Merge branch 'main' into write_fluxes

.github/workflows/code-checks.yml

@@ -17,24 +17,22 @@ on:
 
 jobs:
     ubuntu:
-        name: (${{ matrix.os }})
-        runs-on: ${{ matrix.os }}
-        strategy:
-          matrix:
-            os: ["ubuntu-20.04", "ubuntu-22.04"]
-
+        name: Code checks ubuntu-latest
+        runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
+          with:
+            fetch-depth: 0
 
         - name: Set up Python
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: "3.11"
 
         - name: Install dependencies
           run: |
-            sudo apt-get update -y
-            sudo apt-get install build-essential make openjdk-11-jre-headless
+            sudo apt-get update
+            sudo apt-get install build-essential openjdk-17-jdk
             python -m venv test
             . test/bin/activate
             python -m pip install --upgrade pip

.github/workflows/doc.yml

@@ -17,30 +17,25 @@ on:
 
 jobs:
     ubuntu:
-        name: (${{ matrix.os }} | py-${{ matrix.python-version }})
-        runs-on: ${{ matrix.os }}
-        strategy:
-          matrix:
-            os: ['ubuntu-20.04', 'ubuntu-22.04']
-            python-version: ['3.8', '3.9', '3.10', '3.11']
+        name: Documentation ubuntu-latest
+        runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
+          with:
+            fetch-depth: 0
 
-        - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v4
+        - name: Set up Python
+          uses: actions/setup-python@v5
           with:
-            python-version: ${{ matrix.python-version }}
+            python-version: '3.11'
 
         - name: Install dependencies
           run: |
-            sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
             sudo apt-get update
-            sudo apt-get install build-essential make gcc gfortran gdal-bin libgdal-dev
+            sudo apt-get install build-essential gfortran
             python -m venv test
             . test/bin/activate
             python -m pip install --upgrade pip
-            pip install wheel numpy
-            pip install gdal==$(gdal-config --version)
             pip install -r requirements-dev.txt
 
         - name: Build

.github/workflows/unit-tests.yml

@@ -17,30 +17,28 @@ on:
 
 jobs:
     ubuntu:
-        name: (${{ matrix.os }} | py-${{ matrix.python-version }})
-        runs-on: ${{ matrix.os }}
+        name: Unit tests ubuntu-latest py-${{ matrix.python-version }})
+        runs-on: ubuntu-latest
         strategy:
           matrix:
-            os: ['ubuntu-20.04', 'ubuntu-22.04']
-            python-version: ['3.8', '3.9', '3.10', '3.11']
+            python-version: ['3.9', '3.10', '3.11']
         steps:
-        - uses: actions/checkout@v3
+        - uses: actions/checkout@v4
+          with:
+            fetch-depth: 0
 
         - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: ${{ matrix.python-version }}
 
         - name: Install dependencies
           run: |
-            sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
             sudo apt-get update
-            sudo apt-get install build-essential make gcc gfortran gdal-bin libgdal-dev
+            sudo apt-get install build-essential gfortran
             python -m venv test
             . test/bin/activate
             python -m pip install --upgrade pip
-            pip install wheel numpy
-            pip install gdal==$(gdal-config --version)
             pip install -r requirements-dev.txt
 
         - name: Build

.github/workflows/wheel.yml

@@ -0,0 +1,55 @@
+# This is partially adopted from scipy.
+# See: https://github.com/scipy/scipy/blob/main/.github/workflows/wheels.yml
+# License: 3-clause BSD, https://github.com/scipy/scipy/blob/main/LICENSE.txt
+
+name: Wheels
+
+# Controls when the action will run.
+on:
+
+    push:
+        branches:
+        - main
+
+    pull_request:
+        branches:
+        - main
+        - maintenance/**
+
+    # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheel ${{ matrix.python-version }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    strategy:
+      matrix:
+        buildplat:
+        - [ubuntu-latest, manylinux, x86_64]
+        # Use windows-2019 otherwise there is undefined reference to _setjmpex. This is linked to f90wrap
+        # and f90wrap_abort with FortranDerivedTypeArray
+        - [windows-2019, win, AMD64]
+
+        python-version: ['cp39', 'cp310', 'cp311']
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: ${{ matrix.python-version }}-${{ matrix.buildplat[1] }}*
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
+          name: ${{ matrix.python-version }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}

.gitignore

@@ -22,6 +22,7 @@ parts/
 sdist/
 var/
 wheels/
+wheelhouse/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -60,9 +61,9 @@ f90wrap*.f90
 **/fcore/_m*.py
 
 # Tapenade files
-tapenade/*.msg*
-tapenade/*.f90*
-tapenade/*~
+# Tapenade files
+tapenade/*_db.*
+*_db.msg*
 
 # Temporary files
 tmp*

Dockerfile

@@ -1,23 +1,15 @@
-FROM ubuntu:22.04
+# Derived from Pandas
+FROM python:3.11
+WORKDIR /home/smash
 
-ADD . /app/
-
-WORKDIR /app
-
-RUN apt-get update && apt-get install -y \
+RUN apt-get update && apt-get -y upgrade
+RUN apt-get install -y \
     build-essential \
-    make \
-    openjdk-11-jre-headless \
-    gcc \
-    gfortran \
-    gdal-bin \
-    libgdal-dev \
-    python3-pip
-
-ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
-
-RUN export JAVA_HOME
-
-RUN pip3 install -r requirements-dev.txt
-
-RUN make
+    openjdk-17-jdk \
+    gfortran
+
+RUN python -m pip install --upgrade pip
+COPY requirements-dev.txt /tmp
+RUN python -m pip install -r /tmp/requirements-dev.txt
+RUN git config --global --add safe.directory /home/smash
+CMD ["/bin/bash"]

Makefile

@@ -0,0 +1,59 @@
+#% Meson options (see meson.options)
+use-openmp := true
+
+#% Build smash
+all:
+	pip install -Csetup-args=-Duse-openmp=$(use-openmp) .
+
+#% Build smash in editable mode
+edit:
+	pip install -Csetup-args=-Duse-openmp=$(use-openmp) --no-build-isolation --config-settings=editable-verbose=true --editable .
+
+TAP_FILES := $(addprefix smash/fcore/*/,mwd_*.f90 md_*.f90 forward.f90)
+
+#% Generate tapenade files (adjoint and tangent linear models)
+tap:
+	python tapenade/generate_tapenade.py $(TAP_FILES) --build-dir smash/fcore/forward --openmp -m forward_openmp
+	python tapenade/generate_tapenade.py $(TAP_FILES) --build-dir smash/fcore/forward -m forward
+
+#% Compare tapenade files
+tap-cmp:
+	python tapenade/generate_tapenade.py $(TAP_FILES) --build-dir tapenade --openmp -m forward_openmp
+	python tapenade/generate_tapenade.py $(TAP_FILES) --build-dir tapenade -m forward
+	cmp tapenade/forward_openmp_db.f90 smash/fcore/forward/forward_openmp_db.f90
+	cmp tapenade/forward_db.f90 smash/fcore/forward/forward_db.f90
+
+#% Generate sphinx documentation
+doc:
+	make html -C doc
+
+#% Clean sphinx documentation
+doc-clean:
+	make clean -C doc
+
+#% Testing code with pytest
+test:
+	cd smash/tests ; pytest
+
+#% Testing code with pytest and coverage
+test-coverage:
+	cd smash/tests ; pytest --cov-report term --cov-report html --cov=smash
+
+#% Generate baseline for test with args (see argparser in gen_baseline.py)
+test-baseline:
+	cd smash/tests ; python3 gen_baseline.py
+
+#% Format Python files with ruff and Fortran files with fprettify
+format:
+	ruff format
+	fprettify -e forward_db.f90 -e forward_openmp_db.f90 -e f90wrap -f .f90 --indent 4 -r smash
+
+#% Check Python files with ruff linters
+check:
+	ruff check --fix --exit-non-zero-on-fix
+
+#% Clean
+clean:
+	@rm -rf build
+
+.PHONY: all edit tap tap-cmp doc doc-clean test test-baseline format check clean

README.md

@@ -1,26 +1,26 @@
 <h1 align="center">
 <picture>
-  <source media="(prefers-color-scheme: dark)" srcset="doc/source/_static/corporate_logo_dark.svg">
-  <img src="doc/source/_static/corporate_logo.svg" width="300", hspace=30>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/DassHydro/smash/main/doc/source/_static/corporate_logo_dark.svg">
+  <img src="https://raw.githubusercontent.com/DassHydro/smash/main/doc/source/_static/corporate_logo.svg" width="300", hspace=30>
 </picture>
 <picture>
-  <source media="(prefers-color-scheme: dark)" srcset="doc/source/_static/logo_smash_dark.svg">
-  <img src="doc/source/_static/logo_smash.svg" width="300", hspace=30>
+  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/DassHydro/smash/main/doc/source/_static/logo_smash_dark.svg">
+  <img src="https://raw.githubusercontent.com/DassHydro/smash/main/doc/source/_static/logo_smash.svg" width="300", hspace=30>
 </picture>
 </h1><br>
 
 - **Documentation:** https://smash.recover.inrae.fr
 - **Source code:** https://github.com/DassHydro/smash
-- **Contributors and contact:** https://smash.recover.inrae.fr/contributors/index.html
-- **Contributing:** https://smash.recover.inrae.fr/developers_guide/index.html
+- **Contributing:** https://smash.recover.inrae.fr/contributor_guide/index.html
 - **Scientific references from latest version:** https://smash.recover.inrae.fr/bibliography/index.html
 - **Bug reports:** https://github.com/DassHydro/smash/issues
 
 **smash** is a Python library, that provides a variety of user-friendly routines for hydrological modeling, including data preprocessing, high-dimensional optimization tools, sensitivity and signatures analysis, all interfaced with an efficient Fortran solver.
 
 **smash** offers a range of advanced optimization techniques, including Variational Data Assimilation (VDA), Bayesian estimation, and Artificial Neural Network (ANN) approaches, using an adjoint model generated with the **Tapenade** Automatic Differentiation Engine.
 
+- **Tapenade** website: https://team.inria.fr/ecuador/en/tapenade/
 - **Tapenade** article: https://doi.org/10.1145/2450153.2450158
 - **Tapenade** source code: https://gitlab.inria.fr/tapenade/tapenade.git
 
-Whether you are managing water resources or conducting research on hydrological models, **smash** can provide an easy-to-use yet powerful solution for your work. See [this documentation](https://smash.recover.inrae.fr/getting_started/index.html) for the installation instructions.
+Whether you are managing water resources or conducting research on hydrological models, **smash** can provide an easy-to-use yet powerful solution for your work. See [this documentation](https://smash.recover.inrae.fr/getting_started/index.html) for the installation instructions.