From 88efa616f0494bf85a0da61ff587615fb55b04ad Mon Sep 17 00:00:00 2001 From: ChristianMorland Date: Mon, 15 Jun 2026 08:21:26 +0200 Subject: [PATCH 01/17] add a codemeta.json --- CITATION.cff | 2 +- codemeta.json | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 66 insertions(+), 1 deletion(-) create mode 100644 codemeta.json diff --git a/CITATION.cff b/CITATION.cff index cd1d2cf..560c521 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -40,7 +40,7 @@ authors: orcid: 'https://orcid.org/0000-0002-6719-0190' identifiers: - type: doi - value: 'https://doi.org/10.5281/zenodo.13842384' + value: '10.5281/zenodo.13842384' description: 'Zenodo Archive' repository-code: 'https://github.com/TI-Forest-Sector-Modelling/TiMBA' abstract: |- diff --git a/codemeta.json b/codemeta.json new file mode 100644 index 0000000..f8bf6b6 --- /dev/null +++ b/codemeta.json @@ -0,0 +1,65 @@ +{ + "@context": "https://doi.org/10.5063/schema/codemeta-2.0", + "@type": "SoftwareSourceCode", + "author": [ + { + "@type": "Person", + "name": "TI-FSM" + }, + { + "@id": "https://orcid.org/0000-0001-6600-570X", + "@type": "Person", + "affiliation": { + "@type": "Organization", + "legalName": "Thünen Institue of Forestry" + }, + "familyName": "Morland", + "givenName": "Christian" + }, + { + "@id": "https://orcid.org/0000-0002-3378-1371", + "@type": "Person", + "affiliation": { + "@type": "Organization", + "legalName": "Thünen Institue of Forestry" + }, + "familyName": "Schier", + "givenName": "Franziska" + }, + { + "@id": "https://orcid.org/0000-0002-0630-9434", + "@type": "Person", + "affiliation": { + "@type": "Organization", + "legalName": "Thünen Institue of Forestry" + }, + "familyName": "Tandetzki", + "givenName": "Julia" + }, + { + "@id": "https://orcid.org/0000-0002-6719-0190", + "@type": "Person", + "affiliation": { + "@type": "Organization", + "legalName": "Thünen Institue of Forestry" + }, + "familyName": "Honkomp", + "givenName": "Tomke" + } + ], + "codeRepository": "https://github.com/TI-Forest-Sector-Modelling/TiMBA", + "datePublished": "2025-12-03", + "description": "TiMBA is a partial economic equilibrium model for the\n global forest products market. The model endogenously\n simulates production, consumption and trade of wood and\n wood-based products in 180 countries. TiMBA recursively\n computes the market equilibrium for each country and\n product in a given period by maximizing the social surplus\n in the global forest sector. In the equilibrium processes,\n product supply, demand and price are balanced for each\n simulation period. ", + "identifier": "https://doi.org/10.5281/zenodo.13842384", + "keywords": [ + "research", + "Forest sector model", + "partial equilibrium model", + "optimization", + "wood markets" + ], + "license": "https://spdx.org/licenses/AGPL-3.0-or-later", + "name": "TiMBA (Timber market Model for policy-Based Analysis)", + "url": "https://github.com/TI-Forest-Sector-Modelling/TiMBA", + "version": "1.3.0" +} From 40db9aad7f8d3479e1db48763270950cd18c22f0 Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Fri, 10 Jul 2026 10:34:00 +0200 Subject: [PATCH 02/17] aesthetic changes to pyproject.toml --- pyproject.toml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 37fd44d..4afde8d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ requires = ["setuptools==75.2.0", "wheel", "twine"] build-backend = "setuptools.build_meta" [project] -name = "pytimba" +name = "pytimba" version = "1.3.0" authors = [{name = "TI-FSM", email = "wf-timba@thuenen.de"}] description = "TiMBA is a partial economic equilibrium model for the global forest products market" @@ -11,7 +11,7 @@ readme = "README.md" license = { text = "AGPL-3.0-or-later" } keywords = ["timba", "model", "optimization", "thuenen institute", "economics of forests", "research"] -requires-python = ">=3.9,<3.12 " +requires-python = ">=3.9,<3.12" dependencies = [ "click==8.1.7", "coverage==7.6.3", @@ -24,7 +24,7 @@ dependencies = [ "pandas==1.5.3", "pathlib==1.0.1", "tomli==2.0.2", - "typing==3.7.4.3" , + "typing==3.7.4.3", "PyYAML==6.0.3", "Carbon-Module==1.1.1", ] @@ -36,7 +36,6 @@ classifiers = [ "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3 :: Only", "Operating System :: Microsoft :: Windows", - "Operating System :: Microsoft :: Windows :: Windows 10", "Operating System :: MacOS", "Operating System :: POSIX :: Linux", "Intended Audience :: Science/Research", From a877c7dd919b8ddd082535ccb8ea0381c605c391 Mon Sep 17 00:00:00 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Christian and Schier, Franziska and Tandetzki, Julia and Honkomp, Tomke}, + title = {TiMBA (Timber market Model for policy-Based Analysis)}, + journal = {Journal of Open Source Software} +} From c9567160bc2af8dbf2dd70704ae3be41746b8e1f Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Fri, 10 Jul 2026 11:18:38 +0200 Subject: [PATCH 05/17] Improve citation in README --- README.md | 108 ++++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 92 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 4bdf6de..82ac709 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,7 @@ - [Cite TiMBA](#cite-timba) - [Install TiMBA](#install-timba) + - [Quick start with uv](#quick-start-with-uv) - [Known Issues](#known-issues) - [Installation Process](#installation-process) - [Double check installation and test suite](#double-check-installation-and-test-suite) @@ -45,20 +46,75 @@ In the equilibrium processes, product supply, demand and price are balanced for We are happy that you use TiMBA for your research. When publishing your work in articles, working paper, presentations or elsewhere, please cite the model as -[TI-FSM, Morland, C., Schier, F., Tandetzki, J., Honkomp, T. (2025). TiMBA (Timber market Model for policy-Based Analysis). Journal of Open Source Software, 10(115), 8034, https://doi.org/10.21105/joss.08034](https://joss.theoj.org/papers/10.21105/joss.08034#) +TI-FSM, Morland, C., Schier, F., Tandetzki, J., Honkomp, T. (2025). TiMBA (Timber market Model for policy-Based Analysis). Journal of Open Source Software, 10(115), 8034, [https://doi.org/10.21105/joss.08034](https://doi.org/10.21105/joss.08034) +[Download BibTeX](./citation.bib) The authors' collective is named Thünen Institute Forest Sector Modelling (TI-FSM). The individual authors are listed as -Co-authors in alphabetical order. +Co-authors in alphabetical order. + ## Install TiMBA +### Requirements + The package is developed and tested with Python 3.9 on Windows. TiMBA is compatible with Python versions between 3.9–3.11 -with Windows and Ubuntu OS. The functionality with Python versions and different OS is continuously tested using GitHub -Actions. +under Linux and Windows and macOS. The functionality with Python versions and different OS is continuously tested using GitHub +Actions. + +### Quick start with uv + +The easiest way to get a reproducible, cross-platform environment is to use [uv](https://docs.astral.sh/uv/). + +1. Install uv: + + - **Linux / macOS**: + ```bash + curl -LsSf https://astral.sh/uv/install.sh | sh + ``` + - **Windows**: + ```powershell + powershell -c "irm https://astral.sh/uv/install.ps1 | iex" + ``` + + Alternatively, install uv via pip: + ```bash + pip install uv + ``` + +2. Clone the repository and move into the project folder: + ```bash + git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git + cd TiMBA + ``` + +3. Create the virtual environment and install the project. The project pins Python 3.11 in `.python-version`: + ```bash + uv sync + ``` + + This installs the exact dependency tree from `uv.lock` and installs the package in editable mode. + +4. Verify the installation and run a first period: + ```bash + uv run run_timba --help + uv run run_timba -MP=1 + ``` + +5. Run the test suite: + ```bash + uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover + uv run coverage report + ``` + +6. Build the package: + ```bash + uv build --sdist --wheel + ``` + +If you prefer not to use uv, the pip-based instructions below still work. ### Known Issues -TiMBA currently has compatibility issues on macOS and with Python 3.12 and 3.13. Users may experience unexpected behavior during the optimization -process on macOS, as well as package installation problems when using Python 3.12 and 3.13. -We recommend using Python 3.9–3.11 on Ubuntu or Windows for best results, until full support for Python 3.12 and 3.13 and macOS is implemented. +Python 3.12 and 3.13 are currently not supported because the pinned dependencies (e.g. pandas) are not compatible with those Python versions. +We recommend using Python 3.9–3.11 for best results. macOS is supported through the uv workflow above and is part of the CI matrix; please report any remaining platform-specific issues. ### Installation Process Before proceeding, please ensure that Python is installed on your system. @@ -150,29 +206,49 @@ Enable the virtual environment to isolate TiMBA dependencies. ### Double check installation and test suite -Double check if installation was successful by running following command from terminal: - >run_timba --help +Double check if installation was successful by running the following command from the terminal: + +```bash +run_timba --help +``` + +If you are using uv, run the command with the `uv run` prefix: + +```bash +uv run run_timba --help +``` -The help provides you information about the basic model settings which changed to adapt model runs to your needs +The help provides you information about the basic model settings which can be changed to adapt model runs to your needs (see section [Model settings](#model-settings) for further details). Test if TiMBA is running by executing the model only for the first period: - >run_timba -MP=1 - +```bash +run_timba -MP=1 +# or with uv: +uv run run_timba -MP=1 +``` The TiMBA model comes with a test suite to ensure its functionality. Run the test suite to check the functionality of the package and validate the produced results with those provided by the TI-FSM using the coverage report: - > coverage run - +```bash +python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover +# or with uv: +uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover +``` To reduce the test suite running time, only the first period will be computed and compared. The test suite results will not be saved. -The computed results and provided validation results are compared with a relative tolerance of 5%. +The computed results and provided validation results are compared with a relative tolerance of 5%. The coverage report of the TiMBA model can be accessed using: - > coverage report + +```bash +coverage report +# or with uv: +uv run coverage report +``` ## Use TiMBA From c33d64c551c74c14f414dc20a84f86cd783f0c09 Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Fri, 10 Jul 2026 21:14:37 +0200 Subject: [PATCH 06/17] WIP packaging --- .github/workflows/actions.yml | 26 ++++++++++---------------- .github/workflows/sonarscan.yml | 24 ++++++++++-------------- .python-version | 1 + CHANGELOG.md | 13 +++++++++++++ CONTRIBUTING.md | 21 +++++++++++++++++++++ README.md | 18 ++++++++++++++---- 6 files changed, 69 insertions(+), 34 deletions(-) create mode 100644 .python-version diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml index 6ad90e4..2cb754e 100644 --- a/.github/workflows/actions.yml +++ b/.github/workflows/actions.yml @@ -13,35 +13,29 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest, windows-latest] + os: [ubuntu-latest, windows-latest, macos-latest] python-version: ["3.9", "3.10", "3.11"] - # Add <, macOS-latest> to os to test TiMBA's functionality for macOS. Currently, macOS produces different results - # compared to ubuntu and windows without clear reason. - # Newest Python version 3.12 cannot be tested as Python >3.12.6 is not compatible with pandas < 2.0 runs-on: ${{matrix.os}} steps: - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + + - name: Set up uv and Python ${{ matrix.python-version }} + uses: astral-sh/setup-uv@v5 with: + version: "0.7.8" python-version: ${{ matrix.python-version }} + enable-cache: true - # Install dependencies necessary for the package - name: Install dependencies - run: | - python -m pip install --upgrade pip setuptools wheel - pip install -r requirements.txt - pip install coverage + run: uv sync --python ${{ matrix.python-version }} - # Run tests with coverage (tests excluded, warnings ignored) - name: Run test suite with coverage run: | - python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover - coverage report - coverage xml -o coverage.xml + uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover + uv run coverage report + uv run coverage xml -o coverage.xml - # Upload the coverage XML report as an artifact - name: Upload coverage XML artifact uses: actions/upload-artifact@v4 with: diff --git a/.github/workflows/sonarscan.yml b/.github/workflows/sonarscan.yml index 541bd5e..f5018b6 100644 --- a/.github/workflows/sonarscan.yml +++ b/.github/workflows/sonarscan.yml @@ -18,26 +18,22 @@ jobs: - name: Checkout code uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + - name: Set up uv and Python ${{ matrix.python-version }} + uses: astral-sh/setup-uv@v5 with: + version: "0.7.8" python-version: ${{ matrix.python-version }} + enable-cache: true - # Install dependencies necessary for the package - name: Install dependencies - run: | - python -m pip install --upgrade pip setuptools wheel - pip install -r requirements.txt - pip install coverage + run: uv sync --python ${{ matrix.python-version }} - # Generate a coverage report - name: Run tests with coverage run: | - python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover - coverage report - coverage xml -o coverage.xml + uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover + uv run coverage report + uv run coverage xml -o coverage.xml - # Execute project scan and upload the coverage report to SonarCloud - name: SonarCloud Scan uses: sonarsource/sonarcloud-github-action@v2 with: @@ -45,8 +41,8 @@ jobs: -Dsonar.organization=ti-forest-sector-modelling -Dsonar.projectKey=TI-Forest-Sector-Modelling_TiMBA -Dsonar.projectName=TiMBA - -Dsonar.projectVersion=1.0.3 + -Dsonar.projectVersion=1.3.0 -Dsonar.python.coverage.reportPaths=coverage.xml -Dsonar.exclusions=test/**,**/test_*.py env: - SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} \ No newline at end of file + SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/CHANGELOG.md b/CHANGELOG.md index ab531e9..7169525 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,18 @@ # Changelog +## Unreleased + +### Added +- Migrated dependency management to [uv](https://docs.astral.sh/uv/). +- Added `.python-version` pinning Python 3.11 and a `uv.lock` file for reproducible installs. +- Added macOS to the CI test matrix. +- Documented the uv workflow in `README.md`, `AGENTS.md`, and `CONTRIBUTING.md`. + +### Changed +- Updated GitHub Actions workflows (`actions.yml`, `sonarscan.yml`) to use uv for dependency installation and test execution. +- Cleaned up `pyproject.toml` metadata (`requires-python` and classifiers). +- `requirements.txt` is kept as a fallback for non-uv users. + ## [v1.3.0] - 2025-12-03 ### Added diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 59deec6..c17d460 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -10,6 +10,27 @@ initiate a topic under the [Github discussion section](#https://github.com/TI-Fo Below you can find some guidance that helps us to streamline the integration of your code contributions or facilitate addressing any issues you report. +## Development setup + +TiMBA uses [uv](https://docs.astral.sh/uv/) for dependency management. The project is pinned to Python 3.11 in `.python-version`. + +After installing uv, clone the repository and run: + +```bash +uv sync +``` + +This installs the locked dependencies and the package in editable mode. Most development commands are then run via `uv run`: + +```bash +uv run run_timba --help +uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover +uv run coverage report +uv run build --sdist --wheel +``` + +If you prefer pip, you can still install the project with `pip install -r requirements.txt` and `pip install -e .`. + ## Contributing code ----------------- diff --git a/README.md b/README.md index 82ac709..c761327 100644 --- a/README.md +++ b/README.md @@ -54,15 +54,25 @@ Co-authors in alphabetical order. ## Install TiMBA +The package is developed and tested with Python 3.9 on Windows 11. TiMBA is compatible with Python versions between 3.9–3.11. +The functionality with supported Python versions is continuously tested using GitHub with [operating system images](https://github.com/actions/runner-images#available-images) `windows-latest` and `ubuntu-latest`. +Actions. + ### Requirements -The package is developed and tested with Python 3.9 on Windows. TiMBA is compatible with Python versions between 3.9–3.11 -under Linux and Windows and macOS. The functionality with Python versions and different OS is continuously tested using GitHub -Actions. +- Operating system: Linux or Windows on a x64 architecture. We test Windows 11 + and Ubuntu 24.04, but other Windows and Linux versions are likely to work too. +- The Python package manager [uv](https://docs.astral.sh/uv/). We strongly + recommend to use `uv`, because it provides a very user-friendly, + platform-independent and + + + ### Quick start with uv -The easiest way to get a reproducible, cross-platform environment is to use [uv](https://docs.astral.sh/uv/). +The easiest way to get a reproducible, cross-platform environment is to use +[uv](https://docs.astral.sh/uv/). 1. Install uv: From d91b5c63a279bb9a403132a2e31029e9171a6434 Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Mon, 13 Jul 2026 19:14:35 +0200 Subject: [PATCH 07/17] Section FAIR research software, tested uv --- README.md | 135 ++++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 125 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index c761327..7c20f2b 100644 --- a/README.md +++ b/README.md @@ -36,15 +36,16 @@ -**TiMBA** is a partial economic equilibrium model for the global forest products market. The model endogenously simulates -production, consumption and trade of wood and wood-based products in 180 countries. TiMBA recursively computes the market -equilibrium for each country and product in a given period by maximizing the social surplus in the global forest sector. -In the equilibrium processes, product supply, demand and price are balanced for each simulation period. +**TiMBA** is a partial economic equilibrium model for the global forest products +market. The model endogenously simulates production, consumption and trade of +wood and wood-based products in 180 countries. TiMBA recursively computes the +market equilibrium for each country and product in a given period by maximizing +the social surplus in the global forest sector. In the equilibrium processes, +product supply, demand and price are balanced for each simulation period. ## Cite TiMBA -We are happy that you use TiMBA for your research. When publishing your work in articles, working paper, presentations -or elsewhere, please cite the model as +We are happy that you use TiMBA for your research. When publishing your work in articles, working paper, presentations or elsewhere, please cite the model as TI-FSM, Morland, C., Schier, F., Tandetzki, J., Honkomp, T. (2025). TiMBA (Timber market Model for policy-Based Analysis). Journal of Open Source Software, 10(115), 8034, [https://doi.org/10.21105/joss.08034](https://doi.org/10.21105/joss.08034) [Download BibTeX](./citation.bib) @@ -64,9 +65,9 @@ Actions. and Ubuntu 24.04, but other Windows and Linux versions are likely to work too. - The Python package manager [uv](https://docs.astral.sh/uv/). We strongly recommend to use `uv`, because it provides a very user-friendly, - platform-independent and - + platform-independent and reliable way to install, use and develop TiMBA. +------- BEGIN WIP ------------------ ### Quick start with uv @@ -82,7 +83,8 @@ The easiest way to get a reproducible, cross-platform environment is to use ``` - **Windows**: ```powershell - powershell -c "irm https://astral.sh/uv/install.ps1 | iex" + + powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" ``` Alternatively, install uv via pip: @@ -162,7 +164,7 @@ run_timba(folderpath=Path(r"your_path")) To modify specific parameters, the user can import `parameter_setter` from `TiMBA.main` and set new values: ```python -from timba.main import run_timba, parameter_setter +from TiMBA.main import run_timba, parameter_setter parameters = parameter_setter() parameters.max_period = 2 @@ -214,6 +216,8 @@ Enable the virtual environment to isolate TiMBA dependencies. 7. If the user does not set any folderpath the standard input data will be loaded to the current working directory or the folderpath which is set with: >run_timba -FP your_path +------------------ END WIP ------------------------- + ### Double check installation and test suite Double check if installation was successful by running the following command from the terminal: @@ -471,10 +475,12 @@ This work is the result of great joint efforts of the forest products market ana - [makeareadme.com](https://www.makeareadme.com/) for providing the template this README is leaned on. ## References +- Barker, M., Chue Hong, N.P., Katz, D.S. et al. Introducing the FAIR Principles for research software. Sci Data 9, 622 (2022). https://doi.org/10.1038/s41597-022-01710-x - Buongiorno, J.; Zhu, S.; Zhang, D.; Turner, J.; Tomberlin, D. The Global Forest Products Model; Academic Press: Cambridge, MA, USA, 2003; ISBN 978-0-12-141362-0 - Buongiorno, J. Global modelling to predict timber production and prices: The GFPM approach. Forestry 2015, 88, 291–303. - Buongiorno, J.; and Zhu, S. 2015. Technical change in forest sector models: The GFPM approach. Scand. J. For. Research, 30, 30-48. - GFPM - Global Forest Product Model is available at https://onedrive.live.com/?authkey=%21AEF7RY7oAPlrDPk&id=93BC28B749A1DFB6%21118&cid=93BC28B749A1DFB6 +- Chue Hong, N.P. et al. (2022) “FAIR Principles for Research Software (FAIR4RS Principles)”. Zenodo. Available at: https://doi.org/10.15497/RDA00068. - FAO. Global Forest Resources Assessment: Terms and Definitions; Forest Resources Assessment Working Paper 188; FAO: Rome, Italia, 2020; Available online: http://www.fao.org/3/I8661EN/i8661en.pdf - FAO. Global Forest Resources Assessment. 2022. Available online: https://fra-data.fao.org/ - FAOSTAT. Forestry Production and Trade: Datenbank. Available online: https://www.fao.org/faostat/en/#data/FO @@ -486,4 +492,113 @@ This work is the result of great joint efforts of the forest products market ana - Samuelson, Paul A. Spatial Price Equilibrium and Linear Programming; The American Economic Review, 1952, 42 (3), 283–303; Available online http://www.jstor.org/stable/1810381. - Schier, F.; Morland, C.; Tandetzki, J.; Honkomp, T. (2025). TI-Forest-Sector-Modelling/TiMBA_Additional_Information: Additional Information for TiMBA Setup (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.14928911. - TI-FSM (2025) TiMBA - Timber market Model for policy-Based Analysis: Documentation of model structure, data, and parameters. Braunschweig: Johann Heinrich von Thünen-Institut, 35 p, Thünen Working Paper 263, DOI:10.3220/253-2025-16 +- von Waldow, H. (2024). Research Software Licensing Guide (Version v1.0.2). Zenodo. https://doi.org/10.5281/zenodo.14008091 - World Bank. World Development Indicators|DataBank. Available online: https://databank.worldbank.org/source/world-development-indicators + + +## FAIR research software + +We attempt to adhere as much as possible to the FAIR Principles for research +software (e.g. see Barker et al. 2022 and Chue Hong et al. 2022) and reach high +standards of scientific quality and openness. I you find TiMBA or its +publication lacking in that regard, we very much appreciate your feedback as an +[Issue](https://github.com/TI-Forest-Sector-Modelling/TiMBA/issues/new/choose) +in the GitHub repository or via email to [wf-timba@thuenen.de](mailto:wf-timba@thuenen.de). + +In the following we detail our efforts and considerations. + + +### Findable + +- Zenodo provided DOI with extensive metadata according to the DataCite schema. + - Separate DOIs for each release and one representing all releases. +- A set of SWHID (Software Hash IDentifiers) is created by the [Software + Heritage archive](https://archive.softwareheritage.org/) for each release and + refereneces the code in a very granular fashion. +- An accompanying [software paper](https://doi.org/10.21105/joss.08034) makes + sure the software is also referenced in search indices that focus on journal articles. +- We provide rich metadata also as Linked Data in the form of the file `codemeta.json` in the + [CodeMeta](https://codemeta.github.io/) standard. + + +### Accessible + +- The source code can be accessed in the form of a *git remote* from GitHub, via + *http* from Zenodo, but also by Python package managers through the [Python + Package Index](https://pypi.org/), both as source distribution and as a + *Wheel*. + +- Metadata is preserved to a very high degree of safety in a redundant fashion. + The DataCite type metadata not only preserved by DataCite but also by Zenodo + and in the form of a file `zenodo.json` on GitHub and in the SoftwareHeritage + datacenters. These three repositories also hold the file `codemeta.json`. + +- We are aware that Microsoft GitHub, as a profit driven commercial service, is + tainted by political and company-strategic limitations, in particular with + regard to data safety, security, adherence to scientific community-standards + and long-term viability. However, GitHub's comfortable integration with Zenodo + yields a lot of benefits that we could not achive otherwise with our limited + resources. We hope that a comparable integration will be developed in the + future for better suited Forges such as [Forgejo](https://forgejo.org/) or + self-hosted [GitLab](gitlab.com). + +### Interoperable + +#### Software interoperability + +- TiMBA installs both as executable script (`timba_run`) as well as as a Python + module (`TiMBA`). The script copies its output also to STDOUT and allows to + chain TiMBA with other command line tools in a classical UNIX fashion. + Importing the module allows users to integrate TiMBA into their own Python + programs. + +- We also maintain extensions to TiMBA ([Crabon + Module](https://github.com/TI-Forest-Sector-Modelling/C-Module) and [TiMBA + Charts](https://github.com/TI-Forest-Sector-Modelling/TiMBA_Charts)) in the + form of Python packages that can be used by importing them. These packages + also adhere to FAIR principles, are version-controlled in GitHub and can be + referenced with DOIs registered by Zenodo. + +#### Data interoperability + +- TiMBA relies on a set of required input data. The canonical versions of these + data (a non-trivial scientific output) are also kept [version controlled in + GitHub](https://github.com/TI-Forest-Sector-Modelling/TiMBA_Additional_Information) + and releases are [published to + Zenodo](https://doi.org/10.5281/zenodo.14928910). + +- The main input data file is Office Open XML ("Microsoft Excel") format. We are + aware that this format is not a good choice from a purely technical point of + view and has severe shortcomings with regard to robustness, stability over + time, machine readability, interoperability, platform independence and + accessibility. However, this is the optimal format to make the input + understandable and modifyable by our main target group, who understands + Microsoft Excel very well but might struggle with less common formats and + conventions. This is a cultural and educational problem we can't solve in this + context. We are familiar with and track projects such as [Frictionnless + Data](https://frictionlessdata.io/) with its [Data Package + standard](https://datapackage.org/). We hope to eventually be able to combine + user-friendliness with robust data standards to represent our input data. + +- TiMBA output is written to universally readable CSV-files. We plan to describe + these files with standardized metadata in the future. + +### Reusable + +- TiMBA has dependencies and sub-dependencies which are extensively recorded in + the `uv.lock` file to ensure reproducibility. +- We continually strife to keep and improve software quality. We utilize + automated CI processes (testing for different platforms, linting) in the form + of GitHub workflows. +- We have licensed the software under the [GNU Affero General Public + License](https://www.gnu.org/licenses/agpl-3.0.txt). On the one hand side this + license is most compatible with the potential need to In-license further + dependencies. On the other hand, as a *Copyleft* license, it is very well + suited to support Open Science, reproducibility and transparency (von Waldow, + 2024). +- The scientific background and in particular prior software on which this work + improves, is extensively documented and referenced in this README file. +- Python as a programming language, adherence to an improved (`ruff`-defaults) + PEP 8 style guide, default installation as "editable", user-friendly + formatting of input data, and instructions about how to contribute increase + the chances that this software is being reused in our research community. From 4b48e443513f437f5e8a6c5a3a372b5ff5f5b88b Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Tue, 14 Jul 2026 18:23:36 +0200 Subject: [PATCH 08/17] rewrite install instructions in README --- README.md | 438 ++++++++++++++++++++++-------------------------------- 1 file changed, 179 insertions(+), 259 deletions(-) diff --git a/README.md b/README.md index 7c20f2b..e2ac113 100644 --- a/README.md +++ b/README.md @@ -50,104 +50,68 @@ We are happy that you use TiMBA for your research. When publishing your work in TI-FSM, Morland, C., Schier, F., Tandetzki, J., Honkomp, T. (2025). TiMBA (Timber market Model for policy-Based Analysis). Journal of Open Source Software, 10(115), 8034, [https://doi.org/10.21105/joss.08034](https://doi.org/10.21105/joss.08034) [Download BibTeX](./citation.bib) -The authors' collective is named Thünen Institute Forest Sector Modelling (TI-FSM). The individual authors are listed as -Co-authors in alphabetical order. +The authors' collective is named "Thünen Institute Forest Sector Modelling +(TI-FSM)"". The individual authors are listed as Co-authors in alphabetical +order. ## Install TiMBA -The package is developed and tested with Python 3.9 on Windows 11. TiMBA is compatible with Python versions between 3.9–3.11. -The functionality with supported Python versions is continuously tested using GitHub with [operating system images](https://github.com/actions/runner-images#available-images) `windows-latest` and `ubuntu-latest`. -Actions. +The package is developed and tested with Python 3.9 on Windows 11. TiMBA is +compatible with Python versions between 3.9 - 3.11. The functionality with +supported Python versions is continuously tested using GitHub CI with [operating +system images](https://github.com/actions/runner-images#available-images) +`windows-latest` and `ubuntu-latest`. ### Requirements - Operating system: Linux or Windows on a x64 architecture. We test Windows 11 and Ubuntu 24.04, but other Windows and Linux versions are likely to work too. - The Python package manager [uv](https://docs.astral.sh/uv/). We strongly - recommend to use `uv`, because it provides a very user-friendly, + recommend to use `uv`, because it provides a very user-friendly, quick, platform-independent and reliable way to install, use and develop TiMBA. + +That said, TiMBA can be also installed classically by creating a virtual +environment using [`venv`](https://docs.python.org/3.14/library/venv.html) and +installing with [`pip`](https://pip.pypa.io/en/stable/). To make the virtual +environment use the right Python version (if your system Python doesn't happen +to be version 3.9 - 3.11), you need to install a supported Python the the +operating system level and create the virtual environment with that version, +e.g. `python3.11 -m venv .venv`. + +### Install uv + +- **Linux**: + ```bash + curl -LsSf https://astral.sh/uv/install.sh | sh + ``` +- **Windows**: + ```powershell + powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" +``` -------- BEGIN WIP ------------------ - - -### Quick start with uv - -The easiest way to get a reproducible, cross-platform environment is to use -[uv](https://docs.astral.sh/uv/). - -1. Install uv: - - - **Linux / macOS**: - ```bash - curl -LsSf https://astral.sh/uv/install.sh | sh - ``` - - **Windows**: - ```powershell - - powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" - ``` - - Alternatively, install uv via pip: - ```bash - pip install uv - ``` - -2. Clone the repository and move into the project folder: - ```bash - git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git - cd TiMBA - ``` - -3. Create the virtual environment and install the project. The project pins Python 3.11 in `.python-version`: - ```bash - uv sync - ``` - - This installs the exact dependency tree from `uv.lock` and installs the package in editable mode. - -4. Verify the installation and run a first period: - ```bash - uv run run_timba --help - uv run run_timba -MP=1 - ``` - -5. Run the test suite: - ```bash - uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover - uv run coverage report - ``` - -6. Build the package: - ```bash - uv build --sdist --wheel - ``` - -If you prefer not to use uv, the pip-based instructions below still work. - -### Known Issues -Python 3.12 and 3.13 are currently not supported because the pinned dependencies (e.g. pandas) are not compatible with those Python versions. -We recommend using Python 3.9–3.11 for best results. macOS is supported through the uv workflow above and is part of the CI matrix; please report any remaining platform-specific issues. - -### Installation Process -Before proceeding, please ensure that Python is installed on your system. -It can be downloaded and installed from [Python.org](https://www.python.org/downloads/release/python-3119/). - -## Installation +### Install the TiMBA command line programs -The package can be installed from **PyPI** or directly from **GitHub**: +If you want to use TiMBA as executable program, install it globally like so: -### From PyPI: +``` bash +uv tool install -p 3.11 pytimba +``` +You will then have access to the CLI commands `load_timba`, `run_carbon_module`, `run_timba`. Usage instructions are available with the argument `--help` for each of the commands. +See section [Model settings](#model-settings) for further details. -```bash -pip install timba -```` +### Install TiMBA from PyPi -### Importing and running TiMBA +If you want to use TiMBA as part of your own program, you can install it from PyPi like so: -Once installed, `timba` can be imported with standard settings: +``` bash +uv init -p 3.11 my_timba_program # Create a project skeleton with Python 3.11 +cd my_timba_program # Change into the project directory +uv add pytimba # Install TiMBA into the project's virtual environment. +``` +Use TiMBA in Python modules, for example ```python -from timba.main import run_timba +from TiMBA.main import run_timba run_timba() ``` @@ -155,13 +119,13 @@ run_timba() To change the folder for input and output data, the user can use the `folderpath` option (note: the path must be a `Path` object from `pathlib`): ```python -from timba.main import run_timba +from TiMBA.main import run_timba from pathlib import Path run_timba(folderpath=Path(r"your_path")) ``` -To modify specific parameters, the user can import `parameter_setter` from `TiMBA.main` and set new values: +To modify specific parameters, you can import `parameter_setter` from `TiMBA.main` and set new values: ```python from TiMBA.main import run_timba, parameter_setter @@ -172,102 +136,49 @@ parameters.max_period = 2 run_timba(Parameters=parameters) ``` -### From GitHub: - -1. Clone the repository -Begin by cloning the repository to your local machine using the following command: - >git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git - > -2. Switch to the TiMBA directory -Navigate into the TiMBA project folder on your local machine. - >cd TiMBA - > -3. Create a virtual environment -It is recommended to set up a virtual environment for TiMBA to manage dependencies. The package is tested for - Python versions up to 3.11. With a newer Python version, we can not guarantee the full functionality of the package. - Select the correct Python interpreter. - Show installed versions: - >py -0 - > - - If you have installed multiple versions of Python, activate the correct version using the py-Launcher. - >py -3.11 -m venv venv - > - - If you are using only a single version of Python on your computer: - >python -m venv venv - > -4. Activate the virtual environment -Enable the virtual environment to isolate TiMBA dependencies. - >venv\Scripts\activate - - Or for Linux: - >source venv/bin/activate - -5. Install TiMBA in the editable mode - >pip install -e . - - If the following error occurs: "ERROR: File "setup.py" or "setup.cfg" not found." - you might need to update the pip version you use with: - >python.exe -m pip install --upgrade pip - -6. The package does not come with predefined data. To download the default input data along with additional information needed to run TiMBA use the command - >load_timba -FP your_path - By default, load_timba loads all necessary datasets from the external data repository. - -7. If the user does not set any folderpath the standard input data will be loaded to the current working directory or the folderpath which is set with: - >run_timba -FP your_path - ------------------- END WIP ------------------------- - - -### Double check installation and test suite -Double check if installation was successful by running the following command from the terminal: - -```bash -run_timba --help -``` - -If you are using uv, run the command with the `uv run` prefix: - -```bash -uv run run_timba --help -``` - -The help provides you information about the basic model settings which can be changed to adapt model runs to your needs -(see section [Model settings](#model-settings) for further details). - -Test if TiMBA is running by executing the model only for the first period: +### Install TiMBA from GitHub -```bash -run_timba -MP=1 -# or with uv: -uv run run_timba -MP=1 -``` +To install TiMBA in editable mode, so that you can modify the TiMBA source code, install it directly from GitHub: -The TiMBA model comes with a test suite to ensure its functionality. -Run the test suite to check the functionality of the package and validate the produced results with those provided by the -TI-FSM using the coverage report: +1. Clone the repository and move into the project folder: + ```bash + git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git timba + cd timba + ``` +2. Create the virtual environment and install all dependencies into it: + ```bash + uv sync + ``` +3. Verify the installation and run a first period: + ```bash + uv run run_timba --help + uv run run_timba -MP=1 + ``` -```bash -python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover -# or with uv: -uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover -``` +### Testing TiMBA -To reduce the test suite running time, only the first period will be computed and compared. The test suite results will not be saved. -The computed results and provided validation results are compared with a relative tolerance of 5%. +The TiMBA model comes with a test suite to ensure its functionality. Run the +test suite to check the functionality of the package and validate the produced +results with those provided by the TI-FSM using the coverage report: -The coverage report of the TiMBA model can be accessed using: + ```bash + uv run python -W ignore::DeprecationWarning -m coverage run --rcfile=.coveragerc -m unittest discover + uv run coverage report + ``` + +To reduce the test suite running time, only the first period will be computed +and compared. The test suite results will not be saved. The computed results and +provided validation results are compared with a relative tolerance of 5%. -```bash -coverage report -# or with uv: -uv run coverage report -``` +### Known Issues +Python versions >=3.12 are currently not supported because the pinned +dependencies (e.g. pandas) are not compatible with those Python versions. We +recommend using Python 3.9–3.11 for best results. ## Use TiMBA -The package comes with a built-in CLI to compute the TiMBA for various inputs. While the parametric input can be seen in cmd output calling `run_timba --help` from the terminal, an important part to mention is user input data that need to be imported from a selected folder. You shall not change the following structure within the data folder: -TiMBA is provided with an input file (scenario_input.xlsx), including all input data necessary to run the model. The section [TiMBA extended model description](#timba-extended-model-description-) delivers a detailed description of the included input data. +The package comes with a built-in CLI to compute the TiMBA for various inputs. While arguments are documented in the output of calling `run_timba --help` from the terminal, an important part to mention is user input data that need to be imported from a selected folder. You shall not change the following structure within the data folder: +TiMBA is provided with an input file (scenario_input.xlsx), including all input data necessary to run the model. The section [TiMBA extended model description](#timba-extended-model-description-) provides a detailed description of the included input data. ```bash . `- data @@ -298,11 +209,20 @@ The package will generate a result directory called `output` which is located in ``` **Important output information** -No output file will ever be overwritten by the application itself. New results-files will be generated in the format `results_DT.csv` and will be saved to the output folder as well. The logfile itself won't be overwritten as well but also no new file created on additional runs. Log information simply gets appended to the existing logfile. Removing the logfile ahead of executing the model won't result in errors. +No output file will ever be overwritten by the application itself. New +results-files will be generated in the format +`results_DT.csv` and will be saved to the output folder as +well. The logfile itself won't be overwritten as well but also no new file +created on additional runs. Log information simply gets appended to the existing +logfile. Removing the logfile ahead of executing the model won't result in +errors. ### Model settings -Multiple settings are integrated in TiMBA to allow users to interact with the model and adapt the modelling parameters to their research interests. -Following chapter provides a brief overview of the model settings. A detailed description of the settings is provided in the documentation. + +Multiple settings are integrated in TiMBA to allow users to interact with the +model and adapt the modelling parameters to their research interests. The following +chapter provides a brief overview of the model settings. A detailed description +of the settings is provided in the documentation. Basic model settings include: | Option | Parameter | Type | Default | @@ -340,7 +260,6 @@ Check if CLI command is registered and available on your computer by executing e Default settings can be changed in the following way: (Note: The change of default settings as described below is for demonstration purposes only, and the results have not been validated.): - > run_timba -MP=5 -MB="RCG_specific" -CP="True" - For this example, TiMBA will simulate 5 periods using calculated prices as product prices and shadow prices as world market prices. #### Advanced settings @@ -413,89 +332,6 @@ Several projects are currently extending different components of TiMBA: Frequently check [TiMBA repository](https://github.com/TI-Forest-Sector-Modelling/TiMBA) for new releases. -## Contributing to the project -We welcome contributions, additions and suggestion to further develop or improve the code and the model. To check, discuss and include them into this project, we would like you to share your ideas with us so that we can agree on the requirements needed for accepting your contribution. -You can contact us directly via GitHub by creating issues, or by writing an Email to: - -[wf-timba@thuenen.de](mailto:wf-timba@thuenen.de) - -A scientific documentation will follow and be linked here soon. So far, this README serves as a comprehensive introduction and guidance on how to get started. - - - -## Authors -TiMBA was developed and written by an authors' collective named Thünen Institute Forest Sector Modelling (TI-FSM). - -The individual authors are listed in alphabetical order -- [Christian Morland](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/ehemalige-liste/christian-morland-msc) [(ORCID 0000-0001-6600-570X)](https://orcid.org/0000-0001-6600-570X), -- [Franziska Schier](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/dipl-ing-franziska-schier) [(ORCID 0000-0002-3378-1371)](https://orcid.org/0000-0002-3378-1371), -- [Julia Tandetzki](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/julia-tandetzki-msc) [(ORCID 0000-0002-0630-9434)](https://orcid.org/0000-0002-0630-9434), and -- [Tomke Honkomp](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/tomke-honkomp-msc) [(ORCID 0000-0002-6719-0190)](https://orcid.org/0000-0002-6719-0190). - -## Contribution statement -Within the authors' collective TI-FSM, the authors have contributed over years their individual strengths and knowledge to make the model work: - -| Author | Conceptualization and theoretical framework | Methodology | Data Curation and Management | Formal Analysis | Programming | Writing and Documentation | Visualization | Review and Editing | Supervision | -|:------------------|:-------------------------------------------:|:-----------:|:----------------------------:|:---------------:|:-----------:|:-------------------------:|:-------------:|:------------------:|:-----------:| -| Christian Morland | X | X | X | X | X | X | X | X | | -| Franziska Schier | X | X | X | X | | X | | X | X | -| Julia Tandetzki | X | X | X | X | X | X | X | X | | -| Tomke Honkomp | X | X | X | X | X | X | X | X | | - -## License and copyright note - -Licensed under the GNU AGPL, Version 3.0. - -Copyright ©, 2024, Thuenen Institute, TI-FSM, wf-timba@thuenen.de - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU Affero General Public License as - published by the Free Software Foundation, either version 3 of the - License, or (at your option) any later version. - - This program is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - Affero General Public License for more details. - - You should have received a copy of the GNU Affero General Public - License along with this program. If not, see - . - - - -## Acknowledgements - -This work is the result of great joint efforts of the forest products market analysis team at the Thünen Institute of Forestry and others from 2018 to 2024. In the last years, many people made important contributions to this work. Without their support, reflection, and constructive criticism, this undertaking would not have been as successful as it turns out to be now. We would like express our gratitude to all of them. In particular, we would like to thank -- Pixida GmbH and especially Tobias Hierlmeier for professional support in revising and restructuring the model architecture and code and being valuable help in programming tasks -- Thünen Institute Service Centre for Research Data Management and especially Harald von Waldow for providing expertise, consultation, and support during the release process -- Holger Weimar and Matthias Dieter for the trustful and cooperative working environment, valuable support and critical discussion and the opportunity to keep on going -- Johanna Schliemann for technical support whenever needed -- The Thünen Institut of Forestry and its Head Matthias Dieter for providing financial resources over the years -- [makeareadme.com](https://www.makeareadme.com/) for providing the template this README is leaned on. - -## References -- Barker, M., Chue Hong, N.P., Katz, D.S. et al. Introducing the FAIR Principles for research software. Sci Data 9, 622 (2022). https://doi.org/10.1038/s41597-022-01710-x -- Buongiorno, J.; Zhu, S.; Zhang, D.; Turner, J.; Tomberlin, D. The Global Forest Products Model; Academic Press: Cambridge, MA, USA, 2003; ISBN 978-0-12-141362-0 -- Buongiorno, J. Global modelling to predict timber production and prices: The GFPM approach. Forestry 2015, 88, 291–303. -- Buongiorno, J.; and Zhu, S. 2015. Technical change in forest sector models: The GFPM approach. Scand. J. For. Research, 30, 30-48. -- GFPM - Global Forest Product Model is available at https://onedrive.live.com/?authkey=%21AEF7RY7oAPlrDPk&id=93BC28B749A1DFB6%21118&cid=93BC28B749A1DFB6 -- Chue Hong, N.P. et al. (2022) “FAIR Principles for Research Software (FAIR4RS Principles)”. Zenodo. Available at: https://doi.org/10.15497/RDA00068. -- FAO. Global Forest Resources Assessment: Terms and Definitions; Forest Resources Assessment Working Paper 188; FAO: Rome, Italia, 2020; Available online: http://www.fao.org/3/I8661EN/i8661en.pdf -- FAO. Global Forest Resources Assessment. 2022. Available online: https://fra-data.fao.org/ -- FAOSTAT. Forestry Production and Trade: Datenbank. Available online: https://www.fao.org/faostat/en/#data/FO -- Morland, C.; Schier, F.; Janzen, N.; Weimar, H. Supply and demand functions for global wood markets: Specification and plausibility testing of econometric models within the global forest sector. For. Policy Econ. 2018, 92, 92–105 -- Morland, C.; Tandetzki, J.; & Honkomp, T. (2025). TiMBA Charts (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.15689299 -- Murray, B.C.; McCarl, B.A.; Lee, H.-C. Estimating Leakage from Forest Carbon Sequestration Programs. Land Econ. 2004, 80, 109–124 -- Panayotou, T. Empirical Tests and Policy Analysis of Environmental Degradation at Different Stages of Economic Development; Working Paper No. 238; International Labour Organization: Geneva, Switzerland, 1993; Available online: http://www.ilo.org/public/libdoc/ilo/1993/93B09_31_engl.pdf -- Riahi, K.; van Vuuren, D.P.; Kriegler, E.; Edmonds, J.; O’Neill, B.C.; Fujimori, S.; Bauer, N.; Calvin, K.; Dellink, R.; Fricko, O.; et al. The Shared Socioeconomic Pathways and their energy, land use, and greenhouse gas emissions implications: An overview. Glob. Environ. Chang. 2017, 42, 153–168. -- Samuelson, Paul A. Spatial Price Equilibrium and Linear Programming; The American Economic Review, 1952, 42 (3), 283–303; Available online http://www.jstor.org/stable/1810381. -- Schier, F.; Morland, C.; Tandetzki, J.; Honkomp, T. (2025). TI-Forest-Sector-Modelling/TiMBA_Additional_Information: Additional Information for TiMBA Setup (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.14928911. -- TI-FSM (2025) TiMBA - Timber market Model for policy-Based Analysis: Documentation of model structure, data, and parameters. Braunschweig: Johann Heinrich von Thünen-Institut, 35 p, Thünen Working Paper 263, DOI:10.3220/253-2025-16 -- von Waldow, H. (2024). Research Software Licensing Guide (Version v1.0.2). Zenodo. https://doi.org/10.5281/zenodo.14008091 -- World Bank. World Development Indicators|DataBank. Available online: https://databank.worldbank.org/source/world-development-indicators - - ## FAIR research software We attempt to adhere as much as possible to the FAIR Principles for research @@ -507,7 +343,6 @@ in the GitHub repository or via email to [wf-timba@thuenen.de](mailto:wf-timba@t In the following we detail our efforts and considerations. - ### Findable - Zenodo provided DOI with extensive metadata according to the DataCite schema. @@ -519,7 +354,8 @@ In the following we detail our efforts and considerations. sure the software is also referenced in search indices that focus on journal articles. - We provide rich metadata also as Linked Data in the form of the file `codemeta.json` in the [CodeMeta](https://codemeta.github.io/) standard. - +- We provide machine-actionable citation information in the [Citation File Format + (CFF)](https://citation-file-format.github.io/). ### Accessible @@ -552,7 +388,7 @@ In the following we detail our efforts and considerations. Importing the module allows users to integrate TiMBA into their own Python programs. -- We also maintain extensions to TiMBA ([Crabon +- We also maintain extensions to TiMBA ([Carbon Module](https://github.com/TI-Forest-Sector-Modelling/C-Module) and [TiMBA Charts](https://github.com/TI-Forest-Sector-Modelling/TiMBA_Charts)) in the form of Python packages that can be used by importing them. These packages @@ -602,3 +438,87 @@ In the following we detail our efforts and considerations. PEP 8 style guide, default installation as "editable", user-friendly formatting of input data, and instructions about how to contribute increase the chances that this software is being reused in our research community. + +## Contributing to the project +We welcome contributions, additions and suggestion to further develop or improve the code and the model. To check, discuss and include them into this project, we would like you to share your ideas with us so that we can agree on the requirements needed for accepting your contribution. +You can contact us directly via GitHub by creating issues, or by writing an Email to: + +[wf-timba@thuenen.de](mailto:wf-timba@thuenen.de) + +A scientific documentation will follow and be linked here soon. So far, this README serves as a comprehensive introduction and guidance on how to get started. + + + +## Authors +TiMBA was developed and written by an authors' collective named Thünen Institute Forest Sector Modelling (TI-FSM). + +The individual authors are listed in alphabetical order +- [Christian Morland](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/ehemalige-liste/christian-morland-msc) [(ORCID 0000-0001-6600-570X)](https://orcid.org/0000-0001-6600-570X), +- [Franziska Schier](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/dipl-ing-franziska-schier) [(ORCID 0000-0002-3378-1371)](https://orcid.org/0000-0002-3378-1371), +- [Julia Tandetzki](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/julia-tandetzki-msc) [(ORCID 0000-0002-0630-9434)](https://orcid.org/0000-0002-0630-9434), and +- [Tomke Honkomp](https://www.thuenen.de/de/fachinstitute/waldwirtschaft/personal/wissenschaftliches-personal/tomke-honkomp-msc) [(ORCID 0000-0002-6719-0190)](https://orcid.org/0000-0002-6719-0190). + +## Contribution statement +Within the authors' collective TI-FSM, the authors have contributed over years their individual strengths and knowledge to make the model work: + +| Author | Conceptualization and theoretical framework | Methodology | Data Curation and Management | Formal Analysis | Programming | Writing and Documentation | Visualization | Review and Editing | Supervision | +|:------------------|:-------------------------------------------:|:-----------:|:----------------------------:|:---------------:|:-----------:|:-------------------------:|:-------------:|:------------------:|:-----------:| +| Christian Morland | X | X | X | X | X | X | X | X | | +| Franziska Schier | X | X | X | X | | X | | X | X | +| Julia Tandetzki | X | X | X | X | X | X | X | X | | +| Tomke Honkomp | X | X | X | X | X | X | X | X | | + +## License and copyright note + +Licensed under the GNU AGPL, Version 3.0. + +Copyright ©, 2024, Thuenen Institute, TI-FSM, wf-timba@thuenen.de + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as + published by the Free Software Foundation, either version 3 of the + License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public + License along with this program. If not, see + . + + + +## Acknowledgements + +This work is the result of great joint efforts of the forest products market analysis team at the Thünen Institute of Forestry and others from 2018 to 2024. In the last years, many people made important contributions to this work. Without their support, reflection, and constructive criticism, this undertaking would not have been as successful as it turns out to be now. We would like express our gratitude to all of them. In particular, we would like to thank +- Pixida GmbH and especially Tobias Hierlmeier for professional support in revising and restructuring the model architecture and code and being valuable help in programming tasks +- Thünen Institute Service Centre for Research Data Management and especially Harald von Waldow for providing expertise, consultation, and support during the release process +- Holger Weimar and Matthias Dieter for the trustful and cooperative working environment, valuable support and critical discussion and the opportunity to keep on going +- Johanna Schliemann for technical support whenever needed +- The Thünen Institut of Forestry and its Head Matthias Dieter for providing financial resources over the years +- [makeareadme.com](https://www.makeareadme.com/) for providing the template this README is leaned on. + +## References +- Barker, M., Chue Hong, N.P., Katz, D.S. et al. Introducing the FAIR Principles for research software. Sci Data 9, 622 (2022). https://doi.org/10.1038/s41597-022-01710-x +- Buongiorno, J.; Zhu, S.; Zhang, D.; Turner, J.; Tomberlin, D. The Global Forest Products Model; Academic Press: Cambridge, MA, USA, 2003; ISBN 978-0-12-141362-0 +- Buongiorno, J. Global modelling to predict timber production and prices: The GFPM approach. Forestry 2015, 88, 291–303. +- Buongiorno, J.; and Zhu, S. 2015. Technical change in forest sector models: The GFPM approach. Scand. J. For. Research, 30, 30-48. +- GFPM - Global Forest Product Model is available at https://onedrive.live.com/?authkey=%21AEF7RY7oAPlrDPk&id=93BC28B749A1DFB6%21118&cid=93BC28B749A1DFB6 +- Chue Hong, N.P. et al. (2022) “FAIR Principles for Research Software (FAIR4RS Principles)”. Zenodo. Available at: https://doi.org/10.15497/RDA00068. +- FAO. Global Forest Resources Assessment: Terms and Definitions; Forest Resources Assessment Working Paper 188; FAO: Rome, Italia, 2020; Available online: http://www.fao.org/3/I8661EN/i8661en.pdf +- FAO. Global Forest Resources Assessment. 2022. Available online: https://fra-data.fao.org/ +- FAOSTAT. Forestry Production and Trade: Datenbank. Available online: https://www.fao.org/faostat/en/#data/FO +- Morland, C.; Schier, F.; Janzen, N.; Weimar, H. Supply and demand functions for global wood markets: Specification and plausibility testing of econometric models within the global forest sector. For. Policy Econ. 2018, 92, 92–105 +- Morland, C.; Tandetzki, J.; & Honkomp, T. (2025). TiMBA Charts (v0.2.0). Zenodo. https://doi.org/10.5281/zenodo.15689299 +- Murray, B.C.; McCarl, B.A.; Lee, H.-C. Estimating Leakage from Forest Carbon Sequestration Programs. Land Econ. 2004, 80, 109–124 +- Panayotou, T. Empirical Tests and Policy Analysis of Environmental Degradation at Different Stages of Economic Development; Working Paper No. 238; International Labour Organization: Geneva, Switzerland, 1993; Available online: http://www.ilo.org/public/libdoc/ilo/1993/93B09_31_engl.pdf +- Riahi, K.; van Vuuren, D.P.; Kriegler, E.; Edmonds, J.; O’Neill, B.C.; Fujimori, S.; Bauer, N.; Calvin, K.; Dellink, R.; Fricko, O.; et al. The Shared Socioeconomic Pathways and their energy, land use, and greenhouse gas emissions implications: An overview. Glob. Environ. Chang. 2017, 42, 153–168. +- Samuelson, Paul A. Spatial Price Equilibrium and Linear Programming; The American Economic Review, 1952, 42 (3), 283–303; Available online http://www.jstor.org/stable/1810381. +- Schier, F.; Morland, C.; Tandetzki, J.; Honkomp, T. (2025). TI-Forest-Sector-Modelling/TiMBA_Additional_Information: Additional Information for TiMBA Setup (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.14928911. +- TI-FSM (2025) TiMBA - Timber market Model for policy-Based Analysis: Documentation of model structure, data, and parameters. Braunschweig: Johann Heinrich von Thünen-Institut, 35 p, Thünen Working Paper 263, DOI:10.3220/253-2025-16 +- von Waldow, H. (2024). Research Software Licensing Guide (Version v1.0.2). Zenodo. https://doi.org/10.5281/zenodo.14008091 +- World Bank. World Development Indicators|DataBank. Available online: https://databank.worldbank.org/source/world-development-indicators + + From 7ddfb21bd9310bc1a5d10458eee446d52f30995b Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Tue, 14 Jul 2026 18:29:33 +0200 Subject: [PATCH 09/17] Fix layout --- README.md | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index e2ac113..46fd853 100644 --- a/README.md +++ b/README.md @@ -80,13 +80,14 @@ e.g. `python3.11 -m venv .venv`. ### Install uv -- **Linux**: - ```bash - curl -LsSf https://astral.sh/uv/install.sh | sh - ``` -- **Windows**: - ```powershell - powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" +#### Linux + +```bash +curl -LsSf https://astral.sh/uv/install.sh | sh +``` +#### Windows +```powershell +powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" ``` ### Install the TiMBA command line programs From 6cb00415498b040a0a686df20a6191ec04e060a3 Mon Sep 17 00:00:00 2001 From: Harald von Waldow Date: Tue, 14 Jul 2026 18:36:32 +0200 Subject: [PATCH 10/17] fix reusable section --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 46fd853..63ee178 100644 --- a/README.md +++ b/README.md @@ -435,10 +435,11 @@ In the following we detail our efforts and considerations. 2024). - The scientific background and in particular prior software on which this work improves, is extensively documented and referenced in this README file. -- Python as a programming language, adherence to an improved (`ruff`-defaults) - PEP 8 style guide, default installation as "editable", user-friendly - formatting of input data, and instructions about how to contribute increase - the chances that this software is being reused in our research community. +- Python as a programming language, adherence to an improved + ([`ruff`](https://docs.astral.sh/ruff/)-defaults) PEP8 style guide, + user-friendly formatting of input data, and instructions about how to + contribute increase the chances that this software is being reused in our + research community. ## Contributing to the project We welcome contributions, additions and suggestion to further develop or improve the code and the model. To check, discuss and include them into this project, we would like you to share your ideas with us so that we can agree on the requirements needed for accepting your contribution. 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The model endogenously\n simulates production, consumption and trade of wood and\n wood-based products in 180 countries. TiMBA recursively\n computes the market equilibrium for each country and\n product in a given period by maximizing the social surplus\n in the global forest sector. In the equilibrium processes,\n product supply, demand and price are balanced for each\n simulation period.", + "identifiers": [ + { + "identifier": "https://archive.softwareheritage.org/swh:1:dir:1828c8cf6b8df60176209f7d2f2d8e6f49e68950", + "scheme": "url" + } + ], + "languages": [ + { + "id": "eng", + "title": { + "en": "English" + } + } + ], + "publication_date": "2025-12-03", + "publisher": "Zenodo", + "references": [ + { + "reference": "Buongiorno, J., Zhu, S., Zhang, D., Turner, J., & Tomberlin, D. (2003). The global forest products model: Structure, estimation, and applications. Academic Press. ISBN: 978- 0121413620" + }, + { + "reference": "Buongiorno, J. (2015). Global modelling to predict timber production and prices: The GFPM approach. Forestry, 88(3), 291\u2013303. https://doi.org/10.1093/forestry/cpu047" + }, + { + "reference": "Diamond, S., & Boyd, S. (2016). CVXPY: A Python-embedded modeling language for convex optimization. Journal of Machine Learning Research, 17 (83), 1\u20135." + }, + { + "reference": "Stellato, B., Banjac, G., Goulart, P., Bemporad, A., & Boyd, S. (2020). OSQP: An operator splitting solver for quadratic programs. Mathematical Programming Computation, 12(4), 637\u2013672. https://doi.org/10.1007/s12532-020-00179-2" + }, + { + "reference": "Samuelson, P. A. (1952). Spatial price equilibrium and linear programming. The American Economic Review, 42(3), 283\u2013303. http://www.jstor.org/stable/1810381" + } + ], + "related_identifiers": [ + { + "identifier": "https://github.com/TI-Forest-Sector-Modelling/TiMBA/tree/v1.3.0", + "relation_type": { + "id": "issupplementto", + "title": { + "de": "Erg\u00e4nzt", + "en": "Is supplement to" + } + }, + "resource_type": { + "id": "software", + "title": { + "de": "Software", + "en": "Software" + } + }, + "scheme": "url" + }, + { + "identifier": "10.21105/joss.08034", + "relation_type": { + "id": "ispublishedin", + "title": { + "de": "Ist ver\u00f6ffentlicht in", + "en": "Is published in" + } + }, + "resource_type": { + "id": "publication-article", + "title": { + "de": "Zeitschriftenartikel", + "en": "Journal article" + } + }, + "scheme": "doi" + }, + { + "identifier": "10.5281/zenodo.20925292", + "relation_type": { + "id": "issupplementedby", + "title": { + "de": "Wird erg\u00e4nzt durch", + "en": "Is supplemented by" + } + }, + "resource_type": { + "id": "software", + "title": { + "de": "Software", + "en": "Software" + } + }, + "scheme": "doi" + }, + { + "identifier": "10.5281/zenodo.17814169", + "relation_type": { + "id": "issupplementedby", + "title": { + "de": "Wird erg\u00e4nzt durch", + "en": "Is supplemented by" + } + }, + "resource_type": { + "id": "software", + "title": { + "de": "Software", + "en": "Software" + } + }, + "scheme": "doi" + }, + { + "identifier": "10.5281/zenodo.19466845", + "relation_type": { + "id": "requires", + "title": { + "de": "Setzt voraus", + "en": "Requires" + } + }, + "resource_type": { + "id": "dataset", + "title": { + "de": "Datensatz", + "en": "Dataset" + } + }, + "scheme": "doi" + }, + { + "identifier": "10.5281/zenodo.19466845", + "relation_type": { + "id": "haspart", + "title": { + "de": "Umfasst folgenden Teil", + "en": "Has part" + } + }, + "resource_type": { + "id": "dataset", + "title": { + "de": "Datensatz", + "en": "Dataset" + } + }, + "scheme": "doi" + } + ], + "resource_type": { + "id": "software", + "title": { + "de": "Software", + "en": "Software" + } + }, + "rights": [ + { + "description": { + "en": "" + }, + "id": "agpl-3.0-or-later", + "props": { + "scheme": "spdx", + "url": "https://www.gnu.org/licenses/agpl.txt" + }, + "title": { + "en": "GNU Affero General Public License v3.0 or later" + } + } + ], + "subjects": [ + { + "subject": "research" + }, + { + "subject": "Forest sector model" + }, + { + "subject": "partial equilibrium model" + }, + { + "subject": "optimization" + }, + { + "subject": "wood markets" + } + ], + "title": "TiMBA (Timber market Model for policy-Based Analysis)", + "version": "v1.3.0" + }, + "parent": { + "access": { + "owned_by": { + "user": "1194720" + }, + "settings": { + "accept_conditions_text": null, + "allow_guest_requests": false, + "allow_user_requests": false, + "secret_link_expiration": 0 + } + }, + "communities": { + "default": "09c92e32-50ba-4d88-8c60-9a74a198078d", + "entries": [ + { + "access": { + "member_policy": "open", + "members_visibility": "public", + "record_submission_policy": "open", + "review_policy": "open", + "visibility": "public" + }, + "children": { + "allow": false + }, + "created": "2024-03-26T14:59:31.275326+00:00", + "custom_fields": {}, + "deletion_status": { + "is_deleted": false, + "status": "P" + }, + "id": "09c92e32-50ba-4d88-8c60-9a74a198078d", + "links": {}, + "metadata": { + "curation_policy": "

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", + "organizations": [ + { + "id": "00mr84n67" + } + ], + "title": "Johann Heinrich von Th\u00fcnen-Institut", + "type": { + "id": "organization" + }, + "website": "https://www.thuenen.de/de/" + }, + "revision_id": 7, + "slug": "thuenen", + "updated": "2024-03-26T15:18:00.842375+00:00" + } + ], + "ids": [ + "09c92e32-50ba-4d88-8c60-9a74a198078d" + ] + }, + "id": "13842384", + "pids": { + "doi": { + "client": "datacite", + "identifier": "10.5281/zenodo.13842384", + "provider": "datacite" + } + } + }, + "pids": { + "doi": { + "client": "datacite", + "identifier": "10.5281/zenodo.17806030", + "provider": "datacite" + }, + "oai": { + "identifier": "oai:zenodo.org:17806030", + "provider": "oai" + } + }, + "revision_id": 8, + "stats": { + "all_versions": { + "data_volume": 1869902762.0, + "downloads": 213, + "unique_downloads": 205, + "unique_views": 1797, + "views": 1964 + }, + "this_version": { + "data_volume": 249631555.0, + "downloads": 43, + "unique_downloads": 42, + "unique_views": 199, + "views": 213 + } + }, + "status": "published", + "swh": { + "swhid": "swh:1:dir:e6e6240c08c0b70af91ed91083b3e37fce702214;origin=https://doi.org/10.5281/zenodo.13842384;visit=swh:1:snp:2f6aed0842a62a28ae45836d1833807ac77f2a2d;anchor=swh:1:rel:82b8d27a24ca85e5c57a89bcae5b69d8f9bc047f;path=TI-Forest-Sector-Modelling-TiMBA-b659274" + }, + "updated": "2026-07-08T09:23:34.471797+00:00", + "versions": { + "index": 7, + "is_latest": true + } +} From afa85157bdef70a4b6ee6539c171bcf1f5a07ff4 Mon Sep 17 00:00:00 2001 From: Julia Tandetzki Date: Wed, 15 Jul 2026 14:24:56 +0200 Subject: [PATCH 13/17] Installation via git hub and small tipos --- README.md | 87 +++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 59 insertions(+), 28 deletions(-) diff --git a/README.md b/README.md index 63ee178..05334f1 100644 --- a/README.md +++ b/README.md @@ -137,24 +137,56 @@ parameters.max_period = 2 run_timba(Parameters=parameters) ``` -### Install TiMBA from GitHub +### From GitHub: -To install TiMBA in editable mode, so that you can modify the TiMBA source code, install it directly from GitHub: +Clone the repository Begin by cloning the repository to your local machine using the following command: +```python +git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git +``` +Switch to the TiMBA directory +>Navigate into the TiMBA project folder on your local machine. -1. Clone the repository and move into the project folder: - ```bash - git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git timba - cd timba - ``` -2. Create the virtual environment and install all dependencies into it: - ```bash - uv sync - ``` -3. Verify the installation and run a first period: - ```bash - uv run run_timba --help - uv run run_timba -MP=1 - ``` +```python +cd TiMBA +``` +Create a virtual environment +>It is recommended to set up a virtual environment for TiMBA to manage dependencies. The package is tested for Python versions up to 3.11. With a newer Python version, we can not >guarantee the full functionality of the package. Select the correct Python interpreter. +Show installed versions: + +```python +py -0 +``` +If you have installed multiple versions of Python, activate the correct version using the py-Launcher. +```python +py -3.11 -m venv venv +``` +If you are using only a single version of Python on your computer: +```python +python -m venv venv +``` +Activate the virtual environment +>Enable the virtual environment to isolate TiMBA dependencies. +```python +venv\Scripts\activate +``` +Or for Linux: +```python +source venv/bin/activate +``` +Install TiMBA in the editable mode +```python +pip install -e . +``` +If the following error occurs: "ERROR: File "setup.py" or "setup.cfg" not found." you might need to update the pip version you use with: +```python +python.exe -m pip install --upgrade pip +``` +Double check installation and test suite: +>Double check if installation was successful by running following command from terminal: +```python +timba --help +``` +The help provides you information about the basic model commands. ### Testing TiMBA @@ -337,23 +369,22 @@ Frequently check [TiMBA repository](https://github.com/TI-Forest-Sector-Modellin We attempt to adhere as much as possible to the FAIR Principles for research software (e.g. see Barker et al. 2022 and Chue Hong et al. 2022) and reach high -standards of scientific quality and openness. I you find TiMBA or its -publication lacking in that regard, we very much appreciate your feedback as an -[Issue](https://github.com/TI-Forest-Sector-Modelling/TiMBA/issues/new/choose) +standards of scientific quality and openness. If you find that TiMBA or its documentation could be improved, we would greatly appreciate your feedback. +Please submit it as an [Issue](https://github.com/TI-Forest-Sector-Modelling/TiMBA/issues/new/choose) in the GitHub repository or via email to [wf-timba@thuenen.de](mailto:wf-timba@thuenen.de). In the following we detail our efforts and considerations. ### Findable -- Zenodo provided DOI with extensive metadata according to the DataCite schema. +- Zenodo provides a DOI with extensive metadata according to the DataCite schema. - Separate DOIs for each release and one representing all releases. - A set of SWHID (Software Hash IDentifiers) is created by the [Software Heritage archive](https://archive.softwareheritage.org/) for each release and refereneces the code in a very granular fashion. - An accompanying [software paper](https://doi.org/10.21105/joss.08034) makes sure the software is also referenced in search indices that focus on journal articles. -- We provide rich metadata also as Linked Data in the form of the file `codemeta.json` in the +- We provide rich metadata also as linked data in the form of the file `codemeta.json` in the [CodeMeta](https://codemeta.github.io/) standard. - We provide machine-actionable citation information in the [Citation File Format (CFF)](https://citation-file-format.github.io/). @@ -370,13 +401,13 @@ In the following we detail our efforts and considerations. and in the form of a file `zenodo.json` on GitHub and in the SoftwareHeritage datacenters. These three repositories also hold the file `codemeta.json`. -- We are aware that Microsoft GitHub, as a profit driven commercial service, is - tainted by political and company-strategic limitations, in particular with - regard to data safety, security, adherence to scientific community-standards - and long-term viability. However, GitHub's comfortable integration with Zenodo - yields a lot of benefits that we could not achive otherwise with our limited - resources. We hope that a comparable integration will be developed in the - future for better suited Forges such as [Forgejo](https://forgejo.org/) or +- We recognize that GitHub, a commercial platform owned by Microsoft, is subject +to business and strategic considerations that may raise concerns regarding data +governance, security, adherence to scientific community standards, and long-term +sustainability. Nevertheless, GitHub's seamless integration with Zenodo provides +substantial benefits, including automated archiving and DOI assignment, which would +be difficult to achieve with our current resources. We hope that a comparable integration +will be developed in the future for better suited Forges such as [Forgejo](https://forgejo.org/) or self-hosted [GitLab](gitlab.com). ### Interoperable From b781607c6337b7b8430d11b9688d1321013fb04d Mon Sep 17 00:00:00 2001 From: ChristianMorland Date: Thu, 16 Jul 2026 13:09:56 +0200 Subject: [PATCH 14/17] merge charts and fair README changes --- README.md | 224 ++++++++++------------------- install_TiMBA_ToolBox_from_pip.txt | 1 - 2 files changed, 77 insertions(+), 148 deletions(-) delete mode 100644 install_TiMBA_ToolBox_from_pip.txt diff --git a/README.md b/README.md index e48f224..40f13ce 100644 --- a/README.md +++ b/README.md @@ -13,37 +13,6 @@ [![DOI](https://joss.theoj.org/papers/10.21105/joss.08034/status.svg)](https://doi.org/10.21105/joss.08034) [![License](https://img.shields.io/github/license/TI-Forest-Sector-Modelling/TiMBA?style=flat)](https://github.com/TI-Forest-Sector-Modelling/TiMBA/blob/main/COPYING) ------------------ - - -- [Cite TiMBA](#cite-timba) -- [Install TiMBA](#install-timba) - - [Quick start with uv](#quick-start-with-uv) - - [Known Issues](#known-issues) - - [Installation Process](#installation-process) - - [Double check installation and test suite](#double-check-installation-and-test-suite) -- [Use TiMBA](#use-timba) - - [Model settings](#model-settings) - - [Settings as parameters](#settings-as-parameters) - - [Advanced settings](#advanced-settings) -- [TiMBA extended model description](#timba-extended-model-description) -- [Extensions for TiMBA](#extensions-for-timba) -- [Roadmap and project status](#roadmap-and-project-status) -- [Contributing to the project](#contributing-to-the-project) -- [Authors](#authors) -- [Contribution statement](#contribution-statement) -- [License and copyright note](#license-and-copyright-note) -- [Acknowledgements](#acknowledgements) -- [References](#references) - - - -**TiMBA** is a partial economic equilibrium model for the global forest products -market. The model endogenously simulates production, consumption and trade of -wood and wood-based products in 180 countries. TiMBA recursively computes the -market equilibrium for each country and product in a given period by maximizing -the social surplus in the global forest sector. In the equilibrium processes, -product supply, demand and price are balanced for each simulation period. ----------------- **TiMBA** is a partial economic equilibrium model for the global forest products market. The model endogenously simulates @@ -53,27 +22,6 @@ In the equilibrium processes, product supply, demand and price are balanced for ----------------- -- [TiMBA - Timber market Model for policy-Based Analysis](#timba---timber-market-model-for-policy-based-analysis) - - [1. Cite TiMBA](#1-cite-timba) - - [2. Installation](#2-installation) - - [2.1. PyPI package](#21-pypi-package) - - [2.2. GitHub repository](#22-github-repository) - - [3. Use TiMBA](#3-use-timba) - - [4. Model extensions](#4-model-extensions) - - [5. Project structure](#5-project-structure) - - [6. Model settings](#6-model-settings) - - [6.1. Settings as parameters](#61-settings-as-parameters) - - [6.2. Advanced settings](#62-advanced-settings) - - [7. TiMBA extended model description](#7-timba-extended-model-description) - - [8. Extensions for TiMBA](#8-extensions-for-timba) - - [9. Roadmap and project status](#9-roadmap-and-project-status) - - [10. Contributing to the project](#10-contributing-to-the-project) - - [11. Authors](#11-authors) - - [12. Contribution statement](#12-contribution-statement) - - [13. License and copyright note](#13-license-and-copyright-note) - - [14. Acknowledgements](#14-acknowledgements) - - [15. References](#15-references) - ----------------- @@ -85,27 +33,17 @@ TI-FSM, Morland, C., Schier, F., Tandetzki, J., Honkomp, T. (2025). TiMBA (Timbe [Download BibTeX](./citation.bib) The authors' collective is named "Thünen Institute Forest Sector Modelling -(TI-FSM)"". The individual authors are listed as Co-authors in alphabetical +(TI-FSM)". The individual authors are listed as Co-authors in alphabetical order. -The authors' collective is named Thünen Institute Forest Sector Modelling (TI-FSM). The individual authors are listed as -co-authors in alphabetical order. ## 2. Installation -## Install TiMBA - -The package is developed and tested with Python 3.9 on Windows 11. TiMBA is -compatible with Python versions between 3.9 - 3.11. The functionality with -supported Python versions is continuously tested using GitHub CI with [operating -system images](https://github.com/actions/runner-images#available-images) -`windows-latest` and `ubuntu-latest`. - -### Requirements +### 2.1 Requirements - Operating system: Linux or Windows on a x64 architecture. We test Windows 11 and Ubuntu 24.04, but other Windows and Linux versions are likely to work too. -- The Python package manager [uv](https://docs.astral.sh/uv/). We strongly - recommend to use `uv`, because it provides a very user-friendly, quick, +- The Python package manager [uv](https://docs.astral.sh/uv/). We + recommend to use `uv`, because it provides a user-friendly, quick, platform-independent and reliable way to install, use and develop TiMBA. That said, TiMBA can be also installed classically by creating a virtual @@ -115,48 +53,85 @@ environment use the right Python version (if your system Python doesn't happen to be version 3.9 - 3.11), you need to install a supported Python the the operating system level and create the virtual environment with that version, e.g. `python3.11 -m venv .venv`. -Before proceeding, please ensure that Python is installed on your system. -It can be downloaded and installed from [Python.org](https://www.python.org/downloads/release/python-3119/). ***Known Issues***: -TiMBA currently has compatibility issues on macOS and with Python 3.12 and 3.13. Users may experience unexpected behavior during the optimization -process on macOS, as well as package installation problems when using Python 3.12 and 3.13. -We recommend using Python 3.9–3.11 on Windows or Ubuntu OS for best results until full support of Python 3.12 and 3.13 and macOS is implemented. +TiMBA currently has compatibility issues on macOS and with Python 3.12 or higher Users may experience unexpected behavior during the optimization +process on macOS, as well as package installation problems when using Python 3.12 or higher. +We recommend using Python 3.9–3.11 on Windows or Ubuntu OS for best results until full support for newer Python versions and macOS is implemented. -### Install uv +### 2.2 Install uv -#### Linux +#### 2.2.1 Linux/MacOS ```bash curl -LsSf https://astral.sh/uv/install.sh | sh ``` -#### Windows +#### 2.2.2 Windows ```powershell powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" ``` -### Install the TiMBA command line programs +### 2.3 Install the TiMBA command line programs If you want to use TiMBA as executable program, install it globally like so: ``` bash uv tool install -p 3.11 pytimba ``` -You will then have access to the CLI commands `load_timba`, `run_carbon_module`, `run_timba`. Usage instructions are available with the argument `--help` for each of the commands. + +#### Troubleshooting: `uv` command not found + +If you encounter the following error message: + +``` +'uv' is not recognized as an internal or external command, +operable program or batch file. +``` + +`uv` may be installed successfully, but the installation directory is not available in your `PATH`. + +Check the installation output for the line: + +``` +installing to +``` + +Verify that `uv` is available at this location: + +```powershell +\uv.exe --version +``` + +If this command returns the installed `uv` version, add the directory temporarily to your current terminal session: + +**Windows CMD:** + +```cmd +set PATH=%PATH%; +``` + +For a permanent solution, add `` to your user `PATH` environment variable in Windows. + +Afterwards, rerun: + +```bash +uv tool install -p 3.11 pytimba +``` + +You will then have access to the CLI command `timba` and its subcommands `timba load`, `timba carbon`, `timba run` and `timba dashboard`. Usage instructions are available with the argument `--help` for each of the commands. See section [Model settings](#model-settings) for further details. -### Install TiMBA from PyPi +### 2.3 Install TiMBA from PyPi If you want to use TiMBA as part of your own program, you can install it from PyPi like so: ``` bash -uv init -p 3.11 my_timba_program # Create a project skeleton with Python 3.11 +uv init -p 3.11 # Create a project skeleton with Python 3.11 cd my_timba_program # Change into the project directory uv add pytimba # Install TiMBA into the project's virtual environment. ``` Use TiMBA in Python modules, for example -### 2.1. PyPI package ```bash pip install pytimba @@ -190,7 +165,7 @@ parameters.max_period = 2 run_timba(Parameters=parameters) ``` -### 2.2. GitHub repository +### 2.4. GitHub repository Clone the repository Begin by cloning the repository to your local machine using the following command: ```python @@ -203,8 +178,10 @@ Switch to the TiMBA directory cd TiMBA ``` Create a virtual environment ->It is recommended to set up a virtual environment for TiMBA to manage dependencies. The package is tested for Python versions up to 3.11. With a newer Python version, we can not >guarantee the full functionality of the package. Select the correct Python interpreter. +>It is recommended to set up a virtual environment for TiMBA to manage dependencies. The package is tested for Python versions up to 3.11. With a newer Python version, we can not guarantee the full functionality of the package. Select the correct Python interpreter. + Show installed versions: + 1. Clone the repository Begin by cloning the repository to your local machine using the following command: >git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git @@ -247,34 +224,6 @@ Double check if installation was successful by running following command from te The help provides you information about the basic model commands. -```python -py -0 -``` -If you have installed multiple versions of Python, activate the correct version using the py-Launcher. -```python -py -3.11 -m venv venv -``` -If you are using only a single version of Python on your computer: -```python -python -m venv venv -``` -Activate the virtual environment ->Enable the virtual environment to isolate TiMBA dependencies. -```python -venv\Scripts\activate -``` -Or for Linux: -```python -source venv/bin/activate -``` -Install TiMBA in the editable mode -```python -pip install -e . -``` -If the following error occurs: "ERROR: File "setup.py" or "setup.cfg" not found." you might need to update the pip version you use with: -```python -python.exe -m pip install --upgrade pip -``` Double check installation and test suite: >Double check if installation was successful by running following command from terminal: ```python @@ -282,7 +231,7 @@ timba --help ``` The help provides you information about the basic model commands. -### Testing TiMBA +### 2.5 Testing TiMBA The TiMBA model comes with a test suite to ensure its functionality. Run the test suite to check the functionality of the package and validate the produced @@ -294,20 +243,8 @@ results with those provided by the TI-FSM using the coverage report: ``` To reduce the test suite running time, only the first period will be computed -and compared. The test suite results will not be saved. The computed results and -provided validation results are compared with a relative tolerance of 5%. -To reduce the test suite running time, only the first period will be computed and compared. The test suite results will not be saved. -The computed results and provided validation results are compared with a relative tolerance of 5%. - -### Known Issues -Python versions >=3.12 are currently not supported because the pinned -dependencies (e.g. pandas) are not compatible with those Python versions. We -recommend using Python 3.9–3.11 for best results. - +and compared. The test suite results will not be saved. -## Use TiMBA -The package comes with a built-in CLI to compute the TiMBA for various inputs. While arguments are documented in the output of calling `run_timba --help` from the terminal, an important part to mention is user input data that need to be imported from a selected folder. You shall not change the following structure within the data folder: -TiMBA is provided with an input file (scenario_input.xlsx), including all input data necessary to run the model. The section [TiMBA extended model description](#timba-extended-model-description-) provides a detailed description of the included input data. ## 3. Use TiMBA TiMBA provides a built-in command-line interface (CLI) that enables users to download input data, execute simulations, and analyse model outputs. @@ -439,6 +376,7 @@ Each model run creates a new set of output files using timestamp-based filenames ```text results_D20260708T14-32-18.csv ``` + **Important output information** No output file will ever be overwritten by the application itself. New results-files will be generated in the format @@ -448,19 +386,12 @@ created on additional runs. Log information simply gets appended to the existing logfile. Removing the logfile ahead of executing the model won't result in errors. -### Model settings - -Multiple settings are integrated in TiMBA to allow users to interact with the -model and adapt the modelling parameters to their research interests. The following -chapter provides a brief overview of the model settings. A detailed description -of the settings is provided in the documentation. - -This guarantees that previous simulation results remain available for comparison and documentation. - ## 6. Model settings Multiple settings are integrated for the ***timba run*** command to allow users to interact with the model and adapt the modelling parameters to their research interests. -The following chapter provides a brief overview of the model settings. A detailed description of the settings is provided in the model documentation (TI-FSM 2025). +The following chapter provides a brief overview of the model settings. A detailed description of the settings is provided in the model documentation ([TI-FSM 2025](https://literatur.thuenen.de/digbib_extern/dn069603.pdf)). + +This guarantees that previous simulation results remain available for comparison and documentation. Basic model settings include: @@ -497,6 +428,7 @@ Check if CLI command is registered and available on your computer by executing: - >timba run --help Default settings can be changed in the following way: (Note that the change of default settings as described below is for demonstration purposes only, and the results have not been validated.): + - > timba run -MP=5 -MB="RCG_specific" -CP="True" For this example, TiMBA will simulate 5 periods using calculated prices as product prices and shadow prices as world market prices. @@ -566,7 +498,7 @@ Several projects are currently extending different components of TiMBA: Frequently check [TiMBA repository](https://github.com/TI-Forest-Sector-Modelling/TiMBA) for new releases. -## FAIR research software +## 9. FAIR research software We attempt to adhere as much as possible to the FAIR Principles for research software (e.g. see Barker et al. 2022 and Chue Hong et al. 2022) and reach high @@ -576,7 +508,7 @@ in the GitHub repository or via email to [wf-timba@thuenen.de](mailto:wf-timba@t In the following we detail our efforts and considerations. -### Findable +### 9.1 Findable - Zenodo provides a DOI with extensive metadata according to the DataCite schema. - Separate DOIs for each release and one representing all releases. @@ -590,7 +522,7 @@ In the following we detail our efforts and considerations. - We provide machine-actionable citation information in the [Citation File Format (CFF)](https://citation-file-format.github.io/). -### Accessible +### 9.2 Accessible - The source code can be accessed in the form of a *git remote* from GitHub, via *http* from Zenodo, but also by Python package managers through the [Python @@ -611,9 +543,9 @@ be difficult to achieve with our current resources. We hope that a comparable in will be developed in the future for better suited Forges such as [Forgejo](https://forgejo.org/) or self-hosted [GitLab](gitlab.com). -### Interoperable +### 9.3 Interoperable -#### Software interoperability +#### 9.3.1 Software interoperability - TiMBA installs both as executable script (`timba_run`) as well as as a Python module (`TiMBA`). The script copies its output also to STDOUT and allows to @@ -628,7 +560,7 @@ will be developed in the future for better suited Forges such as [Forgejo](https also adhere to FAIR principles, are version-controlled in GitHub and can be referenced with DOIs registered by Zenodo. -#### Data interoperability +#### 9.3.2 Data interoperability - TiMBA relies on a set of required input data. The canonical versions of these data (a non-trivial scientific output) are also kept [version controlled in @@ -652,7 +584,7 @@ will be developed in the future for better suited Forges such as [Forgejo](https - TiMBA output is written to universally readable CSV-files. We plan to describe these files with standardized metadata in the future. -### Reusable +### 9.4 Reusable - TiMBA has dependencies and sub-dependencies which are extensively recorded in the `uv.lock` file to ensure reproducibility. @@ -673,16 +605,15 @@ will be developed in the future for better suited Forges such as [Forgejo](https contribute increase the chances that this software is being reused in our research community. -## Contributing to the project -We welcome contributions, additions and suggestion to further develop or improve the code and the model. To check, discuss and include them into this project, we would like you to share your ideas with us so that we can agree on the requirements needed for accepting your contribution. + ## 10. Contributing to the project -We welcome contributions, additions, and suggestion to further develop or improve the code and the model. To check, discuss and include them into this project, we would like you to share your ideas with us so that we can agree on the requirements needed for accepting your contribution. +We welcome contributions, additions and suggestion to further develop or improve the code and the model. To check, discuss and include them into this project, we would like you to share your ideas with us so that we can agree on the requirements needed for accepting your contribution. + You can contact us directly via GitHub by creating issues, or by writing an Email to: [wf-timba@thuenen.de](mailto:wf-timba@thuenen.de) -So far, this README serves as a comprehensive introduction and guidance on how to get started. ´The model documentation (TI-FSM 2025) and model validation (TI-FSM 2026) enables a deeper dive. - +So far, this README serves as a comprehensive introduction and guidance on how to get started. ´The model documentation ([TI-FSM 2025]()) and model validation ([TI-FSM 2026]()) enables a deeper dive. ## 11. Authors @@ -736,9 +667,8 @@ This work is the result of great joint efforts of the forest products market ana - The Thünen Institut of Forestry and its Head Matthias Dieter for providing financial resources over the years - [makeareadme.com](https://www.makeareadme.com/) for providing the template this README is leaned on. -## References -- Barker, M., Chue Hong, N.P., Katz, D.S. et al. Introducing the FAIR Principles for research software. Sci Data 9, 622 (2022). https://doi.org/10.1038/s41597-022-01710-x ## 15. References +- Barker, M., Chue Hong, N.P., Katz, D.S. et al. Introducing the FAIR Principles for research software. Sci Data 9, 622 (2022). https://doi.org/10.1038/s41597-022-01710-x - Buongiorno, J.; Zhu, S.; Zhang, D.; Turner, J.; Tomberlin, D. The Global Forest Products Model; Academic Press: Cambridge, MA, USA, 2003; ISBN 978-0-12-141362-0 - Buongiorno, J. Global modelling to predict timber production and prices: The GFPM approach. Forestry 2015, 88, 291–303. - Buongiorno, J.; and Zhu, S. 2015. Technical change in forest sector models: The GFPM approach. Scand. J. For. Research, 30, 30-48. diff --git a/install_TiMBA_ToolBox_from_pip.txt b/install_TiMBA_ToolBox_from_pip.txt deleted file mode 100644 index f08d0ea..0000000 --- a/install_TiMBA_ToolBox_from_pip.txt +++ /dev/null @@ -1 +0,0 @@ -pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ TiMBA_ToolBox From 92bc5e2b460fa4b197e64b7fe866736fad530b39 Mon Sep 17 00:00:00 2001 From: ChristianMorland Date: Thu, 16 Jul 2026 13:27:50 +0200 Subject: [PATCH 15/17] update links and toc --- README.md | 49 +++++++++++++++++++++++++++++++++++++++++++------ 1 file changed, 43 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 40f13ce..5ee7e55 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,44 @@ equilibrium for each country and product in a given period by maximizing the soc In the equilibrium processes, product supply, demand and price are balanced for each simulation period. ----------------- - + + +- [TiMBA - Timber market Model for policy-Based Analysis](#timba---timber-market-model-for-policy-based-analysis) + - [Cite TiMBA](#cite-timba) + - [Installation](#installation) + - [Requirements](#requirements) + - [Install TiMBA with uv](#install-timba-with-uv) + - [Linux/MacOS](#linuxmacos) + - [Windows](#windows) + - [Install the TiMBA command line programs](#install-the-timba-command-line-programs) + - [Troubleshooting: uv command not found](#troubleshooting-uv-command-not-found) + - [Install TiMBA from PyPi](#install-timba-from-pypi) + - [Install TiMBA from GitHub repository](#install-timba-from-github-repository) + - [Testing TiMBA installation](#testing-timba-installation) + - [Use TiMBA](#use-timba) + - [Supplementary modules](#supplementary-modules) + - [Project structure](#project-structure) + - [Model settings](#model-settings) + - [Settings as parameters](#settings-as-parameters) + - [Advanced settings](#advanced-settings) + - [TiMBA extended model description](#timba-extended-model-description) + - [Supplementary modules for TiMBA](#supplementary-modules-for-timba) + - [Roadmap and project status](#roadmap-and-project-status) + - [FAIR research software](#fair-research-software) + - [Findable](#findable) + - [Accessible](#accessible) + - [Interoperable](#interoperable) + - [Software interoperability](#software-interoperability) + - [Data interoperability](#data-interoperability) + - [Reusable](#reusable) + - [Contributing to the project](#contributing-to-the-project) + - [Authors](#authors) + - [Contribution statement](#contribution-statement) + - [License and copyright note](#license-and-copyright-note) + - [Acknowledgements](#acknowledgements) + - [References](#references) + + ----------------- @@ -60,7 +97,7 @@ process on macOS, as well as package installation problems when using Python 3.1 We recommend using Python 3.9–3.11 on Windows or Ubuntu OS for best results until full support for newer Python versions and macOS is implemented. -### 2.2 Install uv +### 2.2 Install TiMBA with uv #### 2.2.1 Linux/MacOS @@ -72,7 +109,7 @@ curl -LsSf https://astral.sh/uv/install.sh | sh powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" ``` -### 2.3 Install the TiMBA command line programs +#### 2.2.4 Install the TiMBA command line programs If you want to use TiMBA as executable program, install it globally like so: @@ -165,7 +202,7 @@ parameters.max_period = 2 run_timba(Parameters=parameters) ``` -### 2.4. GitHub repository +### 2.4. Install TiMBA from GitHub repository Clone the repository Begin by cloning the repository to your local machine using the following command: ```python @@ -231,7 +268,7 @@ timba --help ``` The help provides you information about the basic model commands. -### 2.5 Testing TiMBA +### 2.5 Testing TiMBA installation The TiMBA model comes with a test suite to ensure its functionality. Run the test suite to check the functionality of the package and validate the produced @@ -613,7 +650,7 @@ You can contact us directly via GitHub by creating issues, or by writing an Emai [wf-timba@thuenen.de](mailto:wf-timba@thuenen.de) -So far, this README serves as a comprehensive introduction and guidance on how to get started. ´The model documentation ([TI-FSM 2025]()) and model validation ([TI-FSM 2026]()) enables a deeper dive. +So far, this README serves as a comprehensive introduction and guidance on how to get started. ´The model documentation ([TI-FSM 2025](https://literatur.thuenen.de/digbib_extern/dn069603.pdf)) and model validation ([TI-FSM 2026](https://literatur.thuenen.de/digbib_extern/dn070984.pdf)) enables a deeper dive. ## 11. Authors From bc06520a34ea5a03f748403bad56bb9f2bdb8906 Mon Sep 17 00:00:00 2001 From: ChristianMorland Date: Thu, 16 Jul 2026 13:58:16 +0200 Subject: [PATCH 16/17] update passage about known issues with macOS --- README.md | 71 ++++++++++++++++++++++++++----------------------------- 1 file changed, 34 insertions(+), 37 deletions(-) diff --git a/README.md b/README.md index 5ee7e55..9a7db37 100644 --- a/README.md +++ b/README.md @@ -24,39 +24,39 @@ In the equilibrium processes, product supply, demand and price are balanced for - [TiMBA - Timber market Model for policy-Based Analysis](#timba---timber-market-model-for-policy-based-analysis) - - [Cite TiMBA](#cite-timba) - - [Installation](#installation) - - [Requirements](#requirements) - - [Install TiMBA with uv](#install-timba-with-uv) - - [Linux/MacOS](#linuxmacos) - - [Windows](#windows) - - [Install the TiMBA command line programs](#install-the-timba-command-line-programs) - - [Troubleshooting: uv command not found](#troubleshooting-uv-command-not-found) - - [Install TiMBA from PyPi](#install-timba-from-pypi) - - [Install TiMBA from GitHub repository](#install-timba-from-github-repository) - - [Testing TiMBA installation](#testing-timba-installation) - - [Use TiMBA](#use-timba) - - [Supplementary modules](#supplementary-modules) - - [Project structure](#project-structure) - - [Model settings](#model-settings) - - [Settings as parameters](#settings-as-parameters) - - [Advanced settings](#advanced-settings) - - [TiMBA extended model description](#timba-extended-model-description) - - [Supplementary modules for TiMBA](#supplementary-modules-for-timba) - - [Roadmap and project status](#roadmap-and-project-status) - - [FAIR research software](#fair-research-software) - - [Findable](#findable) - - [Accessible](#accessible) - - [Interoperable](#interoperable) - - [Software interoperability](#software-interoperability) - - [Data interoperability](#data-interoperability) - - [Reusable](#reusable) - - [Contributing to the project](#contributing-to-the-project) - - [Authors](#authors) - - [Contribution statement](#contribution-statement) - - [License and copyright note](#license-and-copyright-note) - - [Acknowledgements](#acknowledgements) - - [References](#references) + - [1. Cite TiMBA](#1-cite-timba) + - [2. Installation](#2-installation) + - [2.1 Requirements](#21-requirements) + - [2.2 Install TiMBA with uv](#22-install-timba-with-uv) + - [2.2.1 Linux/MacOS](#221-linuxmacos) + - [2.2.2 Windows](#222-windows) + - [2.2.4 Install the TiMBA command line programs](#224-install-the-timba-command-line-programs) + - [Troubleshooting: `uv` command not found](#troubleshooting-uv-command-not-found) + - [2.3 Install TiMBA from PyPi](#23-install-timba-from-pypi) + - [2.4. Install TiMBA from GitHub repository](#24-install-timba-from-github-repository) + - [2.5 Testing TiMBA installation](#25-testing-timba-installation) + - [3. Use TiMBA](#3-use-timba) + - [4. Supplementary modules](#4-supplementary-modules) + - [5. Project structure](#5-project-structure) + - [6. Model settings](#6-model-settings) + - [6.1. Settings as parameters](#61-settings-as-parameters) + - [6.2. Advanced settings](#62-advanced-settings) + - [7. TiMBA extended model description](#7-timba-extended-model-description) + - [8. Supplementary modules for TiMBA](#8-supplementary-modules-for-timba) + - [9. Roadmap and project status](#9-roadmap-and-project-status) + - [9. FAIR research software](#9-fair-research-software) + - [9.1 Findable](#91-findable) + - [9.2 Accessible](#92-accessible) + - [9.3 Interoperable](#93-interoperable) + - [9.3.1 Software interoperability](#931-software-interoperability) + - [9.3.2 Data interoperability](#932-data-interoperability) + - [9.4 Reusable](#94-reusable) + - [10. Contributing to the project](#10-contributing-to-the-project) + - [11. Authors](#11-authors) + - [12. Contribution statement](#12-contribution-statement) + - [13. License and copyright note](#13-license-and-copyright-note) + - [14. Acknowledgements](#14-acknowledgements) + - [15. References](#15-references) @@ -92,10 +92,7 @@ operating system level and create the virtual environment with that version, e.g. `python3.11 -m venv .venv`. ***Known Issues***: -TiMBA currently has compatibility issues on macOS and with Python 3.12 or higher Users may experience unexpected behavior during the optimization -process on macOS, as well as package installation problems when using Python 3.12 or higher. -We recommend using Python 3.9–3.11 on Windows or Ubuntu OS for best results until full support for newer Python versions and macOS is implemented. - +TiMBA currently does not work with Python 3.12 or higher. We observe numerical discrepancies (>5% compared to results generated on Windows or Linux) when running TiMBA on macOS which could traced back to the solver OSQP in CVXPY. The results with MacOS have not been validated. We are investigating the issue. ### 2.2 Install TiMBA with uv From 12e8c9214b1dc8ba9fb71e89efd49a27ec28b83b Mon Sep 17 00:00:00 2001 From: ChristianMorland Date: Fri, 17 Jul 2026 11:44:09 +0200 Subject: [PATCH 17/17] final edit of README --- README.md | 40 +++++++++++++++++++++++----------------- 1 file changed, 23 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 07a38b0..b8235f0 100644 --- a/README.md +++ b/README.md @@ -28,10 +28,14 @@ In the equilibrium processes, product supply, demand and price are balanced for - [2. Installation](#2-installation) - [2.1 Requirements](#21-requirements) - [2.2 Install uv](#22-install-uv) + - [2.2.1 Linux](#221-linux) + - [2.2.2 Windows](#222-windows) - [2.3 Install the TiMBA command line programs](#23-install-the-timba-command-line-programs) + - [2.3.1 Troubleshooting: `uv` command not found](#231-troubleshooting-uv-command-not-found) - [2.4 Install TiMBA from PyPi](#24-install-timba-from-pypi) - [2.5 Install TiMBA from GitHub](#25-install-timba-from-github) - - [3. Testing TiMBA](#3-testing-timba) + - [2.5.1 Install from GitHub without 'uv\`](#251-install-from-github-without-uv) + - [2.6. Testing TiMBA](#26-testing-timba) - [3. Use TiMBA](#3-use-timba) - [4. Supplementary modules](#4-supplementary-modules) - [5. Project structure](#5-project-structure) @@ -45,6 +49,8 @@ In the equilibrium processes, product supply, demand and price are balanced for - [10.1 Findable](#101-findable) - [10.2 Accessible](#102-accessible) - [10.3 Interoperable](#103-interoperable) + - [10.3.1 Software interoperability](#1031-software-interoperability) + - [10.3.2 Data interoperability](#1032-data-interoperability) - [10.4 Reusable](#104-reusable) - [11. Contributing to the project](#11-contributing-to-the-project) - [12. Authors](#12-authors) @@ -52,6 +58,8 @@ In the equilibrium processes, product supply, demand and price are balanced for - [14. License and copyright note](#14-license-and-copyright-note) - [15. Acknowledgements](#15-acknowledgements) - [16. References](#16-references) + + ----------------- ## 1. Cite TiMBA @@ -76,22 +84,22 @@ system images](https://github.com/actions/runner-images#available-images) ### 2.1 Requirements - Operating system: Linux or Windows on a x64 architecture. We test Windows 11 - and Ubuntu 24.04, but other Windows and Linux versions are likely to work too. + and Ubuntu 24.04 but other Windows and Linux versions are likely to work, too. - The Python package manager [uv](https://docs.astral.sh/uv/). We recommend to - use `uv`, because it provides a user-friendly, quick, platform-independent - and reliable way to install, use and develop TiMBA. + use `uv`, because it provides a user-friendly, quick, platform-independent, + and reliable way to install, use, and develop TiMBA. That said, TiMBA can be also installed classically by creating a virtual environment using [`venv`](https://docs.python.org/3.14/library/venv.html) and -installing with [`pip`](https://pip.pypa.io/en/stable/). To make the virtual -environment use the right Python version (if your system Python doesn't happen -to be version 3.9 - 3.11), you need to install a supported Python the the -operating system level and create the virtual environment with that version, +installing with [`pip`](https://pip.pypa.io/en/stable/). If your system Python +doesn't happen to be version 3.9 - 3.11, you need to install a supported Python +version to make the virtual environment use. + e.g. `python3.11 -m venv .venv`. ***Known Issues***: TiMBA currently does not work with Python 3.12 or higher. We observe numerical discrepancies -(>5% compared to results generated on Windows or Linux) when running TiMBA on macOS which +(>5% compared to results generated on Windows or Linux) when running TiMBA on MacOS which could traced back to the solver OSQP in CVXPY. The results with MacOS have not been validated. We are investigating the issue. @@ -197,6 +205,7 @@ To install TiMBA in editable mode, so that you can modify the TiMBA source code, uv run timba run --help uv run timba run -MP=1 ``` + #### 2.5.1 Install from GitHub without 'uv` If you want to develop without using `uv`, you can install TiMBA with `venv` and `pip`, for example for Windows like so: @@ -207,17 +216,14 @@ Windows](https://github.com/oleksis/pylauncher/blob/master/docs/launcher.rst) installed. 1. Clone the repository and move into the project folder: - ```bash - git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git timba - cd timba -``` + >git clone https://github.com/TI-Forest-Sector-Modelling/TiMBA.git timba + >cd timba 2. Create a virtual environment - Select the correct Python interpreter. - Show installed versions: + Show installed versions: >py -0 - > + - If you have installed multiple versions of Python, activate the correct version using the py-Launcher. >py -3.11 -m venv venv > @@ -235,7 +241,7 @@ Enable the virtual environment to isolate TiMBA dependencies. you might need to update the pip version you use with: >python.exe -m pip install --upgrade pip -### 3. Testing TiMBA +### 2.6. Testing TiMBA The TiMBA model comes with a test suite to ensure its functionality. Run the test suite to check the functionality of the package and validate the produced