Update doc-live branch to include latest documentation changes

.github/workflows/docs.yml

@@ -8,21 +8,30 @@ on:
     types: [opened, synchronize, reopened]
 
 jobs:
+  check-deltakit-token:
+    name: Check if Deltakit token exists
+    runs-on: ubuntu-latest
+    outputs:
+      exists: ${{ steps.deltakit-token.outputs.exists }}
+    steps:
+        - id: deltakit-token
+          env:
+              DELTAKIT_TOKEN: ${{ secrets.DELTAKIT_TOKEN }}
+          if: ${{ env.DELTAKIT_TOKEN != '' }}
+          run: echo "exists=true" >> $GITHUB_OUTPUT
+
   build-docs:
+    needs: [check-deltakit-token]
+    if: needs.check-deltakit-token.outputs.exists == 'true'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
-
       - name: Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.8.10
+        uses: prefix-dev/setup-pixi@v0.9.1
         with:
-          pixi-version: v0.50.2
+          pixi-version: v0.56.0
 
       - name: Install dependencies
         run: |

.github/workflows/labeled_tests.yml

@@ -44,18 +44,10 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version.version }}
-
       - name: Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.8.10
+        uses: prefix-dev/setup-pixi@v0.9.1
         with:
-          pixi-version: v0.49.0
-
-      - name: Instruct pixi to use specified Python version
-        run: pixi add python=${{ matrix.python-version.version }}
+          pixi-version: v0.56.0
 
       - name: Run ${{ matrix.package }} tests
         run: pixi run -e ${{ matrix.package }}-tests-py${{ matrix.python-version.label }} tests

.github/workflows/static_code_analysis.yml

@@ -21,30 +21,33 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.x'
-
       - name: Set up Pixi
-        uses: prefix-dev/setup-pixi@v0.8.10
+        uses: prefix-dev/setup-pixi@v0.9.1
         with:
-          pixi-version: v0.49.0
+          pixi-version: v0.56.0
 
       - name: Install dependencies
         run: pixi install
 
       - name: typos
         run: pixi run typos
 
-      - name: ruff
+      - name: ruff check
         run: pixi run lint
         if: ${{ always() }}
 
-      - name: mypy
+      - name: ruff format
+        run: pixi run ruff format --check
+        if: ${{ always() }}
+
+      - name: mypy-all (checking packages individually)
         run: pixi run mypy-all
         if: ${{ always() }}
 
+      - name: mypy (checking packages together)
+        run: pixi run mypy .
+        if: ${{ always() }}
+
       - name: deptry
         run: pixi run deptry
         if: ${{ always() }}

.gitignore

@@ -98,15 +98,15 @@ ipython_config.py
 #   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
-#uv.lock
+uv.lock
 
 # poetry
 #   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
 #   This is especially recommended for binary packages to ensure reproducibility, and is more
 #   commonly ignored for libraries.
 #   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
-#poetry.lock
-#poetry.toml
+poetry.lock
+poetry.toml
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
@@ -232,3 +232,8 @@ docs/explorer/simulation/
 
 # mac
 .DS_Store
+
+# Generated by `simulation.md`
+docs/**/measurements.01
+docs/**/dets_from_circuit_sampler.b8
+docs/**/dets_from_dem_sampler.01

.pre-commit-config.yaml

@@ -24,10 +24,38 @@ repos:
       # Run the linter.
       - id: ruff-check
       # Run the formatter.
-      # - id: ruff-format
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.17.0
+    hooks:
+      - id: mypy
+        args:
+          - --config-file=mypy.ini
+        exclude: 'tests|build|tools|conftest\.py$'
+        additional_dependencies:
+          - numpy
+          - matplotlib
+          - seaborn
+          - networkx
+          - plotly
+          - pandas
+          - tqdm
+          - requests
+          - gql
+          - graphql-core
+          - galois
+          - types-seaborn
+          - types-networkx
+          - pandas-stubs
+          - types-tqdm
+          - types-requests
+          - plotly-stubs
+          - scipy-stubs
+          - semver
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.34.0
+    rev: v1.37.1
     hooks:
       - id: typos
 

.readthedocs.yaml

@@ -7,14 +7,6 @@ version: 2
 # Set the OS, Python version, and other tools you might need
 build:
   os: ubuntu-24.04
-  tools:
-    python: "3.13"
   commands:
     - curl -sSf https://pixi.sh/install.sh | sh
-    - /home/docs/.pixi/bin/pixi run sphinx-build -T -b html -d _build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
-
-# Build documentation in the "docs/" directory with Sphinx
-sphinx:
-  builder: html
-  configuration: docs/conf.py
-  fail_on_warning: true
+    - /home/docs/.pixi/bin/pixi run sphinx-build -T -W -b html -d _build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html

CODEOWNERS

@@ -2,7 +2,7 @@
 # the repo. Unless a later match takes precedence,
 # @mdhaber will be requested for review when someone opens
 # a pull request.
-*                   @mdhaber
+*                   @nelimee
 
 # @KentonRL owns any file in deltakit-decode
 # directory anywhere in the repository.

CODE_OF_CONDUCT.md

@@ -14,20 +14,20 @@ diverse, inclusive, and healthy community.
 
 ## Our Standards
 
-Examples of behavior that contributes to a positive environment for our
+Examples of behaviour that contributes to a positive environment for our
 community include:
 
 * Demonstrating empathy and kindness toward other people
 * Being respectful of differing opinions, viewpoints, and experiences
 * Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
+* Accepting responsibility and apologising to those affected by our mistakes,
   and learning from the experience
 * Focusing on what is best not just for us as individuals, but for the
   overall community
 
-Examples of unacceptable behavior include:
+Examples of unacceptable behaviour include:
 
-* The use of sexualized language or imagery, and sexual attention or
+* The use of sexualised language or imagery, and sexual attention or
   advances of any kind
 * Trolling, insulting or derogatory comments, and personal or political attacks
 * Public or private harassment
@@ -39,8 +39,8 @@ Examples of unacceptable behavior include:
 ## Enforcement Responsibilities
 
 Community leaders are responsible for clarifying and enforcing our standards of
-acceptable behavior and will take appropriate and fair corrective action in
-response to any behavior that they deem inappropriate, threatening, offensive,
+acceptable behaviour and will take appropriate and fair corrective action in
+response to any behaviour that they deem inappropriate, threatening, offensive,
 or harmful.
 
 Community leaders have the right and responsibility to remove, edit, or reject
@@ -58,7 +58,7 @@ representative at an online or offline event.
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be
 reported to the community leaders responsible for enforcement at
 deltakit@riverlane.com.
 All complaints will be reviewed and investigated promptly and fairly.
@@ -73,19 +73,19 @@ the consequences for any action they deem in violation of this Code of Conduct:
 
 ### 1. Correction
 
-**Community Impact**: Use of inappropriate language or other behavior deemed
+**Community Impact**: Use of inappropriate language or other behaviour deemed
 unprofessional or unwelcome in the community.
 
 **Consequence**: A private, written warning from community leaders, providing
 clarity around the nature of the violation and an explanation of why the
-behavior was inappropriate. A public apology may be requested.
+behaviour was inappropriate. A public apology may be requested.
 
 ### 2. Warning
 
 **Community Impact**: A violation through a single incident or series
 of actions.
 
-**Consequence**: A warning with consequences for continued behavior. No
+**Consequence**: A warning with consequences for continued behaviour. No
 interaction with the people involved, including unsolicited interaction with
 those enforcing the Code of Conduct, for a specified period of time. This
 includes avoiding interactions in community spaces as well as external channels
@@ -95,7 +95,7 @@ permanent ban.
 ### 3. Temporary Ban
 
 **Community Impact**: A serious violation of community standards, including
-sustained inappropriate behavior.
+sustained inappropriate behaviour.
 
 **Consequence**: A temporary ban from any sort of interaction or public
 communication with the community for a specified period of time. No public or
@@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behaviour,  harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
 **Consequence**: A permanent ban from any sort of public interaction within