-3D)](https://github.com/seung-lab/euclidean-distance-transform-3d).

setup.py

@@ -106,8 +106,14 @@ def build_extension(self, ext):
     ],
 
     install_requires=[
-        'csbdeep>=0.6.0',
+        'csbdeep>=0.6.3',
         'scikit-image',
         'numba',
     ],
+
+    extras_require={
+        "tf1":  ["csbdeep[tf1]>=0.6.3"],
+        "test": ["pytest"],
+    },
+
 )

stardist/version.py

@@ -1 +1 @@
-__version__ = '0.7.2'
+__version__ = '0.7.3'