Update CI

.github/workflows/ci.yaml

@@ -23,19 +23,20 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Cache conda
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         env:
           # Increase this value to reset cache if ci/environment.yml has not changed
           CACHE_NUMBER: 0
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment.yml') }}
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
+          miniconda-version: "latest"
           activate-environment: test_env # Defined in ci/environment*.yml
           auto-update-conda: false
           python-version: ${{ matrix.python-version }}
@@ -51,29 +52,30 @@ jobs:
         run: |
           py.test --cov=./ --cov-report=xml
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           flags: unittests
-          env_vars: OS,PYTHON
           name: codecov-umbrella
           fail_ci_if_error: false
 
   xarray-master:
     name: Build xarray-master
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Cache conda
-      uses: actions/cache@v2
+      uses: actions/cache@v4
       env:
         # Increase this value to reset cache if ci/environment-upstream-dev.yml has not changed
         CACHE_NUMBER: 0
       with:
         path: ~/conda_pkgs_dir
         key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment-upstream-dev.yml') }}
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
+        miniconda-version: "latest"
         activate-environment: test_env # Defined in ci/environment-*.yml
         auto-update-conda: false
         environment-file: ci/environment-xarraymaster.yml
@@ -88,10 +90,10 @@ jobs:
       run: |
         py.test --cov=./ --cov-report=xml
     - name: Upload code coverage to Codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
         flags: unittests
-        env_vars: OS,PYTHON
         name: codecov-umbrella
         fail_ci_if_error: false

ci/environment-py3.9.yml → ci/environment-py3.11.yml

@@ -2,7 +2,7 @@ name: test_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   - xarray
   - dask
   - numpy

ci/environment-py3.10.yml → ci/environment-py3.12.yml

@@ -2,16 +2,19 @@ name: test_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python=3.12
   - xarray
   - dask
   - numpy
   - pytest
   - future
-  - zarr
+  - zarr >=2.15
   - cftime
   - aiohttp
   - pytest-cov
   - codecov
   - fsspec
   - cachetools
+  - setuptools >=68
+  - wheel
+  - pip >=24

ci/environment-py3.8.yml → ci/environment-py3.13.yml

@@ -2,16 +2,19 @@ name: test_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.13
   - xarray
   - dask
   - numpy
   - pytest
   - future
-  - zarr
+  - zarr >=2.15
   - cftime
   - aiohttp
   - pytest-cov
   - codecov
   - fsspec
   - cachetools
+  - setuptools >=68
+  - wheel
+  - pip >=24

ci/environment-xarraymaster.yml

@@ -2,19 +2,21 @@ name: test_env
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.12
   - dask
   - numpy
   - pytest
   - future
-  - zarr
+  - zarr >=2.15
   - cftime
   - aiohttp
   - pytest-cov
   - codecov
   - fsspec
   - cachetools
   - git
-  - pip
+  - setuptools >=68
+  - wheel
+  - pip >=24
   - pip:
     - git+https://github.com/pydata/xarray.git

codecov.yml

@@ -1,23 +1,18 @@
 codecov:
-    require_ci_to_pass: no
-    max_report_age: off
-
-comment: false
+  config: codecov.yml
+  require_ci_to_pass: false
 
 coverage:
-    precision: 2
-    round: down
-    status:
-        project:
-            default:
-                target: 95
-                informational: true
-        patch: off
-        changes: off
-
-ignore:
-    - "xmitgcm/test/*"
-    - "xmitgcm/__init__.py"
-    - "xmitgcm/_version.py"
+  precision: 2
+  round: down
+  status:
+    project:
+      default:
+        target: 90%
+        informational: true
+  ignore:
+    - "xmitgcm/test/test_llcreader.py"
     - "setup.py"
-    - "versioneer.py"
+    - "xmitgcm/llcreader/*"
+
+comment: false

pyproject.toml

@@ -0,0 +1,47 @@
+# TODO fully switch to PEP 621: get rid of versioneer
+[project]
+authors = [{ name = "xmitgcm Developers", email = "[email protected]" }]
+name = "xmitgcm"
+requires-python = ">=3.11"
+description = "Read MITgcm MDS binary files using xarray"
+license = { text = "Apache-2.0" }
+dependencies = [
+  "xarray >= 0.14.1",
+  "dask >= 1.0",
+  "cachetools"
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: OS Independent",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+dynamic = ['version']
+
+#[project.optional-dependencies]
+#...
+
+[project.urls]
+Homepage = "https://github.com/MITgcm/xmitgcm"
+Documentation = "https://xmitgcm.readthedocs.io/"
+
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=42", "setuptools-scm", "wheel"]
+
+[tool.setuptools]
+packages = ["xmitgcm"]
+
+[tool.pytest.ini_options]
+minversion= "6.0"
+testpaths = [
+    "xmitgcm/test",
+    ]
+markers = [
+    "slow: slow tests"
+    ]

setup.py

@@ -1,51 +1,6 @@
- #!/usr/bin/env python
-import os
-import re
-import sys
-import warnings
-import versioneer
+#!/usr/bin/env python
+from setuptools import setup
 
-from setuptools import setup, find_packages
-
-DISTNAME = 'xmitgcm'
-LICENSE = 'Apache'
-AUTHOR = 'Ryan Abernathey'
-AUTHOR_EMAIL = '[email protected]'
-URL = 'https://github.com/MITgcm/xmitgcm'
-CLASSIFIERS = [
-    'Development Status :: 4 - Beta',
-    'License :: OSI Approved :: Apache Software License',
-    'Operating System :: OS Independent',
-    'Intended Audience :: Science/Research',
-    'Programming Language :: Python',
-    'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.7',
-    'Programming Language :: Python :: 3.8',
-    'Programming Language :: Python :: 3.9',
-    'Topic :: Scientific/Engineering',
-]
-
-INSTALL_REQUIRES = ['xarray >= 0.14.1', 'dask >= 1.0', 'cachetools']
-SETUP_REQUIRES = ['pytest-runner']
-TESTS_REQUIRE = ['pytest >= 4.0', 'coverage']
-
-DESCRIPTION = "Read MITgcm mds binary files into xarray"
-def readme():
-    with open('README.rst') as f:
-        return f.read()
-
-setup(name=DISTNAME,
-      version=versioneer.get_version(),
-      cmdclass=versioneer.get_cmdclass(),
-      license=LICENSE,
-      author=AUTHOR,
-      author_email=AUTHOR_EMAIL,
-      classifiers=CLASSIFIERS,
-      description=DESCRIPTION,
-      long_description=readme(),
-      install_requires=INSTALL_REQUIRES,
-      setup_requires=SETUP_REQUIRES,
-      tests_require=TESTS_REQUIRE,
-      url=URL,
-      packages=find_packages(),
-      python_requires='>=3.7')
+setup(
+      use_scm_version={"fallback_version": "9999"},
+     )