Update to packaging tools and logic

.gitattributes

@@ -0,0 +1 @@
+payu/_version.py export-subst

.github/workflows/CD.yml

@@ -1,47 +1,24 @@
 name: CD
 
-on: [push, pull_request]
+on:
+  push:
+    tags:
+      - '*'
 
-jobs:
-  conda:
-    name: build and deploy to conda
-    if: github.repository == 'payu-org/payu' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-      - name: Checkout source
-        uses: actions/checkout@v4
-
-      - name: Setup conda environment
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: "latest"
-          python-version: 3.11
-          environment-file: conda/environment.yml
-          auto-update-conda: false
-          auto-activate-base: false
-          show-channel-urls: true
-
-      - name: Build and upload the conda package
-        uses: uibcdf/[email protected]
-        with:
-          meta_yaml_dir: conda
-          python-version: 3.11
-          user: accessnri
-          label: main
-          token: ${{ secrets.anaconda_token }}
+env:
+  PY_VERSION: 3.11
 
+jobs:
   pypi-build:
     name: Build package for PyPI
-    if: github.repository == 'payu-org/payu' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    if: github.repository == 'payu-org/payu'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.11
+          python-version: ${{ env.PY_VERSION }}
 
       - run: |
           python3 -m pip install --upgrade build && python3 -m build
@@ -54,7 +31,6 @@ jobs:
     # Split build and publish to restrict trusted publishing to just this workflow
     needs: ['pypi-build']
     name: Publish to PyPI.org
-    if: github.repository == 'payu-org/payu' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ubuntu-latest
     permissions:
       # IMPORTANT: this permission is mandatory for trusted publishing
@@ -65,7 +41,34 @@ jobs:
           path: artifact/
 
       - name: Publish package distributions to PyPI
-        # This is version v1.8.10
-        uses: pypa/gh-action-pypi-publish@b7f401de30cb6434a1e19f805ff006643653240e
+        uses: pypa/gh-action-pypi-publish@2f6f737ca5f74c637829c0f5c3acd0e29ea5e8bf # v1.8.11
+        with:
+          packages-dir: artifact/
+
+  conda:
+    name: Build with conda and upload
+    if: github.repository == 'payu-org/payu'
+    runs-on: ubuntu-latest
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Setup conda environment
+        uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a # v3.0.1
         with:
-          packages_dir: artifact/
+          miniconda-version: "latest"
+          python-version: ${{ env.PY_VERSION }}
+          environment-file: conda/environment.yml
+          auto-update-conda: false
+          auto-activate-base: false
+          show-channel-urls: true
+
+      - name: Build and upload the conda package
+        uses: uibcdf/action-build-and-upload-conda-packages@c6e7a90ad5e599d6cde76e130db4ee52ad733ecf # v1.2.0
+        with:
+          meta_yaml_dir: conda
+          python-version: ${{ env.PY_VERSION }}
+          user: accessnri
+          label: main
+          token: ${{ secrets.anaconda_token }}

.github/workflows/CI.yml

@@ -12,34 +12,50 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+env:
+  PY_VERSION: 3.11
+
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
+  pypa-build:
+    name: PyPA build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PY_VERSION }}
+
+      - run: |
+          python3 -m pip install --upgrade build && python3 -m build
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./dist
+
   conda-build:
     name: Conda Build
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
       - name: Setup conda environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@11b562958363ec5770fef326fe8ef0366f8cbf8a # v3.0.1
         with:
           miniconda-version: "latest"
-          python-version: 3.11
+          python-version: ${{ env.PY_VERSION }}
           environment-file: conda/environment.yml
           auto-update-conda: false
           auto-activate-base: false
           show-channel-urls: true
 
       - name: Run conda build
         shell: bash -el {0}
-        # For the build, these environment variables would usually be set based on repo tags,
-        # but they can be these defaults instead since we don't use the build
-        env:
-          GIT_DESCRIBE_TAG: test
-          GIT_DESCRIBE_NUMBER: 0
         run: conda build . --no-anaconda-upload
 
-  build:
+  tests:
+    name: Tests
     runs-on: ubuntu-latest
 
     # Run the job for different versions of python
@@ -76,18 +92,18 @@ jobs:
           PYTHONPATH=. pytest --cov=payu -s test;
 
       - name: Coveralls
-        uses: AndreMiras/coveralls-python-action@develop
+        uses: AndreMiras/coveralls-python-action@f5fd5c309b39d01599fb92c72d4f7409ea78aec9 # v20201129
         with:
           parallel: true
 
       - name: Make docs
         run: cd docs && make html
 
   coveralls_finish:
-    needs: build
+    name: Coveralls Finished
+    needs: tests
     runs-on: ubuntu-latest
     steps:
-    - name: Coveralls Finished
-      uses: AndreMiras/coveralls-python-action@develop
+    - uses: AndreMiras/coveralls-python-action@f5fd5c309b39d01599fb92c72d4f7409ea78aec9 # v20201129
       with:
         parallel-finished: true

.pylintrc

@@ -0,0 +1,5 @@
+[MAIN]
+
+# Files or directories to be skipped. They should be base names, not
+# paths.
+ignore=_version.py

conda/environment.yml

@@ -7,3 +7,4 @@ dependencies:
   - anaconda-client
   - conda-build
   - conda-verify
+  - versioneer

conda/meta.yaml

@@ -1,51 +1,45 @@
+{% set data = load_setup_py_data(setup_file='../setup.py', from_recipe_dir=True) %}
+{% set version = data.get('version') %}
+{% set pyproj = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
+{% set project = pyproj.get('project') %}
+
 package:
     name: payu
-    version: {{ GIT_DESCRIBE_TAG }}
+    version: "{{ version }}"
 
 build:
     noarch: python
-    number: {{ GIT_DESCRIBE_NUMBER }}
-    script: "{{ PYTHON }}  -m pip install . --no-deps"
+    number: 0
+    script: "{{ PYTHON }}  -m pip install . -vv"
     entry_points:
-        - payu = payu.cli:parse
-        - payu-run = payu.subcommands.run_cmd:runscript
-        - payu-collate = payu.subcommands.collate_cmd:runscript
-        - payu-profile = payu.subcommands.profile_cmd:runscript
-        - payu-sync = payu.subcommands.sync_cmd:runscript
-        - payu-branch = payu.subcommands.branch_cmd:runscript
-        - payu-clone = payu.subcommands.clone_cmd:runscript
-        - payu-checkout = payu.subcommands.checkout_cmd:runscript
+        {% for name, script in project.get('scripts', {}).items() %}
+        - {{ name }} = {{ script }}
+        {% endfor %}
 
 source:
-    git_url: ../
+    path: ../
 
 requirements:
-    build:
-        - python <=3.11
-        - pbr
-        - setuptools
+    host:
+        - python
+        - pip
+        - setuptools >=61.0.0
+        - versioneer
     run:
-        - python <=3.11
-        - f90nml >=0.16
-        - yamanifest >=0.3.4
-        - PyYAML
-        - python-dateutil
-        - tenacity
-        - requests
-        - cftime
-        # The following two requirements are from the security
-        # extra for the pypi package
-        - pyOpenSSL >=0.14
-        - cryptography>=1.3.4
-        - GitPython >=3.1.40
-        - ruamel.yaml >=0.18.5
+        - python >=3.9
+        {% for dep in project.get('dependencies', []) %}
+        - {{ dep }}
+        {% endfor %}
 
 test:
     imports:
         - payu
     commands:
         - payu list
 
-
 about:
     home: https://github.com/payu-org/payu/
+    license: Apache Software
+    license_family: APACHE
+    summary: "A climate model workflow manager for supercomputing environments"
+    doc_url: https://payu.readthedocs.io/en/latest/

payu/__init__.py

@@ -3,4 +3,5 @@
 :copyright: Copyright 2011 Marshall Ward, see AUTHORS for details.
 :license: Apache License, Version 2.0, see LICENSE for details.
 """
-__version__ = '1.0.19'
+from . import _version
+__version__ = _version.get_versions()['version']