GazzolaLab · armantekinalp · Apr 19, 2022 · Apr 12, 2022 · Apr 12, 2022 · Apr 12, 2022
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -26,7 +26,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
-      
+
       # Ref: https://docs.github.com/en/free-pro-team@latest/actions/guides/building-and-testing-python
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
@@ -36,9 +36,9 @@ jobs:
       # You can test your matrix by printing the current Python version
       - name: Display Python version
         run: python -c "import sys; print(sys.version)"
-      
+
       # Cache the pip requirmenets for other tests. If requirements cached use them to speed up the build.
-      # Ref: https://github.com/actions/cache/blob/main/examples.md#python---pip 
+      # Ref: https://github.com/actions/cache/blob/main/examples.md#python---pip
       - name: Cache pip Linux
         uses: actions/cache@v2
         if: startsWith(runner.os, 'Linux')
@@ -55,7 +55,7 @@ jobs:
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
-            
+
       - name: Cache pip Windows
         uses: actions/cache@v2
         if: startsWith(runner.os, 'Windows')
@@ -72,34 +72,34 @@ jobs:
           pip install -r requirements.txt
           echo update test requirements
           pip install -r tests/requirements.txt
-    
+
       # Runs a single command using the runners shell
       - name: Welcome message
         run: echo Hello, world! Welcome MiV-OS Build, lets start testing!
-      
+
       # Formatting test with black and flake8
       - name: Black and Flake8 formatting tests
         if: startsWith(runner.os, 'macOS')
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.8" ]]; then 
+          if [[ "${{ matrix.python-version }}" == "3.8" ]]; then
             black --version
             black --check miv tests
             flake8 --version
-            flake8 miv tests 
+            flake8 miv tests
           fi
-          
+
       # General PyTest for all matrix strategy
-      - name: PyTest
+      - name: PyTest and MyPy
         run: |
-          pytest
-          
+          make ci
+
       # Set environment variables for coverage test. Coverage test is done using python 3.8
       # Test MiV-OS using pytest
       - name: Test MiV-OS using pytest
         if: startsWith(runner.os, 'macOS')
         run: |
-          if [[ "${{ matrix.python-version }}" == "3.8" ]]; then 
+          if [[ "${{ matrix.python-version }}" == "3.8" ]]; then
             echo "CODECOV_TOKEN=4e35faf2-dc6b-442c-99f3-90d088ccd9f6" >> $GITHUB_ENV
-            python3 -m pytest --cov=MiV-OS --cov-report=xml
+            python3 -m pytest --cov=miv --cov-report=xml
             codecov
           fi
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -5,8 +5,6 @@ repos:
   - id: trailing-whitespace
   - id: check-json
   - id: end-of-file-fixer
-  - id: name-tests-test
-    args: ['--django']
   - id: requirements-txt-fixer
 - repo: https://github.com/psf/black
   rev: 21.12b0

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.8"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt
diff --git a/Makefile b/Makefile
@@ -1,4 +1,11 @@
 test:
 	@python -m pytest
 
-all:test
+mypy:
+	@mypy --ignore-missing-imports miv
+
+coverage:
+	@pytest --cov=miv tests/
+
+all:test mypy
+ci: test mypy
diff --git a/README.md b/README.md
@@ -29,7 +29,7 @@ $ pip install MiV-OS
 ## Documentation
 [![Documentation Status][badge-docs-status]][link-docs-status]
 
-Documentation of the package is available [here][link-docs-website]
+Documentation of the package is available [here][link-docs-status]
 
 ## Contribution
 

diff --git a/docs/README.md b/docs/README.md
@@ -6,6 +6,12 @@ In addition, we utilize the following extensions to enhance the documentation :c
 - `numpydoc`: We favor [numpy documentation style](https://numpydoc.readthedocs.io/en/latest/format.html) for API documentation.
 - `myst_parser`: We like to write documentation and guidelines in `markdown` format.
 
+## Key things to remember
+
+- Please DON'T IGNORE any `errors` or `warnings` during the compilation stage.
+- If you are uploading any `ipynb` or notebook-style, make sure you excluded the input-output cells.
+    - Currently, we don't use the `runnable` notebook directly on the documentation. If you think otherwise, please leave an issue so that we can discuss.
+
 ## Build documentation
 
 The `sphinx` is already initialized in `docs` directory. In order to build the documentation, you will need additional packages listed in `docs/requirements.txt`.

diff --git a/docs/api/_toctree/DetectionAPI/miv.signal.spike.SpikeDetectionProtocol.rst b/docs/api/_toctree/DetectionAPI/miv.signal.spike.SpikeDetectionProtocol.rst
@@ -0,0 +1,16 @@
+miv.signal.spike.SpikeDetectionProtocol
+=======================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: SpikeDetectionProtocol
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~SpikeDetectionProtocol.__init__
diff --git a/docs/api/_toctree/DetectionAPI/miv.signal.spike.ThresholdCutoff.rst b/docs/api/_toctree/DetectionAPI/miv.signal.spike.ThresholdCutoff.rst
@@ -0,0 +1,16 @@
+miv.signal.spike.ThresholdCutoff
+================================
+
+.. currentmodule:: miv.signal.spike
+
+.. autoclass:: ThresholdCutoff
+   :members: align_to_minimum, compute_spike_threshold, detect_threshold_crossings, get_next_minimum
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~ThresholdCutoff.align_to_minimum
+      ~ThresholdCutoff.compute_spike_threshold
+      ~ThresholdCutoff.detect_threshold_crossings
+      ~ThresholdCutoff.get_next_minimum
diff --git a/docs/api/_toctree/FilterAPI/miv.signal.filter.ButterBandpass.rst b/docs/api/_toctree/FilterAPI/miv.signal.filter.ButterBandpass.rst
@@ -0,0 +1,4 @@
+miv.signal.filter.ButterBandpass
+================================
+
+.. autoclass:: miv.signal.filter.ButterBandpass
diff --git a/docs/api/_toctree/FilterAPI/miv.signal.filter.FilterCollection.rst b/docs/api/_toctree/FilterAPI/miv.signal.filter.FilterCollection.rst
@@ -0,0 +1,7 @@
+miv.signal.filter.FilterCollection
+==================================
+
+.. currentmodule:: miv.signal.filter
+
+.. autoclass:: FilterCollection
+   :members: append, insert
diff --git a/docs/api/_toctree/FilterAPI/miv.signal.filter.FilterProtocol.rst b/docs/api/_toctree/FilterAPI/miv.signal.filter.FilterProtocol.rst
@@ -0,0 +1,4 @@
+miv.signal.filter.FilterProtocol
+================================
+
+.. autoclass:: miv.signal.filter.FilterProtocol
diff --git a/docs/api/_toctree/StatisticsAPI/miv.statistics.summarizer.StatisticsSummary.rst b/docs/api/_toctree/StatisticsAPI/miv.statistics.summarizer.StatisticsSummary.rst
@@ -0,0 +1,13 @@
+miv.statistics.summarizer.StatisticsSummary
+===========================================
+
+.. currentmodule:: miv.statistics.summarizer
+
+.. autoclass:: StatisticsSummary
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~StatisticsSummary.__init__
+      ~StatisticsSummary.spikestamps_summary
diff --git a/docs/api/signal.rst b/docs/api/signal.rst
@@ -1,13 +1,34 @@
-************************
-Signal Processing Module
-************************
+*************************
+Signal Processing Modules
+*************************
 
-.. automodule:: miv.signal.filter.continuous_signal_filter
-   :members:
 
-***********************
-Spike Detection Modules
-***********************
+Filter
+######
 
-.. automodule:: miv.signal.spike.detection
-   :members:
+.. currentmodule:: miv.signal.filter
+
+.. automodule:: miv.signal.filter
+
+   .. autosummary::
+       :nosignatures:
+       :toctree: _toctree/FilterAPI
+
+       FilterProtocol
+       ButterBandpass
+       FilterCollection
+
+Spike Detection
+###############
+
+.. automodule:: miv.signal.spike
+
+   .. autosummary::
+       :nosignatures:
+       :toctree: _toctree/DetectionAPI
+
+       SpikeDetectionProtocol
+       ThresholdCutoff
+
+Spike Sorting
+#############
diff --git a/docs/api/statistics.rst b/docs/api/statistics.rst
@@ -1,3 +1,41 @@
 ******************
 Statistics Modules
 ******************
+
+Statistics Tools
+================
+
+Spikestamps
+-----------
+
+.. currentmodule:: miv.statistics
+
+.. automodule:: miv.statistics.summarizer
+
+   .. autosummary::
+      :nosignatures:
+      :toctree: _toctree/StatisticsAPI
+
+      StatisticsSummary
+
+Useful External Packages
+########################
+
+scipy statistics
+================
+
+`scipy <https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.describe.html>`_
+
+.. autosummary::
+
+   scipy.stats.describe
+
+elephant.statistics
+===================
+
+`elephant documentation: <https://elephant.readthedocs.io/en/latest/reference/statistics.html>`_
+
+.. autosummary::
+
+   elephant.statistics.mean_firing_rate
+   elephant.statistics.instantaneous_rate
diff --git a/docs/conf.py b/docs/conf.py
@@ -37,22 +37,26 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
     "sphinx.ext.autosectionlabel",
     "sphinx_autodoc_typehints",
     #'sphinx.ext.napoleon',
     "sphinx.ext.viewcode",
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
     "sphinx_rtd_theme",
     "sphinx.ext.mathjax",
     "numpydoc",
-    "myst_parser",
+    # "myst_parser", # Moving onto jupyter-notebook style
+    "myst_nb",
 ]
 
 myst_enable_extensions = [
     "amsmath",
     "colon_fence",
     "deflist",
     "dollarmath",
-    "fieldlist",
+    # "fieldlist",
     "html_admonition",
     "html_image",
 ]
@@ -67,16 +71,24 @@
     "README.md",  # File reserved to explain how documentationing works.
 ]
 
-autodoc_default_flags = [
-    "members",
-    "private-members",
-    "special-members",
-    "show-inheritance",
-]
+autodoc_default_options = {
+    # "members": False,
+    "member-order": "bysource",
+    "special-members": "",
+    "exclude-members": "__weakref__",
+    "show-inheritance": True,
+}
 autosectionlabel_prefix_document = True
+autosummary_generate = True
+autosummary_generate_overwrite = False
 
 source_parsers = {}
-source_suffix = [".rst", ".md"]
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "myst-nb",
+    ".myst": "myst-nb",
+    ".ipynb": "myst-nb",
+}
 
 master_doc = "index"
 # -- Options for HTML output -------------------------------------------------
@@ -101,3 +113,6 @@
 
 # -- Options for numpydoc ---------------------------------------------------
 numpydoc_show_class_members = False
+
+# -- Options for myst-nb ---------------------------------------------------
+jupyter_execute_notebooks = "off"
diff --git a/docs/examples/spike_detection.rst b/docs/examples/spike_detection.rst
@@ -0,0 +1,6 @@
+Spike Detection Example
+#######################
+
+.. literalinclude:: ../../examples/post_processing/spike_detection.py
+   :linenos:
+   :language: python