Enh/add doctest runner (NeuralEnsemble#503)

* fixed asset doctest formatting

* fixed doctests in granger.py

* fixed granger doctest np.random.seed

* fix datasets.py example

* fixed doctests in gpfa.py

* fix doctest signal_processing.py

* display plot from elephant.signal_processing.cross_correlation_function

* display plot from elephant.signal_processing.hilbert¶

* fix doctest spade.py

* update spade doctests

* doctest fix fast_fca.py

* fix doctest spectral.py

* fix doctest spike_train_correlation.py

* doctest for spike_train_correlation.py

* doctest for spike_train_surrogates.py

* fixed doctests in spike_train_synchrony.py

* fixed doctests in statistics.py

* doctest for spike_train_synchrony.py

* fixed doctests in sta.py

* display figure in elephant.sta.spike_field_coherence

* fix doctests statistics.py

* changes in test_sta.py

* fixed doctests in unitary_event_analysis.py

* fix doctests unitary_event_analysis.py

* signal_processing.py old results

* fix pep8 in spade.py

* add doctest runner

* add mpi4py to doctest runner

* change installation order

* install openmpi library

* remove trailing spaces from CI.yml

* add doctest runner

* add mpi4py to doctest runner

* change installation order

* install openmpi library

* remove trailing spaces from CI.yml

* Revert "remove trailing spaces from CI.yml"

This reverts commit bd833ed.

* Revert "install openmpi library"

This reverts commit b9eefef.

* Revert "change installation order"

This reverts commit 8671d61.

* Revert "add mpi4py to doctest runner"

This reverts commit 55709b5.

* Revert "add doctest runner"

This reverts commit 80de439.

* skip doctest cell_assembly_detection.py

* skip doctest change_point_detection.py

* skip second doctest change_point_detection.py

* skip second doctest cubic.py

* skip second doctest phase_analysis.py

* skip second doctest signal_processing.py

* skip second doctest spade.py

* skip doctest spike_train_correlation.py

* skip doctest spike_train_surrogates.py

* skip doctest statistics.py

* skip doctest change_point_detection.py

* skip doctest spike_train_correlation.py

* skip doctest spike_train_surrogates.py

* skip doctest statistics.py

* skip doctest unitary_event_analysis.py

* fix pep8

.github/workflows/CI.yml

@@ -415,3 +415,65 @@ jobs:
           activate base
           cd doc
           make html
+
+  # install dependencies and elephant with pip and run tests with pytest
+  doctests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
+        python-version: ["3.10"]
+
+        # OS [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest]
+
+      # do not cancel all in-progress jobs if any matrix job fails
+      fail-fast: false
+
+    steps:
+      # used to reset cache every month
+      - name: Get current year-month
+        id: date
+        run: echo "::set-output name=date::$(date +'%Y-%m')"
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache test_env
+        uses: actions/cache@v3
+        with:
+          path: ~/test_env
+          # Look to see if there is a cache hit for the corresponding requirements files
+          # cache will be reset on changes to any requirements or every month
+          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
+            -${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('**/CI.yml') }}-${{ hashFiles('setup.py') }}
+            -${{ steps.date.outputs.date }}
+
+      - name: Install dependencies
+        run: |
+          # create an environment and install everything
+          python -m venv ~/test_env
+          source ~/test_env/bin/activate
+          sudo apt install -y libopenmpi-dev openmpi-bin
+
+          python -m pip install --upgrade pip
+          pip install mpi4py
+          pip install -r requirements/requirements-tests.txt
+          pip install -r requirements/requirements.txt
+          pip install -r requirements/requirements-extras.txt
+          pip install pytest-cov coveralls
+          pip install -e .
+
+      - name: List packages
+        run: |
+          source ~/test_env/bin/activate
+          pip list
+          python --version
+
+      - name: Run doctests
+        run: |
+          source ~/test_env/bin/activate
+          pytest elephant --doctest-modules --ignore=elephant/test/

elephant/spade.py

@@ -74,8 +74,11 @@
 
 >>> patterns = spade(spiketrains, bin_size=10 * pq.ms, winlen=1,
 ...                  dither=5 * pq.ms, min_spikes=6, n_surr=10,
-...                  psr_param=[0, 0, 3])['patterns']
->>> patterns[0]
+...                  psr_param=[0, 0, 3])['patterns']  # doctest:+ELLIPSIS
+Time for data mining: ...
+Time for pvalue spectrum computation: ...
+
+>>> patterns[0] # doctest: +SKIP
 {'itemset': (4, 3, 0, 2, 5, 1),
  'windows_ids': (9,
   16,
@@ -314,9 +317,19 @@ def spade(spiketrains, bin_size, winlen, min_spikes=2, min_occ=2,
 
     >>> from elephant.spade import spade
     >>> import quantities as pq
+    >>> from elephant.spike_train_generation import compound_poisson_process
+
+    >>> np.random.seed(30)
+    >>> spiketrains = compound_poisson_process(rate=15*pq.Hz,
+    ...     amplitude_distribution=[0, 0.95, 0, 0, 0, 0, 0.05], t_stop=5*pq.s)
+
     >>> bin_size = 3 * pq.ms # time resolution to discretize the spiketrains
     >>> winlen = 10 # maximal pattern length in bins (i.e., sliding window)
-    >>> result_spade = spade(spiketrains, bin_size, winlen)
+
+    >>> result_spade = spade(
+    ...                     spiketrains, bin_size, winlen) # doctest: +ELLIPSIS
+    Time for data mining: ...
+
 
     """
     if HAVE_MPI:  # pragma: no cover