diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index c217fed9..60e0cfff 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -4,54 +4,85 @@ on: workflow_dispatch: inputs: version: - description: 'New version' + description: New semantic version (for example, 2.3.1) required: true +permissions: + contents: write + jobs: - update-and-build: + update-build-and-release: runs-on: ubuntu-latest + env: + VERSION: ${{ inputs.version }} steps: - - name: Check out the repo - uses: actions/checkout@v2 + - name: Check out the repository + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Validate version + shell: bash + run: | + if [[ ! "$VERSION" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then + echo "Version must use MAJOR.MINOR.PATCH without a prefix." + exit 1 + fi + if git rev-parse "$VERSION" >/dev/null 2>&1; then + echo "Git tag $VERSION already exists." + exit 1 + fi + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.12" + + - name: Install Poetry + run: python -m pip install "poetry>=1.8,<3" - - name: Update pyproject.toml version + - name: Set version, install, test, and build run: | - sed -i "s/^version = .*/version = \"${{ github.event.inputs.version }}\"/" pyproject.toml - git config --global user.name 'GitHub Actions' - git config --global user.email 'actions@github.com' - git commit -am "ci: Version bump ${{ github.event.inputs.version }}" - git push + poetry version "$VERSION" + poetry install --no-interaction + poetry run pytest + poetry build + + - name: Commit and tag the version + run: | + git config user.name "GitHub Actions" + git config user.email "actions@github.com" + git add pyproject.toml + git commit -m "chore: release $VERSION" + git tag "$VERSION" + git push origin "HEAD:${GITHUB_REF_NAME}" + git push origin "$VERSION" - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 + uses: docker/setup-buildx-action@v3 - - name: Login to Docker Hub - uses: docker/login-action@v1 + - name: Log in to Docker Hub + uses: docker/login-action@v3 with: username: ${{ vars.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_TOKEN }} - - name: Build and push Docker Image - uses: docker/build-push-action@v2 + - name: Build and push Docker image + uses: docker/build-push-action@v6 with: context: . file: ./Dockerfile - platforms: linux/amd64 #,linux/arm64 future ;) + platforms: linux/amd64 push: true - tags: ${{ vars.DOCKER_IMAGE_NAME }}:${{ github.event.inputs.version }}, ${{ vars.DOCKER_IMAGE_NAME }}:latest - - - name: Push version bump commit - run: | - git tag ${{ github.event.inputs.version }} - git push origin ${{ github.event.inputs.version }} - git push + tags: | + ${{ vars.DOCKER_IMAGE_NAME }}:${{ env.VERSION }} + ${{ vars.DOCKER_IMAGE_NAME }}:latest - - name: Create GitHub Release - uses: actions/create-release@v1 + - name: Create GitHub release and upload Python artifacts env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - tag_name: ${{ github.event.inputs.version }} - release_name: Release ${{ github.event.inputs.version }} - draft: false - prerelease: false + GH_TOKEN: ${{ github.token }} + run: | + gh release create "$VERSION" dist/* \ + --title "Release $VERSION" \ + --generate-notes \ + --verify-tag diff --git a/.github/workflows/soil-raster-tests.yml b/.github/workflows/soil-raster-tests.yml new file mode 100644 index 00000000..cf99025c --- /dev/null +++ b/.github/workflows/soil-raster-tests.yml @@ -0,0 +1,32 @@ +name: Soil raster compatibility + +on: + push: + pull_request: + +jobs: + regression-tests: + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, windows-latest] + python-version: ["3.8", "3.12"] + runs-on: ${{ matrix.os }} + + steps: + - name: Check out repository + uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install Poetry + run: python -m pip install poetry + + - name: Install dependencies + run: poetry install + + - name: Test one-band and two-band soil rasters + run: poetry run pytest -q pythia/tests/raster_functions_test.py diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..45dcfb3f --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,36 @@ +# Changelog + +## Unreleased + +### Fixed + +- Restored backward compatibility with legacy one-band GHR soil rasters. +- Automatically detect one-band legacy and two-band encoded soil rasters. +- Resolve legacy raster IDs through `GHR.db` and provide actionable errors for + missing database records and DSSAT `.SOL` files. +- Prevent out-of-bounds soil raster access and support coordinate reprojection. +- Read only the requested two-band raster pixel instead of loading both bands + for every lookup. +- Corrected and documented the Sri Lanka example workflow; its existing + one-band `ggcmi_soils_2.tif` does not require conversion. +- Fixed plugin hook execution so context is passed once and plugin return values + are composed correctly. + +### Added + +- Added `--configure-example` and `--validate-example` commands for the + downloadable Sri Lanka data. +- Added a reproducible example-data packager that removes local/generated files, + restores portable JSON templates, enforces the GitHub asset size limit, and + writes a SHA-256 checksum. +- Expanded installation, conceptual, input configuration, troubleshooting, and + release documentation. +- Updated the release workflow to test and build wheel/source artifacts before + publishing them. + +### Testing + +- Added self-contained regression coverage for both soil raster formats, + including the Sri Lanka coordinate and profile reported by users. +- Added tests for repeatable example configuration, archive portability, and + plugin hook execution. diff --git a/README.md b/README.md index cb65e556..981703b3 100644 --- a/README.md +++ b/README.md @@ -1,123 +1,207 @@ -# DSSAT-Pythia Installation Guide +# Pythia + +Pythia is an extensible framework for running point-based crop models over +spatial data. It turns raster and vector inputs into DSSAT experiments, runs +DSSAT, and can aggregate the resulting outputs. + +The usual workflow is: + +1. read a JSON configuration; +2. select locations from a vector or raster data set; +3. resolve weather, soil, cultivar, and management inputs for each location; +4. create DSSAT experiment directories; +5. run DSSAT and optionally aggregate results. + +## Requirements + +- Python 3.8 or newer (the automated tests cover Python 3.8 and 3.12); +- a working [DSSAT installation](https://get.dssat.net/); +- Git and [Poetry](https://python-poetry.org/docs/#installation) only when + building Pythia from source. + +R and RStudio are optional and are needed only for separate post-processing +scripts. They are not required to install or run Pythia. + +On Windows, enable **Developer Mode** (or run with privileges that permit +symbolic links). Pythia uses links while preparing DSSAT work directories. -## Software Requirements -To install and run DSSAT-Pythia on your PC, you will need the following software: +## Install a released build -1. **DSSAT**: - Download and install DSSAT from [DSSAT website](https://get.dssat.net/request/?sft=4). +Download the Pythia `.whl` file for your operating environment from the +[GitHub release](https://github.com/DSSAT/pythia/releases/latest). For an +isolated command that is available outside the source directory, `pipx` is the +recommended installation method: -2. **Python 3.8**: - Download the Python 3.8 installer for Windows or macOS from [Python 3.8 release page](https://www.python.org/downloads/release/python-389/). - - During installation, select “Customize installation.” - - Select all options under “Optional Features” and “Advanced Options.” - - Note: DSSAT-Pythia only works with Python 3.8. If you have another version, uninstall it and download Python 3.8 from the above link. +```console +python3 -m pip install --user pipx +python3 -m pipx ensurepath +pipx install /path/to/pythia-VERSION-py3-none-any.whl +``` -3. **Git**: - Download and install Git from [Git download page](https://git-scm.com/download/win). +Open a new terminal, then verify exactly which command is being used: -4. **Community Version of Visual Studio**: - Download and install Visual Studio from [Visual Studio website](https://visualstudio.microsoft.com/downloads/). - Select the **Desktop development with C++** workload during installation. +```console +command -v pythia +pythia --help +pipx list +``` -5. **RStudio**: - To use RStudio on your PC, install both R and RStudio: - - Download and install R from [CRAN website](https://cran.rstudio.com/). - - Download and install RStudio from [RStudio website](https://posit.co/download/rstudio-desktop/). +On Windows PowerShell, use `py` instead of `python3` and +`Get-Command pythia` instead of `command -v pythia`. ---- +To replace an older pipx installation with a new local wheel: +```console +pipx install --force /path/to/pythia-VERSION-py3-none-any.whl +``` -## Steps to Install DSSAT-Pythia on PC +Do not install into a Homebrew- or system-managed Python with +`--break-system-packages`. A virtual environment or pipx avoids modifying that +Python installation. -1. Enable **Developer Mode**: - - Open Windows Settings > Update & Security > For Developers. - - Switch on Developer Mode and restart the computer. +## Build and install from source -2. Open the **Command Prompt** in the C Drive: - - Open the C drive and type `cmd` in the address bar and press Enter. +```console +git clone https://github.com/DSSAT/pythia.git +cd pythia +python3 -m pip install --user poetry +poetry install +poetry run pytest +poetry build +pipx install --force dist/pythia-VERSION-py3-none-any.whl +``` -3. Clone the DSSAT-Pythia repository: - ```bash - git clone https://github.com/dssat/pythia.git pythia - ``` +Keep the committed `poetry.lock`; it makes dependency resolution repeatable. +During development, commands can also be run without a global installation: -4. Navigate to the cloned directory: - ```bash - cd pythia - ``` +```console +poetry run pythia --help +``` -5. Delete the `poetry.lock` file: - ```bash - del poetry.lock - ``` +## Download and configure the Sri Lanka example -6. Install Poetry: - ```bash - pip install poetry - ``` +Download `Pythia-Example-Data-VERSION.zip` from the same GitHub release as the +Pythia wheel and extract it. The resulting layout includes: -7. Install DSSAT-Pythia: - ```bash - \poetry install - \poetry build - ``` - - On Windows, poetry will be found in "C:\Users\username\AppData\Local\Programs\Python\Python38\Scripts" - -8. Install the Pythia wheel file: - - Navigate to the `dist` folder and install the `.whl` file: - ```bash - cd dist - pip install pythia-2.3.0-py3-none-any.whl - ``` - - **Note**: Check the version in the `dist` folder and adjust the command if necessary. +```text +Simulation_Data/ +├── eGHR/ +│ ├── GHR.db +│ └── LK.SOL +├── raster/ +│ └── ggcmi_soils_2.tif +├── Sri_Lanka/ +│ ├── SL_Maize.json +│ ├── SL_Rice.json +│ └── SL_Rice_env.json +├── weather_data/Sri_Lanka/ +└── OUTPUT/ +``` -9. Add the path to `pythia.exe` to your environment variables. +The three JSON files intentionally contain portable placeholders. Replace them +and validate all referenced files with one command: -10. Close the command prompt. +```console +pythia --configure-example /path/to/Simulation_Data \ + --dssat-executable /path/to/dscsm048 +``` ---- +Windows PowerShell example: -## Troubleshooting - -- If you encounter any issues during installation, delete the folder `C:\pythia` and repeat the installation steps. - ---- - -## Input Files Setup - -1. Download the `InputFiles.zip` folder from [Google Drive link](https://drive.google.com/file/d/1vlBeWEavNggcuhRMgmO79aHTYZ7aq_Im/view?usp=sharing), unzip it, and save the `Simulation_Data` folder in `C:\pythia\`. +```powershell +pythia --configure-example C:\Pythia\Simulation_Data ` + --dssat-executable C:\DSSAT48\DSCSM048.EXE +``` -2. Open the folder `C:\pythia\Simulation_Data\OUTPUT\Sri_Lanka` and remove all folders (if any). +This command: + +- replaces `<>` with the extracted directory; +- replaces `<>` with the DSSAT executable; +- keeps each portable source as `*.json.template`; +- checks the example structure and every referenced input path. - **Note**: Remove the contents from the `OUTPUT` folder every time you run the model. +It is safe to run the command again after moving the data or DSSAT. Confirm the +current configuration at any time: + +```console +pythia --validate-example /path/to/Simulation_Data +``` + +## Run the examples + +Run the complete setup, simulation, and analysis sequence: + +```console +pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Maize.json +pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Rice.json +pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Rice_env.json +``` ---- +For troubleshooting or HPC workflows, the stages can be run separately: + +```console +pythia --setup CONFIG.json +pythia --run-dssat CONFIG.json +pythia --analyze CONFIG.json +``` -## Running the Model +Use `--clean-work-dir` only when an existing work directory should be removed +before a new run. Results are written to the `workDir` defined in each JSON, +below `Simulation_Data/OUTPUT/Sri_Lanka` in the bundled examples. -1. Open the command prompt at `C:\pythia\Simulation_Data\Sri_Lanka` by typing `cmd` in the folder address bar. +## Configuration overview + +The main JSON fields are: + +| Field | Purpose | +| --- | --- | +| `workDir` | Generated DSSAT experiments and outputs | +| `templateDir` | DSSAT experiment templates | +| `weatherDir` | Weather files used by the experiments | +| `ghr_root` | `GHR.db` and DSSAT `.SOL` files | +| `default_setup` | Values and spatial lookup functions shared by runs | +| `dssat.executable` | DSSAT command-line executable | +| `runs` | Crop, management, year, and harvest-area scenarios | +| `analytics_setup` | Output aggregation options | + +See the [configuration reference](docs/json.rst) and the +[conceptual and operational guide](docs/understanding_pythia.rst) for details. + +## Soil raster compatibility -2. Run the following commands to simulate maize and rice: - ```bash - pythia --all C:/pythia/Simulation_Data/Sri_Lanka/SL_Maize.json - pythia --all C:/pythia/Simulation_Data/Sri_Lanka/SL_Rice.json - ``` +Pythia automatically supports both soil raster formats: -3. To view the output: - - Open the `.json` file in `C:\pythia\Simulation_Data\Sri_Lanka\`. - - Find the working directory in `"workDir": "C:/pythia/Simulation_Data/OUTPUT/Sri_Lanka/…"` and navigate to that folder. - - The output will be available in `.csv` format. +| Format | Raster bands | Supporting data | +| --- | ---: | --- | +| Legacy GHR | 1 | `GHR.db` plus the referenced `.SOL` files | +| Encoded profile | 2 | Referenced `.SOL` files under `ghr_root` | ---- +The Sri Lanka example intentionally uses the legacy one-band +`ggcmi_soils_2.tif`. Do not add a second band. Pythia reads the numeric cell +identifier, resolves it through `eGHR/GHR.db`, and loads the matching profile +from the `.SOL` files. See the [soil raster guide](docs/soil_rasters.rst) for +format detection, diagnostics, and migration guidance. -## Plotting Output in RStudio - -1. Open the R code file: `C:\pythia\Simulation_Data\OUTPUT\ACASA_Sri_Lanka_maize.R`. - -2. Install all required packages and modify the file location on line 22 to match the output `.csv` file. - -3. Run the R script to generate the yield plot. - -4. The plot will be saved at the location specified in line 62. +## Troubleshooting - **Note**: If you encounter errors reading the `.csv` file, open the file and delete all columns except `LATITUDE`, `LONGITUDE`, and `HWAH`. +- **`pythia: command not found`** — reopen the terminal after `pipx ensurepath`, + then inspect `pipx list` and `command -v pythia`. +- **More than one executable is found** — remove the obsolete installation and + keep the pipx path first in `PATH`. +- **Placeholders remain in JSON** — rerun `--configure-example` with absolute + paths. +- **A referenced file is missing** — run `--validate-example`; it reports the + exact configuration and path. +- **A one-band raster is rejected as requiring two bands** — an older/regressed + Pythia build is being executed. Install the release containing the legacy GHR + compatibility fix and confirm the executable path again. +- **Windows reports a symbolic-link error** — enable Developer Mode and open a + new terminal. + +## Developer and release documentation + +- [Release procedure](docs/RELEASING.md) +- [Example-data packaging instructions](docs/EXAMPLE_DATA_RELEASE.md) +- [Change log](CHANGELOG.md) + +Pythia is distributed under the BSD 3-Clause license. diff --git a/docs/EXAMPLE_DATA_RELEASE.md b/docs/EXAMPLE_DATA_RELEASE.md new file mode 100644 index 00000000..682a5b1d --- /dev/null +++ b/docs/EXAMPLE_DATA_RELEASE.md @@ -0,0 +1,68 @@ +# Preparing the example-data release asset + +The source directory is expected to be named `Simulation_Data` and to contain +the three portable configurations under `Sri_Lanka/`. Each configuration must +contain both tokens: + +```text +<> +<> +``` + +The packager can also use the `*.json.template` backups created after local +testing, so personal absolute paths are never published. + +## 1. Validate and test locally + +```console +poetry run pythia --configure-example /path/to/Simulation_Data \ + --dssat-executable /path/to/dscsm048 +poetry run pythia --validate-example /path/to/Simulation_Data +poetry run pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Maize.json +poetry run pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Rice.json +poetry run pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Rice_env.json +``` + +Review the results, then build the release asset. There is no need to restore +the active JSON files manually: the original portable templates are used. + +## 2. Create the ZIP and checksum + +```console +poetry run python scripts/prepare_example_release.py \ + /path/to/Simulation_Data \ + /path/to/Pythia-Example-Data-VERSION.zip +``` + +The command validates required data, inserts `release/Simulation_Data_README.md`, +and creates a SHA-256 file beside the archive. It excludes generated output, +`.history`, macOS metadata, logs, bytecode, and local template backups. The ZIP +always contains a top-level `Simulation_Data/` directory and an empty +`OUTPUT/` directory. + +The command rejects an archive at or above GitHub's 2 GiB per-file release +asset limit. If that happens, split stable supporting data into clearly named +archives and document that all parts must be extracted into the same +`Simulation_Data` directory. + +## 3. Inspect before upload + +```console +unzip -l /path/to/Pythia-Example-Data-VERSION.zip +shasum -a 256 /path/to/Pythia-Example-Data-VERSION.zip +``` + +Extract into a new temporary directory, configure it using the installed wheel, +and repeat one maize and one rice run. This is the final check that the release +does not depend on the repository or on the maintainer's filesystem. + +## 4. Attach to the GitHub release + +Upload both files: + +- `Pythia-Example-Data-VERSION.zip` +- `Pythia-Example-Data-VERSION.zip.sha256` + +The release notes must state that legacy one-band soil rasters remain supported, +that users do not need to convert `ggcmi_soils_2.tif`, and that the new example +package is configured with `pythia --configure-example`. diff --git a/docs/RELEASING.md b/docs/RELEASING.md index a9827a69..648f47b4 100644 --- a/docs/RELEASING.md +++ b/docs/RELEASING.md @@ -1,26 +1,55 @@ -# Pythia - Release Guide +# Pythia release guide -## Versioning +Pythia uses [semantic versioning](https://semver.org/): increment `MAJOR` for +incompatible changes, `MINOR` for backward-compatible features, and `PATCH` for +backward-compatible fixes. The one-band soil compatibility correction should +therefore be a patch release from 2.3.0 (for example, 2.3.1). -When it comes to managing software releases for Pythia, understanding how to properly version each release is crucial. Pythia follows the principles of [semantic versioning](https://semver.org/), a widely adopted system designed to give meaning to version numbers. In semantic versioning, a version number is made up of three parts: ``MAJOR.MINOR.PATCH``, with each part serving a specific purpose: +## Before triggering the release - - **MAJOR** version when you make incompatible API changes, - - **MINOR** version when you add functionality in a backwards compatible manner, and - - **PATCH** version when you make backwards compatible bug fixes. +1. Work in a branch and review `git status` and `git diff`. +2. Update `CHANGELOG.md`, README, and any affected reference documentation. +3. Run: -This system helps developers and users understand the scope and impact of each release. Here's a breakdown of when to increment each part of the version number: + ```console + poetry install + poetry run pytest + poetry build + ``` - - Increment the **MAJOR** version when there are significant changes that break backward compatibility with the previous versions. This could include changes to the software's architecture, removal of functionalities, or any other changes that would require users to make modifications to their existing setups. - - Increment the **MINOR** version when new features or functionalities are added in a backward-compatible manner. This means that the new version adds value to the software without disrupting the existing functionalities or forcing changes in the users' setups. - - Increment the **PATCH** version for minor changes that fix bugs without adding new features or changing existing ones. These should not affect the software's functionality beyond the specific fixes. +4. Install the wheel in a clean pipx environment and check: -## Release Process -Pythia is released through GitHub Actions. Once a release is triggered, the CI/CD pipeline will automatically build the software and publish a Docker image to Dockerhub. A GitHub release is also created. + ```console + pipx install --force dist/pythia-VERSION-py3-none-any.whl + pythia --help + ``` -In order to deploy new versions of Pythia, go to "([Actions > Release](https://github.com/DSSAT/pythia/actions/workflows/release.yml) > Run Workflow > fill in the version number, follow [versioning](#versioning) to figure out this information > Run workflow). +5. Prepare and test the Sri Lanka archive by following + [EXAMPLE_DATA_RELEASE.md](EXAMPLE_DATA_RELEASE.md). +6. Commit the reviewed source, documentation, tests, and scripts. Open and merge + a pull request before creating the release. -![image](https://github.com/DSSAT/pythia/assets/18128642/a5db0435-9d17-4be8-82c8-54adcbcf860d) +Do not delete `poetry.lock`; update it with Poetry when dependency constraints +change. -> **IMPORTANT:** The version number must strictly match what is described in [versioning](#versioning). **Do not** add any kind of prefix or suffix that is not semantically valid. - -> **IMPORTANT:** The version number on ``pyproject.toml`` is automatically updated by the CI/CD pipeline. **Do not** change it manually. +## GitHub release workflow + +Open [Actions → Release](https://github.com/DSSAT/pythia/actions/workflows/release.yml), +choose **Run workflow**, enter a plain semantic version such as `2.3.1`, and +run it from the intended branch. Do not add a `v` prefix. + +The workflow validates the version, updates `pyproject.toml`, builds and tests +the package, pushes the version commit and tag, builds the Docker image, creates +the GitHub release, and attaches the Python wheel and source archive. + +After the workflow succeeds, manually attach the tested example ZIP and its +`.sha256` file. Confirm that the release page contains all four kinds of +artifact: + +- Python wheel; +- Python source distribution; +- example-data ZIP and SHA-256 checksum; +- Docker image with the version and `latest` tags. + +Finally, download the public assets rather than using local copies and repeat +the installation, `--validate-example`, maize, and rice smoke tests. diff --git a/docs/index.rst b/docs/index.rst index 61dfed5b..fd0dafe1 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,4 +3,6 @@ :caption: Pythia Documentation about - json \ No newline at end of file + understanding_pythia + json + soil_rasters diff --git a/docs/json.rst b/docs/json.rst index 57fd22a8..e6e9449b 100644 --- a/docs/json.rst +++ b/docs/json.rst @@ -45,7 +45,11 @@ sample ghr_root :Type: directory string - :Description: The location of the eGHR (ehanced Global High Resolution) soils data. + :Description: The location of the eGHR (enhanced Global High Resolution) + soils data. For a legacy one-band soil raster, this directory must + contain ``GHR.db`` and the referenced ``.SOL`` files. For a two-band + encoded raster, ``GHR.db`` is not required, but the ``.SOL`` files are. + See :doc:`soil_rasters`. Default Setup (default_setup) ----------------------------- diff --git a/docs/soil_rasters.rst b/docs/soil_rasters.rst new file mode 100644 index 00000000..9fded7f5 --- /dev/null +++ b/docs/soil_rasters.rst @@ -0,0 +1,76 @@ +Soil raster formats +=================== + +Pythia supports both the original one-band GHR soil raster and the newer +two-band encoded soil raster. The format is detected automatically; existing +one-band projects do not need to convert their raster or change their JSON +configuration. + +Legacy one-band GHR raster +-------------------------- + +Each raster cell contains a numeric key. Pythia looks that key up in the +``profile_map`` table of ``GHR.db`` to obtain the DSSAT soil profile ID. + +The directory configured by ``ghr_root`` must contain: + +* ``GHR.db``; +* the country ``.SOL`` files referenced by the database. + +For example, a cell value of ``5130973`` in the Sri Lanka data maps through +``GHR.db`` to profile ``LK04202172``. Pythia then reads ``LK.SOL``. + +Example configuration:: + + { + "ghr_root": "C:/pythia/Simulation_Data/eGHR", + "default_setup": { + "id_soil": "lookup_ghr::raster::C:/pythia/Simulation_Data/raster/ggcmi_soils_2.tif" + } + } + +Two-band encoded raster +----------------------- + +The newer format stores the profile ID directly: + +* band 1 contains the encoded two- or four-letter prefix; +* band 2 contains the numeric part of the profile ID; +* ``0`` is the default ``nodata`` value for rasters created by Pythia. + +For a two-letter prefix, the numeric part is padded to eight digits. For a +four-letter prefix, it is padded to six digits. For example, band values +``6682`` and ``5142095`` decode to ``BR05142095``. + +Create a raster from one or more DSSAT ``.SOL`` files:: + + pythia --create-raster --raster-input cli \ + --raster-output data/soils.tif \ + --raster-sol-path data/soils \ + --raster-recursive + +Troubleshooting +--------------- + +``GHR.db was not found`` + A one-band raster was detected, but ``ghr_root`` does not contain the + legacy database. Correct ``ghr_root`` or restore ``GHR.db``. + +``was not found in GHR.db`` + The raster cell contains an ID that is not present in ``profile_map``. + Ensure that the raster and database came from the same input-data release. + +``DSSAT soil file was not found`` + The profile was resolved, but its country ``.SOL`` file is missing from + ``ghr_root``. + +``expected 1 legacy band or 2 encoded bands`` + The selected file is not a supported Pythia soil raster. + +Migration guidance +------------------ + +Existing one-band projects should continue using their raster, ``GHR.db`` and +``.SOL`` files together. Conversion to the two-band format is optional. Never +replace only the raster: the raster, database and soil files must describe the +same profile collection. diff --git a/docs/understanding_pythia.rst b/docs/understanding_pythia.rst new file mode 100644 index 00000000..825d3185 --- /dev/null +++ b/docs/understanding_pythia.rst @@ -0,0 +1,89 @@ +Understanding Pythia and DSSAT +============================== + +Purpose and scope +----------------- + +DSSAT simulates crop growth at a point from weather, soil, crop, and management +inputs. Pythia provides the spatial orchestration around that point model. It +selects geographic locations, resolves the appropriate inputs for each one, +creates DSSAT experiments, executes them, and optionally combines their +outputs. + +Pythia does not replace DSSAT and it does not turn DSSAT itself into a raster +model. Each selected cell or feature becomes an independent point simulation. +The quality and meaning of the final spatial product therefore depend on the +resolution, coordinate reference system, coverage, and quality of every input. + +From maps to experiments +------------------------ + +Pythia uses two common kinds of spatial data: + +* a **vector** represents locations or boundaries as points, lines, or + polygons with an attribute table; +* a **raster** is a grid whose cells contain values such as a soil identifier, + harvest area, or another spatial variable. + +A JSON configuration connects those spatial sources to DSSAT inputs. Lookup +expressions such as ``raster::...``, ``xy_from_vector::...``, and +``lookup_ghr::...`` tell Pythia how to derive a value at each simulation +location. The DSSAT experiment template supplies the text structure into which +those values are written. + +Operational workflow +-------------------- + +The workflow has three independently callable stages: + +``--setup`` + Select sites, evaluate spatial lookups, and create the DSSAT working + directories and experiment files. + +``--run-dssat`` + Execute the configured DSSAT command for the prepared experiments. + +``--analyze`` + Read model results and produce the configured aggregate outputs. + +``--all`` runs the three stages in that order. Running stages separately is +useful for inspecting generated inputs, scheduling experiments on a cluster, +or diagnosing failures. + +Inputs that must agree +---------------------- + +Before a large simulation, check the following relationships on a small area: + +* site coordinates overlap the weather, soil, and harvest-area data; +* all layers use compatible coordinate reference systems; +* raster cell values use the units and missing-value conventions expected by + the relevant lookup function; +* soil identifiers resolve to profiles present in the configured ``.SOL`` + files; +* the crop and cultivar identifiers exist in the DSSAT cultivar files; +* years requested in ``runs`` are covered by the weather data; +* the DSSAT executable can run one generated experiment outside Pythia. + +Configuration structure +----------------------- + +``workDir``, ``templateDir``, ``weatherDir``, and ``ghr_root`` establish the +file layout. ``default_setup`` describes shared experiment values and spatial +lookups. ``runs`` contains one or more scenarios that override or add crop, +management, and time settings. ``dssat.executable`` identifies the DSSAT +command, and ``analytics_setup`` controls post-processing. + +For a field-by-field reference, see :doc:`json`. For the supported one- and +two-band soil formats, see :doc:`soil_rasters`. The downloadable Sri Lanka +package provides complete maize and rice configurations that can be configured +without editing paths manually; follow the root project README. + +Practical validation strategy +----------------------------- + +Start with ``pythia --validate-example`` when using the released example data. +Then run ``--setup`` and inspect a generated experiment before invoking DSSAT. +Run one small scenario, compare its output with a known DSSAT run, and only then +increase the spatial or temporal scope. This separates configuration problems +from DSSAT model errors and from resource limitations. diff --git a/poetry.lock b/poetry.lock index 4a6a296c..ffb4330e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.4.1 and should not be changed by hand. 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["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources ; python_version < \"3.9\"", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.1" -python-versions = "^3.8" -content-hash = "7d6da9988fc2582ebfed8a651c76f4badbd1c008b259f43f4df90c469240a52f" +python-versions = ">=3.8,<4.0" +content-hash = "d9460bd01696cbd2877ed77ecd23eb6509b14b024025490b4ecb877581ab3231" diff --git a/pyproject.toml b/pyproject.toml index 4601b465..da42c8c2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,8 +26,8 @@ rasterio = [ jinja2 = "^3.0" rtree = "^0.8" -[tool.poetry.dev-dependencies] -pytest = "^5.1" +[tool.poetry.group.dev.dependencies] +pytest = ">=7.4,<9" flake8 = "^3.9.2" neovim = "^0.3.1" python-lsp-server = {extras = ["all"], version = "^1.2.4"} @@ -36,13 +36,11 @@ python-lsp-black = "^1.0.0" pylsp-rope = "^0.1.7" pyls-flake8 = "^0.4.0" ipython = "^8.1.0" +black = "^22.8.0" [tool.poetry.scripts] pythia = "pythia.cli:main" -[tool.poetry.group.dev.dependencies] -black = "^22.8.0" - [build-system] requires = ["setuptools", "poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" \ No newline at end of file +build-backend = "poetry.core.masonry.api" diff --git a/pythia/cli.py b/pythia/cli.py index 695e4b45..fe7346be 100644 --- a/pythia/cli.py +++ b/pythia/cli.py @@ -8,6 +8,7 @@ import pythia.analytics import pythia.config import pythia.dssat +import pythia.example_data import pythia.io import pythia.peerless import pythia.plugin @@ -16,7 +17,9 @@ def _build_raster_cfg_from_cli(args) -> dict: if not args.raster_output: - raise ValueError("Missing --raster-output when using --create-raster --raster-input cli.") + raise ValueError( + "Missing --raster-output when using --create-raster --raster-input cli." + ) # For now: .SOL-based CLI input if not args.raster_sol_path: @@ -45,16 +48,33 @@ def main(): parser = argparse.ArgumentParser(prog="pythia") # Positional arguments - parser.add_argument("config", nargs="?", default=None, help="JSON configuration file to run") - + parser.add_argument( + "config", nargs="?", default=None, help="JSON configuration file to run" + ) # General run flags - parser.add_argument("--all", action="store_true", help="Run all the steps in pythia") - parser.add_argument("--export-runlist", action="store_true", help="Export a list of all the directories to be run") - parser.add_argument("--setup", action="store_true", help="Setup DSSAT run structure and files") - parser.add_argument("--run-dssat", action="store_true", help="Run DSSAT over the run structure") - parser.add_argument("--analyze", action="store_true", help="Run the analysis for the DSSAT runs") - parser.add_argument("--clean-work-dir", action="store_true", help="Clean the work directory prior to run") + parser.add_argument( + "--all", action="store_true", help="Run all the steps in pythia" + ) + parser.add_argument( + "--export-runlist", + action="store_true", + help="Export a list of all the directories to be run", + ) + parser.add_argument( + "--setup", action="store_true", help="Setup DSSAT run structure and files" + ) + parser.add_argument( + "--run-dssat", action="store_true", help="Run DSSAT over the run structure" + ) + parser.add_argument( + "--analyze", action="store_true", help="Run the analysis for the DSSAT runs" + ) + parser.add_argument( + "--clean-work-dir", + action="store_true", + help="Clean the work directory prior to run", + ) parser.add_argument( "--logfile-prefix", default="pythia", @@ -62,9 +82,28 @@ def main(): ) parser.add_argument("--quiet", action="store_true", help="Enjoy the silence") + example_group = parser.add_mutually_exclusive_group() + example_group.add_argument( + "--configure-example", + metavar="SIMULATION_DATA", + help="Configure the downloadable Sri Lanka example-data directory", + ) + example_group.add_argument( + "--validate-example", + metavar="SIMULATION_DATA", + help="Validate a configured Sri Lanka example-data directory", + ) + parser.add_argument( + "--dssat-executable", + help="DSSAT executable used with --configure-example", + ) # Raster creation mode - parser.add_argument("--create-raster", action="store_true", help="Create or update a soil raster GeoTIFF") + parser.add_argument( + "--create-raster", + action="store_true", + help="Create or update a soil raster GeoTIFF", + ) parser.add_argument( "--raster-input", @@ -78,31 +117,68 @@ def main(): help="Path to raster build JSON config (used when --create-raster --raster-input json).", ) - parser.add_argument("--raster-output", help="Output GeoTIFF path (used when --create-raster --raster-input cli).") + parser.add_argument( + "--raster-output", + help="Output GeoTIFF path (used when --create-raster --raster-input cli).", + ) parser.add_argument( "--raster-sol-path", action="append", default=[], help="Path to a .SOL file or a directory containing .SOL files. Repeatable.", ) - parser.add_argument("--raster-base", help="Optional base raster (.tif) to update instead of creating a new one.") + parser.add_argument( + "--raster-base", + help="Optional base raster (.tif) to update instead of creating a new one.", + ) rec_group = parser.add_mutually_exclusive_group() - rec_group.add_argument("--raster-recursive", dest="raster_recursive", action="store_true") - rec_group.add_argument("--raster-no-recursive", dest="raster_recursive", action="store_false") + rec_group.add_argument( + "--raster-recursive", dest="raster_recursive", action="store_true" + ) + rec_group.add_argument( + "--raster-no-recursive", dest="raster_recursive", action="store_false" + ) parser.set_defaults(raster_recursive=False) args = parser.parse_args() - + if args.configure_example: + if not args.dssat_executable: + parser.error("--dssat-executable is required with --configure-example.") + try: + configured = pythia.example_data.configure_example_data( + args.configure_example, args.dssat_executable + ) + except pythia.example_data.ExampleDataError as exc: + parser.error(str(exc)) + print("Configured and validated example files:") + for path in configured: + print(f" {path}") + return + + if args.validate_example: + try: + validated = pythia.example_data.validate_example_data(args.validate_example) + except pythia.example_data.ExampleDataError as exc: + parser.error(str(exc)) + print("Example data is valid:") + for path in validated: + print(f" {path}") + return + # Raster creation workflow if args.create_raster: if not args.raster_input: - parser.error("--raster-input is required when using --create-raster (choose: json or cli).") + parser.error( + "--raster-input is required when using --create-raster (choose: json or cli)." + ) if args.raster_input == "json": if not args.raster_config: - parser.error("Missing --raster-config when using --create-raster --raster-input json.") + parser.error( + "Missing --raster-config when using --create-raster --raster-input json." + ) raster_main(args.raster_config, None) return @@ -129,7 +205,6 @@ def main(): parser.error("Invalid --raster-input value.") return - # Normal Pythia run workflow if not args.config: parser.print_help() @@ -157,6 +232,7 @@ def main(): print("Cleaning the work directory") if os.path.exists(config["workDir"]): import shutil + shutil.rmtree(config["workDir"]) config["exportRunlist"] = args.export_runlist @@ -183,4 +259,3 @@ def main(): "Pythia completed: %s", datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"), ) - \ No newline at end of file diff --git a/pythia/example_data.py b/pythia/example_data.py new file mode 100644 index 00000000..30a0416a --- /dev/null +++ b/pythia/example_data.py @@ -0,0 +1,190 @@ +"""Configure and validate the downloadable Pythia example data package.""" + +import json +import os +import shutil +import tempfile +from pathlib import Path +from typing import Dict, Iterable, List + + +DATA_ROOT_TOKEN = "<>" +DSSAT_EXECUTABLE_TOKEN = "<>" +EXAMPLE_CONFIGS = ("SL_Maize.json", "SL_Rice.json", "SL_Rice_env.json") + + +class ExampleDataError(ValueError): + """Raised when the example-data package is incomplete or misconfigured.""" + + +def _config_paths(data_root: Path) -> Iterable[Path]: + sri_lanka = data_root / "Sri_Lanka" + for name in EXAMPLE_CONFIGS: + yield sri_lanka / name + + +def _template_path(config_path: Path) -> Path: + return config_path.with_suffix(config_path.suffix + ".template") + + +def _release_template(config_path: Path) -> Path: + """Return the reusable template, including after a local configuration.""" + backup = _template_path(config_path) + if backup.is_file(): + return backup + return config_path + + +def _replace_tokens(value, replacements: Dict[str, str]): + if isinstance(value, str): + for token, replacement in replacements.items(): + value = value.replace(token, replacement) + return value + if isinstance(value, list): + return [_replace_tokens(item, replacements) for item in value] + if isinstance(value, dict): + return {key: _replace_tokens(item, replacements) for key, item in value.items()} + return value + + +def _strings(value): + if isinstance(value, str): + yield value + elif isinstance(value, list): + for item in value: + yield from _strings(item) + elif isinstance(value, dict): + for item in value.values(): + yield from _strings(item) + + +def _referenced_paths(config: dict) -> Iterable[Path]: + for key in ("workDir", "templateDir", "weatherDir", "ghr_root"): + if config.get(key): + yield Path(config[key]) + + dssat = config.get("dssat", {}) + if dssat.get("executable"): + yield Path(dssat["executable"]) + + setup = config.get("default_setup", {}) + for include in setup.get("include", []): + yield Path(include) + + template_dir = config.get("templateDir") + if template_dir and setup.get("template"): + yield Path(template_dir) / setup["template"] + + for value in _strings(config): + parts = value.split("::") + for marker in ("raster", "vector"): + if marker in parts: + index = parts.index(marker) + if index + 1 < len(parts): + yield Path(parts[index + 1]) + + +def validate_example_data(data_root, allow_placeholders=False) -> List[Path]: + """Validate package structure and all paths referenced by its JSON examples.""" + root = Path(data_root).expanduser().resolve() + errors = [] + + required = ( + root / "Sri_Lanka", + root / "weather_data" / "Sri_Lanka", + root / "eGHR" / "GHR.db", + root / "eGHR" / "LK.SOL", + root / "raster" / "ggcmi_soils_2.tif", + root / "raster" / "spam2010V2r0_global_H_MAIZ_H.tif", + root / "raster" / "spam2010V2r0_global_H_RICE_I.tif", + ) + for path in required: + if not path.exists(): + errors.append(f"Required example-data path is missing: {path}") + + configs = list(_config_paths(root)) + for config_path in configs: + if not config_path.is_file(): + errors.append(f"Example configuration is missing: {config_path}") + continue + source_path = ( + _release_template(config_path) if allow_placeholders else config_path + ) + try: + source_text = source_path.read_text(encoding="utf-8") + config = json.loads(source_text) + except (OSError, json.JSONDecodeError) as exc: + errors.append(f"Invalid JSON file {source_path}: {exc}") + continue + + has_root_token = DATA_ROOT_TOKEN in source_text + has_dssat_token = DSSAT_EXECUTABLE_TOKEN in source_text + if allow_placeholders: + if not has_root_token: + errors.append(f"Data-root placeholder is missing from {source_path}") + if not has_dssat_token: + errors.append(f"DSSAT placeholder is missing from {source_path}") + continue + + if has_root_token or has_dssat_token: + errors.append( + f"Example is not configured yet: {config_path}. " + "Run 'pythia --configure-example ...' first." + ) + continue + + for path in _referenced_paths(config): + # workDir is intentionally created by Pythia. + if str(path) == str(config.get("workDir")): + continue + if not path.exists(): + errors.append( + f"Referenced path does not exist in {config_path}: {path}" + ) + + if errors: + raise ExampleDataError("\n".join(errors)) + return configs + + +def _atomic_json_write(path: Path, config: dict) -> None: + fd, temporary_name = tempfile.mkstemp( + prefix=f".{path.name}.", suffix=".tmp", dir=str(path.parent) + ) + try: + with os.fdopen(fd, "w", encoding="utf-8") as output: + json.dump(config, output, indent=2, ensure_ascii=False) + output.write("\n") + os.replace(temporary_name, str(path)) + except Exception: + try: + os.unlink(temporary_name) + except OSError: + pass + raise + + +def configure_example_data(data_root, dssat_executable) -> List[Path]: + """Replace release placeholders and validate the configured examples.""" + root = Path(data_root).expanduser().resolve() + dssat_path = Path(dssat_executable).expanduser().resolve() + if not dssat_path.is_file(): + raise ExampleDataError(f"DSSAT executable was not found: {dssat_path}") + + validate_example_data(root, allow_placeholders=True) + replacements = { + DATA_ROOT_TOKEN: root.as_posix(), + DSSAT_EXECUTABLE_TOKEN: dssat_path.as_posix(), + } + + configured = [] + for config_path in _config_paths(root): + backup = _template_path(config_path) + if not backup.exists(): + shutil.copy2(str(config_path), str(backup)) + config = json.loads(backup.read_text(encoding="utf-8")) + _atomic_json_write(config_path, _replace_tokens(config, replacements)) + configured.append(config_path) + + validate_example_data(root) + return configured diff --git a/pythia/example_release.py b/pythia/example_release.py new file mode 100644 index 00000000..0f8b35ea --- /dev/null +++ b/pythia/example_release.py @@ -0,0 +1,98 @@ +"""Build a portable release archive from a Simulation_Data directory.""" + +import hashlib +import json +import zipfile +from pathlib import Path +from typing import Iterable, Tuple + +from pythia.example_data import EXAMPLE_CONFIGS, validate_example_data + + +GITHUB_ASSET_LIMIT = 2 * 1024 * 1024 * 1024 +IGNORED_NAMES = {".DS_Store", ".history", "__MACOSX", "__pycache__"} + + +def _is_excluded(relative: Path) -> bool: + if any(part in IGNORED_NAMES for part in relative.parts): + return True + if relative.parts and relative.parts[0] == "OUTPUT": + return True + return relative.suffix in {".log", ".pyc", ".template"} + + +def _release_files(root: Path) -> Iterable[Tuple[Path, Path]]: + """Yield (source, archive-relative-path), substituting clean JSON templates.""" + example_names = set(EXAMPLE_CONFIGS) + for source in sorted(root.rglob("*")): + if not source.is_file(): + continue + relative = source.relative_to(root) + if _is_excluded(relative): + continue + if relative.parent == Path("Sri_Lanka") and relative.name in example_names: + template = source.with_suffix(source.suffix + ".template") + yield (template if template.is_file() else source), relative + else: + yield source, relative + + +def _sha256(path: Path) -> str: + digest = hashlib.sha256() + with path.open("rb") as stream: + for block in iter(lambda: stream.read(1024 * 1024), b""): + digest.update(block) + return digest.hexdigest() + + +def build_example_archive(data_root, output, package_readme=None): + """Validate and create a deterministic, portable ZIP plus SHA-256 file.""" + root = Path(data_root).expanduser().resolve() + destination = Path(output).expanduser().resolve() + if destination.suffix.lower() != ".zip": + raise ValueError("The release archive must use the .zip extension.") + if root == destination or root in destination.parents: + raise ValueError("Write the release archive outside Simulation_Data.") + + validate_example_data(root, allow_placeholders=True) + destination.parent.mkdir(parents=True, exist_ok=True) + + archive_root = "Simulation_Data" + with zipfile.ZipFile( + destination, "w", compression=zipfile.ZIP_DEFLATED, allowZip64=True + ) as archive: + archive.writestr(f"{archive_root}/OUTPUT/", b"") + if package_readme: + readme = Path(package_readme).expanduser().resolve() + archive.write(readme, f"{archive_root}/README.md") + for source, relative in _release_files(root): + archive.write(source, (Path(archive_root) / relative).as_posix()) + + size = destination.stat().st_size + if size >= GITHUB_ASSET_LIMIT: + raise ValueError( + f"Archive is {size / 1024**3:.2f} GiB; GitHub release assets must be " + "smaller than 2 GiB. Split the data into multiple archives." + ) + + checksum = _sha256(destination) + checksum_path = destination.with_suffix(destination.suffix + ".sha256") + checksum_path.write_text(f"{checksum} {destination.name}\n", encoding="utf-8") + return destination, checksum_path, size + + +def inspect_archive(path) -> dict: + """Return a small manifest used by release checks and tests.""" + archive_path = Path(path) + with zipfile.ZipFile(archive_path) as archive: + names = archive.namelist() + bad = [ + name + for name in names + if any(part in IGNORED_NAMES for part in Path(name).parts) + ] + configs = {} + for name in EXAMPLE_CONFIGS: + member = f"Simulation_Data/Sri_Lanka/{name}" + configs[name] = json.loads(archive.read(member).decode("utf-8")) + return {"members": names, "excluded_members": bad, "configs": configs} diff --git a/pythia/functions.py b/pythia/functions.py index a91f4d34..d4d21cce 100644 --- a/pythia/functions.py +++ b/pythia/functions.py @@ -1,16 +1,24 @@ import datetime import logging -import os +import math +import sqlite3 +from functools import lru_cache from pathlib import Path -from typing import Optional +from typing import Dict, Optional, Tuple +import numpy as np import rasterio +from rasterio.crs import CRS +from rasterio.errors import RasterioIOError +from rasterio.warp import transform as transform_coordinates +from rasterio.windows import Window import pythia.io import pythia.soil_handler import pythia.template import pythia.util + def extract_raster(s): """ Extracts the raster filepath from a DSSAT-style lookup string. It scans for the @@ -77,6 +85,7 @@ def auto_planting_window(k, run, context, _): "plast": pythia.util.to_iso_date(last), } + def auto_planting_window_doy(k, run, context, _): """multiple rasters not yet supported""" args = run[k].split("::")[1:] @@ -93,6 +102,7 @@ def auto_planting_window_doy(k, run, context, _): "plast": pythia.util.to_iso_date(last), } + def auto_planting_window_doy_shape(k, run, context, _): """multiple rasters not yet supported""" args = run[k].split("::")[1:] @@ -102,7 +112,7 @@ def auto_planting_window_doy_shape(k, run, context, _): idx = args.index("vector") cell_doy = finder(args[idx + 1], context["lng"], context["lat"], args[idx + 2]) - first = datetime.datetime(run["startYear"], 1, 1) + datetime.timedelta(int(cell_doy) + int(args[idx + 3]) ) + first = datetime.datetime(run["startYear"], 1, 1) + datetime.timedelta(int(cell_doy) + int(args[idx + 3])) td = datetime.timedelta(days=int(args[idx + 4])) last = first + td return { @@ -111,6 +121,7 @@ def auto_planting_window_doy_shape(k, run, context, _): "plast": pythia.util.to_iso_date(last), } + def lookup_hc27(k, run, context, _): args = run[k].split("::")[1:] if "raster" in args: @@ -126,7 +137,7 @@ def lookup_wth(k, run, context, _): if "vector" in args: idx = args.index("vector") cell_id = finder(args[idx + 1], context["lng"], context["lat"], args[idx + 2]) - return {k: args[0], "wthFile": "{}.WTH".format(int(cell_id))} + return {k: args[0], "wthFile": "{}.WTH".format(cell_id)} def generate_ic_layers(k, run, context, _): @@ -153,7 +164,10 @@ def decode_prefix(prefix_code: int) -> str: b = int(s[2:]) if not (32 <= a <= 126 and 32 <= b <= 126): raise ValueError("invalid 2-letter ascii pair") - return chr(a) + chr(b) + prefix = chr(a) + chr(b) + if not prefix.isalpha(): + raise ValueError("invalid 2-letter ascii prefix") + return prefix b0 = (code >> 24) & 0xFF b1 = (code >> 16) & 0xFF @@ -164,7 +178,10 @@ def decode_prefix(prefix_code: int) -> str: if not (32 <= x <= 126): raise ValueError("invalid packed-ascii byte") - return bytes([b0, b1, b2, b3]).decode("ascii") + prefix = bytes([b0, b1, b2, b3]).decode("ascii") + if not prefix.isalpha(): + raise ValueError("invalid 4-letter ascii prefix") + return prefix def build_profile_code_from_bands(prefix_code: int, numeric_id: int) -> str: @@ -172,49 +189,300 @@ def build_profile_code_from_bands(prefix_code: int, numeric_id: int) -> str: n = int(numeric_id) if len(prefix) == 2: + if n < 0 or n > 99999999: + raise ValueError("numeric ID does not fit the 2-letter profile format") return f"{prefix}{n:08d}" if len(prefix) == 4: + if n < 0 or n > 999999: + raise ValueError("numeric ID does not fit the 4-letter profile format") return f"{prefix}{n:06d}" raise ValueError("invalid decoded prefix length") +def _point_to_raster_pixel(src, lat: float, lon: float) -> Optional[Tuple[int, int]]: + """Return a checked raster pixel for a WGS84 latitude/longitude pair.""" + x = float(lon) + y = float(lat) + + if not math.isfinite(x) or not math.isfinite(y): + logging.error("Invalid non-finite coordinates: (%s, %s).", lat, lon) + return None + + try: + if src.crs is not None and src.crs != CRS.from_epsg(4326): + xs, ys = transform_coordinates(CRS.from_epsg(4326), src.crs, [x], [y]) + x, y = xs[0], ys[0] + except Exception as exc: + logging.error( + "Could not transform point (%s, %s) to raster CRS %s: %s", + lat, + lon, + src.crs, + exc, + ) + return None + + bounds = src.bounds + if not (bounds.left <= x <= bounds.right and bounds.bottom <= y <= bounds.top): + logging.warning("Point (%s, %s) is outside raster '%s'.", lat, lon, src.name) + return None + + try: + row, col = src.index(x, y) + except Exception as exc: + logging.warning( + "Could not locate point (%s, %s) in raster '%s': %s", + lat, + lon, + src.name, + exc, + ) + return None + + if row < 0 or row >= src.height or col < 0 or col >= src.width: + logging.warning("Point (%s, %s) is outside raster '%s'.", lat, lon, src.name) + return None + return row, col + + +def _integer_band_value(value, band: int, lat: float, lon: float) -> Optional[int]: + if np.ma.is_masked(value): + return None + try: + number = float(value) + except (TypeError, ValueError, OverflowError): + logging.error( + "Invalid value in soil raster band %d at (%s, %s): %r.", + band, + lat, + lon, + value, + ) + return None + if not math.isfinite(number) or not number.is_integer(): + logging.error( + "Soil raster band %d must contain integer values at (%s, %s); found %r.", + band, + lat, + lon, + value, + ) + return None + return int(number) + + +def _get_profile_from_dataset(src, lat: float, lon: float) -> Optional[str]: + if src.count != 2: + logging.error( + "Encoded soil raster '%s' must have exactly 2 bands. Found %d.", + src.name, + src.count, + ) + return None + + pixel = _point_to_raster_pixel(src, lat, lon) + if pixel is None: + return None + row, col = pixel + + try: + values = src.read( + indexes=(1, 2), + window=Window(col, row, 1, 1), + masked=True, + ) + except Exception as exc: + logging.error( + "Could not read soil raster '%s' at (%s, %s): %s", + src.name, + lat, + lon, + exc, + ) + return None + + b1 = _integer_band_value(values[0, 0, 0], 1, lat, lon) + b2 = _integer_band_value(values[1, 0, 0], 2, lat, lon) + if b1 is None and b2 is None: + return None + if b1 is None or b2 is None: + logging.error( + "Incomplete encoded soil profile at (%s, %s) in '%s'.", + lat, + lon, + src.name, + ) + return None + + try: + return build_profile_code_from_bands(b1, b2) + except (TypeError, ValueError, OverflowError) as exc: + logging.error( + "Failed to decode soil raster bands at (%s, %s): b1=%d b2=%d (%s).", + lat, + lon, + b1, + b2, + exc, + ) + return None + + def get_profile_from_raster(lat: float, lon: float, raster_path: Path) -> Optional[str]: + """Resolve a profile from a two-band encoded soil raster.""" + raster_path = Path(raster_path) if not raster_path.exists(): - logging.error("Raster not found: %s", str(raster_path)) + logging.error("Soil raster not found: %s", str(raster_path)) return None - with rasterio.open(str(raster_path)) as src: - try: - row, col = src.index(lon, lat) - except Exception: - logging.warning("Point (%s, %s) outside raster.", lat, lon) - return None + try: + with rasterio.open(str(raster_path)) as src: + return _get_profile_from_dataset(src, lat, lon) + except (OSError, RasterioIOError) as exc: + logging.error("Could not open soil raster '%s': %s", raster_path, exc) + return None - if src.count < 2: - logging.error("Raster '%s' must have 2 bands. Found %d.", str(raster_path), src.count) - return None - b1 = src.read(1)[row, col] - b2 = src.read(2)[row, col] +@lru_cache(maxsize=8) +def _load_ghr_profiles_cached(db_path: str, modified_ns: int) -> Dict[int, str]: + """Load the legacy profile map; ``modified_ns`` invalidates stale cache entries.""" + del modified_ns + profiles = {} + with sqlite3.connect(db_path) as conn: + cursor = conn.execute( + "SELECT id, profile FROM profile_map " + "WHERE profile IS NOT NULL AND TRIM(profile) != ''" + ) + for soil_id, profile in cursor.fetchall(): + profiles[int(soil_id)] = str(profile).strip() + return profiles - nodata = src.nodata if src.nodata is not None else 0 - try: - b1i = int(b1) - b2i = int(b2) - except Exception: - logging.error("Non-integer band values at (%s, %s): b1=%s b2=%s", lat, lon, str(b1), str(b2)) - return None +def _ghr_database_path(config) -> Path: + ghr_root = config.get("ghr_root") if config else None + if not ghr_root: + raise ValueError("Missing 'ghr_root' in the Pythia configuration.") - if b1i == int(nodata) and b2i == int(nodata): - return None + db_path = Path(ghr_root) / "GHR.db" + if not db_path.is_file(): + raise FileNotFoundError( + "Legacy one-band soil raster detected, but GHR.db was not found " + f"under ghr_root: {ghr_root}" + ) + return db_path.resolve() - try: - return build_profile_code_from_bands(b1i, b2i) - except Exception: - logging.error("Failed to decode bands at (%s, %s): b1=%d b2=%d", lat, lon, b1i, b2i) - return None + +def build_ghr_cache(config) -> Dict[int, str]: + """Load the complete legacy profile map for API compatibility. + + Runtime lookups query and cache individual IDs to avoid copying the full GHR + database into every worker process, especially on Windows. + """ + resolved = _ghr_database_path(config) + return _load_ghr_profiles_cached(str(resolved), resolved.stat().st_mtime_ns) + + +@lru_cache(maxsize=32768) +def _lookup_ghr_profile_cached( + db_path: str, modified_ns: int, soil_id: int +) -> Optional[str]: + del modified_ns + with sqlite3.connect(db_path) as conn: + row = conn.execute( + "SELECT profile FROM profile_map " + "WHERE id = ? AND profile IS NOT NULL AND TRIM(profile) != ''", + (soil_id,), + ).fetchone() + if row is None: + return None + return str(row[0]).strip() + + +def _lookup_ghr_profile(config, soil_id: int) -> Optional[str]: + resolved = _ghr_database_path(config) + return _lookup_ghr_profile_cached( + str(resolved), resolved.stat().st_mtime_ns, soil_id + ) + + +def _legacy_profile_from_context(k, context, config) -> Optional[str]: + if k not in context: + logging.error( + "Legacy one-band soil raster requires the raster value in context[%r].", + k, + ) + return None + + try: + value = float(str(context[k])) + if not math.isfinite(value) or not value.is_integer(): + raise ValueError + soil_id = int(value) + except (TypeError, ValueError, OverflowError): + logging.error("Invalid legacy soil ID in context[%r]: %r.", k, context[k]) + return None + + try: + profile = _lookup_ghr_profile(config, soil_id) + except (FileNotFoundError, OSError, ValueError, sqlite3.DatabaseError) as exc: + logging.error("Could not load the legacy GHR soil mapping: %s", exc) + return None + + if not profile: + logging.error( + "Legacy soil ID %d at (%s, %s) was not found in GHR.db.", + soil_id, + context.get("lat"), + context.get("lng"), + ) + return None + return profile + + +@lru_cache(maxsize=256) +def _soil_profiles_in_file(path: str, modified_ns: int): + del modified_ns + profiles = set() + with open(path, "r", encoding="utf-8", errors="ignore") as soil_file: + for line in soil_file: + if line.startswith("*"): + profile = line[1:].strip().split(maxsplit=1) + if profile: + profiles.add(profile[0].upper()) + return profiles + + +def _soil_file_for_profile(profile_code: str, config) -> Optional[Path]: + ghr_root = config.get("ghr_root") if config else None + if not ghr_root: + logging.error("Missing 'ghr_root' in the Pythia configuration.") + return None + + soil_path = Path(ghr_root) / f"{profile_code[:2].upper()}.SOL" + if not soil_path.is_file(): + logging.error( + "Soil profile %s resolved successfully, but its DSSAT soil file was not found: %s", + profile_code, + soil_path, + ) + return None + try: + resolved = soil_path.resolve() + profiles = _soil_profiles_in_file( + str(resolved), resolved.stat().st_mtime_ns + ) + except OSError as exc: + logging.error("Could not read DSSAT soil file '%s': %s", soil_path, exc) + return None + if profile_code.upper() not in profiles: + logging.error( + "Soil profile %s was not found inside DSSAT soil file: %s", + profile_code, + soil_path, + ) + return None + return soil_path def lookup_ghr(k, run, context, config): @@ -229,6 +497,9 @@ def lookup_ghr(k, run, context, config): return None raster_path = Path(args[raster_idx + 1]) + if not raster_path.is_file(): + logging.error("Soil raster not found: %s", raster_path) + return None try: lat = float(context["lat"]) @@ -237,17 +508,43 @@ def lookup_ghr(k, run, context, config): logging.error("lookup_ghr: Invalid lat/lng in context.") return None - profile_code = get_profile_from_raster(lat, lon, raster_path) + try: + with rasterio.open(str(raster_path)) as src: + if src.count == 1: + logging.debug("Using legacy one-band GHR soil lookup for %s.", raster_path) + if _point_to_raster_pixel(src, lat, lon) is None: + return None + profile_code = _legacy_profile_from_context(k, context, config) + elif src.count == 2: + logging.debug("Using two-band encoded soil lookup for %s.", raster_path) + profile_code = _get_profile_from_dataset(src, lat, lon) + else: + logging.error( + "Unsupported soil raster '%s': expected 1 legacy band or 2 encoded bands; found %d.", + raster_path, + src.count, + ) + return None + except (OSError, RasterioIOError) as exc: + logging.error("Could not open soil raster '%s': %s", raster_path, exc) + return None + if not profile_code: - logging.error("lookup_ghr: No profile found for (%s, %s) in %s", lat, lon, str(raster_path)) + logging.error( + "lookup_ghr: No profile found for (%s, %s) in %s", + lat, + lon, + str(raster_path), + ) return None - sol_prefix = profile_code[:2].upper() - sol_path = os.path.join(config["ghr_root"], f"{sol_prefix}.SOL") + sol_path = _soil_file_for_profile(profile_code, config) + if sol_path is None: + return None return { k: profile_code, - "soilFiles": [sol_path], + "soilFiles": [str(sol_path)], } @@ -290,7 +587,7 @@ def split_fert_dap_percent(k, run, context, _): def assign_by_raster_value(k, run, context, _): init_args = run[k].split("::")[1:] if "raster" in init_args: - args = init_args[init_args.index("raster") + 2 :] + args = init_args[init_args.index("raster") + 2:] else: logging.error("Need to specify a raster for %s:assign_by_value", k) return None diff --git a/pythia/io.py b/pythia/io.py index 4dc67513..39534dc6 100644 --- a/pythia/io.py +++ b/pythia/io.py @@ -22,13 +22,14 @@ def get_site_raster_value(dataset, band, site): lng, lat = site - row, col = dataset.index(lng, lat) - data = [] try: + row, col = dataset.index(lng, lat) + if row < 0 or row >= dataset.height or col < 0 or col >= dataset.width: + return None data = band[row, col] if data is ma.masked: data = None - except IndexError: + except (IndexError, TypeError, ValueError): data = None return data diff --git a/pythia/plugin.py b/pythia/plugin.py index 004bc730..68fca0d4 100644 --- a/pythia/plugin.py +++ b/pythia/plugin.py @@ -102,10 +102,12 @@ def run_plugin_functions(hook, plugins, **kwargs): _return = {**kwargs} if hook in plugins: for plugin_fun in plugins[hook]: - plugin_fun_return = plugin_fun["fun"](plugin_fun.get("config", {}), _return, **kwargs) + plugin_fun_return = plugin_fun["fun"]( + plugin_fun.get("config", {}), **_return + ) _return = { **_return, - **({} if plugin_fun_return is None else plugin_fun_return) + **({} if plugin_fun_return is None else plugin_fun_return), } return _return diff --git a/pythia/plugins/test_plugin/__init__.py b/pythia/plugins/test_plugin/__init__.py index c5c21508..a03b4afb 100644 --- a/pythia/plugins/test_plugin/__init__.py +++ b/pythia/plugins/test_plugin/__init__.py @@ -4,23 +4,44 @@ def initialize(config, plugins, full_config): logging.info("[TEST PLUGIN] Initializing plugin") - plugins = register_plugin_function(PluginHook.post_config, sample_function, config, plugins) - plugins = register_plugin_function(PluginHook.post_build_context, contexted_function, config, plugins) - plugins = register_plugin_function(PluginHook.post_peerless_pixel_success, on_peerless_success, config, plugins) - plugins = register_plugin_function(PluginHook.post_peerless_pixel_skip, on_peerless_skip, config, plugins) - plugins = register_plugin_function(PluginHook.post_run_pixel_success, on_run_pixel_success, config, plugins) - plugins = register_plugin_function(PluginHook.post_run_pixel_failed, on_run_pixel_failed, config, plugins) + plugin_config = config.get("params", {}) + plugins = register_plugin_function( + PluginHook.post_config, sample_function, plugin_config, plugins + ) + plugins = register_plugin_function( + PluginHook.post_build_context, contexted_function, plugin_config, plugins + ) + plugins = register_plugin_function( + PluginHook.post_peerless_pixel_success, + on_peerless_success, + plugin_config, + plugins, + ) + plugins = register_plugin_function( + PluginHook.post_peerless_pixel_skip, on_peerless_skip, plugin_config, plugins + ) + plugins = register_plugin_function( + PluginHook.post_run_pixel_success, + on_run_pixel_success, + plugin_config, + plugins, + ) + plugins = register_plugin_function( + PluginHook.post_run_pixel_failed, on_run_pixel_failed, plugin_config, plugins + ) return plugins -def sample_function(config={}, **kwargs): +def sample_function(config=None, **kwargs): + config = config or {} retval = config.get("value", 1) logging.info("[TEST PLUGIN] Running the sample_function()") return {**kwargs, "config": config, "retval": retval} -def contexted_function(context={}, **kwargs): +def contexted_function(config=None, context=None, **kwargs): logging.info("[TEST PLUGIN] Running the contexted_function()") + context = dict(context or {}) context["context_value"] = context.get("context_value", 2) + 1 return {**kwargs, "context": context} diff --git a/pythia/tests/example_data_test.py b/pythia/tests/example_data_test.py new file mode 100644 index 00000000..191848da --- /dev/null +++ b/pythia/tests/example_data_test.py @@ -0,0 +1,122 @@ +import json +from pathlib import Path + +import pytest + +from pythia.example_data import ( + DATA_ROOT_TOKEN, + DSSAT_EXECUTABLE_TOKEN, + EXAMPLE_CONFIGS, + ExampleDataError, + configure_example_data, + validate_example_data, +) +from pythia.example_release import build_example_archive, inspect_archive + + +def _make_example_package(tmp_path: Path) -> Path: + root = tmp_path / "Simulation Data" + required = ( + "weather_data/Sri_Lanka/0001.WTH", + "eGHR/GHR.db", + "eGHR/LK.SOL", + "raster/ggcmi_soils_2.tif", + "raster/spam2010V2r0_global_H_MAIZ_H.tif", + "raster/spam2010V2r0_global_H_RICE_I.tif", + "Sri_Lanka/templates/example.X", + "Sri_Lanka/shapes/Sri_Lanka.shp", + "Sri_Lanka/CUL_files/example.CUL", + ) + for relative in required: + path = root / relative + path.parent.mkdir(parents=True, exist_ok=True) + path.write_bytes(b"test") + + for name in EXAMPLE_CONFIGS: + config = { + "workDir": f"{DATA_ROOT_TOKEN}/OUTPUT/example", + "templateDir": f"{DATA_ROOT_TOKEN}/Sri_Lanka/templates", + "weatherDir": f"{DATA_ROOT_TOKEN}/weather_data/Sri_Lanka", + "ghr_root": f"{DATA_ROOT_TOKEN}/eGHR", + "default_setup": { + "include": [f"{DATA_ROOT_TOKEN}/Sri_Lanka/CUL_files/example.CUL"], + "template": "example.X", + "sites": f"xy_from_vector::{DATA_ROOT_TOKEN}/Sri_Lanka/shapes/Sri_Lanka.shp", + "id_soil": f"lookup_ghr::raster::{DATA_ROOT_TOKEN}/raster/ggcmi_soils_2.tif", + }, + "dssat": {"executable": DSSAT_EXECUTABLE_TOKEN}, + "runs": [ + { + "harvestArea": f"raster::{DATA_ROOT_TOKEN}/raster/spam2010V2r0_global_H_MAIZ_H.tif" + } + ], + } + (root / "Sri_Lanka" / name).write_text(json.dumps(config), encoding="utf-8") + return root + + +def test_configure_and_validate_example_data(tmp_path): + root = _make_example_package(tmp_path) + executable = tmp_path / "dscsm048" + executable.write_text("executable", encoding="utf-8") + + assert len(validate_example_data(root, allow_placeholders=True)) == 3 + configured = configure_example_data(root, executable) + assert len(configured) == 3 + assert len(validate_example_data(root)) == 3 + + for path in configured: + text = path.read_text(encoding="utf-8") + assert DATA_ROOT_TOKEN not in text + assert DSSAT_EXECUTABLE_TOKEN not in text + assert root.as_posix() in text + assert executable.as_posix() in text + assert path.with_suffix(".json.template").is_file() + + second_executable = tmp_path / "DSSAT48.exe" + second_executable.write_text("executable", encoding="utf-8") + configure_example_data(root, second_executable) + for path in configured: + text = path.read_text(encoding="utf-8") + assert second_executable.as_posix() in text + assert executable.as_posix() not in text + + +def test_unconfigured_example_is_rejected(tmp_path): + root = _make_example_package(tmp_path) + with pytest.raises(ExampleDataError, match="not configured yet"): + validate_example_data(root) + + +def test_missing_required_file_is_reported(tmp_path): + root = _make_example_package(tmp_path) + (root / "eGHR" / "GHR.db").unlink() + with pytest.raises(ExampleDataError, match="GHR.db"): + validate_example_data(root, allow_placeholders=True) + + +def test_release_archive_is_portable_and_excludes_local_files(tmp_path): + root = _make_example_package(tmp_path) + (root / ".history").mkdir() + (root / ".history" / "old.json").write_text("{}", encoding="utf-8") + (root / "OUTPUT" / "old-run").mkdir(parents=True) + (root / "OUTPUT" / "old-run" / "result.csv").write_text("result", encoding="utf-8") + (root / ".DS_Store").write_bytes(b"local") + + executable = tmp_path / "dscsm048" + executable.write_text("executable", encoding="utf-8") + configure_example_data(root, executable) + + readme = tmp_path / "README.md" + readme.write_text("example", encoding="utf-8") + archive, checksum, _ = build_example_archive(root, tmp_path / "example.zip", readme) + manifest = inspect_archive(archive) + + assert checksum.is_file() + assert manifest["excluded_members"] == [] + assert "Simulation_Data/OUTPUT/" in manifest["members"] + assert "Simulation_Data/OUTPUT/old-run/result.csv" not in manifest["members"] + for config in manifest["configs"].values(): + serialized = json.dumps(config) + assert DATA_ROOT_TOKEN in serialized + assert DSSAT_EXECUTABLE_TOKEN in serialized diff --git a/pythia/tests/plugin_test.py b/pythia/tests/plugin_test.py index fa197a57..593bdd9c 100644 --- a/pythia/tests/plugin_test.py +++ b/pythia/tests/plugin_test.py @@ -82,7 +82,7 @@ def test_plugin_manual_execution(): plugins1 = load_plugins(config, plugins) for plugin in plugins1[PluginHook.post_config]: - assert 1 == plugin["fun"]() + assert 1 == plugin["fun"](plugin["config"])["retval"] def test_plugin_auto_execution(): @@ -94,7 +94,9 @@ def test_plugin_auto_execution(): context1 = run_plugin_functions( PluginHook.post_build_context, plugins1, context=context ).get("context") - context2 = run_plugin_functions(PluginHook.post_build_context, plugins1).get("context", None) + context2 = run_plugin_functions(PluginHook.post_build_context, plugins1).get( + "context", None + ) assert context1 != context assert context1["context_value"] == 8 assert context2["context_value"] == 3 diff --git a/pythia/tests/raster_functions_test.py b/pythia/tests/raster_functions_test.py index 3cfc0bdc..3fc2724e 100644 --- a/pythia/tests/raster_functions_test.py +++ b/pythia/tests/raster_functions_test.py @@ -1,233 +1,292 @@ -""" -====================================================================== - Basic Functional Tests for pythia.functions ----------------------------------------------------------------------- -This file contains lightweight tests designed to validate individual -helper functions used throughout the Pythia workflow, including: - - - ASCII/soil-code builders - - Raster path parsing - - String parsing helpers - - Fertilizer splitting logic - - Value assignment via raster - - Date manipulation helpers - - Soil lookup via raster (core integration test) - -These tests DO NOT simulate a full Pythia run - they only confirm that -key low-level pieces behave correctly in isolation. -====================================================================== -""" - +import logging +import sqlite3 from pathlib import Path -import pythia.functions as fn +import numpy as np +import pytest +import rasterio +from rasterio.transform import from_origin -def test_prefix_and_profile_code_from_bands(): - print("\n=== Running test_prefix_and_profile_code_from_bands ===") - - # 66='B', 82='R' => "6682" (legacy 2-letter encoding) - prefix_code = 6682 - prefix = fn.decode_prefix(prefix_code) - print("decode_prefix(6682) =", prefix) - assert prefix == "BR", "decode_prefix failed for 2-letter encoding" - - code = fn.build_profile_code_from_bands(prefix_code, 5142095) - print("build_profile_code_from_bands(6682, 5142095) =", code) - assert code == "BR05142095", "build_profile_code_from_bands failed" +import pythia.functions as fn +import pythia.io + + +SRI_LANKA_LAT = 8.541666666666686 +SRI_LANKA_LON = 81.12500000000011 +# Values from the public Sri Lanka example at the coordinate reported by users. +PROFILE_ID = "LK04202172" +LEGACY_SOIL_ID = 5130973 + + +def _write_raster(path: Path, bands, nodata=0, crs="EPSG:4326") -> Path: + data = np.asarray(bands, dtype="uint32") + if data.ndim == 2: + data = data[np.newaxis, :, :] + with rasterio.open( + path, + "w", + driver="GTiff", + width=data.shape[2], + height=data.shape[1], + count=data.shape[0], + dtype=data.dtype, + nodata=nodata, + crs=crs, + transform=from_origin(80.0, 10.0, 1.0, 1.0), + ) as dst: + dst.write(data) + return path + + +def _write_soil_file(ghr_root: Path, profile_id=PROFILE_ID) -> Path: + soil_path = ghr_root / f"{profile_id[:2]}.SOL" + soil_path.write_text( + "*{0} Test soil\n" + "@SITE COUNTRY LAT LONG\n" + " TEST SRI_LANKA 8.54 81.12\n" + "@ SLB SBDM SLLL SDUL\n" + " 20 1.2 0.10 0.20\n" + " 60 1.3 0.12 0.25\n\n".format(profile_id), + encoding="utf-8", + ) + return soil_path + + +def _write_ghr_database(ghr_root: Path, soil_id=LEGACY_SOIL_ID, profile=PROFILE_ID) -> Path: + db_path = ghr_root / "GHR.db" + with sqlite3.connect(str(db_path)) as conn: + conn.execute("CREATE TABLE profile_map (id INTEGER PRIMARY KEY, profile TEXT)") + conn.execute( + "INSERT INTO profile_map (id, profile) VALUES (?, ?)", + (soil_id, profile), + ) + return db_path + + +@pytest.fixture +def soil_data(tmp_path): + # A path with spaces exercises the same Path-based code used for Windows paths. + root = tmp_path / "Simulation Data" / "soil" + root.mkdir(parents=True) + soil_file = _write_soil_file(root) + database = _write_ghr_database(root) + + legacy_values = np.zeros((3, 3), dtype="uint32") + legacy_values[1, 1] = LEGACY_SOIL_ID + legacy_raster = _write_raster(root / "ggcmi_soils_2.tif", legacy_values) + + prefix_values = np.zeros((3, 3), dtype="uint32") + numeric_values = np.zeros((3, 3), dtype="uint32") + prefix_values[1, 1] = 7675 # ASCII decimal pairs: L=76, K=75 + numeric_values[1, 1] = 4202172 + encoded_raster = _write_raster( + root / "encoded_soils.tif", + np.stack([prefix_values, numeric_values]), + ) + + return { + "root": root, + "soil_file": soil_file, + "database": database, + "legacy_raster": legacy_raster, + "encoded_raster": encoded_raster, + } - print("[OK] test_prefix_and_profile_code_from_bands") +def _lookup(raster_path, ghr_root, context=None): + run = {"id_soil": f"lookup_ghr::raster::{raster_path}"} + base_context = {"lat": SRI_LANKA_LAT, "lng": SRI_LANKA_LON} + if context: + base_context.update(context) + return fn.lookup_ghr( + "id_soil", + run, + base_context, + {"ghr_root": str(ghr_root)}, + ) -def test_extract_raster(): - print("\n=== Running test_extract_raster ===") - s = "lookup_ghr::raster::../rasters/eGHR_soils_raster.tif" - print("Input string:", s) +def test_prefix_and_profile_code_from_bands(): + assert fn.decode_prefix(6682) == "BR" + assert fn.build_profile_code_from_bands(6682, 5142095) == "BR05142095" + assert fn.build_profile_code_from_bands(7675, 4202172) == PROFILE_ID - raster_path = fn.extract_raster(s) - print("Extracted path:", raster_path) - expected = "../rasters/eGHR_soils_raster.tif" - print("Expected path :", expected) +@pytest.mark.parametrize( + "prefix_code,numeric_id", + [(3333, 1), (6682, -1), (6682, 100000000)], +) +def test_invalid_encoded_profile_values(prefix_code, numeric_id): + with pytest.raises(ValueError): + fn.build_profile_code_from_bands(prefix_code, numeric_id) - assert raster_path == expected, f"Expected {expected}, got {raster_path}" - print("[OK] test_extract_raster") +def test_extract_raster(): + value = "lookup_ghr::raster::../rasters/eGHR_soils_raster.tif" + assert fn.extract_raster(value) == "../rasters/eGHR_soils_raster.tif" def test_string_to_number(): - print("\n=== Running test_string_to_number ===") - assert fn.string_to_number("10") == 10 assert fn.string_to_number("3.14") == 3.14 - - # Should log an error and return None - result = fn.string_to_number("abc") - print("string_to_number('abc') →", result) - assert result is None - - print("[OK] test_string_to_number") + assert fn.string_to_number("abc") is None def test_split_fert_dap_percent(): - print("\n=== Running test_split_fert_dap_percent ===") - - run = { - "fert": "split_fert_dap_percent::100::2::10::50::20::50" - } - context = {} - - out = fn.split_fert_dap_percent("fert", run, context, None) - apps = out["fert"] - - print("Resulting applications:", apps) - - assert len(apps) == 2, "Should have 2 applications" - - # Application 1 - assert apps[0]["fdap"] == 10 - assert abs(apps[0]["famn"] - 50.0) < 1e-6 - - # Application 2 - assert apps[1]["fdap"] == 20 - assert abs(apps[1]["famn"] - 50.0) < 1e-6 - - print("[OK] test_split_fert_dap_percent") + run = {"fert": "split_fert_dap_percent::100::2::10::50::20::50"} + applications = fn.split_fert_dap_percent("fert", run, {}, None)["fert"] + assert applications == [ + {"fdap": 10, "famn": 50.0}, + {"fdap": 20, "famn": 50.0}, + ] def test_assign_by_raster_value(): - print("\n=== Running test_assign_by_raster_value ===") - run = { "treat": "assign_by_raster_value::raster::dummy.tif::1::OptionA::2::OptionB" } - context = {"treat": 2} - - out = fn.assign_by_raster_value("treat", run, context, None) - print("assign_by_raster_value →", out) - - assert out["treat"] == "OptionB", "Assignment based on raster value failed" - - print("[OK] test_assign_by_raster_value") + assert fn.assign_by_raster_value("treat", run, {"treat": 2}, None) == { + "treat": "OptionB" + } def test_date_offset(): - print("\n=== Running test_date_offset ===") - - run = { - "harvest": "date_offset::$pdate::10" + run = {"harvest": "date_offset::$pdate::10"} + result = fn.date_offset("harvest", run, {"pdate": "2020-01-01"}, None) + assert result["harvest"] == "2020-01-11" + + +def test_legacy_one_band_lookup_uses_ghr_database(soil_data): + result = _lookup( + soil_data["legacy_raster"], + soil_data["root"], + {"id_soil": float(LEGACY_SOIL_ID)}, + ) + assert result == { + "id_soil": PROFILE_ID, + "soilFiles": [str(soil_data["soil_file"])], } - context = {"pdate": "2020-01-01"} - - out = fn.date_offset("harvest", run, context, None) - print("date_offset →", out) - - assert out["harvest"] == "2020-01-11" - - print("[OK] test_date_offset") - - -def test_get_profile_from_raster(): - print("\n=== Running test_get_profile_from_raster ===") - raster_path = Path("rasters/eGHR_soils_raster.tif") # adjust to your path - lat, lon = -9.208, -72.041 # known valid point from your README - profile_code = fn.get_profile_from_raster(lat, lon, raster_path) - print("get_profile_from_raster →", profile_code) - - assert profile_code is not None, "Raster lookup failed" - assert len(profile_code) >= 3 - assert profile_code[:2].isalpha() +def test_two_band_lookup_remains_supported(soil_data): + result = _lookup(soil_data["encoded_raster"], soil_data["root"]) + assert result == { + "id_soil": PROFILE_ID, + "soilFiles": [str(soil_data["soil_file"])], + } - print("[OK] test_get_profile_from_raster") +def test_get_profile_from_two_band_raster(soil_data): + result = fn.get_profile_from_raster( + SRI_LANKA_LAT, + SRI_LANKA_LON, + soil_data["encoded_raster"], + ) + assert result == PROFILE_ID -def test_lookup_ghr_integration(): - print("\n=== Running test_lookup_ghr_integration ===") +def test_lookup_and_generate_initial_condition_layers(soil_data): + lookup = _lookup( + soil_data["legacy_raster"], + soil_data["root"], + {"id_soil": LEGACY_SOIL_ID}, + ) + context = {**lookup} run = { - "id_soil": "lookup_ghr::raster::rasters/eGHR_soils_raster.tif" - } - context = { - "lat": -9.208, - "lng": -72.041, - } - config = { - "ghr_root": "eGHR" # adjust to your real SOL path + "ic_layers": "generate_ic_layers::$id_soil", + "icin": 50, + "icsw%": 50, } + result = fn.generate_ic_layers("ic_layers", run, context, None) + assert len(result["ic_layers"]) == 2 + assert result["ic_layers"][0]["icbl"] == "20" - print("Extracting raster path from run['id_soil']...") - raster_path_str = fn.extract_raster(run["id_soil"]) - print("→", raster_path_str) - - print("\nCalling lookup_ghr...") - result = fn.lookup_ghr("id_soil", run, context, config) - print("lookup_ghr output:", result) - - assert result is not None, "lookup_ghr returned None" - assert "id_soil" in result - assert "soilFiles" in result - assert len(result["soilFiles"]) == 1 - sol_path = Path(result["soilFiles"][0]) - print("Resolved SOL path:", sol_path) +def test_legacy_lookup_reports_missing_database(tmp_path, caplog): + root = tmp_path / "soil" + root.mkdir() + _write_soil_file(root) + values = np.zeros((3, 3), dtype="uint32") + values[1, 1] = LEGACY_SOIL_ID + raster_path = _write_raster(root / "legacy.tif", values) - assert sol_path.exists(), "SOL file does not exist — adjust ghr_root" + with caplog.at_level(logging.ERROR): + result = _lookup(raster_path, root, {"id_soil": LEGACY_SOIL_ID}) - print("[OK] test_lookup_ghr_integration") - - -def test_lookup_ghr_and_ic_layers(): - print("\n=== Running test_lookup_ghr_and_ic_layers ===") - - run = { - "id_soil": "lookup_ghr::raster::rasters/eGHR_soils_raster.tif", - "ic_layers": "generate_ic_layers::$id_soil", - # parâmetros mínimos que calculateICLayerData usa: - "icin": 50, # N inicial total (exemplo) - "icsw%": 50, # água disponível inicial (exemplo) - } - - context = { - "lat": -9.208, - "lng": -72.041, - } - config = { - "ghr_root": "eGHR" - } + assert result is None + assert "GHR.db was not found" in caplog.text - # 1) Resolve solo e soilFiles - lookup = fn.lookup_ghr("id_soil", run, context, config) - context.update(lookup) - # 2) Gera camadas IC - ic_result = fn.generate_ic_layers("ic_layers", run, context, None) - print("generate_ic_layers →", ic_result) +def test_legacy_lookup_reports_unknown_id(soil_data, caplog): + with caplog.at_level(logging.ERROR): + result = _lookup( + soil_data["legacy_raster"], + soil_data["root"], + {"id_soil": 999}, + ) + assert result is None + assert "was not found in GHR.db" in caplog.text - assert ic_result is not None - assert "ic_layers" in ic_result - assert isinstance(ic_result["ic_layers"], list) - assert len(ic_result["ic_layers"]) > 0 - print("[OK] test_lookup_ghr_and_ic_layers") +def test_lookup_reports_missing_sol_file(soil_data, caplog): + soil_data["soil_file"].unlink() + with caplog.at_level(logging.ERROR): + result = _lookup( + soil_data["legacy_raster"], + soil_data["root"], + {"id_soil": LEGACY_SOIL_ID}, + ) + assert result is None + assert "DSSAT soil file was not found" in caplog.text -if __name__ == "__main__": - print("\n============================================") - print(" Running Basic Tests for pythia.functions") - print("============================================\n") +def test_lookup_reports_profile_missing_inside_sol_file(soil_data, caplog): + soil_data["soil_file"].write_text("*LK99999999 Another soil\n", encoding="utf-8") + with caplog.at_level(logging.ERROR): + result = _lookup( + soil_data["legacy_raster"], + soil_data["root"], + {"id_soil": LEGACY_SOIL_ID}, + ) + assert result is None + assert "was not found inside DSSAT soil file" in caplog.text + + +@pytest.mark.parametrize( + "lat,lon", + [(91.0, 81.0), (-91.0, 81.0), (8.0, 181.0), (8.0, -181.0)], +) +def test_coordinates_outside_raster_return_none(soil_data, lat, lon): + assert fn.get_profile_from_raster(lat, lon, soil_data["encoded_raster"]) is None + + +def test_partially_missing_encoded_profile_returns_none(tmp_path): + prefix = np.zeros((3, 3), dtype="uint32") + numeric = np.zeros((3, 3), dtype="uint32") + prefix[1, 1] = 7675 + raster_path = _write_raster( + tmp_path / "partial.tif", + np.stack([prefix, numeric]), + ) + assert fn.get_profile_from_raster(SRI_LANKA_LAT, SRI_LANKA_LON, raster_path) is None + + +def test_unsupported_band_count_is_rejected(tmp_path, caplog): + root = tmp_path / "soil" + root.mkdir() + _write_soil_file(root) + raster_path = _write_raster( + root / "three-bands.tif", + np.zeros((3, 3, 3), dtype="uint32"), + ) + with caplog.at_level(logging.ERROR): + result = _lookup(raster_path, root) + assert result is None + assert "expected 1 legacy band or 2 encoded bands" in caplog.text - test_prefix_and_profile_code_from_bands() - test_extract_raster() - test_string_to_number() - test_split_fert_dap_percent() - test_assign_by_raster_value() - test_date_offset() - test_get_profile_from_raster() - test_lookup_ghr_integration() - test_lookup_ghr_and_ic_layers() - print("\n============================================") - print(" All tests finished successfully.") - print("============================================\n") +def test_peer_raster_read_rejects_negative_and_overflowing_indexes(soil_data): + with rasterio.open(soil_data["legacy_raster"]) as dataset: + band = dataset.read(1, masked=True) + assert pythia.io.get_site_raster_value(dataset, band, (79.0, 11.0)) is None + assert pythia.io.get_site_raster_value(dataset, band, (84.0, 8.0)) is None diff --git a/release/RELEASE_NOTES_2.3.1.md b/release/RELEASE_NOTES_2.3.1.md new file mode 100644 index 00000000..9cdfefb4 --- /dev/null +++ b/release/RELEASE_NOTES_2.3.1.md @@ -0,0 +1,45 @@ +# Pythia 2.3.1 + +This patch release restores compatibility with existing one-band GHR soil +rasters, including the `ggcmi_soils_2.tif` distributed with the Sri Lanka +example. It also retains support for the newer two-band encoded profile format. + +## Action required for current users + +If Pythia reports that a one-band soil raster “must have 2 bands,” install the +2.3.1 wheel. **Do not convert or add a band to the existing raster.** For a +legacy one-band input, keep these resources together: + +- the soil raster referenced by `id_soil`; +- `GHR.db` under the configured `ghr_root`; +- the `.SOL` files referenced by `GHR.db`, also under `ghr_root`. + +Existing JSON configurations remain compatible and require no schema change. + +## Updated Sri Lanka example + +Download `Pythia-Example-Data-2.3.1.zip` from this release, extract it, and run: + +```console +pythia --configure-example /path/to/Simulation_Data \ + --dssat-executable /path/to/dscsm048 +pythia --validate-example /path/to/Simulation_Data +pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Maize.json +``` + +The configuration command prepares all three examples: maize, rice, and rice +with environment modifications. It saves the portable originals as +`*.json.template` and can be rerun after moving DSSAT or `Simulation_Data`. + +## Additional improvements + +- automatic one-band/two-band soil format detection; +- checked raster bounds and coordinate reprojection; +- actionable errors for missing GHR mappings and `.SOL` profiles; +- pixel-level reads for two-band rasters instead of loading full rasters; +- corrected plugin context execution; +- expanded installation, configuration, troubleshooting, and release guides; +- regression tests for both soil formats and the reported Sri Lanka location. + +Verify the downloaded example archive against +`Pythia-Example-Data-2.3.1.zip.sha256` before extracting it. diff --git a/release/Simulation_Data_README.md b/release/Simulation_Data_README.md new file mode 100644 index 00000000..e58a6437 --- /dev/null +++ b/release/Simulation_Data_README.md @@ -0,0 +1,41 @@ +# Pythia Sri Lanka example data + +This directory accompanies a Pythia release. It contains three configurations: + +- `Sri_Lanka/SL_Maize.json` +- `Sri_Lanka/SL_Rice.json` +- `Sri_Lanka/SL_Rice_env.json` + +The configurations are portable templates. After installing both Pythia and +DSSAT, configure all three at once: + +```console +pythia --configure-example /path/to/Simulation_Data \ + --dssat-executable /path/to/dscsm048 +``` + +On Windows, for example: + +```powershell +pythia --configure-example C:\Pythia\Simulation_Data ` + --dssat-executable C:\DSSAT48\DSCSM048.EXE +``` + +The command replaces `<>` and +`<>`, preserves the original files as +`*.json.template`, and checks every referenced input. It is safe to run the +command again if the directory or DSSAT executable changes. + +Validate and run an example: + +```console +pythia --validate-example /path/to/Simulation_Data +pythia --all /path/to/Simulation_Data/Sri_Lanka/SL_Maize.json +``` + +Results are written below `OUTPUT/Sri_Lanka`. The bundled one-band +`raster/ggcmi_soils_2.tif` is intentional: compatible Pythia releases resolve +its numeric GHR identifiers through `eGHR/GHR.db` and the `.SOL` files. + +For installation, detailed commands, Windows notes, and troubleshooting, see +the README on the Pythia release page. diff --git a/scripts/prepare_example_release.py b/scripts/prepare_example_release.py new file mode 100644 index 00000000..cc6513d2 --- /dev/null +++ b/scripts/prepare_example_release.py @@ -0,0 +1,34 @@ +#!/usr/bin/env python3 +"""Create the portable Simulation_Data archive attached to a Pythia release.""" + +import argparse +from pathlib import Path + +from pythia.example_release import build_example_archive + + +def main(): + parser = argparse.ArgumentParser( + description="Validate and package the Pythia Sri Lanka example data." + ) + parser.add_argument("source", help="Path to the Simulation_Data directory") + parser.add_argument("output", help="Destination .zip path") + parser.add_argument( + "--readme", + default=str( + Path(__file__).parents[1] / "release" / "Simulation_Data_README.md" + ), + help="README inserted at the root of Simulation_Data", + ) + args = parser.parse_args() + + archive, checksum, size = build_example_archive( + args.source, args.output, args.readme + ) + print(f"Created: {archive}") + print(f"Size: {size / 1024**2:.1f} MiB") + print(f"Checksum: {checksum}") + + +if __name__ == "__main__": + main()