Merge pull request #1503 from nextstrain/docs/myst

CHANGELOG.md

@@ -177,14 +177,12 @@ Nextclade CLI will warn users when input datasets contains extra files which are
 
 We added one more build variant to Bioconda distribution channel - for Linux operating system on 64-bit ARM hardware architecture. It uses `nextclade-aarch64-unknown-linux-gnu` executable underneath. This can be useful if you prefer to manage Nextclade CLI installation on your Linux ARM machine or in a Docker ARM container with Conda package manager. However, because Nextclade CLI is a self-contained single-file executable, we still recommend [direct downloads from GitHub Releases](https://github.com/nextstrain/nextclade/releases) rather than Conda or other installation methods.
 
-## Nextclade CLI 3.3.1
+## Nextclade 3.3.1
 
 ### Fix crash when using `--verbosity` option
 
 Nextclade was crashing with internal error when `--verbosity` option was present. This has been fixed.
 
-## Nextclade Web 3.3.1
-
 ### Restrict Safari browser support to >= 16.5
 
 Nextclade reports WebWorker-related errors when analysis is started on Safari browser. The minimum working version of Safari we were able to successfully test Nextclade on is 16.5. We still recommend using Chrome or Firefox for the best experience.
@@ -249,7 +247,7 @@ Due to popular demand, we are bringing back `--input-pcr-primers` argument for N
 
 Results table stripes are always alternating now, regardless of sorting and filtering applied. This is only a visual change and does not affect any functionality.
 
-## Nextclade CLI 3.0.1
+## Nextclade 3.0.1
 
 #### Bug fixes
 
@@ -261,11 +259,11 @@ Results table stripes are always alternating now, regardless of sorting and filt
 
 - Added a section to the v3 migration guide about the renamed default path for translations, a breaking change. The new default output path for translations is `nextclade.cds_translation.{cds}.fasta`. Before v3, the default path was `nextclade_gene_{gene}.translation.fasta`. You can emulate the old (default) behavior by passing `--output-translations="nextclade_gene_{cds}.translation.fasta"` to `nextclade3`.
 
-## Nextclade Web 3.0.1
+### Fix links
 
 Fixed links on navigation bar: "Docs" and "CLI"
 
-## 3.0.0
+## Nextclade 3.0.0
 
 We are happy to present a major release of Nextclade, containing new features and bug fixes.
 
@@ -544,4 +542,4 @@ The change in genome annotation handling had significant consequences for coordi
 
 ## Older versions
 
-For changes in Nextclade v2 and below, see [docs/changes/CHANGELOG.old.md](docs/changes/CHANGELOG.old.md)
+For changes in older versions, see [docs/changes/CHANGELOG.old.md](https://github.com/nextstrain/nextclade/blob/master/docs/changes/CHANGELOG.old.md)

docs/conf.py

@@ -13,33 +13,29 @@
 import os
 import sys
 from datetime import datetime
-sys.path.insert(0, os.path.abspath('.'))
 
-# At top on conf.py (with other import statements)
-import recommonmark
-from recommonmark.transform import AutoStructify
+sys.path.insert(0, os.path.abspath('.'))
 
 # -- Project information -----------------------------------------------------
 
 project = 'Nextclade'
 copyright = f'2020-{datetime.now().year}, Trevor Bedford and Richard Neher'
 author = 'The Nextstrain Team'
 
-
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'recommonmark',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.mathjax',
-    'sphinx_markdown_tables',
-    'sphinxarg.ext',
-    'sphinx.ext.autodoc',
-    'sphinx_tabs.tabs',
-    'nextstrain.sphinx.theme',
+  'myst_parser',
+  'sphinx.ext.intersphinx',
+  'sphinx.ext.mathjax',
+  'sphinx_markdown_tables',
+  'sphinxarg.ext',
+  'sphinx.ext.autodoc',
+  'sphinx_tabs.tabs',
+  'nextstrain.sphinx.theme',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -49,10 +45,28 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    "README.md"
-    "dev/**/*"
+  "README.md",
+  "assets/**",
+  "build/**",
+  "changes/CHANGELOG.old.md",
+  "dev/docs-meta.md",
+  "dev/old-versions.md",
 ]
 
+myst_enable_extensions = [
+  "amsmath",
+  "dollarmath",
+  "linkify",
+  "strikethrough",
+]
+myst_heading_anchors = 6
+myst_gfm_only = False  # For math to work. GitHub renders this syntax just fine though.
+myst_linkify_fuzzy_links = False
+myst_url_schemes = ["mailto", "http", "https"]
+
+suppress_warnings = [
+  "myst.header"
+]
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -67,30 +81,18 @@
 html_static_path = ['_static']
 
 html_css_files = [
-    'css/custom.css',
+  'css/custom.css',
 ]
 
 html_favicon = '_static/favicon.ico'
 
 html_theme_options = {
-    'logo_only': False,
-    'collapse_navigation': False,
-    'titles_only': True,
+  'logo_only': False,
+  'collapse_navigation': False,
+  'titles_only': True,
 }
 
-
 # -- Cross-project references ------------------------------------------------
 
 intersphinx_mapping = {
 }
-
-
-# At the bottom of conf.py
-def setup(app):
-    app.add_config_value('recommonmark_config', {
-        'url_resolver': lambda url: github_doc_root + url,
-        'auto_toc_tree_section': 'Contents',
-        'enable_math': True,
-        'enable_inline_math': True,
-    }, True)
-    app.add_transform(AutoStructify)