Merge pull request #512 from grahamgower/release-prep

Prepare for release

.github/workflows/docs.yaml

@@ -37,7 +37,7 @@ jobs:
       - name: Build Docs
         run: |
           cd docs
-          make dist
+          make
 
       - name: Checkout docs site
         if: (!github.event.pull_request)

CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## 0.2.3 - 2023-05-04
+
+- Fixed the use of numpy strings for deme names.
+  ({user}`terhorst`, {user}`grahamgower`, {issue}`495`, {pr}`505`)
+- Added `Graph.rename_demes()` method to return a graph with renamed demes.
+  ({user}`aabiddanda`, {pr}`499`)
+
 ## 0.2.2 - 2022-04-28
 
 Better conformance to the spec. Minor discrepancies between

docs/Makefile

@@ -7,10 +7,5 @@ DEMES_VERSION:=$(shell PYTHONPATH=${PYTHONPATH} \
 dev:
 	./build.sh
 
-dist:
-	@echo Building distribution for demes version ${DEMES_VERSION}
-	sed -i s/__DEMES_VERSION__/${DEMES_VERSION}/g _config.yml
-	./build.sh
-
 clean:
 	rm -fR _build

docs/_config.yml

@@ -3,9 +3,8 @@
 
 title: Demes manual
 author: PopSim Consortium
-copyright: "2021"
+copyright: "2021-2023"
 only_build_toc_files: true
-# logo: logo.png
 
 execute:
   execute_notebooks: cache
@@ -15,19 +14,6 @@ repository:
   branch: main
   path_to_book: docs
 
-launch_buttons:
-  # Disable binder launch button on pages with python code.
-  binderhub_url: ""
-
-html:
-  use_issues_button: true
-  use_repository_button: true
-  use_edit_page_button: true
-  # Do not edit this - the version placeholder is replaced by the
-  # current version during a distribution build in the Makefile
-  extra_navbar: demes __DEMES_VERSION__
-  extra_footer: demes __DEMES_VERSION__
-
 sphinx:
     extra_extensions:
     - sphinx.ext.autodoc
@@ -49,3 +35,18 @@ sphinx:
 
       # Don't use fully-qualified type names. E.g. demes.demes.Graph
       autodoc_typehints: none
+
+      html_show_sphinx: false
+      # https://piccolo-theme.readthedocs.io/
+      html_theme: "piccolo_theme"
+      # some custom css to fix piccolo/notebook in dark modes
+      html_static_path: ["_static"]
+      html_css_files: ["custom.css"]
+
+      html_theme_options:
+          globaltoc_collapse: false
+          globaltoc_maxdepth: -1
+          globaltoc_includehidden: true
+
+          ## piccolo_theme options
+          source_url: https://github.com/popsim-consortium/demes-python

docs/_static/custom.css

@@ -0,0 +1,26 @@
+/*
+ * Fixes for images with transparent backgrounds and notebook output
+ * when using dark mode with piccolo_theme.
+ */
+.cell_output img {
+    background-color: white !important;
+}
+section img {
+    background-color: white !important;
+}
+div.cell summary {
+    background-color: #eeffcc !important;
+    color: #252630 !important;
+}
+div.cell_output,
+div.cell_input
+{
+    background: inherit !important;
+}
+
+.cell_output .output.text_plain,
+.cell_output .output.traceback,
+.cell_output .output.stream,
+.cell_output .output.stderr {
+    background: inherit !important;
+}

docs/_toc.yml

@@ -1,6 +1,7 @@
 format: jb-article
-root: introduction
+root: index
 sections:
+- file: introduction
 - file: installation
 - file: quickstart
 - file: api

docs/index.md

@@ -0,0 +1 @@
+<meta http-equiv="refresh" content="0; URL=introduction.html" />

requirements/docs.txt

@@ -1,4 +1,5 @@
 demesdraw==0.3.1
 jupyter-book==0.15.1
+piccolo_theme==0.15.0
 sphinx_issues==3.0.1
 sphinxcontrib-programoutput==0.17

setup.cfg

@@ -12,11 +12,6 @@ classifiers =
     Operating System :: OS Independent
     Intended Audience :: Science/Research
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Bio-Informatics
 project_urls =