diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 38fb4e49..3a860804 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -32,26 +32,25 @@ jobs:
steps:
- uses: actions/checkout@v4
- - name: Setup micromamba
- uses: mamba-org/setup-micromamba@v1
+ - uses: prefix-dev/setup-pixi@v0.8.1
with:
- environment-file: ci/environment.yml
- cache-environment: true
- create-args: >-
- python=${{matrix.python-version}}
+ pixi-version: v0.39.2
+ environments: ${{ matrix.environment }}
+ # we can freeze the environment and manually bump the dependencies to the
+ # latest version time to time.
+ frozen: true
- name: Install virtualizarr
run: |
python -m pip install -e . --no-deps
- - name: Conda list information
+ - name: List installed libraries
run: |
- micromamba env list
- micromamba list
+ pixi list
- name: Running Tests
run: |
- python -m pytest --run-network-tests --verbose --cov=virtualizarr --cov-report=xml
+ pixi run test-xml-cov
- name: Upload code coverage to Codecov
uses: codecov/codecov-action@v3.1.4
diff --git a/.github/workflows/min-deps.yml b/.github/workflows/min-deps.yml
deleted file mode 100644
index c236a9ef..00000000
--- a/.github/workflows/min-deps.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-name: min-deps
-
-on:
- push:
- branches: [ "main" ]
- paths-ignore:
- - 'docs/**'
- pull_request:
- branches: [ "main" ]
- paths-ignore:
- - 'docs/**'
- schedule:
- - cron: "0 0 * * *"
-
-concurrency:
- group: ${{ github.workflow }}-${{ github.ref }}
- cancel-in-progress: true
-
-env:
- PIP_ROOT_USER_ACTION: ignore
-
-jobs:
- test-min-deps:
- name: ${{ matrix.python-version }}-build
- runs-on: ubuntu-latest
- defaults:
- run:
- shell: bash -l {0}
- strategy:
- matrix:
- python-version: ["3.12"]
- steps:
- - uses: actions/checkout@v4
-
- - name: Setup micromamba
- uses: mamba-org/setup-micromamba@v1
- with:
- environment-file: ci/min-deps.yml
- cache-environment: true
- create-args: >-
- python=${{matrix.python-version}}
-
- - name: Install virtualizarr
- run: |
- python -m pip install -e . --no-deps
-
- - name: Conda list information
- run: |
- micromamba env list
- micromamba list
-
- - name: Running Tests
- run: |
- python -m pytest --verbose --cov=virtualizarr --cov-report=xml
-
- - name: Upload code coverage to Codecov
- uses: codecov/codecov-action@v3.1.4
- with:
- file: ./coverage.xml
- flags: unittests
- env_vars: OS,PYTHON
- name: codecov-umbrella
- fail_ci_if_error: false
diff --git a/.github/workflows/upstream.yml b/.github/workflows/upstream.yml
deleted file mode 100644
index 74867ea5..00000000
--- a/.github/workflows/upstream.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-name: upstream
-
-on:
- push:
- branches: [ "main" ]
- paths-ignore:
- - 'docs/**'
- pull_request:
- branches: [ "main" ]
- paths-ignore:
- - 'docs/**'
- schedule:
- - cron: "0 0 * * *"
-
-concurrency:
- group: ${{ github.workflow }}-${{ github.ref }}
- cancel-in-progress: true
-
-env:
- PIP_ROOT_USER_ACTION: ignore
-
-jobs:
- test-upstream:
- name: ${{ matrix.python-version }}-build
- runs-on: ubuntu-latest
- defaults:
- run:
- shell: bash -l {0}
- strategy:
- matrix:
- python-version: ["3.12"]
- steps:
- - uses: actions/checkout@v4
-
- - name: Setup micromamba
- uses: mamba-org/setup-micromamba@v1
- with:
- environment-file: ci/upstream.yml
- cache-environment: true
- create-args: >-
- python=${{matrix.python-version}}
-
- - name: Install virtualizarr
- run: |
- python -m pip install -e . --no-deps
-
- - name: Conda list information
- run: |
- micromamba env list
- micromamba list
-
- - name: Running Tests
- run: |
- python -m pytest --verbose --cov=virtualizarr --cov-report=xml
-
- - name: Upload code coverage to Codecov
- uses: codecov/codecov-action@v3.1.4
- with:
- file: ./coverage.xml
- flags: unittests
- env_vars: OS,PYTHON
- name: codecov-umbrella
- fail_ci_if_error: false
diff --git a/.gitignore b/.gitignore
index fc7e85e5..f46cb46e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -180,3 +180,10 @@ examples/
.ionide
# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode
+
+# Pixi folder
+.pixi/
+
+# python virtual environment
+.venv
+venv
diff --git a/.readthedocs.yml b/.readthedocs.yml
index db97ed7c..6a64750f 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,24 +1,19 @@
# Read the Docs configuration file
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-# Required
version: 2
-
-# Set the version of Python and other tools you might need
build:
- os: ubuntu-20.04
+ os: ubuntu-22.04
tools:
- python: "mambaforge-4.10"
+ # this ensures a viable `mamba` is on `$PATH``
+ python: mambaforge-latest
+ commands:
+ - mamba install -c conda-forge -c nodefaults pixi
+ - pixi install --environment docs
+ - pixi run docs
+ - pixi run readthedocs
# Build documentation in the doc/ directory with Sphinx
sphinx:
configuration: docs/conf.py
fail_on_warning: true
-
-# Optionally declare the Python requirements required to build your docs
-conda:
- environment: ci/doc.yml
-python:
- install:
- - method: pip
- path: .
diff --git a/ci/doc.yml b/ci/doc.yml
deleted file mode 100644
index ccc3ded6..00000000
--- a/ci/doc.yml
+++ /dev/null
@@ -1,15 +0,0 @@
-name: virtualizarr-docs
-channels:
- - conda-forge
- - nodefaults
-dependencies:
- - python>=3.10
- - "sphinx"
- - pip
- - pip:
- - "myst_nb"
- - "pydata_sphinx_theme"
- - "sphinx_copybutton"
- - "sphinx_design"
- - "sphinx_togglebutton"
- - "sphinx-autodoc-typehints"
diff --git a/ci/environment.yml b/ci/environment.yml
deleted file mode 100644
index 08dbf246..00000000
--- a/ci/environment.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-name: virtualizarr-tests
-channels:
- - conda-forge
- - nodefaults
-dependencies:
- - h5netcdf
- - h5py
- - hdf5
- - netcdf4
- - xarray>=2024.10.0
- - kerchunk>=0.2.5
- - numpy>=2.0.0
- - ujson
- - packaging
- - universal_pathlib
- - hdf5plugin
- - numcodecs
- # Testing
- - codecov[toml]
- - pre-commit
- - mypy
- - ruff
- - pandas-stubs
- - pytest-mypy
- - pytest-cov
- - pytest
- - pooch
- - scipy
- - fsspec
- - s3fs
- - fastparquet
- - imagecodecs>=2024.6.1
- # for opening tiff files
- - tifffile
- # for opening FITS files
- - astropy
- - pip
- - pip:
- - imagecodecs-numcodecs==2024.6.1
diff --git a/ci/min-deps.yml b/ci/min-deps.yml
deleted file mode 100644
index a0a0cf20..00000000
--- a/ci/min-deps.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-name: virtualizarr-min-deps
-channels:
- - conda-forge
- - nodefaults
-dependencies:
- - h5py
- - hdf5
- - netcdf4
- - xarray>=2024.10.0
- - numpy>=2.0.0
- - numcodecs
- - packaging
- - ujson
- - universal_pathlib
- # Testing
- - codecov[toml]
- - pre-commit
- - mypy
- - ruff
- - pandas-stubs
- - pytest-mypy
- - pytest-cov
- - pytest
- - pooch
- - fsspec
diff --git a/ci/upstream.yml b/ci/upstream.yml
deleted file mode 100644
index ed9bf6fa..00000000
--- a/ci/upstream.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: virtualizarr-upstream
-channels:
- - conda-forge
- - nodefaults
-dependencies:
- - xarray>=2024.10.0,<2025.0.0
- - h5netcdf
- - h5py
- - hdf5
- - netcdf4
- - numpy>=2.0.0
- - packaging
- - ujson
- - universal_pathlib
- - hdf5plugin
- - numcodecs
- - imagecodecs>=2024.6.1
- # Testing
- - codecov[toml]
- - pre-commit
- - mypy
- - ruff
- - pandas-stubs
- - pytest-asyncio
- - pytest-mypy
- - pytest-cov
- - pytest
- - pooch
- - fsspec
- - pip
- - pip:
- - icechunk==0.1.0a8 # Installs zarr v3 beta 3 as dependency
- # - git+https://github.com/fsspec/kerchunk@main # kerchunk is currently incompatible with zarr-python v3 (https://github.com/fsspec/kerchunk/pull/516)
- - imagecodecs-numcodecs==2024.6.1
diff --git a/pyproject.toml b/pyproject.toml
index 8421819e..062f6862 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,34 +21,47 @@ classifiers = [
requires-python = ">=3.10"
dynamic = ["version"]
dependencies = [
- "xarray>=2024.10.0,<2025.0.0",
+ "xarray>=2024.10.0",
"numpy>=2.0.0",
"packaging",
"universal-pathlib",
"numcodecs",
"ujson",
+ "zarr"
]
[project.optional-dependencies]
-hdf_reader = [
+remote = [
"fsspec",
+ "requests",
+ "aiohttp",
+ "s3fs",
+]
+hdf_reader = [
+ "virtualizarr[remote]",
"h5py",
"hdf5plugin",
"imagecodecs",
"imagecodecs-numcodecs==2024.6.1",
- "numcodecs"
+
]
icechunk = [
- "icechunk==0.1.0a8",
+ "icechunk==0.1.0a12",
]
-test = [
- "codecov",
+kerchunk = [
+ "virtualizarr[remote]",
"fastparquet",
- "fsspec",
"h5py",
- "kerchunk>=0.2.5",
- "mypy",
+ "kerchunk @ git+https://github.com/fsspec/kerchunk@main",
"netcdf4",
+ "scipy",
+ "tifffile",
+ "astropy",
+
+]
+test = [
+ "codecov",
+ "mypy",
"numcodecs",
"pandas-stubs",
"pooch",
@@ -57,14 +70,24 @@ test = [
"pytest-mypy",
"pytest",
"ruff",
- "s3fs",
- "scipy",
- "virtualizarr[hdf_reader]"
+ "virtualizarr[hdf_reader]",
+ "virtualizarr[icechunk]",
+ "virtualizarr[kerchunk]",
+ "virtualizarr[remote]"
+]
+docs = [
+ "sphinx",
+ "myst_nb",
+ "pydata_sphinx_theme",
+ "sphinx_copybutton",
+ "sphinx_design",
+ "sphinx_togglebutton",
+ "sphinx-autodoc-typehints",
]
[project.urls]
-Home = "https://github.com/TomNicholas/VirtualiZarr"
-Documentation = "https://github.com/TomNicholas/VirtualiZarr/blob/main/README.md"
+Home = "https://github.com/zarr-developers/VirtualiZarr"
+Documentation = "https://github.com/zarr-developers/VirtualiZarr/blob/main/README.md"
[build-system]
requires = [
@@ -74,6 +97,41 @@ requires = [
"check-manifest"
]
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
+
+[tool.pixi.environments]
+test = { features = ["test", "remote", "hdf_reader", "kerchunk", "icechunk"], solve-group = "default" }
+hdf-reader = { features = ["hdf_reader"], solve-group = "default" }
+kerchunk = { features = ["kerchunk"], solve-group = "default" }
+icechunk = { features = ["icechunk"], solve-group = "default" }
+docs = { features = ["docs"], solve-group = "default" }
+
+[tool.pixi.feature.hdf_reader.dependencies]
+netcdf4 = ">=1.7.2,<2"
+hdf5 = ">=1.14.4,<2"
+h5netcdf = ">=1.5.0,<2"
+
+[tool.pixi.feature.kerchunk.dependencies]
+netcdf4 = ">=1.7.2,<2"
+hdf5 = ">=1.14.4,<2"
+h5netcdf = ">=1.5.0,<2"
+
+[tool.pixi.pypi-dependencies]
+virtualizarr = { path = ".", editable = true }
+
+[tool.pixi.feature.test.tasks]
+test = { cmd = "pytest --run-network-tests" }
+test-no-network = { cmd = "pytest" }
+test-cov = { cmd = "pytest --run-network-tests --verbose --cov=virtualizarr --cov=term-missing" }
+test-xml-cov = { cmd = "pytest --run-network-tests --verbose --cov=virtualizarr --cov-report=xml" }
+test-html-cov = { cmd = "pytest --run-network-tests --verbose --cov=virtualizarr --cov-report=html" }
+
+[tool.pixi.feature.docs.tasks]
+docs = { cmd = "make html", cwd = "docs" }
+readthedocs = "rm -rf $READTHEDOCS_OUTPUT/html && cp -r docs/_build/html $READTHEDOCS_OUTPUT/html"
+
[tool.setuptools_scm]
fallback_version = "9999"