kernelmix 0.3.0__tar.gz → 0.3.1__tar.gz

{kernelmix-0.3.0 → kernelmix-0.3.1}/CHANGELOG.md

@@ -1,15 +1,18 @@
 # Changelog
 
-## Unreleased
+## 0.3.1
+
+- Use complete documentation and image URLs in the PyPI description.
+- Add the PyPI installation command to the guides and reference manual.
+
+## 0.3.0
 
 - Add reproducible fitted-posterior comparisons with R and independent extension checks.
 - Add searchable documentation with grouped API pages and common questions.
 
 - Clarify model support, priors and notation; connect the guides and reference manual around analysis tasks.
 - Add a reproducible public-data ozone example, saved results and residual plots.
-- Document original-study gaps and platform verification limits.
-
-## 0.3.0
+- Document original-study gaps and platform verification.
 
 - Matérn 3/2 and rational-quadratic kernels; predictive-process and random-Fourier GP bases.
 - Random slopes with full covariance; Gaussian AR1, exponential and fixed residual correlations.

{kernelmix-0.3.0 → kernelmix-0.3.1}/CITATION.cff

@@ -2,7 +2,7 @@ cff-version: 1.2.0
 message: "Please cite KernelMix and the method papers listed in the README."
 title: "KernelMix: Bayesian kernel machine regression for exposure mixtures"
 type: software
-version: 0.3.0
+version: 0.3.1
 authors:
   - family-names: Chapagain
     given-names: Nilson

{kernelmix-0.3.0 → kernelmix-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kernelmix
-Version: 0.3.0
+Version: 0.3.1
 Summary: Bayesian kernel machine regression for exposure mixtures
 Author: Nilson Chapagain
 License-Expression: GPL-2.0-only
@@ -36,27 +36,27 @@ To handle different outcome types, the package combines this exposure function w
 
 | Task | Start here |
 | --- | --- |
-| Choose an outcome model and priors | [Models and assumptions](docs/methods.md) |
-| Fit, inspect, predict and compare exposures | [Analysis tutorial](docs/tutorial.md) |
-| Model clusters, kernels or detailed survival records | [Structured models](docs/structured.md) |
-| Find arguments and result fields | [API reference](docs/api.md) |
-| Check numerical evidence and limitations | [Evidence](docs/reproduction.md) |
+| Choose an outcome model and priors | [Models and assumptions](https://nilson01.github.io/kernelmix/methods/) |
+| Fit, inspect, predict and compare exposures | [Analysis tutorial](https://nilson01.github.io/kernelmix/tutorial/) |
+| Model clusters, kernels or detailed survival records | [Structured models](https://nilson01.github.io/kernelmix/structured/) |
+| Find arguments and result fields | [API reference](https://nilson01.github.io/kernelmix/reference/) |
+| Check numerical evidence and limitations | [Evidence](https://nilson01.github.io/kernelmix/reproduction/) |
 
 ## Install
 
-Install directly from GitHub:
-
 ```sh
-python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@main"
+python -m pip install kernelmix
 ```
 
-Or, from a downloaded source folder:
+For plots, use `python -m pip install "kernelmix[plots]"`.
+
+Or install the released source directly from GitHub:
 
 ```sh
-python -m pip install ".[plots]"
+python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@v0.3.1"
 ```
 
-Python 3.10 or later is required. Omit `[plots]` if plots are not needed.
+Python 3.10 or later is required.
 
 ## Example
 
@@ -85,7 +85,7 @@ sigma2              0.2159    0.08346     0.1142     0.4188
 
 These short chains illustrate the output and trigger mixing warnings. For an analysis, use longer runs and inspect agreement between chains and effective sample sizes, which account for dependence between draws.
 
-![Exposure response curve with pointwise 95% credible intervals](docs/figures/response.png)
+![Exposure response curve with pointwise 95% credible intervals](https://nilson01.github.io/kernelmix/figures/response.png)
 
 The curve varies the first exposure with the second at its median, relative to the all-median exposure profile. It describes a fitted association; a causal interpretation requires additional assumptions.
 
@@ -93,10 +93,10 @@ The curve varies the first exposure with the second at its median, relative to t
 
 Browse the [searchable documentation](https://nilson01.github.io/kernelmix/).
 
-The [common questions](docs/faq.md) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](docs/airquality.md) includes source data and saved results. Download the [reference manual](docs/manual.pdf) for offline reading. Contributors can find [development checks](docs/development.md) separately.
+The [common questions](https://nilson01.github.io/kernelmix/faq/) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](https://nilson01.github.io/kernelmix/airquality/) includes source data and saved results. Download the [reference manual](https://nilson01.github.io/kernelmix/manual.pdf) for offline reading. Contributors can find [development checks](https://nilson01.github.io/kernelmix/development/) separately.
 
 ## References and license
 
-[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](docs/methods.md).
+[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](https://nilson01.github.io/kernelmix/methods/).
 
-We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](docs/reproduction.md) records results and limits. See [NOTICE](NOTICE) for attribution and [LICENSE](LICENSE) for GPL-2.0-only terms.
+We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](https://nilson01.github.io/kernelmix/reproduction/) records results and limits. See [NOTICE](https://github.com/nilson01/kernelmix/blob/main/NOTICE) for attribution and [LICENSE](https://github.com/nilson01/kernelmix/blob/main/LICENSE) for GPL-2.0-only terms.

{kernelmix-0.3.0 → kernelmix-0.3.1}/README.md

@@ -7,27 +7,27 @@ To handle different outcome types, the package combines this exposure function w
 
 | Task | Start here |
 | --- | --- |
-| Choose an outcome model and priors | [Models and assumptions](docs/methods.md) |
-| Fit, inspect, predict and compare exposures | [Analysis tutorial](docs/tutorial.md) |
-| Model clusters, kernels or detailed survival records | [Structured models](docs/structured.md) |
-| Find arguments and result fields | [API reference](docs/api.md) |
-| Check numerical evidence and limitations | [Evidence](docs/reproduction.md) |
+| Choose an outcome model and priors | [Models and assumptions](https://nilson01.github.io/kernelmix/methods/) |
+| Fit, inspect, predict and compare exposures | [Analysis tutorial](https://nilson01.github.io/kernelmix/tutorial/) |
+| Model clusters, kernels or detailed survival records | [Structured models](https://nilson01.github.io/kernelmix/structured/) |
+| Find arguments and result fields | [API reference](https://nilson01.github.io/kernelmix/reference/) |
+| Check numerical evidence and limitations | [Evidence](https://nilson01.github.io/kernelmix/reproduction/) |
 
 ## Install
 
-Install directly from GitHub:
-
 ```sh
-python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@main"
+python -m pip install kernelmix
 ```
 
-Or, from a downloaded source folder:
+For plots, use `python -m pip install "kernelmix[plots]"`.
+
+Or install the released source directly from GitHub:
 
 ```sh
-python -m pip install ".[plots]"
+python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@v0.3.1"
 ```
 
-Python 3.10 or later is required. Omit `[plots]` if plots are not needed.
+Python 3.10 or later is required.
 
 ## Example
 
@@ -56,7 +56,7 @@ sigma2              0.2159    0.08346     0.1142     0.4188
 
 These short chains illustrate the output and trigger mixing warnings. For an analysis, use longer runs and inspect agreement between chains and effective sample sizes, which account for dependence between draws.
 
-![Exposure response curve with pointwise 95% credible intervals](docs/figures/response.png)
+![Exposure response curve with pointwise 95% credible intervals](https://nilson01.github.io/kernelmix/figures/response.png)
 
 The curve varies the first exposure with the second at its median, relative to the all-median exposure profile. It describes a fitted association; a causal interpretation requires additional assumptions.
 
@@ -64,10 +64,10 @@ The curve varies the first exposure with the second at its median, relative to t
 
 Browse the [searchable documentation](https://nilson01.github.io/kernelmix/).
 
-The [common questions](docs/faq.md) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](docs/airquality.md) includes source data and saved results. Download the [reference manual](docs/manual.pdf) for offline reading. Contributors can find [development checks](docs/development.md) separately.
+The [common questions](https://nilson01.github.io/kernelmix/faq/) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](https://nilson01.github.io/kernelmix/airquality/) includes source data and saved results. Download the [reference manual](https://nilson01.github.io/kernelmix/manual.pdf) for offline reading. Contributors can find [development checks](https://nilson01.github.io/kernelmix/development/) separately.
 
 ## References and license
 
-[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](docs/methods.md).
+[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](https://nilson01.github.io/kernelmix/methods/).
 
-We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](docs/reproduction.md) records results and limits. See [NOTICE](NOTICE) for attribution and [LICENSE](LICENSE) for GPL-2.0-only terms.
+We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](https://nilson01.github.io/kernelmix/reproduction/) records results and limits. See [NOTICE](https://github.com/nilson01/kernelmix/blob/main/NOTICE) for attribution and [LICENSE](https://github.com/nilson01/kernelmix/blob/main/LICENSE) for GPL-2.0-only terms.

kernelmix-0.3.1/docs/installation.md

@@ -0,0 +1,23 @@
+# Installation
+
+Python 3.10 or later is required. KernelMix uses NumPy and SciPy; R is not required for fitting or prediction.
+
+## From PyPI
+
+```sh
+python -m pip install kernelmix
+```
+
+For plots, install Matplotlib through the plotting extra:
+
+```sh
+python -m pip install "kernelmix[plots]"
+```
+
+## From GitHub
+
+```sh
+python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@v0.3.1"
+```
+
+Start with the [analysis tutorial](tutorial.md) for fitting, diagnostics, prediction and exposure summaries. The [ozone example](airquality.md) includes observed data and saved results.

{kernelmix-0.3.0 → kernelmix-0.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "kernelmix"
-version = "0.3.0"
+version = "0.3.1"
 description = "Bayesian kernel machine regression for exposure mixtures"
 readme = "README.md"
 requires-python = ">=3.10"

{kernelmix-0.3.0 → kernelmix-0.3.1}/src/kernelmix/__init__.py

@@ -25,7 +25,7 @@ from .priors import Prior
 from .result import BKMRFit, Prediction, SurvivalPrediction
 from .structured_result import CompetingRiskPrediction, RandomCoefficientPrediction, StructuredFit
 
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 __all__ = [
     "StructuredFit", "RandomCoefficientPrediction", "CompetingRiskPrediction", "kernel_matrix",
     "fit", "Prior", "BKMRFit", "Prediction", "gaussian_kernel", "diagnose",

{kernelmix-0.3.0 → kernelmix-0.3.1}/src/kernelmix.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: kernelmix
-Version: 0.3.0
+Version: 0.3.1
 Summary: Bayesian kernel machine regression for exposure mixtures
 Author: Nilson Chapagain
 License-Expression: GPL-2.0-only
@@ -36,27 +36,27 @@ To handle different outcome types, the package combines this exposure function w
 
 | Task | Start here |
 | --- | --- |
-| Choose an outcome model and priors | [Models and assumptions](docs/methods.md) |
-| Fit, inspect, predict and compare exposures | [Analysis tutorial](docs/tutorial.md) |
-| Model clusters, kernels or detailed survival records | [Structured models](docs/structured.md) |
-| Find arguments and result fields | [API reference](docs/api.md) |
-| Check numerical evidence and limitations | [Evidence](docs/reproduction.md) |
+| Choose an outcome model and priors | [Models and assumptions](https://nilson01.github.io/kernelmix/methods/) |
+| Fit, inspect, predict and compare exposures | [Analysis tutorial](https://nilson01.github.io/kernelmix/tutorial/) |
+| Model clusters, kernels or detailed survival records | [Structured models](https://nilson01.github.io/kernelmix/structured/) |
+| Find arguments and result fields | [API reference](https://nilson01.github.io/kernelmix/reference/) |
+| Check numerical evidence and limitations | [Evidence](https://nilson01.github.io/kernelmix/reproduction/) |
 
 ## Install
 
-Install directly from GitHub:
-
 ```sh
-python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@main"
+python -m pip install kernelmix
 ```
 
-Or, from a downloaded source folder:
+For plots, use `python -m pip install "kernelmix[plots]"`.
+
+Or install the released source directly from GitHub:
 
 ```sh
-python -m pip install ".[plots]"
+python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@v0.3.1"
 ```
 
-Python 3.10 or later is required. Omit `[plots]` if plots are not needed.
+Python 3.10 or later is required.
 
 ## Example
 
@@ -85,7 +85,7 @@ sigma2              0.2159    0.08346     0.1142     0.4188
 
 These short chains illustrate the output and trigger mixing warnings. For an analysis, use longer runs and inspect agreement between chains and effective sample sizes, which account for dependence between draws.
 
-![Exposure response curve with pointwise 95% credible intervals](docs/figures/response.png)
+![Exposure response curve with pointwise 95% credible intervals](https://nilson01.github.io/kernelmix/figures/response.png)
 
 The curve varies the first exposure with the second at its median, relative to the all-median exposure profile. It describes a fitted association; a causal interpretation requires additional assumptions.
 
@@ -93,10 +93,10 @@ The curve varies the first exposure with the second at its median, relative to t
 
 Browse the [searchable documentation](https://nilson01.github.io/kernelmix/).
 
-The [common questions](docs/faq.md) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](docs/airquality.md) includes source data and saved results. Download the [reference manual](docs/manual.pdf) for offline reading. Contributors can find [development checks](docs/development.md) separately.
+The [common questions](https://nilson01.github.io/kernelmix/faq/) explain prediction scales, missing values, selection and diagnostics. The [observed ozone example](https://nilson01.github.io/kernelmix/airquality/) includes source data and saved results. Download the [reference manual](https://nilson01.github.io/kernelmix/manual.pdf) for offline reading. Contributors can find [development checks](https://nilson01.github.io/kernelmix/development/) separately.
 
 ## References and license
 
-[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](docs/methods.md).
+[Bobb et al. (2015)](https://doi.org/10.1093/biostatistics/kxu058) introduced BKMR for exposure-mixture analysis. [Bobb et al. (2018)](https://doi.org/10.1186/s12940-018-0413-y) described the R software and its binary-outcome extension. KernelMix implements these methods separately in Python and adds count and survival likelihoods, defined in the [model guide](https://nilson01.github.io/kernelmix/methods/).
 
-We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](docs/reproduction.md) records results and limits. See [NOTICE](NOTICE) for attribution and [LICENSE](LICENSE) for GPL-2.0-only terms.
+We compare selected Gaussian and probit posterior summaries and conditional calculations, including random intercepts, with installed R [`bkmr`](https://cran.r-project.org/package=bkmr) 0.2.2. The [evidence summary](https://nilson01.github.io/kernelmix/reproduction/) records results and limits. See [NOTICE](https://github.com/nilson01/kernelmix/blob/main/NOTICE) for attribution and [LICENSE](https://github.com/nilson01/kernelmix/blob/main/LICENSE) for GPL-2.0-only terms.

{kernelmix-0.3.0 → kernelmix-0.3.1}/tools/build_manual.py

@@ -42,6 +42,9 @@ def main():
                     url = (f'https://github.com/nilson01/kernelmix/blob/{options.revision}/'
                            + image.relative_to(root).as_posix())
                     text = text.replace(url, str(vector))
+                    text = text.replace(
+                        "https://nilson01.github.io/kernelmix/figures/" + image.name, str(vector)
+                    )
             # Keep short tables and code blocks with their immediate headings.
             def short_table(match):
                 heading, table = match.group(1) or '', match.group(2)

kernelmix-0.3.0/docs/installation.md

@@ -1,19 +0,0 @@
-# Installation
-
-Python 3.10 or later is required. KernelMix uses NumPy and SciPy; R is not required for fitting or prediction. Matplotlib is an optional plotting dependency.
-
-Install directly from GitHub:
-
-```sh
-python -m pip install "kernelmix[plots] @ git+https://github.com/nilson01/kernelmix.git@main"
-```
-
-Or, from a downloaded source folder:
-
-```sh
-python -m pip install ".[plots]"
-```
-
-Omit `[plots]` if plots are not needed.
-
-Start with the [analysis tutorial](tutorial.md). It explains the required arrays, fitting, diagnostics, prediction and exposure summaries. The [ozone example](airquality.md) includes observed data and saved results.