remove strategy (#16)

* remove strategy

* change github install-poetry action

* fix github action cache

.github/workflows/build.yml

@@ -15,26 +15,30 @@ jobs:
         python-version: [3.7, 3.8]
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Check out repository
+      uses: actions/checkout@v2
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install Poetry
-      uses: dschep/[email protected]
+      uses: snok/[email protected]
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
 
     - name: Cache Poetry virtualenv
+      id: cached-poetry-dependencies
       uses: actions/cache@v2
-      id: cache
       with:
-        path: ~/.cache
-        key: poetry-${{ hashFiles('**/poetry.lock') }}
+        path: .venv
+        key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install Decendencies
       run: poetry install
-      if: steps.cache.outputs.cache-hit != 'true'
+      if: steps.cached-poetry-dependences.outputs.cache-hit != 'true'
 
     - name: Run pytest
       run: poetry run pytest tests

.github/workflows/upload.yml

@@ -10,26 +10,30 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Check out repository
+      uses: actions/checkout@v2
 
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: '3.x'
 
     - name: Install Poetry
-      uses: dschep/[email protected]
+      uses: snok/[email protected]
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
 
     - name: Cache Poetry virtualenv
+      id: cached-poetry-dependencies
       uses: actions/cache@v2
-      id: cache
       with:
-        path: ~/.cache
-        key: poetry-${{ hashFiles('**/poetry.lock') }}
+        path: .venv
+        key: venv-${{ runner.os}}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install Decendencies
       run: poetry install
-      if: steps.cache.outputs.cache-hit != 'true'
+      if: steps.cached-poetroy-dependencies.outputs.cache-hit != 'true'
 
     - name: Build and Publish
       run: |

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "hotaru"
-version = "3.3.1"
+version = "3.3.2"
 description = "High performance Optimizer to extract spike Timing And cell location from calcium imaging data via lineaR impUlse"
 license = "GPL-3.0-only"
 authors = ["TAKEKAWA Takashi <[email protected]>"]

src/hotaru/footprint/clean.py

@@ -10,8 +10,6 @@
 
 
 def clean_footprint(data, mask, gauss, radius, batch, verbose):
-    strategy = tf.distribute.get_strategy()
-
     dataset = tf.data.Dataset.from_tensor_slices(data)
     dataset = unmasked(dataset, mask)
     dataset = dataset.batch(batch)
@@ -27,7 +25,7 @@ def clean_footprint(data, mask, gauss, radius, batch, verbose):
     ps = tf.TensorArray(tf.int32, nk)
     fs = tf.TensorArray(tf.float32, nk)
     i = tf.constant(0)
-    for data in strategy.experimental_distribute_dataset(dataset):
+    for data in dataset:
         gl, ll, rl, yl, xl = _prepare(data, mask, gauss, radius)
         nx = tf.size(rl)
         for k in tf.range(nx):

src/hotaru/footprint/make.py

@@ -10,8 +10,6 @@
 
 
 def make_segment(dataset, mask, gauss, radius, peaks, shard, batch, verbose):
-    strategy = tf.distribute.get_strategy()
-
     ts, rs, ys, xs = peaks[:, 0], peaks[:, 1], peaks[:, 2], peaks[:, 3]
     nk = ts.size
 
@@ -29,7 +27,7 @@ def make_segment(dataset, mask, gauss, radius, peaks, shard, batch, verbose):
     prog = tf.keras.utils.Progbar(nk, verbose=verbose)
     fps = tf.TensorArray(tf.float32, 0, True)
     e = K.constant(0, tf.int32)
-    for imgs in strategy.experimental_distribute_dataset(dataset):
+    for imgs in dataset:
         s, e = e, e + tf.shape(imgs)[0]
         gl, yl, xl = _prepare(
             imgs, s, e, ts, rs, ys, xs, gauss, radius,