docs: furo theme (#64)

* docs: furo theme
* add schema check
* drop CircleCI
* sphinx==4.0 & nbsphinx==0.8.6

.github/workflows/ci_schema.yml

@@ -0,0 +1,20 @@
+name: CI action schema
+on: # Trigger the workflow on push or pull request, but only for the master branch
+  push: {}
+  pull_request:
+    branches: [master]
+
+jobs:
+  validate-schema:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Install pkg
+        run: |
+          pip install check-jsonschema
+
+      - name: GH Workflows
+        run: |
+          check-jsonschema .github/workflows/*.yml --schemafile "https://json.schemastore.org/github-workflow"

.github/workflows/ci_testing.yml

@@ -13,13 +13,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04, windows-2019, macOS-10.15]
-        python-version: [2.7, 3.6, 3.8]
-        requires: ['minimal', 'latest']
-        exclude:
-          - python-version: 2.7
-            requires: 'minimal'
-          - python-version: 3.8
+        os: [ubuntu-20.04, windows-2019, macOS-10.15]
+        python-version: [3.6, 3.9]
+        requires: ['latest']
+        include:
+          - os: "ubuntu-18.04"
+            python-version: 2.7
+            requires: 'latest'
+          - os: "ubuntu-18.04"
+            python-version: 3.6
             requires: 'minimal'
 
     # Timeout: https://stackoverflow.com/a/59076067/4521646

.github/workflows/docs-check.yml

@@ -1,8 +1,11 @@
 name: "Docs check"
 # https://github.com/marketplace/actions/sphinx-build
 
-on:
-- pull_request
+# see: https://help.github.com/en/actions/reference/events-that-trigger-workflows
+on:  # Trigger the workflow on push or pull request,  but only for the master branch
+  push:
+    branches: [master]
+  pull_request: {}
 
 jobs:
 
@@ -36,8 +39,8 @@ jobs:
       - name: Test Documentation
         run: |
           # First run the same pipeline as Read-The-Docs
-          cd docs
           make doctest
+        working-directory: ./docs
 
   make-docs:
     runs-on: ubuntu-20.04
@@ -70,10 +73,10 @@ jobs:
 
       - name: Make Documentation
         run: |
-          cd docs
           make clean
           make html --debug --jobs 2 SPHINXOPTS="-W"
           make latexpdf
+        working-directory: ./docs
 
       - name: Upload built docs
         uses: actions/upload-artifact@v2

docs/requirements.txt

@@ -1,8 +1,9 @@
-sphinx>=2.0, <3.0
+sphinx>=4.0, <4.1  # assert 'Verbatim' in lines[0]
 m2r  # fails with multi-line text
 myst-parser
-nbsphinx>=0.8.5
+nbsphinx==0.8.6  # freeze for some "Unexpected indentation" in notebooks
 pandoc
-docutils<0.15  # higher version breaks py2
+docutils  # >0.15 higher version breaks py2
 imgconverter
 ipython
+furo

docs/source/conf.py

@@ -75,7 +75,7 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 
-needs_sphinx = '2.2'
+needs_sphinx = '4.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -143,7 +143,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 # http://www.sphinx-doc.org/en/master/usage/theming.html#builtin-themes
-html_theme = 'nature'
+html_theme = "furo"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

notebooks/ANHIR_evaluation-board.ipynb

@@ -8,9 +8,11 @@
    "source": [
     "# ANHIR: Evaluation Board\n",
     "\n",
-    "This notebook serves as visualisation for challenge results in several forms - standard tables and charts. First, all submissions have to be recomputed, so they also contain the detail about each image registration pair. One of the perspective to validate is the difference between training and testing.\n",
+    "This notebook serves as visualisation for challenge results in several forms - standard tables and charts.\n",
+    "First, all submissions have to be recomputed, so they also contain the detail about each image registration pair.\n",
+    "One of the perspective to validate is the difference between training and testing.\n",
     "\n",
-    "The ANHIR challenge is hosted on https://anhir.grand-challenge.org.\n",
+    "**The ANHIR challenge is hosted on https://anhir.grand-challenge.org.**\n",
     "\n",
     "These particular results are for ANHIR workshop hosted at ISBI 2019 in Venice, Italy.\n",
     "In case you want to get some further evaluation related to new submission, you may contact one of the ANHIR administrators because the full submission is required, see https://anhir.grand-challenge.org/Organizers."
@@ -3506,15 +3508,6 @@
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
    "version": "3.6.9"
-  },
-  "pycharm": {
-   "stem_cell": {
-    "cell_type": "raw",
-    "metadata": {
-     "collapsed": false
-    },
-    "source": []
-   }
   }
  },
  "nbformat": 4,