leapfrog-goals 0.0.1__tar.gz

leapfrog_goals-0.0.1/.gitignore

@@ -0,0 +1,12 @@
+*.pyc
+__pycache__
+.coverage*
+.idea
+.vscode
+.direnv
+.venv
+/dist
+docs/_build
+.mypy_cache
+.pytest_cache
+build

leapfrog_goals-0.0.1/.python-version

@@ -0,0 +1 @@
+3.13

leapfrog_goals-0.0.1/CMakeLists.txt

@@ -0,0 +1,18 @@
+cmake_minimum_required(VERSION 3.15...3.27)
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX)
+
+# Try to import all Python components potentially needed by nanobind
+find_package(Python 3.10
+  REQUIRED COMPONENTS Interpreter Development.Module
+  OPTIONAL_COMPONENTS Development.SABIModule)
+
+# Import nanobind through CMake's find_package mechanism
+find_package(nanobind CONFIG REQUIRED)
+
+# set C++ to require 20
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+nanobind_add_module(_core MODULE src/main.cpp)
+target_include_directories(_core PRIVATE ../leapfrog-core/include)
+install(TARGETS _core DESTINATION ${SKBUILD_PROJECT_NAME})

leapfrog_goals-0.0.1/LICENSE.txt

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2025-present Rob Ashton <robertashton94@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

leapfrog_goals-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: leapfrog-goals
+Version: 0.0.1
+Summary: Python interface for Leapfrog Goals model
+Author-Email: Rob Ashton <robertashton94@gmail.com>
+Project-URL: Documentation, https://github.com/hivtools/leapfrog#readme
+Project-URL: Issues, https://github.com/hivtools/leapfrog/issues
+Project-URL: Source, https://github.com/hivtools/leapfrog
+Requires-Python: >=3.10
+Requires-Dist: h5py>3.11.0
+Requires-Dist: numpy>1.24.4
+Description-Content-Type: text/markdown
+
+# goals
+
+## Installation (TODO)
+
+```bash
+pip install leapfrog-goals
+```
+
+## Usage
+
+
+### Get parameters
+
+In the following example you will need parameters - inputs to the model. We have provided utilities to easily get test parameters (we use hdf5 file format to store these). If you already have different parameters in the correct shape you can skip this section.
+
+```python
+from leapfrog_goals import read_h5_file
+
+parameters_child = read_h5_file("../leapfrogr/tests/testthat/testdata/child_parms_full.h5")
+```
+
+We need to add a good way to import the goals parameters, for now add manually.
+
+```python
+import numpy as np
+parameters_child["ex_input"] = np.full((81, 2), 1)
+```
+
+
+### Run model
+
+Here are a couple of ways to run the model
+
+```python
+from leapfrog_goals import run_goals
+
+# Run the model
+run_goals(parameters_child)
+
+# Can specify which years to output from the model
+run_goals(parameters_child, [1970, 1971, 2000])
+```
+
+
+### Run model from initial state (TODO)
+
+You can also run the model from an initial state. For example, to run the model in two parts
+
+```python
+from leapfrog_goals import run_goals, run_goals_from_state, get_time_slice
+
+# Run model until year 2000
+ret = run_goals(parameters_child, range(1970, 2001))
+
+run_goals_from_state(
+    # parameters
+    parameters_child,
+
+    # get the last time slice of the state returned by run model so we
+    # can continue from where the model left off
+    get_time_slice(ret, 30),
+
+    # simulation start year, this should be the year the previous
+    # argument represents
+    2000,
+
+    # years you want the model to output
+    range(2001, 2031)
+)
+```
+
+
+### Run model for a single year
+
+The previous two functions will return a dictionary with values that are have one more
+dimension (time dimension) than the state specified in the [model config](../leapfrog-core/model_schemas/configs/DpConfig.json). This means if you want to carry on from that initial single year state you would have to use the `get_time_slice` utility at index 1. Example:
+
+```python
+from leapfrog_goals import run_goals, run_goals_from_state, get_time_slice
+
+ret_single_year = run_goals(parameters_child, [1970])
+
+for year in range(1970, 2030):
+    ret_single_year = run_goals_from_state(
+        parameters_child,
+        get_time_slice(ret_single_year, 0),
+        year,
+        [year + 1]
+    )
+```
+
+This is tedious for two reasons:
+1. Repeatedly getting the time slice for one time dimension (initial one is unavoidable since we use run model and don't have any initial state)
+1. Specifying output year as `year + 1`
+
+So to make projecting for a single year more ergonomic we decided to create a separate function
+that returns the time slice for a single year:
+
+```python
+from leapfrog_goals import run_goals, run_goals_single_year, get_time_slice
+
+ret_single_year = get_time_slice(run_goals(parameters_child, [1970]), 0)
+
+for year in range(1970, 2030):
+    ret_single_year = run_goals_single_year(
+        parameters_child,
+        ret_single_year,
+        year
+    )
+```
+
+## Development
+
+This project uses [scikit-build-core](https://github.com/scikit-build/scikit-build-core) with [nanobind](https://github.com/wjakob/nanobind) to build the C++ project. You'll need a recent version of CMake (>3.15) and Python (>3.7).
+
+We use [uv](https://docs.astral.sh/uv/) to manage the project:
+* Sync the virtual env `uv sync`
+* Run tests `uv run pytest`
+* Lint `uvx ruff check .`
+* Format `uvx ruff format`
+* Format imports  `uvx ruff check --select I --fix`
+
+uv will rebuild automatically if you make a change to the C++ code however if you need to force recompilation use `--reinstall-package leapfrog-goals`.
+
+For local installation run `pip install .`
+
+## License
+
+`leapfrog-goals` is distributed under the terms of [MIT](https://spdx.org/licenses/MIT.html) license.

leapfrog_goals-0.0.1/README.md

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+# goals
+
+## Installation (TODO)
+
+```bash
+pip install leapfrog-goals
+```
+
+## Usage
+
+
+### Get parameters
+
+In the following example you will need parameters - inputs to the model. We have provided utilities to easily get test parameters (we use hdf5 file format to store these). If you already have different parameters in the correct shape you can skip this section.
+
+```python
+from leapfrog_goals import read_h5_file
+
+parameters_child = read_h5_file("../leapfrogr/tests/testthat/testdata/child_parms_full.h5")
+```
+
+We need to add a good way to import the goals parameters, for now add manually.
+
+```python
+import numpy as np
+parameters_child["ex_input"] = np.full((81, 2), 1)
+```
+
+
+### Run model
+
+Here are a couple of ways to run the model
+
+```python
+from leapfrog_goals import run_goals
+
+# Run the model
+run_goals(parameters_child)
+
+# Can specify which years to output from the model
+run_goals(parameters_child, [1970, 1971, 2000])
+```
+
+
+### Run model from initial state (TODO)
+
+You can also run the model from an initial state. For example, to run the model in two parts
+
+```python
+from leapfrog_goals import run_goals, run_goals_from_state, get_time_slice
+
+# Run model until year 2000
+ret = run_goals(parameters_child, range(1970, 2001))
+
+run_goals_from_state(
+    # parameters
+    parameters_child,
+
+    # get the last time slice of the state returned by run model so we
+    # can continue from where the model left off
+    get_time_slice(ret, 30),
+
+    # simulation start year, this should be the year the previous
+    # argument represents
+    2000,
+
+    # years you want the model to output
+    range(2001, 2031)
+)
+```
+
+
+### Run model for a single year
+
+The previous two functions will return a dictionary with values that are have one more
+dimension (time dimension) than the state specified in the [model config](../leapfrog-core/model_schemas/configs/DpConfig.json). This means if you want to carry on from that initial single year state you would have to use the `get_time_slice` utility at index 1. Example:
+
+```python
+from leapfrog_goals import run_goals, run_goals_from_state, get_time_slice
+
+ret_single_year = run_goals(parameters_child, [1970])
+
+for year in range(1970, 2030):
+    ret_single_year = run_goals_from_state(
+        parameters_child,
+        get_time_slice(ret_single_year, 0),
+        year,
+        [year + 1]
+    )
+```
+
+This is tedious for two reasons:
+1. Repeatedly getting the time slice for one time dimension (initial one is unavoidable since we use run model and don't have any initial state)
+1. Specifying output year as `year + 1`
+
+So to make projecting for a single year more ergonomic we decided to create a separate function
+that returns the time slice for a single year:
+
+```python
+from leapfrog_goals import run_goals, run_goals_single_year, get_time_slice
+
+ret_single_year = get_time_slice(run_goals(parameters_child, [1970]), 0)
+
+for year in range(1970, 2030):
+    ret_single_year = run_goals_single_year(
+        parameters_child,
+        ret_single_year,
+        year
+    )
+```
+
+## Development
+
+This project uses [scikit-build-core](https://github.com/scikit-build/scikit-build-core) with [nanobind](https://github.com/wjakob/nanobind) to build the C++ project. You'll need a recent version of CMake (>3.15) and Python (>3.7).
+
+We use [uv](https://docs.astral.sh/uv/) to manage the project:
+* Sync the virtual env `uv sync`
+* Run tests `uv run pytest`
+* Lint `uvx ruff check .`
+* Format `uvx ruff format`
+* Format imports  `uvx ruff check --select I --fix`
+
+uv will rebuild automatically if you make a change to the C++ code however if you need to force recompilation use `--reinstall-package leapfrog-goals`.
+
+For local installation run `pip install .`
+
+## License
+
+`leapfrog-goals` is distributed under the terms of [MIT](https://spdx.org/licenses/MIT.html) license.

leapfrog_goals-0.0.1/pyproject.toml

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+[project]
+name = "leapfrog-goals"
+version = "0.0.1"
+description = "Python interface for Leapfrog Goals model"
+readme = "README.md"
+authors = [
+    { name = "Rob Ashton", email = "robertashton94@gmail.com" }
+]
+requires-python = ">=3.10"
+dependencies = [
+    "h5py>3.11.0",
+    "numpy>1.24.4",
+]
+
+[project.urls]
+Documentation = "https://github.com/hivtools/leapfrog#readme"
+Issues = "https://github.com/hivtools/leapfrog/issues"
+Source = "https://github.com/hivtools/leapfrog"
+
+[tool.scikit-build]
+minimum-version = "build-system.requires"
+build-dir = "build/{wheel_tag}"
+build.verbose = false
+cmake.build-type = "Release"
+install.strip = true
+
+[build-system]
+requires = ["scikit-build-core>=0.10", "nanobind>=1.3.2"]
+build-backend = "scikit_build_core.build"
+
+[dependency-groups]
+dev = [
+    "deepdiff>=8.4.2",
+    "docopt>=0.6.2",
+    "pytest>=8.3.5",
+]
+
+# Needed for full C++17 support on macOS
+[tool.cibuildwheel.macos.environment]
+MACOSX_DEPLOYMENT_TARGET = "10.14"
+
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+]

leapfrog_goals-0.0.1/src/leapfrog_goals/__init__.py

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+from typing import TypeAlias, Union, cast
+
+import h5py
+import numpy as np
+from h5py._hl.dataset import Dataset
+
+from leapfrog_goals._core import (
+    get_goals_ss_py,
+    run_base_model,
+    run_base_model_from_state,
+    run_base_model_single_year,
+)
+
+LeapfrogParameters: TypeAlias = dict[str, Union[np.ndarray, int, float]]
+LeapfrogDataSingleYear: TypeAlias = LeapfrogParameters
+LeapfrogData: TypeAlias = dict[str, np.ndarray]
+LeapfrogRange: TypeAlias = Union[range, list]
+LeapfrogStateSpace: TypeAlias = dict[str, int | float]
+
+
+def read_h5_file(file_path: str) -> LeapfrogParameters:
+    ret = {}
+    f = h5py.File(file_path, "r")
+    for key in list(f.keys()):
+        dset = cast(Dataset, f[key])
+        if dset.size == 1:
+            val = dset[0]
+            if isinstance(val, bytes):
+                ret[key] = val.decode("utf-8")
+            else:
+                ret[key] = val
+        else:
+            ret[key] = np.transpose(np.array(f[key]))
+    f.close()
+    return ret
+
+
+def save_h5_file(dat: Union[LeapfrogParameters, LeapfrogData], file_path: str) -> None:
+    f = h5py.File(file_path, "w")
+    for key in list(dat.keys()):
+        arr = dat[key]
+        if isinstance(arr, np.ndarray):
+            f.create_dataset(key, data=np.transpose(arr))
+        else:
+            f[key] = dat[key]
+    f.close()
+
+
+def get_time_slice(state: LeapfrogData, index: int) -> LeapfrogDataSingleYear:
+    return {
+        k: v[..., index] if v.ndim > 1 else v[index].item() for (k, v) in state.items()
+    }
+
+
+def concat_on_time_dim(state1, state2):
+    return {k: np.concatenate((state1[k], state2[k]), axis=-1) for k in state1.keys()}
+
+
+def run_goals(
+    parameters: LeapfrogParameters,
+    output_years: LeapfrogRange = range(1970, 2031),
+):
+    return run_base_model(parameters, output_years)
+
+
+def run_goals_from_state(
+    parameters: LeapfrogParameters,
+    initial_state: LeapfrogDataSingleYear,
+    simulation_start_year: int,
+    output_years: LeapfrogRange = range(1970, 2031),
+):
+    return run_base_model_from_state(
+        parameters, initial_state, simulation_start_year, output_years
+    )
+
+
+def run_goals_single_year(
+    parameters: LeapfrogParameters,
+    initial_state: LeapfrogDataSingleYear,
+    simulation_start_year: int,
+):
+    return run_base_model_single_year(parameters, initial_state, simulation_start_year)
+
+
+def get_goals_ss(configuration: str) -> LeapfrogStateSpace:
+    return get_goals_ss_py(configuration)

leapfrog_goals-0.0.1/src/leapfrog_goals/_core.pyi

@@ -0,0 +1,23 @@
+from leapfrog_goals import (
+    LeapfrogData,
+    LeapfrogDataSingleYear,
+    LeapfrogParameters,
+    LeapfrogRange,
+    LeapfrogStateSpace,
+)
+
+def run_base_model(
+    parameters: LeapfrogParameters, output_years: LeapfrogRange
+) -> LeapfrogData: ...
+def run_base_model_from_state(
+    parameters: LeapfrogParameters,
+    initial_state: LeapfrogDataSingleYear,
+    simulation_start_year: int,
+    output_years: LeapfrogRange,
+) -> LeapfrogData: ...
+def run_base_model_single_year(
+    parameters: LeapfrogParameters,
+    initial_state: LeapfrogDataSingleYear,
+    simulation_start_year: int,
+) -> LeapfrogDataSingleYear: ...
+def get_leapfrog_ss_py(configuration: str) -> LeapfrogStateSpace: ...

leapfrog_goals-0.0.1/src/main.cpp

@@ -0,0 +1,53 @@
+#include "../../leapfrog-core/include/leapfrog_py.hpp"
+
+template<typename ...Args>
+auto sim_model(Args&&... args) {
+  return simulate_model<leapfrog::Goals>(std::forward<Args>(args)...);
+};
+
+
+nb::dict run_base_model(
+  const nb::dict parameters,
+  const std::vector<int> output_years
+) {
+  return sim_model(parameters, output_years);
+}
+
+nb::dict run_base_model_from_state(
+  const nb::dict parameters,
+  const nb::dict initial_state,
+  int simulation_start_year,
+  const std::vector<int> output_years
+) {
+  return sim_model(parameters, output_years, initial_state, simulation_start_year);
+}
+
+nb::dict run_base_model_single_year(
+  const nb::dict parameters,
+  const nb::dict initial_state,
+  int simulation_start_year
+) {
+  return sim_model(parameters, initial_state, simulation_start_year);
+}
+
+
+nb::dict get_leapfrog_ss() {
+  return leapfrog::get_ss_py<leapfrog::Goals>();
+}
+
+NB_MODULE(_core, m) {
+  m.doc() = "Leapfrog-Goals python interface";
+
+  m.def("run_base_model", &run_base_model, R"pbdoc(
+      Run the goals model.
+  )pbdoc");
+  m.def("run_base_model_from_state", &run_base_model_from_state, R"pbdoc(
+      Run the goals model from an initial state.
+  )pbdoc");
+  m.def("run_base_model_single_year", &run_base_model_single_year, R"pbdoc(
+      Run the goals model from an initial state for a single year.
+  )pbdoc");
+  m.def("get_goals_ss_py", &get_leapfrog_ss, R"pbdoc(
+    Get the state space dimensions for the Goals model,
+  )pbdoc");
+}

leapfrog_goals-0.0.1/tests/test_goals.py

@@ -0,0 +1,63 @@
+import numpy as np
+from deepdiff import DeepDiff
+
+from leapfrog_goals import (
+    read_h5_file,
+    run_goals,
+)
+
+
+def assert_equal(obj1, obj2):
+    assert len(DeepDiff(obj1, obj2, ignore_nan_inequality=True)) == 0
+
+
+def test_goals_model():
+    parameters = read_h5_file(
+        "../leapfrogr/tests/testthat/testdata/child_parms_full.h5"
+    )
+    parameters["ex_input"] = np.full((81, 2), 1)
+    ret = run_goals(parameters)
+    returned_vars = list(ret.keys())
+    expected_vars = [
+        "p_totpop",
+        "births",
+        "p_deaths_background_totpop",
+        "p_hivpop",
+        "p_deaths_background_hivpop",
+        "h_hivpop",
+        "h_artpop",
+        "h_hiv_deaths_no_art",
+        "p_infections",
+        "h_hiv_deaths_art",
+        "h_art_initiation",
+        "h_deaths_excess_nonaids_no_art",
+        "h_deaths_excess_nonaids_on_art",
+        "p_deaths_excess_nonaids",
+        "p_hiv_deaths",
+        "p_net_migration_hivpop",
+        "hiv_births",
+        "hiv_births_by_mat_age",
+        "prevalence_15to49_hts",
+        "incidence_15to49_hts",
+        "artcoverage_15to49_hts",
+        "hc1_hivpop",
+        "hc2_hivpop",
+        "hc1_artpop",
+        "hc2_artpop",
+        "hc1_noart_aids_deaths",
+        "hc2_noart_aids_deaths",
+        "hc1_art_aids_deaths",
+        "hc2_art_aids_deaths",
+        "hc_art_init",
+        "hc_art_need_init",
+        "ctx_need",
+        "infection_by_type",
+        "mtct_by_source_tr",
+        "mtct_by_source_women",
+        "mtct_by_source_hc_infections",
+        "pmtct_coverage_at_delivery",
+        "ex_output",
+    ]
+    returned_vars.sort()
+    expected_vars.sort()
+    assert_equal(returned_vars, expected_vars)

leapfrog_goals-0.0.1/uv.lock

@@ -0,0 +1,407 @@
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+resolution-markers = [
+    "python_full_version >= '3.11'",
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+]
+
+[[package]]
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