Merge pull request #17 from MerlinDumeur/cleanup

Cleanup

.github/workflows/ci.yml

@@ -36,7 +36,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     needs: linter-check
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.10", "3.8"]
@@ -54,17 +54,89 @@ jobs:
           path: ~/conda_pkgs_dir
           key:
             ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
-            hashFiles('etc/example-environment.yml') }}
+            hashFiles('env.yml') }}
       - name: Setup python ${{ matrix.python-version }} with conda
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          environment-file: env.yml
+          environment-file: meta.yml
           use-only-tar-bz2: true
       - name: Testing
         run: |
-          conda install -c conda-forge pytest pytest-xdist
-          pip uninstall pymultifracs
+          conda install -c conda-forge pytest pytest-xdist pytest-cov
           pip install -e .
-          pytest -n auto -x
+          pytest -n auto -x --cov=./ --cov-report=xml
+
+  build-docs:
+    if: github.repository == 'neurospin/pymultifracs'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Cache conda
+        uses: actions/cache@v2
+        env:
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            doc-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('meta.yml') }}
+      - name: Setup python with conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.11
+          environment-file: meta.yml
+          use-only-tar-bz2: true
+      - name: Build doc
+        run: |
+          conda install -c conda-forge sphinx numpydoc pydata-sphinx-theme
+          pip install -e .
+          cd doc
+          make html
+      
+  upload-docs:
+    if: github.repository == 'neurospin/pymultifracs'
+    runs-on: ubuntu-latest
+    needs: [build-docs]
+    steps:
+      - name: Archive artifact
+        shell: sh
+        if: runner.os == 'Linux'
+        run: |
+          tar \
+            --dereference --hard-dereference \
+            --directory doc/_build/ \
+            -cvf "$RUNNER_TEMP/artifact.tar" \
+            --exclude=.git \
+            --exclude=.github \
+            .
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: github-pages
+          path: ${{ runner.temp }}/artifact.tar
+          retention-days: 1
+          if-no-files-found: error
+
+  deploy-docs:
+    needs: upload-docs
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Specify runner + deployment step
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/[email protected] # or the latest "vX.X.X" version tag for this action
+

.gitignore

@@ -3,6 +3,9 @@
 
 # Compiled python modules.
 *.pyc
+*.so
+*.c
+pymultifracs/*.html
 
 # Setuptools distribution folder.
 python_code/pymultifracs/dist/
@@ -42,3 +45,7 @@ pymultifracs/todo.txt
 notebooks/Dev*.ipynb
 coverage.xml
 notebooks/figures
+
+examples/*.html
+data/
+examples/*.mat

README.rst

@@ -1,6 +1,6 @@
 .. -*- mode: rst -*-
 
-|Codecov|_ |Binder|_ |CircleCI|_
+|Codecov|_ |Binder|_
 
 .. |Codecov| image:: https://codecov.io/gh/neurospin/pymultifracs/branch/master/graph/badge.svg
 .. _Codecov: https://codecov.io/gh/neurospin/pymultifracs

doc/_templates/autosummary/class.rst

@@ -3,14 +3,3 @@
 .. currentmodule:: {{ module }}
 
 .. autoclass:: {{ objname }}
-
-   .. rubric:: Methods
-   .. autosummary::
-
-   {% for item in methods %}
-   {%- if item not in ["__init__"] and item[0] != '_'%}
-      ~{{ name }}.{{ item }}
-   {%- endif %}
-   {%- endfor %}
-
-.. include:: {{fullname}}.examples

doc/_templates/autosummary/function.rst

@@ -1,12 +1,5 @@
-{{ fullname }}
-{{ underline }}
+{{ fullname | escape | underline }}
 
 .. currentmodule:: {{ module }}
 
 .. autofunction:: {{ objname }}
-
-.. include:: {{ fullname }}.examples
-
-.. raw:: html
-
-    <div style='clear:both'></div>

doc/conf.py

@@ -18,27 +18,30 @@
 # -- Project information -----------------------------------------------------
 
 project = 'PyMultiFracs'
-copyright = '2020-2021, M. Dumeur, P. Ciuciu, V. van Wassenhove, P. Abry'
+copyright = '2020-2023, M. Dumeur, P. Ciuciu, V. van Wassenhove, P. Abry'
 author = 'M. Dumeur, P. Ciuciu, V. van Wassenhove, P. Abry'
 
 # The full version, including alpha/beta/rc tags
-release = '1.0'
+release = '0.2'
 
 
 # -- General configuration ---------------------------------------------------
 
+needs_sphinx = "2.0"
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.autosummary',
+              'sphinx.ext.coverage',
               'sphinx.ext.intersphinx',
               # 'sphinx.ext.linkcode',
               'numpydoc',
-              'sphinx_autodoc_typehints',
+            #   'sphinx_autodoc_typehints',
               # 'sphinx_gallery.notebook',
-              'sphinx_bootstrap_theme',
-              'nbsphinx',
+            #   'sphinx_bootstrap_theme',
+            #   'nbsphinx',
               'sphinx.ext.mathjax']
 
 # Add any paths that contain templates here, relative to this directory.
@@ -60,32 +63,47 @@
 #
 # html_theme = 'alabaster'
 
-html_theme = 'bootstrap'
+html_theme = 'pydata_sphinx_theme'
 
 html_theme_options = {
-    'navbar_title': 'PyMultiFracs',  # we replace this with an image
-    'source_link_position': "nav",  # default
-    'bootswatch_theme': "flatly",  # yeti paper lumen
-    'navbar_sidebarrel': False,  # Render the next/prev links in navbar?
-    'navbar_pagenav': False,
-    'navbar_class': "navbar",
-    'bootstrap_version': "3",  # default
-    # 'navbar_site_name': '',
-    'navbar_links': [
-        # ("Install", "install"),
-        # ("Tutorials", "auto_tutorials/index"),
-        ("Examples", "examples"),
-        # ("Glossary", "glossary"),
-        ("API", "reference"),
-        ("Theory", 'theory')
-        # ("Contribute", "install/contributing"),
+    "icon_links": [
+        dict(
+            name="GitHub",
+            url="https://github.com/neurospin/pymultifracs/",
+            icon="fa-brands fa-square-github",
+        ),
     ],
+    "icon_links_label": "External Links",  # for screen reader
+    "use_edit_page_button": False,
+    "navigation_with_keys": False,
+    "show_toc_level": 1,
+    "article_header_start": [],  # disable breadcrumbs
+    # "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "footer_start": ["copyright"],
+    "secondary_sidebar_items": ["page-toc"],
 }
 
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+# html_logo = "_static/.svg"
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = "_static/favicon.ico"
+
 # 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']
+html_static_path = ["_static"]
+# html_css_files = [
+#     "style.css",
+# ]
+
+# Custom sidebar templates, maps document names to template names.
+# html_sidebars = {
+#     "index": ["sidebar-quicklinks.html"],
+# }
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
@@ -95,22 +113,25 @@
 html_show_sphinx = False
 
 
-def setup(app):
-    app.add_stylesheet("style.css")  # also can be a full URL
-    app.add_stylesheet("font-awesome.css")
-    app.add_stylesheet("font-source-code-pro.css")
-    app.add_stylesheet("font-source-sans-pro.css")
+# def setup(app):
+#     app.add_stylesheet("style.css")  # also can be a full URL
+#     app.add_stylesheet("font-awesome.css")
+#     app.add_stylesheet("font-source-code-pro.css")
+#     app.add_stylesheet("font-source-sans-pro.css")
 
 
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://numpy.org/devdocs', None),
-    'scipy': ('https://scipy.github.io/devdocs', None),
-    'matplotlib': ('https://matplotlib.org', None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
     'sklearn': ('https://scikit-learn.org/stable', None),
     'joblib': ('https://joblib.readthedocs.io/en/latest', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable', None),
     'seaborn': ('https://seaborn.pydata.org/', None),
+    # "numba": ("https://numba.readthedocs.io/en/latest", None),
+    # "joblib": ("https://joblib.readthedocs.io/en/latest", None),
+    # "statsmodels": ("https://www.statsmodels.org/dev", None),
 }
 
 # numpydoc

doc/docenv.yml

@@ -0,0 +1,17 @@
+name: pymultifracs-doc
+channels:
+  - conda-forge
+dependencies:
+  - python>=3.7
+  - numpy>=1.17.3
+  - scipy>=1.3.1
+  - pywavelets>=1.1.1
+  - seaborn>=0.9.0
+  - scikit-learn>=0.21.34
+  - statsmodels
+  - sphinx
+  - numpydoc
+  - pydata-sphinx-theme
+  - pip
+  - pip:
+    - recombinator

doc/index.rst

@@ -9,4 +9,3 @@ Contents
 
    reference
    theory
-

doc/reference.rst

@@ -13,17 +13,6 @@ Multifractal Analysis
     :toctree: _autosummary
 
     mf_analysis
-    mf_analysis_full
-    minimal_mf_analysis
-
-Classes gathering the output of multifractal analysis
-
-.. autosummary::
-    :toctree: _autosummary
-    :template: namedtuple.rst
-
-    MFractalData
-    MFractalVar
 
 Dataclasses
 ```````````
@@ -40,6 +29,13 @@ Used to compute and store intermediary results
     structurefunction.StructureFunction
     mfspectrum.MultifractalSpectrum
 
+Storing the multifractal analysis output
+
+.. autosummary::
+    :toctree: _autosummary
+
+    utils.MFractalVar
+
 Wavelet Analysis
 ----------------
 
@@ -55,7 +51,6 @@ Wavelet Analysis
 
 .. autosummary::
     :toctree: _autosummary
-    :template: namedtuple.rst
 
     WaveletTransform
 
@@ -90,6 +85,19 @@ Computing and Plotting PSDs
 
 .. autosummary::
     :toctree: _autosummary
-    :template: namedtuple.rst
 
-    PSD
+    PSD
+
+
+Utility functions
+-----------------
+
+.. currentmodule:: pymultifracs.utils
+
+:py:mod:`pymultifracs.utils`:
+
+.. autosummary::
+    :toctree: _autosummary
+
+    scale2freq
+    freq2scale