Refactor

.github/pull_request_template.md

@@ -26,7 +26,7 @@ Check relevant points.
 
 # Checklist:
 
-- [ ] updated version number in setup.py/pyproject.toml
+- [ ] updated version number in pyproject.toml
 - [ ] updated environment.yml and the lock file
 - [ ] added changes to History.rst
 - [ ] updated the latest version in README file

.github/workflows/conda-deployment.yml

@@ -0,0 +1,43 @@
+name: conda-deployment
+
+on: [push]
+
+jobs:
+  Main-package:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
+    env:
+      OS: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          mamba-version: "*"
+          use-mamba: true
+          auto-update-conda: false
+          auto-activate-base: false
+          environment-file: environment.yml
+          activate-environment: test
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+          channel-priority: true
+          show-channel-urls: true
+
+      - name: Install dev-dependencies
+        shell: bash -el {0}
+        run: |
+            pip install pytest
+            pip install .[test] --no-deps --verbose
+
+      - name: Run tests
+        shell: bash -el {0}
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          pytest -sv -m "not plot"

.github/workflows/github-release.yml

@@ -0,0 +1,36 @@
+name: gitHub-release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  create-release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup GitHub CLI
+        run: |
+          type -p curl >/dev/null || (sudo apt update && sudo apt install curl -y)
+          curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg \
+          && sudo chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg \
+          && echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
+          && sudo apt update \
+          && sudo apt install gh -y
+
+      - name: Extract tag name
+        run: echo "TAG_NAME=${GITHUB_REF#refs/tags/}" >> $GITHUB_ENV
+
+
+      - name: Create GitHub Release
+        id: create_release
+        run: |
+          gh release create $TAG_NAME --title "$TAG_NAME"  --notes-from-tag
+        env:
+          GH_TOKEN: ${{ secrets.CREATE_RELEASE }}

.github/workflows/pypi-deployment.yml

@@ -0,0 +1,43 @@
+name: pypi-deployment
+
+on: [push]
+
+jobs:
+  Main-Package:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.12"]
+    env:
+      OS: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+
+      - name: Install GDAL
+        run: |
+            python -m pip install --upgrade pip
+            pip install --no-cache-dir Cython
+            pip install --find-links=https://girder.github.io/large_image_wheels --no-cache GDAL==3.10.0
+
+      - name: Test GDAL installation
+        run: |
+            python -c "from osgeo import gdal"
+            gdalinfo --version
+
+      - name: Install dependencies
+        run: |
+            pip install .[dev,test]
+
+      - name: Run Tests
+        run: |
+          python -m pytest -vvv --cov=src/Hapi --cov-report=xml
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v3

.github/workflows/pypi.yml → .github/workflows/pypi-release.yml

@@ -1,7 +1,7 @@
 # This workflows will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
-name: pypi-package
+name: pypi-release
 
 on:
     release:

.gitignore

@@ -186,3 +186,33 @@ examples/Hydrodynamic models/test_case/results/q/New folder/*
 examples/Hydrodynamic models/test_case/results/h/New folder/*
 examples/Hydrodynamic models/test_case/results/USbnd/New folder/*
 tests/mo/*
+/tests/rrm/data/test_results/extract_parameter/01_TT.tif
+/tests/rrm/data/test_results/extract_parameter/02_RFCF.tif
+/tests/rrm/data/test_results/extract_parameter/03_SFCF.tif
+/tests/rrm/data/test_results/extract_parameter/04_CFMAX.tif
+/tests/rrm/data/test_results/extract_parameter/05_CWH.tif
+/tests/rrm/data/test_results/extract_parameter/06_CFR.tif
+/tests/rrm/data/test_results/extract_parameter/07_FC.tif
+/tests/rrm/data/test_results/extract_parameter/08_BETA.tif
+/tests/rrm/data/test_results/extract_parameter/09_ETF.tif
+/tests/rrm/data/test_results/extract_parameter/10_LP.tif
+/tests/rrm/data/test_results/extract_parameter/11_K0.tif
+/tests/rrm/data/test_results/extract_parameter/12_K1.tif
+/tests/rrm/data/test_results/extract_parameter/13_K2.tif
+/tests/rrm/data/test_results/extract_parameter/14_UZL.tif
+/tests/rrm/data/test_results/extract_parameter/15_PERC.tif
+/tests/rrm/data/test_results/extract_parameter/16_MAXBAS.tif
+/tests/rrm/data/test_results/extract_parameter/17_K_muskingum.tif
+/tests/rrm/data/test_results/extract_parameter/18_X_muskingum.tif
+/tests/rrm/data/test_results/extract_parameter/ID1.tif
+
+/tests/rrm/data/test_results/prepare_inputs/0_precip_2009.01.01.tif
+/tests/rrm/data/test_results/prepare_inputs/1_precip_2009.01.02.tif
+/tests/rrm/data/test_results/prepare_inputs/2_precip_2009.01.03.tif
+/tests/rrm/data/test_results/prepare_inputs/3_precip_2009.01.04.tif
+/tests/rrm/data/test_results/prepare_inputs/4_precip_2009.01.05.tif
+/tests/rrm/data/test_results/prepare_inputs/5_precip_2009.01.06.tif
+/tests/rrm/data/test_results/prepare_inputs/6_precip_2009.01.07.tif
+/tests/rrm/data/test_results/prepare_inputs/7_precip_2009.01.08.tif
+/tests/rrm/data/test_results/prepare_inputs/8_precip_2009.01.09.tif
+/tests/rrm/data/test_results/prepare_inputs/9_precip_2009.01.10.tif

.pre-commit-config.yaml

@@ -1,16 +1,21 @@
 fail_fast: true
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v5.0.0
     hooks:
+      - id: check-toml
+        name: "[py -  check] check toml"
       - id: end-of-file-fixer
         name: "[py -  check] validate yaml"
+      - id: no-commit-to-branch
+        name: "[git -  check] no commit to branch"
+        args: [ --branch=main ]
       - id: trailing-whitespace
         name: "[file - format] trim trailing whitespace"
         args: [ --markdown-linebreak-ext=md ]
       - id: check-added-large-files
         name: "[file -  check] large file"
-        args: [ --maxkb=5000 ]
+        args: [ --maxkb=2000 ]
       - id: check-docstring-first
         name: "[py   -  check] docstring first"
         files: /examples
@@ -38,52 +43,46 @@ repos:
         name: "[reqs - format] fix requirements.txt"
       - id: check-yaml
         name: "[yaml -  check] validate yaml"
-#  - repo: https://github.com/pre-commit/mirrors-isort
-#    rev: v5.10.1
-#    hooks:
-#      - id: isort
-#        name: "[py   - format] isort"
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.4
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
     hooks:
-      - id: docformatter
-        name: "[py   - format] docformatter"
-        args: [ -i, --wrap-summaries, "0" ]
-
-  - repo: https://github.com/PyCQA/pydocstyle
-    rev: 6.1.1
+      - id: flake8
+        additional_dependencies: [Flake8-pyproject]
+        name: "[py   - check] flake8"
+        exclude: ^(examples/|tests/)
+#   - repo: https://github.com/pycqa/docformatter
+#     rev: v1.4
+#     hooks:
+#      - id: docformatter
+#        name: "[py   - format] docformatter"
+#        description: 'Formats docstrings to follow PEP 257.'
+#        entry: docformatter
+#        args: [-i]
+#        language: python
+#        types: [python]
+  - repo: https://github.com/pycqa/pydocstyle
+    rev: 6.3.0
     hooks:
       - id: pydocstyle
         name: "[py   - check] pydocstyle"
-        files: ^Hapi/
-
-  - repo: https://gitlab.com/pycqa/flake8
-    rev: 4.0.1
+        files: ^src/.*\.py$
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
     hooks:
-      - id: flake8
-        name: "[py   - check] flake8"
-        language_version: python3.9
-        exclude: ^(examples/|tests/)
-
-  #- repo: https://github.com/psf/black
-  #  rev: 22.8.0
-  #  hooks:
-  #    - id: black
-  - repo: https://github.com/ambv/black
-    rev: 22.8.0
+      - id: isort
+        name: "[py   - format] isort"
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
     hooks:
       - id: black
-        name: "[py   - format] black"
-        language_version: python3.9
   - repo: https://github.com/lovesegfault/beautysh
     rev: v6.2.1
     hooks:
       - id: beautysh
         name: "[bash - format] beautysh"
 
-  # pre-commit-shell: Checks shell scripts against shellcheck.
   - repo: https://github.com/detailyang/pre-commit-shell
-    rev: v1.0.6
+    rev: 1.0.5
     hooks:
       - id: shell-lint
         name: "[bash -   lint] shell-lint"
@@ -108,7 +107,7 @@ repos:
     hooks:
       - id: pytest-check
         name: pytest-check
-        entry: pytest -vvv --cov=Hapi
+        entry: pytest -vvv --cov=Hapi --cov-report term-missing
         language: system
         pass_filenames: false
         always_run: true

HISTORY.rst

@@ -49,3 +49,19 @@ History
 * add smoothDikeLevel, getReach and updateReach
 * bump up denpendencies versions
 * move un-necessary functions to serapeum-utils
+
+
+2.0.0 (2025-01-**)
+------------------
+
+Dev
+---
+- Add conda/pypi workfkow
+- Add github release workfkow
+- Add pypi release workfkow
+- remove coverall
+- remove flake8 separate config file
+- move the main packge files inside src directory
+- move the hydrodymanic model to separate repo (serapis)
+- move the plot module to the cleopatra package
+- replace the setup.py by pyproject.toml