From 081dbc16a4c58b0cd8f49bf606ebf6d4548fd877 Mon Sep 17 00:00:00 2001
From: update-deploy-bot <you@example.com>
Date: Wed, 7 Jan 2026 20:44:59 +0000
Subject: [PATCH 1/2] updating manifest.json and requirements.txt

---
 manifest.json      | 245 +++++++++++++++++++++++++++++++++++++++++++++
 metapop/version.py |   8 ++
 requirements.txt   | 153 ++++++++++++++++++++++++++++
 3 files changed, 406 insertions(+)
 create mode 100644 manifest.json
 create mode 100644 metapop/version.py
 create mode 100644 requirements.txt

diff --git a/manifest.json b/manifest.json
new file mode 100644
index 0000000..8f04f59
--- /dev/null
+++ b/manifest.json
@@ -0,0 +1,245 @@
+{
+  "version": 1,
+  "locale": "en_US.UTF-8",
+  "metadata": {
+    "appmode": "python-streamlit",
+    "entrypoint": "app"
+  },
+  "python": {
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+    "package_manager": {
+      "name": "pip",
+      "version": "25.3",
+      "package_file": "requirements.txt"
+    }
+  },
+  "environment": {
+    "python": {
+      "requires": "~=3.10.0"
+    }
+  },
+  "files": {
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+    },
+    ".github/CODEOWNERS": {
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+    },
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+    },
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+    },
+    ".github/ISSUE_TEMPLATE/scientific-improvement.md": {
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+    },
+    ".github/actions/pre-commit/action.yaml": {
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+    },
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+    },
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+    },
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+    },
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+    },
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+    },
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+    },
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+    },
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+      "checksum": "9ad5683b5439b9fd311ac4531c0ee607"
+    },
+    "LICENSE": {
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+    },
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+    },
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+    },
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+    },
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+    },
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+    },
+    "poetry.lock": {
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+    },
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+    },
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+    },
+    "scripts/comparison/comparison_config.yaml": {
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+    },
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+    },
+    "scripts/connectivity/config.yaml": {
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+    },
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+    },
+    "scripts/extract_to_docx/extract_to_docx.py": {
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+    },
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+    },
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+    },
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+    },
+    "scripts/misc/baseline_immunity_sketch.ipynb": {
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+    },
+    "scripts/misc/example_new_beta_calculation.py": {
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+    },
+    "scripts/misc/immunity_interpolation.py": {
+      "checksum": "9a364b2f5cfb4e082f30a4dbd2ab71d8"
+    },
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+    },
+    "scripts/misc/make_plots.qmd": {
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+    },
+    "scripts/misc/run_abc.py": {
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+    },
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+    },
+    "scripts/one_pop/one_pop_plots.R": {
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+    },
+    "scripts/one_pop/one_pop_simulate.py": {
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+    },
+    "scripts/timing/timing_config.yaml": {
+      "checksum": "70a9186688fba83f236e0a4673e8c886"
+    },
+    "scripts/timing/timing_results_post_processing.R": {
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+    },
+    "scripts/timing/timing_simulate.py": {
+      "checksum": "428a75b802f6a6e152a69fa2f0411fa4"
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+    },
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+    },
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+    },
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+    },
+    "tests/test_vaccine_schedules.py": {
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+    }
+  }
+}
diff --git a/metapop/version.py b/metapop/version.py
new file mode 100644
index 0000000..09158a8
--- /dev/null
+++ b/metapop/version.py
@@ -0,0 +1,8 @@
+# This file is automatically generated by the Makefile.
+# Do not edit this file directly.
+# This file contains the version information for the metapop package.
+__all__ = ["__version__", "__versiondate__", "__git_commit__"]
+
+__version__ = "1.0.2"
+__versiondate__ = "2026-01-07"
+__git_commit__ = "75073745348f3fa25002223069281c49531364e6"  # pragma: allowlist secret
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..06e45f0
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,153 @@
+altair==5.5.0
+anyio==4.12.1
+argon2-cffi==25.1.0
+argon2-cffi-bindings==25.1.0
+arrow==1.4.0
+asttokens==3.0.1
+async-lru==2.0.5
+attrs==25.4.0
+babel==2.17.0
+beautifulsoup4==4.14.3
+bleach==6.3.0
+blinker==1.9.0
+bs4==0.0.2
+build==1.3.0
+cachetools==6.2.4
+certifi==2026.1.4
+cffi==2.0.0
+cfgv==3.5.0
+charset-normalizer==3.4.4
+click==8.3.1
+comm==0.2.3
+contourpy==1.3.2
+cycler==0.12.1
+debugpy==1.8.19
+decorator==5.2.1
+defusedxml==0.7.1
+detect-secrets==1.5.0
+distlib==0.4.0
+exceptiongroup==1.3.1
+executing==2.2.1
+fastjsonschema==2.21.2
+filelock==3.20.2
+fonttools==4.61.1
+fqdn==1.5.1
+gitdb==4.0.12
+GitPython==3.1.46
+greenlet==3.3.0
+griddler @ git+https://github.com/CDCgov/pygriddler.git@cb52684efa4e54df092a7364a0d7198ef9f39a9c
+h11==0.16.0
+httpcore==1.0.9
+httpx==0.28.1
+identify==2.6.15
+idna==3.11
+iniconfig==2.3.0
+ipykernel==6.31.0
+ipython==8.38.0
+ipywidgets==8.1.8
+isoduration==20.11.0
+jedi==0.19.2
+Jinja2==3.1.6
+json5==0.13.0
+jsonpointer==3.0.0
+jsonschema==4.26.0
+jsonschema-specifications==2025.9.1
+jupyter==1.1.1
+jupyter-console==6.6.3
+jupyter-events==0.12.0
+jupyter-lsp==2.3.0
+jupyter_client==8.7.0
+jupyter_core==5.9.1
+jupyter_server==2.17.0
+jupyter_server_terminals==0.5.3
+jupyterlab==4.5.1
+jupyterlab_pygments==0.3.0
+jupyterlab_server==2.28.0
+jupyterlab_widgets==3.0.16
+kiwisolver==1.4.9
+lark==1.3.1
+MarkupSafe==3.0.3
+matplotlib==3.10.8
+matplotlib-inline==0.2.1
+mistune==3.2.0
+narwhals==2.15.0
+nbclient==0.10.4
+nbconvert==7.16.6
+nbformat==5.10.4
+nest-asyncio==1.6.0
+nodeenv==1.10.0
+notebook==7.5.1
+notebook_shim==0.2.4
+numpy==2.2.6
+overrides==7.7.0
+packaging==25.0
+pandas==2.3.3
+pandocfilters==1.5.1
+parso==0.8.5
+pexpect==4.9.0
+pillow==11.3.0
+platformdirs==4.5.1
+playwright==1.57.0
+pluggy==1.6.0
+polars==1.36.1
+polars-runtime-32==1.36.1
+pre_commit==4.5.1
+progressbar2==4.5.0
+prometheus_client==0.23.1
+prompt_toolkit==3.0.52
+protobuf==6.33.2
+psutil==7.2.1
+ptyprocess==0.7.0
+pure_eval==0.2.3
+pyarrow==19.0.1
+pycparser==2.23
+pydeck==0.9.1
+pyee==13.0.0
+Pygments==2.19.2
+PyJWT==2.10.1
+pypandoc==1.16.2
+pyparsing==3.3.1
+pyproject_hooks==1.2.0
+pytest==8.4.2
+python-dateutil==2.9.0.post0
+python-json-logger==4.0.0
+python-utils==3.9.1
+pytz==2025.2
+PyYAML==6.0.3
+pyzmq==27.1.0
+referencing==0.37.0
+requests==2.32.5
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rfc3987-syntax==1.1.0
+rpds-py==0.30.0
+rsconnect_python==1.28.2
+scipy==1.14.1
+seaborn==0.13.2
+semver==3.0.4
+Send2Trash==2.0.0
+six==1.17.0
+smmap==5.0.2
+soupsieve==2.8.1
+st-flexible-callout-elements==0.1.0
+stack-data==0.6.3
+streamlit @ https://github.com/k88hudson-cfa/streamlit/releases/download/v1.46.1-508.5/streamlit-1.46.1-py3-none-any.whl
+tenacity==9.1.2
+terminado==0.18.1
+tinycss2==1.4.0
+toml==0.10.2
+tomli==2.3.0
+tornado==6.5.4
+traitlets==5.14.3
+typing_extensions==4.15.0
+tzdata==2025.3
+uri-template==1.3.0
+urllib3==2.6.3
+virtualenv==20.36.0
+watchdog==6.0.0
+wcwidth==0.2.14
+webcolors==25.10.0
+webencodings==0.5.1
+websocket-client==1.9.0
+widgetsnbextension==4.0.15
+metapop==1.0.2

From e68aa689c22ae42d4c0d396b6505b0cd316f82b2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 20 Feb 2026 15:57:10 +0000
Subject: [PATCH 2/2] Bump protobuf from 6.31.1 to 6.33.5

Bumps [protobuf](https://github.com/protocolbuffers/protobuf) from 6.31.1 to 6.33.5.
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Commits](https://github.com/protocolbuffers/protobuf/commits)

---
updated-dependencies:
- dependency-name: protobuf
  dependency-version: 6.33.5
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 06e45f0..192094f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -95,7 +95,7 @@ pre_commit==4.5.1
 progressbar2==4.5.0
 prometheus_client==0.23.1
 prompt_toolkit==3.0.52
-protobuf==6.33.2
+protobuf==6.33.5
 psutil==7.2.1
 ptyprocess==0.7.0
 pure_eval==0.2.3