Putting trajectory calculation into separate repo

.github/workflows/python-package.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: pism-ragis
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        python -m pytest

.pre-commit-config.yaml

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+exclude: "docs|node_modules|migrations|.git|.tox"
+default_stages: [commit]
+fail_fast: true
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        exclude: conda/meta.yaml
+
+  # Can run individually with `pre-commit run black --all-files`
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+
+  # Can run individually with `pre-commit run isort --all-files`
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args:
+          - --profile
+          - black
+
+  # Can run individually with `pre-commit run flake8 --all-files`
+  # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
+  # https://github.com/pre-commit/pre-commit/issues/1206
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        entry: pflake8
+        additional_dependencies: [flake8-isort, pyproject-flake8]
+
+  # Can run individually with `pre-commit run mypy --all-files`
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.0
+    hooks:
+      - id: mypy
+
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
+        args:
+          [
+            "-rn", # Only display messages
+            "-sn", # Don't display the score
+          ]
+
+  # - repo: https://github.com/srstevenson/nb-clean
+  #   rev: 3.1.0
+  #  hooks:
+  #    - id: nb-clean
+
+  - repo: local
+    hooks:
+     - id: pytest # pytest is a pre-commit hook
+       name: pytest
+       entry: pytest tests
+       language: system
+       types: [python]
+       exclude: ^venv/ ^.git/ ^.vscode/ ^.DS_Store ^uq/ ^hindcasts/
+       always_run: true
+       pass_filenames: false

.pylintrc

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+[MASTER]
+jobs=4 #number of processes to use
+[BASIC]
+good-names=nameOfYourProject #names to be considered ok
+[pre-commit-hook]
+disable=E0401, C0301, C0103, R0903, R0913, R0914, W0102, E1126, C0302, R0911, R1705, W0702, R0912, R0915

README.md

@@ -1 +1 @@
-# trajectory
+# trajectory

pyproject.toml

@@ -0,0 +1,135 @@
+[project]
+name = "trajectory"
+version = "0.1.0"
+maintainers = [{name = "Andy Aschwanden", email = "[email protected]"}]
+description = """Calculate trajectories for a static flow field"""
+readme = "README.md"
+requires-python = ">3.8"
+license = {text = "GPL 3.0"}
+classifiers = [
+        "License :: OSI Approved :: Apache Software License",
+        "Natural Language :: English",
+        "Operating System :: MacOS :: MacOS X",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: POSIX :: Linux",
+        "Programming Language :: Python :: 3.10",
+        "Topic :: Scientific/Engineering :: Postprocessing",
+        ]
+dynamic = ["dependencies"]
+
+[tool.setuptools.packages.find]
+include = ["trajectory"]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+py-modules = ["trajectory"]
+
+[tool.poetry]
+name = "trajectory"
+version = "0.1.0"
+description = """Calculate trajectories"""
+authors = ["Andy Aschwanden <[email protected]>"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.13"
+gdal = ">=3.7.2"
+geopandas = ">=0.14.0"
+joblib = ">=1.3.2"
+matplotlib = ">=3.8.0"
+pandas = ">=1.5.3"
+shapely = ">=2.0.2"
+xarray = "^2022.10.0"
+pyogrio = "^0.7.2"
+pyarrow = "^14.0.0"
+tqdm = "^4.66.1"
+
+[tool.poetry.urls]
+
+"homepage" = "https://github.com/pism/trajectory"
+"repository" = "https://github.com/pism/trajectory"
+"bug tracker" = "https://github.com/pism/trajectory/issues"
+
+[tool.flake8]
+# https://pep8.readthedocs.io/en/latest/intro.html#error-codes
+ignore = """
+    E203,
+    E501,
+    W503,
+    W605,
+    C901,
+    F841,
+    E722,
+    E402,
+    F722,
+    """
+# Max width of Github code review is 119 characters
+max-line-length = 119
+max-complexity = 18
+exclude = [
+    ".tox",
+    ".git",
+    "*/migrations/*",
+    ".mypy_cache",
+    ".pytest_cache",
+    "*__init__.py",
+    "venv"
+    ]
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = "True"
+force_grid_wrap = 0
+use_parentheses = "True"
+line_length = 88
+
+[tool.pycodestyle]
+max-line-length = 119
+exclude = [
+    ".tox",
+    ".git",
+    "*/migrations/*",
+    ".mypy_cache",
+    ".pytest_cache",
+    "*__init__.py",
+    "venv"
+    ]
+
+[tool.mypy]
+python_version = 3.11
+check_untyped_defs = "True"
+ignore_missing_imports = "True"
+warn_unused_ignores = "True"
+warn_redundant_casts = "True"
+warn_unused_configs = "True"
+
+[tool.black]
+line-length = 88
+target-version = ['py311']
+include = '\.pyi?$'
+exclude = '''
+/(
+      \.eggs
+    | \.git
+    | \.mypy_cache
+    | _build
+    | conda
+    | docs
+ )/
+'''
+
+[tool.pylint.messages_control]
+disable = """
+    too-many-lines,
+    no-else-return,
+    bare-except
+"""
+
+[tool.pylint.format]
+max-line-length = 120

requirements.txt

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+dask>=2023.10.1
+joblib>=1.3.2
+matplotlib>=3.8.0
+pandas>=2.0.3
+pydoe>=0.3.8
+salib>=1.4.7
+scipy>=1.10.1
+shapely>=2.0.2
+h5netcdf
+xarray>=2023.10.1
+pyogrio>=0.7.2
+pyarrow>=14.0.0
+tqdm>=4.66.1
+openpyxl>=3.1.2
+toml
+types-toml