Merge branch 'update-0.2.2' into Info_theory_enhancement

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/ci-sphinx.yml

@@ -22,14 +22,17 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
+        with:
+          submodules: recursive
       - name: Setup Poetry
         uses: snok/install-poetry@v1
       - name: Poetry install docs dependencies
         run: |
             poetry --version
             poetry config virtualenvs.in-project true
             #poetry config virtualenvs.create false
-            poetry install -E docs
+            poetry lock --no-update
+            poetry install -E "docs experiment"
       - name: Sphinx Build Check
         run: |
             source .venv/bin/activate
@@ -45,9 +48,9 @@ jobs:
                 echo Doc build success
                 exit 0
             fi
-      - name: Sphinx Link Check
-        run: |
-            source .venv/bin/activate
-            cd docs
-            make clean
-            make linkcheck
+    #- name: Sphinx Link Check
+        #run: |
+            #source .venv/bin/activate
+            #cd docs
+            #make clean
+            #make linkcheck

.github/workflows/main.yml

@@ -42,7 +42,8 @@ jobs:
       - name: Install dependencies
         run: |
           poetry config virtualenvs.in-project true
-          poetry install
+          poetry lock --no-update
+          poetry install -E "docs experiment"
       # Test MiV-OS using pytest
       - name: Run tests
         run: |
@@ -78,7 +79,8 @@ jobs:
       - name: Install dependencies
         run: |
           poetry config virtualenvs.in-project true
-          poetry install
+          poetry lock --no-update
+          poetry install -E "docs experiment"
       # Set environment variables for coverage test. Coverage test is done using python 3.8
       - name: Run style checks
         run: |

.gitignore

@@ -203,6 +203,7 @@ TODO.md
 *.png
 *.eps
 *.pdf
+*.svg
 
 # data files
 *.dat
@@ -234,3 +235,6 @@ outcmaes/*
 
 # csv files
 *.csv
+
+# Emacs backup:
+*~

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "docs/MiV-Shared-Docs"]
+	path = docs/MiV-Shared-Docs
+	url = https://github.com/GazzolaLab/MiV-Shared-Docs

.readthedocs.yaml

@@ -1,18 +1,26 @@
 # .readthedocs.yaml
 version: 2
 
+submodules:
+  include: all
+
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-20.04
-  tools: {python: "3.10"}
+  tools: 
+    python: "3.10"
   jobs:
-    pre_create_environment:
-      - asdf plugin add poetry
-      - asdf install poetry latest
-      - asdf global poetry latest
-      - poetry config virtualenvs.create false  # Key
-    post_install:
-      - poetry install -E docs
+    post_create_environment:
+      - pip install --upgrade pip
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - experiment
+  system_packages: true
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

RELEASE.md

@@ -1,3 +1,29 @@
+# Release Note (version 0.2.1)
+
+## What's Changed
+
+* Test Cases + Bug fix binned_spiketrain by @Gauravu2 in https://github.com/GazzolaLab/MiV-OS/pull/93
+* Shift documentation theme to PyData by @skim0119 in https://github.com/GazzolaLab/MiV-OS/pull/94
+* Initial implementation of MiV HDF5-based data format by @iraikov in https://github.com/GazzolaLab/MiV-OS/pull/90
+* TTL event readout from OpenEphys dataset by @skim0119 in https://github.com/GazzolaLab/MiV-OS/pull/99
+* Add core datatypes: SpikeTrain by @skim0119 in https://github.com/GazzolaLab/MiV-OS/pull/102
+* Setup dependabot by @skim0119 in https://github.com/GazzolaLab/MiV-OS/pull/103
+* Documentation theme updated to `pydata-theme`
+
+## New Contributors
+
+* @iraikov made their first contribution in https://github.com/GazzolaLab/MiV-OS/pull/90
+* @dependabot made their first contribution in https://github.com/GazzolaLab/MiV-OS/pull/107
+
+## Dependency Version Upgrade
+
+* build(deps-dev): bump flake8 from 4.0.1 to 5.0.4 by @dependabot in https://github.com/GazzolaLab/MiV-OS/pull/107
+* build(deps): bump codecov/codecov-action from 2 to 3 by @dependabot in https://github.com/GazzolaLab/MiV-OS/pull/105
+* build(deps): bump actions/setup-python from 2.2.2 to 4.2.0 by @dependabot in https://github.com/GazzolaLab/MiV-OS/pull/104
+* build(deps-dev): bump pylint from 2.14.5 to 2.15.0 by @dependabot in https://github.com/GazzolaLab/MiV-OS/pull/111
+
+**Full Changelog**: https://github.com/GazzolaLab/MiV-OS/compare/v0.2.0...v0.2.1
+
 # Release Note (version 0.2.0)
 
 [Milestone](https://github.com/GazzolaLab/MiV-OS/issues/30)

docs/.gitignore

@@ -1,2 +1,3 @@
 _external_assets
 _assets
+**/datasets

docs/_templates/miv-switcher.html

@@ -0,0 +1,23 @@
+<div class="dropdown">
+    <button type="button" class="version-switcher__button btn btn-sm navbar-btn dropdown-toggle" data-toggle="dropdown">
+<style>
+  border-color: var(--pst-color-border);
+  color: var(--pst-color-text-base);
+
+  &:hover {
+    color: var(--pst-color-text-base);
+  }
+</style>
+        OS <!-- this text may get changed later by javascript -->
+    </button>
+    <div class="dropdown-menu list-group-flush py-0">
+    <!-- dropdown will be populated by javascript on page load -->
+
+    <a class="list-group-item list-group-item-action py-1" href="https://miv-simulator.readthedocs.io/en/latest/">
+        <span>Simulator</span>
+    </a>
+    <a class="list-group-item list-group-item-action py-1" href="https://miv-oh.readthedocs.io/en/latest/">
+        <span>OH</span>
+    </a>
+    </div>
+</div>

docs/api/index.rst

@@ -0,0 +1,22 @@
+API Documentation
+=================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API
+
+   io
+   signal
+   sorting
+   statistics
+   causality
+   visualization
+   signal_generator
+   coding
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/api/io.rst

@@ -1,8 +1,26 @@
 **************************************
-Data Managing Module (:mod:`miv.io`)
+IO Module (:mod:`miv.io`)
 **************************************
 
+Python Data Managing
+====================
+
 .. automodule:: miv.io.data
 
 .. automodule:: miv.io.binary
    :members:
+
+External Datafile (H5)
+======================
+
+.. automodule:: miv.io.file
+   :members:
+
+Serial Communication Helper
+===========================
+
+.. automodule:: miv.io.serial.arduino
+   :members:
+
+.. automodule:: miv.io.serial.stimjim
+   :members:

docs/conf.py

@@ -15,16 +15,15 @@
 
 import os
 import sys
-
-# import sphinx_rtd_theme
+from urllib.request import urlretrieve
 
 sys.path.insert(0, os.path.abspath("../"))
 
 from miv import get_version
 
 # -- Project information -----------------------------------------------------
 
-project = "Mind-in-Vitro MiV-OS"
+project = "Mind-in-Vitro"
 copyright = "2022, GazzolaLab"
 author = "Gazzola Lab"
 
@@ -40,13 +39,13 @@
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "sphinx.ext.autosectionlabel",
+    "sphinx.ext.mathjax",
     "sphinx_autodoc_typehints",
     #'sphinx.ext.napoleon',
     "sphinx.ext.viewcode",
     "sphinx_togglebutton",
     "sphinx_copybutton",
-    "sphinx_rtd_theme",
-    "sphinx.ext.mathjax",
+    "sphinxcontrib.mermaid",
     "numpydoc",
     # "myst_parser", # Moving onto jupyter-notebook style
     "myst_nb",
@@ -97,23 +96,66 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
-html_theme = "sphinx_book_theme"
+html_theme = "pydata_sphinx_theme"
+html_logo = "MiV-Shared-Docs/_static/assets/logo1.svg"
+html_favicon = html_logo
+html_sourcelink_suffix = ""
 html_theme_options = {
-    "repository_url": "https://github.com/GazzolaLab/MiV-OS",
-    "use_repository_button": True,
+    "logo": {
+        # "link": "https://mindinvitro.illinois.edu/",
+        "text": "Open Software"
+    },
+    # Navbar Configuration
+    "navbar_start": ["navbar-logo", "miv-switcher.html"],
+    "navbar_center": ["navbar-nav"],
+    # "navbar_end": ["navbar-icon-links"],
+    # Header Link
+    "external_links": [
+        # {"name": "link-one-name", "url": "https://<link-one>"},
+    ],
+    "icon_links": [
+        {
+            # Label for this link
+            "name": "GitHub",
+            "url": "https://github.com/GazzolaLab/MiV-OS",  # required
+            # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
+            # The type of image to be used (see below for details)
+            "icon": "fab fa-github-square",
+            "type": "fontawesome",
+        }
+    ],
+    # Sidebar Configuraion
+    "left_sidebar_end": [],
+    # Theme (https://help.farbox.com/pygments.html)
+    # "pygment_light_style": "default",
+    # "pygment_dark_style": "native",
+    "use_edit_page_button": True,
 }
 html_title = "MiV-OS"
-# html_logo = ""
-# pygments_style = "sphinx"
+
+html_context = {
+    "default_mode": "dark",
+    "github_user": "GazzolaLab",
+    "github_repo": "MiV-OS",
+    "github_version": "main",
+    "doc_path": "docs",
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static", "_static/assets"]
+html_static_path = ["_static"]
 html_css_files = ["css/*", "css/logo.css"]
 
 # -- Options for numpydoc ---------------------------------------------------
 numpydoc_show_class_members = False
 
 # -- Options for myst-nb ---------------------------------------------------
-nb_execution_mode = "off"
+nb_execution_mode = "cache"
+myst_heading_anchors = 3
+
+# External Data Download
+# urlretrieve(  # Logo image file
+#    "https://raw.githubusercontent.com/skim0119/MiV-OS/assets_logo/docs/_static/assets/logo1.svg",
+#    html_logo,
+# )