Merge pull request #978 from samuelgarcia/gh_actions_and_datalad

Continue github actions.

Author: JuliaSprenger

.github/workflows/full-test.yml

@@ -1,4 +1,4 @@
-name: Full spikeinterface tests
+name: neo.io and neo.rawio tests
 
 on:
   pull_request:
@@ -18,14 +18,17 @@ jobs:
       - uses: actions/checkout@v2
         with:
           python-version: 3.8
-      - name: Which python
-        run: |
-          which python
+      - name: Get current year-month
+        id: date
+        run: echo "::set-output name=date::$(date+'%Y-%m')"
       - uses: actions/cache@v2
+        # the cache for python package is reset:
+        #   * every month
+        #   * when requirements/requirements_testing change
         id: cache-venv
         with:
-          path: ./test_env
-          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}
+          path: ~/test_env
+          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements_testing.txt') }}-${{ steps.date.outputs.date }}
           restore-keys: |
             ${{ runner.os }}-venv-
       - name: Install dependencies
@@ -36,26 +39,27 @@ jobs:
           git config --global user.email "neo_ci@fake_mail.com"
           git config --global user.name "neo CI"
           # create an environement and install everything
-          python -m venv test_env
-          source ./test_env/bin/activate
+          python -m venv ~/test_env
+          source ~/test_env/bin/activate
           python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install -r requirements_testing.txt
           pip install -e .
+      - name: Get ephy_testing_data current head hash
+        # the key depend on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
+        id: vars
+        run: |
+          echo "::set-output name=HASH_EPHY_DATASET::$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)"
       - uses: actions/cache@v2
         id: cache-datasets
-        env:
-          # the key depend on the last comit repo https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git
-          HASH_EPHY_DATASET: git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1
         with:
           path: ~/ephy_testing_data
-          key: ${{ runner.os }}-datasets-${{ env.HASH_EPHY_DATASET }}
+          key: ${{ runner.os }}-datasets-${{ steps.vars.outputs.HASH_EPHY_DATASET }}
           restore-keys: |
             ${{ runner.os }}-datasets
       - name: Test with pytest
         run: |
-          source ./test_env/bin/activate
-          # onbly rawiotest is tested at the moment
+          source ~/test_env/bin/activate
+          # only neo.rawio and neo.io
           pytest --cov=neo neo/test/rawiotest
-          # TODO uncomment this soon
-          # pytest --cov=neo neo/test/iotest
+          pytest --cov=neo neo/test/iotest

.travis.yml

@@ -30,6 +30,7 @@ before_install:
   - pip install "numpy==$NUMPY_VERSION"
 install:
   - pip install -r requirements.txt
+  - pip install nose
   - pip install coveralls
   - pip install .
   - pip install pillow

neo/io/kwikio.py

@@ -198,8 +198,12 @@ def read_spiketrain(self, cluster_id, model,
             w = pq.Quantity(w, raw_data_units)
         else:
             w = None
+        if model.duration > 0.:
+            t_stop = model.duration
+        else:
+            t_stop = np.max(model.spike_times[idx])
         sptr = SpikeTrain(times=model.spike_times[idx],
-                          t_stop=model.duration, waveforms=w, units='s',
+                          t_stop=t_stop, waveforms=w, units='s',
                           sampling_rate=model.sample_rate * pq.Hz,
                           file_origin=self.filename,
                           **{'cluster_id': cluster_id})

neo/test/iotest/common_io_test.py

@@ -176,12 +176,6 @@ def able_to_write_or_read(self, writeread=False, readwrite=False):
 
         return True
 
-    #~ def get_filename_path(self, filename):
-        #~ '''
-        #~ Get the path to a filename in the current temporary file directory
-        #~ '''
-        #~ return os.path.join(self.local_test_dir, filename)
-
     def get_local_base_folder(self):
         return get_local_testing_data_folder()
 

neo/test/iotest/test_nixio.py

@@ -711,7 +711,7 @@ def rquant(shape, unit, incr=False):
 
     @classmethod
     def create_all_annotated(cls):
-        times = cls.rquant(10, pq.s)
+        times = cls.rquant(10, pq.s, incr=True)
         times_ann = {cls.rword(6): cls.rquant(10, pq.ms)}
         signal = cls.rquant((10, 10), pq.V)
         signal_ann = {cls.rword(6): cls.rquant(10, pq.uV)}
@@ -744,8 +744,8 @@ def create_all_annotated(cls):
         event.annotate(**cls.rdict(4))
         seg.events.append(event)
 
-        spiketrain = SpikeTrain(times=times, t_stop=pq.s, units=pq.s,
-                                array_annotations=times_ann)
+        spiketrain = SpikeTrain(times=times, t_stop=10*pq.s,
+                        units=pq.s, array_annotations=times_ann)
         d = cls.rdict(6)
         d["quantity"] = pq.Quantity(10, "mV")
         d["qarray"] = pq.Quantity(range(10), "mA")
@@ -859,7 +859,7 @@ def test_signals_write(self):
         anotherblock.segments.append(seg)
         irsig = IrregularlySampledSignal(
             signal=np.random.random((20, 30)),
-            times=self.rquant(20, pq.ms, True),
+            times=self.rquant(20, pq.ms, incr=True),
             units=pq.A
         )
         seg.irregularlysampledsignals.append(irsig)
@@ -875,7 +875,7 @@ def test_signals_write(self):
         self.write_and_compare([block, anotherblock])
 
         block.segments[0].irregularlysampledsignals.append(
-            IrregularlySampledSignal(times=np.random.random(10),
+            IrregularlySampledSignal(times=np.sort(np.random.random(10)),
                                      signal=np.random.random((10, 13)),
                                      units="mV", time_units="s",
                                      dtype=np.float,

neo/utils/datasets.py

@@ -12,8 +12,8 @@
 
 
 global local_testing_data_folder
-if os.getenv('TESTING_DATA_FOLDER', default=None) is not None:
-    local_testing_data_folder = Path(os.getenv('TESTING_DATA_FOLDER'))
+if os.getenv('EPHY_TESTING_DATA_FOLDER', default=None) is not None:
+    local_testing_data_folder = Path(os.getenv('EPHY_TESTING_DATA_FOLDER'))
 else:
     # set in home
     local_testing_data_folder = Path.home() / 'ephy_testing_data'
@@ -52,6 +52,8 @@ def download_dataset(repo=None, remote_path=None, local_folder=None):
     local_path:
         The local path of the downloaded file or folder
     """
+    assert HAVE_DATALAD, 'You need to install datalad'
+
     if repo is None:
         # Use gin NeuralEnsemble/ephy_testing_data
         repo = 'https://gin.g-node.org/NeuralEnsemble/ephy_testing_data'
@@ -72,10 +74,7 @@ def download_dataset(repo=None, remote_path=None, local_folder=None):
         return
 
     dataset.get(remote_path)
-    
+
     local_path = local_folder / remote_path
 
     return local_path
-
-
-

requirements.txt

@@ -1,5 +1,2 @@
-# essential
 numpy>=1.13.0,!=1.16.0
 quantities>=0.12.1
-# for running tests
-nose>=1.1.2

requirements_testing.txt

@@ -6,7 +6,7 @@ h5py
 igor
 klusta
 tqdm
-nixio>=1.5.0b2
+nixio>=1.5.0
 matplotlib
 ipython
 coverage