First commit to setup the project skeleton

.conda/env_build.yml

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+channels:
+    - accessnri
+    - conda-forge
+    - nodefaults
+
+dependencies:
+    - anaconda-client
+    - conda-build
+    - conda-verify
+    - versioneer

.conda/env_dev.yml

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+name: um-modify
+channels:
+    - accessnri
+    - conda-forge
+    - coecms
+    - nodefaults
+
+dependencies:
+    - python >=3.10
+    - mule
+    - numpy <2
+    - versioneer
+    - xarray
+    - hypothesis
+    - ipykernel
+    - pip
+    - pytest
+    - pytest-cov
+    - ruff

.conda/meta.yaml

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+{% set version = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True).get('version') %}
+{% set project = load_file_data('../pyproject.toml', from_recipe_dir=True).get('project') %}
+
+package:
+    name: {{ project.get('name') }}
+    version: "{{ version }}"
+
+build:
+    noarch: python
+    number: 0
+    entry_points:
+        {% for name, script in project.get('scripts').items() %}
+        - {{ name }} = {{ script }}
+        {% endfor %}
+
+source:
+    path: ../src
+
+requirements:
+    host:
+        - python
+        - pip
+        - setuptools >=61.0.0
+        - versioneer
+    run:
+        {% for dep in project.get('dependencies') %}
+        - {{ dep }}
+        {% endfor %}
+
+test:
+    commands:
+    {% for name, script in project.get('scripts').items() %}
+        - {{ name }} --help
+    {% endfor %}
+
+about:
+    home: {{ project.get('urls').get('Repository') }}
+    license: Apache Software
+    license_file: LICENSE
+    summary: {{ project.get('description') }}
+    license_family: Apache
+

.gitattributes

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+src/um-modify/_version.py export-subst

.github/workflows/CD.yml

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+name: CD
+
+on:
+  push:
+    tags:        
+      - '**' 
+
+jobs:
+  get-package-name:
+    name: Get package name
+    runs-on: ubuntu-latest
+    outputs:
+      package-name: ${{ steps.get-package-name.outputs.package-name }}
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+          fetch-tags: true
+          fetch-depth: 0
+
+      - name: Get name
+        id: get-package-name
+        run: |
+          echo "package-name=$(yq '.project.name' pyproject.toml)" >> $GITHUB_OUTPUT
+  
+  release-conda-package:
+    name: Build with conda and release
+    runs-on: ubuntu-latest
+    needs: get-package-name
+    env:
+      BUILD_FOLDER: ${{github.workspace}}/build
+      PACKAGE_PATH: ${{github.workspace}}/build/noarch/*.tar.bz2
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+        with:
+            fetch-tags: true
+            fetch-depth: 0 
+
+      - name: Setup conda build environment
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ vars.PY_VERSION }} 
+          environment-file: .conda/env_build.yml
+          auto-activate-base: false
+          auto-update-conda: false
+          show-channel-urls: true
+
+      - name: Build conda package
+        shell: bash -el {0}
+        run: |
+          conda build . --no-anaconda-upload --output-folder=${{env.BUILD_FOLDER}} -c accessnri -c conda-forge
+        # Channels needed for the conda recipe tests
+
+      - name: Upload conda package to Anaconda.org
+        shell: bash -el {0}
+        run: |
+          anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload --user ${{ secrets.ANACONDA_USER_NAME }} ${{env.PACKAGE_PATH}}
+      
+      - name: Create Release
+        uses: softprops/action-gh-release@c062e08bd532815e2082a85e87e3ef29c3e6d191 #v2.0.8
+        with:
+          tag_name: ${{ github.ref_name }}
+          name: ${{needs.get-package-name.outputs.package-name}} ${{ github.ref_name }}
+          generate_release_notes: true
+          fail_on_unmatched_files: true
+          files: |
+            ${{env.PACKAGE_PATH}}

.github/workflows/CI.yml

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+name: CI
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  changes:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: read
+    outputs:
+      tracked-files: ${{ steps.filter.outputs.tracked-files }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Filter files
+        uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 #v3.0.2
+        id: filter
+        with:
+          filters: |
+            tracked-files:
+              - 'setup.py'
+              - 'pyproject.toml'
+              - '.conda/**'
+              - 'src/**'
+
+  verify-conda-build:
+    name: Verify Conda Build
+    runs-on: ubuntu-latest
+    needs: changes
+    # Only run if there are changes in the tracked files
+    if: ${{ needs.changes.outputs.tracked-files == 'true' }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup conda build environment
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ vars.PY_VERSION }} 
+          environment-file: .conda/env_build.yml
+          auto-activate-base: false
+          auto-update-conda: false
+          show-channel-urls: true
+
+      - name: Verify conda recipe
+        shell: bash -el {0}
+        run: conda-verify .conda --ignore C2105,C2122
+        # C2105: invalid package version for 'replace_landsurface' 
+        # (there is no git tag in this test so versioneer outputs a 
+        # version that conda-verify recognizes as 'invalid')
+        # C2122: invalid license family
+        # Reference --> https://github.com/conda/conda-verify?tab=readme-ov-file#checks
+
+      - name: Build conda package
+        shell: bash -el {0}
+        run: conda build . --no-anaconda-upload --output-folder=./build -c accessnri -c conda-forge 
+        # channels needed for the conda recipe tests
+
+      - name: Verify conda package
+        shell: bash -el {0}
+        run: conda-verify ./build/noarch/*.tar.bz2 --ignore C1105,C1115,C1141
+        # C1105: invalid version number for 'replace_landsurface' 
+        # (there is no git tag in this test so versioneer outputs a 
+        # version that conda-verify recognizes as 'invalid')
+        # C1115: Found invalid license
+        # C1141: Found python file without a corresponding pyc file
+        # Reference --> https://github.com/conda/conda-verify?tab=readme-ov-file#checks
+
+  tests:
+    name: Tests
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4.1.7
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ matrix.python-version }}
+          environment-file: .conda/env_dev.yml
+          activate-environment: um-modify
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Install source
+        shell: bash -l {0}
+        run: python3 -m pip install --no-deps --no-build-isolation -e .
+
+      - name: List installed packages
+        shell: bash -l {0}
+        run: conda list
+
+      - name: Test of um-modify entry point
+        shell: bash -l {0}
+        run: um-modify --help
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: python3 -m pytest -s -v

.gitignore

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+.coverage
+__pycache__/
+*.py[cod]
+.*_cache/
+.vscode/

README.md

@@ -1,57 +1,3 @@
-# General Repository Template
+# um-modify
 
-A general template repository for default settings when creating new repositories.
-
-This repository uses the Apache-2.0 license. `COPYRIGHT.txt` contains a current copyright statement which should be included at the top of all files.
-
-When creating a new repository you [can use this repository as a template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template), to automate the creation of the correct license and COPYRIGHT statement.
-
-## COPYRIGHT Header
-
-Best practice suggests adding a copyright statement at the top of every source code file, or text file where it is possible to add a copyright statement without interfering with the purpose of the file. The reasoning is if a file is separated from the repository in which it resides then it may not be possible to ascertain it's licensing, which may hamper re-use.
-
-Making this as short and concise as possible reduces the overhead in including such a copyright statement. To that end using [SPDX identifiers](https://spdx.dev/ids/) is simple, efficient, portable and machine-readable.
-
-### Examples
-
-An example, short, copyright statement is reproduced below, as it might appear in different coding languages. Copy and add to files as appropriate: 
-
-#### plaintext
-It is common to include copyright statements at the bottom of a text document or website page
-```text
-© 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details. 
-SPDX-License-Identifier: Apache-2.0
-```
-
-#### python
-For code it is more common to include the copyright in a comment at the top
-```python
-# Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-# SPDX-License-Identifier: Apache-2.0
-```
-
-#### shell
-```bash
-# Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-# SPDX-License-Identifier: Apache-2.0
-```
-
-##### FORTRAN
-```fortran
-! Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-! SPDX-License-Identifier: Apache-2.0
-```
-
-#### C/C++ 
-```c
-// Copyright 2022 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
-// SPDX-License-Identifier: Apache-2.0
-```
-
-### Notes
-
-Note that the date is the first time the project is created. 
-
-The date signifies the year from which the copyright notice applies. **NEVER** replace with a later year, only ever add later years or a year range. 
-
-It is not necessary to include subsequent years in the copyright statement at all unless updates have been made at a later time, and even then it is largely discretionary: they are not necessary as copyright is contingent on the lifespan of copyright holder +50 years as per the [Berne Convention](https://en.wikipedia.org/wiki/Berne_Convention).
+`um-modify` is a standalone Python module used to modify the data of a UM file.

pyproject.toml

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+[project]
+name = "um-modify"
+authors = [
+  {name = "Davide Marchegiani", email="davide.marchegiani@anu.edu.au"},
+]
+maintainers = [
+    { name = "ACCESS-NRI", email = "access.nri@anu.edu.au" }
+]
+description = "Package to modify the data of a UM file."
+license = { file = "LICENSE" }
+readme = "README.md"
+keywords = ["ACCESS-CM2", "ACCESS-ESM1.5", "ACCESS-ESM1.6", "Unified Model"]
+dynamic = ["version"]
+requires-python = ">=3.10"
+dependencies = [
+    "mule",
+    "numpy < 2",
+    "versioneer",
+]
+
+[project.urls]
+Repository = "https://github.com/ACCESS-NRI/um-modify"
+
+[project.scripts]
+um-modify = "TODO" # TODO: Add the script
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools>64", 
+    "versioneer[toml]"
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "src/um_modify/_version.py"
+versionfile_build = "um_modify/_version.py"
+tag_prefix = ""
+parentdir_prefix = "um-modify-"
+
+[tool.pytest.ini_options]
+testpaths = ["src"]
+addopts = ["--cov=src"]
+
+[tool.coverage.run]
+branch = true
+source = ["src/"]
+
+[tool.coverage.report]
+omit = ["src/*/_version.py"]
+skip_empty = true
+show_missing = true

setup.py

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+import versioneer
+from setuptools import setup
+
+setup(
+    version=versioneer.get_version(),
+    cmdclass=versioneer.get_cmdclass(),
+)