sciris 3.2.8__tar.gz → 3.3.0__tar.gz

sciris-3.3.0/.claude-plugin/marketplace.json

@@ -0,0 +1,18 @@
+{
+  "name": "sciris-marketplace",
+  "owner": {
+    "name": "Sciris"
+  },
+  "metadata": {
+    "description": "Sciris skills for Claude Code"
+  },
+  "plugins": [
+    {
+      "name": "sciris",
+      "source": "./claude_plugin",
+      "description": "Skills covering all Sciris features: arrays, dicts, files, plotting, parallelization, dates, printing, utilities, and advanced features",
+      "version": "0.1.0",
+      "keywords": ["sciris", "scientific-python"]
+    }
+  ]
+}

sciris-3.3.0/.github/workflows/publish_docs.yaml

@@ -0,0 +1,44 @@
+# Note: this workflow only runs manually or on pushes to tagged versions.
+
+name: Publish docs
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+jobs:
+  publish:
+    name: Quarto
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+
+    - name: Install Sciris
+      run: |
+        pip install -e .
+        pip install -r docs/requirements.txt
+
+    - name: Set up Quarto
+      uses: quarto-dev/quarto-actions/setup@v2
+
+    - name: Install Quarto interlinks
+      working-directory: ./docs
+      run: quarto add sciris/quartopydoc --no-prompt
+
+    - name: Publish docs
+      working-directory: ./docs
+      run: |
+        git config --global user.name "github-actions"
+        git config --global user.email "github-actions@users.noreply.github.com"
+        ./publish

{sciris-3.2.8 → sciris-3.3.0}/.github/workflows/schedule_tests.yaml

@@ -1,8 +1,9 @@
 name: Sciris cron tests
 on:
+  workflow_call:
   workflow_dispatch:
   schedule:
-    - cron: "0 0 * * *" # Run every day at midnight
+    - cron: "0 12 * * *" # Run every day at noon
 
 jobs:
   ci-tests:

sciris-3.3.0/.github/workflows/test_docs.yaml

@@ -0,0 +1,40 @@
+# Test that the docs build successfully on pushes to main and PRs targeting main.
+
+name: Test docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Render
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+
+    - name: Install Sciris
+      run: |
+        pip install -e .
+        pip install -r docs/requirements.txt
+
+    - name: Set up Quarto
+      uses: quarto-dev/quarto-actions/setup@v2
+
+    - name: Install Quarto interlinks
+      working-directory: ./docs
+      run: quarto add sciris/quartopydoc --no-prompt
+
+    - name: Render docs
+      working-directory: ./docs
+      run: ./render

{sciris-3.2.8 → sciris-3.3.0}/.github/workflows/test_downstream.yaml

@@ -1,6 +1,7 @@
-name: Sciris downstream tests
+name: Downstream
 on:
   workflow_dispatch:
+  workflow_call:
   push:
     branches:
       - main
@@ -32,16 +33,12 @@ jobs:
       - name: Check out Covasim
         uses: actions/checkout@v2
         with:
-          repository: 'institutefordiseasemodeling/covasim'
+          repository: 'starsimhub/covasim'
           path: 'covasim'
 
       - name: Install Covasim
         working-directory: ./covasim
-        run: pip install -e .
-
-      - name: Install Covasim tests
-        working-directory: ./covasim/tests
-        run: pip install -r requirements_test.txt
+        run: pip install -e .[test]
 
       - name: Run Covasim tests
         working-directory: ./covasim/tests
@@ -78,13 +75,17 @@ jobs:
       - name: Check out HPVsim
         uses: actions/checkout@v2
         with:
-          repository: 'institutefordiseasemodeling/hpvsim'
+          repository: 'starsimhub/hpvsim'
           path: 'hpvsim'
 
       - name: Install HPVsim
         working-directory: ./hpvsim
         run: pip install -e .
 
+      - name: Download HPVsim data
+        working-directory: ./hpvsim
+        run: hpvsim-download-data
+
       - name: Install HPVsim tests
         working-directory: ./hpvsim/tests
         run: pip install -r requirements.txt
@@ -184,4 +185,4 @@ jobs:
         if: always()
         with:
           name: test_results
-          path: atomica/tests/atomica-test-results.xml
+          path: atomica/tests/atomica-test-results.xml

{sciris-3.2.8 → sciris-3.3.0}/.github/workflows/test_sciris.yaml

@@ -1,6 +1,7 @@
-name: Sciris CI tests
+name: Sciris CI
 on:
   workflow_dispatch:
+  workflow_call:
   pull_request:
 
 jobs:
@@ -12,7 +13,7 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python-version: '3.9'
+            python-version: '3.10'
           - os: ubuntu-latest
             python-version: '3.13'
           - os: ubuntu-latest
@@ -22,7 +23,8 @@ jobs:
           - os: macos-latest
             python-version: '3.13'
     runs-on: ${{ matrix.os }}
-    name: CI tests
+
+    name: Tests
     steps:
       - name: Checkout sources
         uses: actions/checkout@v2

{sciris-3.2.8 → sciris-3.3.0}/.gitignore

@@ -66,8 +66,8 @@ instance/
 # Scrapy stuff:
 .scrapy
 
-# Sphinx documentation
-docs/_build/
+# Quarto documentation
+docs/_site/
 
 # PyBuilder
 target/

sciris-3.3.0/.pytest_cache/README.md

@@ -0,0 +1,8 @@
+# pytest cache directory #
+
+This directory contains data from the pytest's cache plugin,
+which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
+
+**Do not** commit this to version control.
+
+See [the docs](https://docs.pytest.org/en/latest/cache.html) for more information.