Merge branch 'develop' into feature-globally-germ-aware-fpr

.github/workflows/autodeploy.yml

@@ -8,7 +8,7 @@ on:
     branches: [ "master" ]
     # Pattern matched against refs/tags
     tags:        
-      - '*'           # Push events to every tag not containing '/' (use '**' for hierarchical tags)
+      - 'v*'           # Push events to every tag not containing '/' (use '**' for hierarchical tags)
 
   # Dont allow running manually from Actions tab -- use manualdeploy for this
   #workflow_dispatch:
@@ -35,7 +35,7 @@ jobs:
       - name: Build wheels
         uses: pypa/[email protected]
         env:
-          CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
+          CIBW_BUILD: cp37-* cp38-* cp39-* cp310-*
           CIBW_BUILD_VERBOSITY: 1
           CIBW_BEFORE_ALL_LINUX: ./.github/ci-scripts/before_install.sh
 

.github/workflows/extras.yml

@@ -46,7 +46,7 @@ jobs:
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        # Installing with -e to keep installation local (for NOSE_NOPATH)
+        # Installing with -e to keep installation local
         # but still compile Cython extensions
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace

.github/workflows/notebook.yml

@@ -52,7 +52,7 @@ jobs:
     - name: Install package
       run: |
         python -m pip install --upgrade pip
-        # Installing with -e to keep installation local (for NOSE_NOPATH)
+        # Installing with -e to keep installation local
         # but still compile Cython extensions
         python -m pip install -e .[testing]
         python setup.py build_ext --inplace

.gitignore

@@ -20,8 +20,10 @@ hooks/etc/permissions.yml
 .ropeproject
 .vscode
 doc/_autosummary
+doc/autoapi
 doc/build
-.venv
+.venv*
+
 
 # Test Metadata #
 #################
@@ -66,6 +68,7 @@ dist/*
 /pygsti.egg-info
 /pyGSTi.egg-info
 parsetab_string.py
+*.pyd
 
 # These are handwritten, not generated by cython, and should not be ignored
 !/pygsti/objects/replib/fastreps.cpp

.readthedocs.yaml

@@ -0,0 +1,58 @@
+# Read the Docs configuration file for Sphinx projects
+
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+
+# Required
+
+version: 2
+
+
+# Set the OS, Python version and other tools you might need
+
+build:
+
+  os: ubuntu-22.04
+
+  tools:
+
+    python: "3.11"
+
+    # You can also specify other tool versions:
+
+    # nodejs: "19"
+
+    # rust: "1.64"
+
+    # golang: "1.19"
+
+
+# Build documentation in the "docs/" directory with Sphinx
+
+sphinx:
+
+   configuration: doc/conf.py
+
+
+# Optionally build your docs in additional formats such as PDF and ePub
+
+# formats:
+
+#    - pdf
+
+#    - epub
+
+
+# Optional but recommended, declare the Python requirements required
+
+# to build your documentation
+
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+
+python:
+
+    install:    
+       - requirements: rtd-requirements.txt
+
+       - method: pip
+         path: .

CHANGELOG

@@ -1,5 +1,26 @@
 # CHANGELOG
 
+## [0.9.11.2] - 2023-08-11
+
+### Fixed
+
+- Fixed FAQ hyperlinks (#304)
+- Removed deprecated functions for NumPy 1.25+ (#335)
+- Fixed pickling of TPPOVM objects (#336)
+- Updated the ReadTheDocs builds (#331)
+- Fixed dataset pickling (#326)
+- Removed deprecated functions for notebook 7+ (#337)
+
+### Changed
+
+- Slight performance improvements for GST fitting (#305)
+
+## [0.9.11.1] - 2023-05-19
+
+### Fixed
+
+- Guarded an optional markupsafe import for report generation
+
 ## [0.9.11] - 2023-05-16
 
 ### Added

doc/_templates/index.rst

@@ -0,0 +1,15 @@
+API Reference
+=============
+
+This page contains auto-generated API reference documentation [#f1]_.
+
+.. toctree::
+   :titlesonly:
+
+   {% for page in pages %}
+   {% if page.top_level_object and page.display %}
+   {{ page.include_path }}
+   {% endif %}
+   {% endfor %}
+
+.. [#f1] Created with `sphinx-autoapi <https://github.com/readthedocs/sphinx-autoapi>`_

doc/_templates/python/attribute.rst

@@ -0,0 +1 @@
+{% extends "python/data.rst" %}

doc/_templates/python/class.rst

@@ -0,0 +1,60 @@
+{% if obj.display %}
+.. py:{{ obj.type }}:: {{ obj.short_name }}{% if obj.args %}({{ obj.args }}){% endif %}
+
+{% for (args, return_annotation) in obj.overloads %}
+      {{ " " * (obj.type | length) }}   {{ obj.short_name }}{% if args %}({{ args }}){% endif %}
+
+{% endfor %}
+
+
+   {% if obj.bases %}
+   {% if "show-inheritance" in autoapi_options %}
+   Bases: {% for base in obj.bases %}{{ base|link_objs }}{% if not loop.last %}, {% endif %}{% endfor %}
+   {% endif %}
+
+
+   {% if "show-inheritance-diagram" in autoapi_options and obj.bases != ["object"] %}
+   .. autoapi-inheritance-diagram:: {{ obj.obj["full_name"] }}
+      :parts: 1
+      {% if "private-members" in autoapi_options %}
+      :private-bases:
+      {% endif %}
+
+   {% endif %}
+   {% endif %}
+   {% if obj.docstring %}
+   {{ obj.docstring|indent(3) }}
+   {% endif %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_classes = obj.classes|selectattr("display")|list %}
+   {% else %}
+   {% set visible_classes = obj.classes|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for klass in visible_classes %}
+   {{ klass.render()|indent(3) }}
+   {% endfor %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_properties = obj.properties|selectattr("display")|list %}
+   {% else %}
+   {% set visible_properties = obj.properties|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for property in visible_properties %}
+   {{ property.render()|indent(3) }}
+   {% endfor %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_attributes = obj.attributes|selectattr("display")|list %}
+   {% else %}
+   {% set visible_attributes = obj.attributes|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for attribute in visible_attributes %}
+   {{ attribute.render()|indent(3) }}
+   {% endfor %}
+   {% if "inherited-members" in autoapi_options %}
+   {% set visible_methods = obj.methods|selectattr("display")|list %}
+   {% else %}
+   {% set visible_methods = obj.methods|rejectattr("inherited")|selectattr("display")|list %}
+   {% endif %}
+   {% for method in visible_methods %}
+   {{ method.render()|indent(3) }}
+   {% endfor %}
+{% endif %}

doc/_templates/python/data.rst

@@ -0,0 +1,37 @@
+{% if obj.display %}
+.. py:{{ obj.type }}:: {{ obj.name }}
+   {%- if obj.annotation is not none %}
+
+   :type: {%- if obj.annotation %} {{ obj.annotation }}{%- endif %}
+
+   {%- endif %}
+
+   {%- if obj.value is not none %}
+
+   :value: {% if obj.value is string and obj.value.splitlines()|count > 1 -%}
+                Multiline-String
+
+    .. raw:: html
+
+        <details><summary>Show Value</summary>
+
+    .. code-block:: python
+
+        """{{ obj.value|indent(width=8,blank=true) }}"""
+
+    .. raw:: html
+
+        </details>
+
+            {%- else -%}
+              {%- if obj.value is string -%}
+                {{ "%r" % obj.value|string|truncate(100) }}
+              {%- else -%}
+                {{ obj.value|string|truncate(100) }}
+              {%- endif -%}
+            {%- endif %}
+   {%- endif %}
+
+
+   {{ obj.docstring|indent(3) }}
+{% endif %}

doc/_templates/python/exception.rst

@@ -0,0 +1 @@
+{% extends "python/class.rst" %}