POMtool 100.0.0__tar.gz

pomtool-100.0.0/LICENSE.md

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+Copyright 2025 Ossi Noita
+
+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.

pomtool-100.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: POMtool
+Version: 100.0.0
+Summary: Scientific command line tool
+License: MIT
+Requires-Python: ==3.11.*
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy==2.3.2
+Requires-Dist: PyYAML==6.0.2
+Requires-Dist: scimath==5.0.0
+Requires-Dist: scipy==1.16.1
+Requires-Dist: traits==7.0.2
+Dynamic: license-file
+
+# POM tool
+
+## Description
+This is commpand line interface (CLI) tool to create population of model and calibrate your model. It can calculate biomarkers, and calibrate either your model or your population based on those parameters.
+
+## Installation
+There are few options how to start using POMtool.
+
+### pipx
+Using pipx you can download package and install it as command line interface. In addition, it is recommended to set your version
+```
+pipx install "POMtool~=100.0"
+```
+However, typically you do not have correct python version. as your default.
+
+POMtool version 100.0 requires python 3.11, so using python, so you would need to use 
+```
+pipx install --python <path/to/correct/python> "POMtool~=100.0"
+```
+
+For example, if you have python3.11 installed, you can use
+```
+pipx install --python python3.11 "POMtool~=100.0"
+```
+For pyenv installation, point to correct shim
+```
+pipx install --python ~/.pyenv/versions/3.11.11/bin/python "POMtool~=100.0"
+```
+
+### Clone
+Clone the repository and run inside the repository:
+```
+./POMtool.py run --help
+```
+
+To follow other examples, create alias for `POMtool`, or keep using `./POMtool.py` directly. For example with:
+```
+./POMtool.py run --help && alias POMtool="python $(pwd)/POMtool.py"
+```
+
+### pip
+Using pip is also possible. Just create virtual environment with correct python version. For most use cases, you should use `pipx` instead.
+
+## Using
+Use -h to get help-file for the CLI. Currently, this is only tested on python, newer python version might not work.
+
+Every config should describe model. This section describes how model you are interested can be run and how to input parameters to it.
+
+You have two options what to do with model, you can run POM-experiment (experiment), or model optimization (optimization).
+
+In POM-experiment first model is run for each set of parameters as described in `experiment`. After that `biomarkers` are calculated. With biomarkers, we can calibrate our population based on protocols described in `calibration`.
+
+In optimization, parameters are changed with goal to match biomarkers given as arguments. Biomarkers are calculated as given in `biomarkers` and `optimization` describes optimization process.
+
+To create your own config, check examples directory. All examples there are runnable (at moment of writing, only one example). 
+
+## Future
+* More ways to use the tool will be made available as the project progresses
+* Improvements to this document are added, as issues arise
+* More examples will be provided, and some example projects will be made public for best practices
+* Some thoughts can also be found from roadmap
+
+## Acknowledgements
+Initial production of this tool was partly funded by [SMASH-HCM](https://smash-hcm.eu/), which is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Education and Culture Executive Agency (EACEA). Neither the European Union nor EACEA can be held responsible for them.
+
+## Authors
+Ossi Noita - Original concept and current maintainer
+Olli Ylinen - Major contributions to optimization, biomarkers, and testing

pomtool-100.0.0/README.md

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+# POM tool
+
+## Description
+This is commpand line interface (CLI) tool to create population of model and calibrate your model. It can calculate biomarkers, and calibrate either your model or your population based on those parameters.
+
+## Installation
+There are few options how to start using POMtool.
+
+### pipx
+Using pipx you can download package and install it as command line interface. In addition, it is recommended to set your version
+```
+pipx install "POMtool~=100.0"
+```
+However, typically you do not have correct python version. as your default.
+
+POMtool version 100.0 requires python 3.11, so using python, so you would need to use 
+```
+pipx install --python <path/to/correct/python> "POMtool~=100.0"
+```
+
+For example, if you have python3.11 installed, you can use
+```
+pipx install --python python3.11 "POMtool~=100.0"
+```
+For pyenv installation, point to correct shim
+```
+pipx install --python ~/.pyenv/versions/3.11.11/bin/python "POMtool~=100.0"
+```
+
+### Clone
+Clone the repository and run inside the repository:
+```
+./POMtool.py run --help
+```
+
+To follow other examples, create alias for `POMtool`, or keep using `./POMtool.py` directly. For example with:
+```
+./POMtool.py run --help && alias POMtool="python $(pwd)/POMtool.py"
+```
+
+### pip
+Using pip is also possible. Just create virtual environment with correct python version. For most use cases, you should use `pipx` instead.
+
+## Using
+Use -h to get help-file for the CLI. Currently, this is only tested on python, newer python version might not work.
+
+Every config should describe model. This section describes how model you are interested can be run and how to input parameters to it.
+
+You have two options what to do with model, you can run POM-experiment (experiment), or model optimization (optimization).
+
+In POM-experiment first model is run for each set of parameters as described in `experiment`. After that `biomarkers` are calculated. With biomarkers, we can calibrate our population based on protocols described in `calibration`.
+
+In optimization, parameters are changed with goal to match biomarkers given as arguments. Biomarkers are calculated as given in `biomarkers` and `optimization` describes optimization process.
+
+To create your own config, check examples directory. All examples there are runnable (at moment of writing, only one example). 
+
+## Future
+* More ways to use the tool will be made available as the project progresses
+* Improvements to this document are added, as issues arise
+* More examples will be provided, and some example projects will be made public for best practices
+* Some thoughts can also be found from roadmap
+
+## Acknowledgements
+Initial production of this tool was partly funded by [SMASH-HCM](https://smash-hcm.eu/), which is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Education and Culture Executive Agency (EACEA). Neither the European Union nor EACEA can be held responsible for them.
+
+## Authors
+Ossi Noita - Original concept and current maintainer
+Olli Ylinen - Major contributions to optimization, biomarkers, and testing

pomtool-100.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "POMtool"
+version = "100.0.0"
+description = "Scientific command line tool"
+readme = "README.md"
+license = { text = "MIT" }
+
+requires-python = "==3.11.*"
+
+dependencies = [
+    "numpy==2.3.2",
+    "PyYAML==6.0.2",
+    "scimath==5.0.0",
+    "scipy==1.16.1",
+    "traits==7.0.2",
+]
+
+[project.scripts]
+POMtool = "pomtool.main:run"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]

pomtool-100.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

pomtool-100.0.0/src/POMtool.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: POMtool
+Version: 100.0.0
+Summary: Scientific command line tool
+License: MIT
+Requires-Python: ==3.11.*
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy==2.3.2
+Requires-Dist: PyYAML==6.0.2
+Requires-Dist: scimath==5.0.0
+Requires-Dist: scipy==1.16.1
+Requires-Dist: traits==7.0.2
+Dynamic: license-file
+
+# POM tool
+
+## Description
+This is commpand line interface (CLI) tool to create population of model and calibrate your model. It can calculate biomarkers, and calibrate either your model or your population based on those parameters.
+
+## Installation
+There are few options how to start using POMtool.
+
+### pipx
+Using pipx you can download package and install it as command line interface. In addition, it is recommended to set your version
+```
+pipx install "POMtool~=100.0"
+```
+However, typically you do not have correct python version. as your default.
+
+POMtool version 100.0 requires python 3.11, so using python, so you would need to use 
+```
+pipx install --python <path/to/correct/python> "POMtool~=100.0"
+```
+
+For example, if you have python3.11 installed, you can use
+```
+pipx install --python python3.11 "POMtool~=100.0"
+```
+For pyenv installation, point to correct shim
+```
+pipx install --python ~/.pyenv/versions/3.11.11/bin/python "POMtool~=100.0"
+```
+
+### Clone
+Clone the repository and run inside the repository:
+```
+./POMtool.py run --help
+```
+
+To follow other examples, create alias for `POMtool`, or keep using `./POMtool.py` directly. For example with:
+```
+./POMtool.py run --help && alias POMtool="python $(pwd)/POMtool.py"
+```
+
+### pip
+Using pip is also possible. Just create virtual environment with correct python version. For most use cases, you should use `pipx` instead.
+
+## Using
+Use -h to get help-file for the CLI. Currently, this is only tested on python, newer python version might not work.
+
+Every config should describe model. This section describes how model you are interested can be run and how to input parameters to it.
+
+You have two options what to do with model, you can run POM-experiment (experiment), or model optimization (optimization).
+
+In POM-experiment first model is run for each set of parameters as described in `experiment`. After that `biomarkers` are calculated. With biomarkers, we can calibrate our population based on protocols described in `calibration`.
+
+In optimization, parameters are changed with goal to match biomarkers given as arguments. Biomarkers are calculated as given in `biomarkers` and `optimization` describes optimization process.
+
+To create your own config, check examples directory. All examples there are runnable (at moment of writing, only one example). 
+
+## Future
+* More ways to use the tool will be made available as the project progresses
+* Improvements to this document are added, as issues arise
+* More examples will be provided, and some example projects will be made public for best practices
+* Some thoughts can also be found from roadmap
+
+## Acknowledgements
+Initial production of this tool was partly funded by [SMASH-HCM](https://smash-hcm.eu/), which is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Education and Culture Executive Agency (EACEA). Neither the European Union nor EACEA can be held responsible for them.
+
+## Authors
+Ossi Noita - Original concept and current maintainer
+Olli Ylinen - Major contributions to optimization, biomarkers, and testing

pomtool-100.0.0/src/POMtool.egg-info/SOURCES.txt

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+LICENSE.md
+README.md
+pyproject.toml
+src/POMtool.egg-info/PKG-INFO
+src/POMtool.egg-info/SOURCES.txt
+src/POMtool.egg-info/dependency_links.txt
+src/POMtool.egg-info/entry_points.txt
+src/POMtool.egg-info/requires.txt
+src/POMtool.egg-info/top_level.txt
+src/pomtool/__init__.py
+src/pomtool/biomarker.py
+src/pomtool/calibration.py
+src/pomtool/experiment.py
+src/pomtool/log.py
+src/pomtool/loss_function.py
+src/pomtool/main.py
+src/pomtool/merge.py
+src/pomtool/model.py
+src/pomtool/optimization.py
+src/pomtool/utility.py

pomtool-100.0.0/src/POMtool.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pomtool-100.0.0/src/POMtool.egg-info/entry_points.txt

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+[console_scripts]
+POMtool = pomtool.main:run

pomtool-100.0.0/src/POMtool.egg-info/requires.txt

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+numpy==2.3.2
+PyYAML==6.0.2
+scimath==5.0.0
+scipy==1.16.1
+traits==7.0.2

pomtool-100.0.0/src/POMtool.egg-info/top_level.txt

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+pomtool