Merge pull request #174 from DassHydro/maintenance/1.0.x

Maintenance/1.0.x

.github/workflows/code-checks.yml

@@ -0,0 +1,48 @@
+# This workflow will check code (tapenade compare and ruff check)
+name: Code Checks
+
+on:
+
+    push:
+        branches:
+        - main
+
+    pull_request:
+        branches:
+        - main
+        - maintenance/**
+
+    # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    ubuntu:
+        name: Code checks ubuntu-latest
+        runs-on: ubuntu-latest
+        steps:
+        - uses: actions/checkout@v4
+          with:
+            fetch-depth: 0
+
+        - name: Set up Python
+          uses: actions/setup-python@v5
+          with:
+            python-version: "3.11"
+
+        - name: Install dependencies
+          run: |
+            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
+            pip install ruff
+
+        - name: Tapenade Compare
+          run: |
+            make tap-cmp
+
+        - name: Ruff Check
+          run: |
+            . test/bin/activate
+            make check

.github/workflows/doc.yml

@@ -1,4 +1,4 @@
-# This workflow will generate the documentation
+# This workflow will build the doc
 name: Documentation
 
 on:
@@ -17,25 +17,33 @@ on:
 
 jobs:
     ubuntu:
-        name: (${{ matrix.os }})
-        runs-on: ${{ matrix.os }}
-        strategy:
-          matrix:
-            os: ["ubuntu-20.04", "ubuntu-22.04"]
+        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
+          uses: actions/setup-python@v5
+          with:
+            python-version: '3.11'
+
         - name: Install dependencies
           run: |
             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
-            if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        
-        - name: Build and Install
+            pip install -r requirements-dev.txt
+
+        - name: Build
           run: |
+            . test/bin/activate
             make
-        
-        - name: Generate Documentation
+
+        - name: Build Documentation
           run: |
+            . test/bin/activate
             make doc

.github/workflows/unit-tests.yml

@@ -17,25 +17,36 @@ on:
 
 jobs:
     ubuntu:
-        name: (${{ matrix.os }})
-        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: ['3.9', '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@v5
+          with:
+            python-version: ${{ matrix.python-version }}
+
         - name: Install dependencies
           run: |
             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
-            if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
-        
-        - name: Build and Install
+            pip install -r requirements-dev.txt
+
+        - name: Build
           run: |
+            . test/bin/activate
             make
-        
+
         - name: Run Tests
           run: |
+            . test/bin/activate
             make test

.github/workflows/wheel.yml

@@ -0,0 +1,52 @@
+# 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]
+
+        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

@@ -1,12 +1,74 @@
-**/__pycache__
-__pycache__
+# https://github.com/github/gitignore/blob/main/Python.gitignore
 
-**/.f2py*
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+wheelhouse/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Fortran module files
+*.mod
+*.smod
+
+# Fortran wrapping files
 .f2py*
+src.*
+f90wrap*.f90
+**/fcore/_m*.py
 
+# Tapenade files
 tapenade/*.msg*
 tapenade/*.f90*
 tapenade/*~
 
-**/tmp*
+# Temporary files
 tmp*
+*.kate-swp
+
+# Documentation files
+doc/source/api_reference/**/smash
+doc/*-dataset

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"]