Use pixi for simplified environment/CI management

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/workflows/test-build-push.yml

@@ -14,59 +14,32 @@ jobs:
   pytest:
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-14]
-        deps:
-          - label: Latest
-            # we can't specify `tophu` for conda, not available on mac
-            # Numba pin: https://github.com/numba/numba/blob/release0.61/numba/__init__.py#L42-L45
-            spec: >-
-              isce3-cpu
-              dask
-              numpy<2.3
-
+        os: [ubuntu-latest, macos-latest]
       fail-fast: true
-    name: ${{ matrix.os }} • ${{ matrix.deps.label }}
+    name: ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      - name: Setup environment
-        uses: mamba-org/setup-micromamba@v2
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
         with:
-          environment-file: conda-env.yml
-          environment-name: dolphin-env
-          # persist on the same day.
-          cache-environment-key: environment-${{ steps.date.outputs.date }}
-          cache-downloads-key: downloads-${{ steps.date.outputs.date }}
-          generate-run-shell: false
-          create-args: ${{ matrix.deps.spec }}
-          condarc: |
-            channels:
-              - conda-forge
-      - name: Install
-        # TODO: remove ortools pin when fixed: https://github.com/google/or-tools/issues/4674
-        run: |
-          python -m pip install --no-deps .
-      - name: Install test dependencies
-        # Remove pytest pin when fixed: https://github.com/pytest-dev/pytest-cov/issues/693
+          pixi-version: v0.48.2
+          # cache: true
+      - name: Install environment
         run: |
-          python -m pip install -r tests/requirements.txt "pytest<8.4" "ortools!=9.13.*"
-          python -m pip install --no-deps \
-            git+https://github.com/isce-framework/tophu@main \
-            "snaphu>=0.4.0"
+          pixi install --environment test
       - name: Enable numba boundscheck for better error catching
         run: |
           echo "NUMBA_BOUNDSCHECK=1" >> $GITHUB_ENV
           echo "TQDM_DISABLE=1" >> $GITHUB_ENV
-      - name: Test (with numba boundscheck on)
+      - name: Test
+        # Run the task "test" inside the "test" environment with verbose output
         run: |
-          pytest -n0 --capture=no -vv
-      # https://community.codecov.com/t/numba-jitted-methods-are-not-captured-by-codecov/2649
-      # - name: Coverage report
-      #   uses: codecov/codecov-action@v2
+          pixi run --environment test test -vv
 
   dockerize: # Based on Mintpy: https://github.com/insarlab/MintPy/blob/5ca554fef324b816f9130feec567e2cf463e41d2/.github/workflows/build-n-publish-to-pypi.yml
     name: Build Docker image and push to GitHub Container Registry

.readthedocs.yaml

@@ -6,19 +6,16 @@ version: 2
 mkdocs:
   configuration: mkdocs.yml
 
-# Conda is causing "excessive memory usage"
-# https://docs.readthedocs.io/en/stable/guides/conda.html#making-builds-faster-with-mamba
 build:
-  os: "ubuntu-20.04"
-  tools:
-    python: "mambaforge-4.10"
-
-conda:
-  environment: conda-env.yml
-
-python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+  os: ubuntu-24.04
+  commands:
+    - asdf plugin add pixi
+    - asdf install pixi latest
+    - asdf global pixi latest
+    - pixi install -e docs
+    - pixi shell --environment docs
+    # Avoiding problems from the local extension in docs/mdx_bib.py  :
+    # Config value 'markdown_extensions': Failed to load extension 'docs.mdx_bib'
+    # ModuleNotFoundError: No module named 'docs'
+    - export PYTHONPATH="${PYTHONPATH}:${PWD}"
+    - mkdocs build --clean --site-dir $READTHEDOCS_OUTPUT/html --config-file mkdocs.yml

pyproject.toml

@@ -8,6 +8,24 @@ description = "Workflows for generating surface displacement maps using InSAR"
 readme = { file = "README.md", content-type = "text/markdown" }
 requires-python = ">=3.10"
 
+dependencies = [
+  "h5py>=3.6",
+  "jax>=0.4.19",
+  "numba>=0.56",
+  "numpy>=1.23",
+  "opera-utils>=0.16",
+  "pydantic>=2.1",
+  "pyproj>=3.3",
+  "rasterio>=1.3",
+  "ruamel_yaml>=0.15",
+  "scipy>=1.9",
+  "snaphu>=0.4.1",
+  "threadpoolctl>=3.0",
+  "tqdm>=4.60",
+  "typing_extensions>=3.10",
+  "tyro>=0.9.20",
+]
+
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",
   "Intended Audience :: Science/Research",
@@ -24,7 +42,90 @@ license = { file = "LICENSE.txt" }
 # see section: setuptools_scm
 # https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#dynamic-metadata
 # dependencies will be read from text files
-dynamic = ["version", "dependencies", "optional-dependencies"]
+dynamic = ["version"]
+
+# extra requirements: `pip install dolphin[docs]` or `pip install .[docs]`
+[project.optional-dependencies]
+docs = [
+  "black[jupyter]",
+  "markdown",
+  "mkdocs",
+  "mkdocs-gen-files",
+  "mkdocs-jupyter==0.25.0",
+  "mkdocs-literate-nav",
+  "mkdocs-material",
+  "mkdocs-section-index",
+  "mkdocstrings-python",
+  "nbdime",
+  "pybtex",
+  "pymdown-extensions",
+]
+test = [
+  "asv",
+  "black[jupyter]",
+  "boto3",
+  "moto[server]",
+  "nbdime",
+  "pooch",
+  "pre-commit",
+  "pytest",
+  "pytest-cov",
+  "pytest-randomly",
+  "pytest-xdist",
+  "shapely",
+  "snaphu>=0.4.1",
+  "spurt>=0.1.1",
+  "ortools!=9.13.*",
+  "xarray>=2025",
+]
+all = ["dolphin[test,docs]"]
+
+# Pixi configuration
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-64", "osx-arm64"]
+
+[tool.pixi.dependencies]
+git = "*"
+gdal = ">=3.3"
+libgdal-netcdf = "*"
+libgdal-hdf5 = "*"
+h5py = ">=3.6"
+hdf5 = "!=1.12.2"
+jax = ">=0.4.19"
+numba = ">=0.56"
+numpy = ">=1.23"
+opera-utils = ">=0.4.1"
+pydantic = ">=2.1"
+pyproj = ">=3.3"
+rasterio = ">=1.3"
+"ruamel.yaml" = ">=0.15"
+scipy = ">=1.12"
+threadpoolctl = ">=3.0"
+tqdm = ">=4.60"
+typing_extensions = ">=3.10"
+tyro = ">=0.9.20"
+
+# Like running pip install -e .
+[tool.pixi.pypi-dependencies]
+dolphin = { path = ".", editable = true }
+
+[tool.pixi.tasks]
+test = "python -m pytest"
+check = "pre-commit run --all-files"
+
+[tool.pixi.feature.test.dependencies]
+isce3-cpu = "*"
+dask = "*"
+
+[tool.pixi.feature.test.pypi-dependencies]
+tophu = { git = "https://github.com/scottstanie/tophu.git", rev = "303470c203bfddb59bf4debdecd1fd949d0c8d54" }
+
+[tool.pixi.environments]
+default = { features = [], solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
+docs = { features = ["docs"], solve-group = "default" }
+all = { features = ["all", "docs", "test"], solve-group = "default" }
 
 [project.urls]
 Homepage = "https://github.com/isce-framework/dolphin"
@@ -34,14 +135,6 @@ Homepage = "https://github.com/isce-framework/dolphin"
 [project.scripts]
 dolphin = "dolphin.cli:main"
 
-[tool.setuptools.dynamic]
-dependencies = { file = ["requirements.txt"] }
-
-# extra requirements: `pip install dolphin[docs]` or `pip install .[docs]`
-[tool.setuptools.dynamic.optional-dependencies.docs]
-file = ["docs/requirements.txt"]
-[tool.setuptools.dynamic.optional-dependencies.test]
-file = ["tests/requirements.txt"]
 
 [tool.setuptools_scm]
 # https://github.com/pypa/setuptools_scm#configuration-parameters
@@ -112,7 +205,6 @@ exclude = ["scripts"]
 # Whether to allow unused variadic arguments, like *args and **kwargs.
 ignore-variadic-names = true
 
-
 [tool.black]
 preview = true
 

src/dolphin/_show_versions.py

@@ -12,7 +12,6 @@
 import re
 import sys
 from importlib.metadata import metadata
-from typing import Optional
 
 import dolphin
 
@@ -35,21 +34,14 @@ def _get_sys_info() -> dict[str, str]:
     }
 
 
-def _get_version(module_name: str) -> Optional[str]:
-    if module_name in sys.modules:
-        mod = sys.modules[module_name]
-    else:
-        try:
-            mod = importlib.import_module(module_name.replace("-", "_"))
-        except ImportError:
-            return None
+def _get_version(name: str) -> str | None:
     try:
-        return mod.__version__
-    except AttributeError:
-        return mod.version
+        return importlib.metadata.version(name)
+    except importlib.metadata.PackageNotFoundError:
+        return None
 
 
-def _get_unwrapping_options() -> dict[str, Optional[str]]:
+def _get_unwrapping_options() -> dict[str, str | None]:
     """Information on possible phase unwrapping libraries.
 
     Returns
@@ -65,7 +57,7 @@ def _get_unwrapping_options() -> dict[str, Optional[str]]:
     return out
 
 
-def _get_deps_info() -> dict[str, Optional[str]]:
+def _get_deps_info() -> dict[str, str | None]:
     """Overview of the installed version of main dependencies.
 
     Returns
@@ -85,11 +77,11 @@ def _get_deps_info() -> dict[str, Optional[str]]:
     # Replace 'ruamel-yaml' with 'ruamel.yaml'
     deps = [dep.replace("ruamel-yaml", "ruamel.yaml") for dep in deps]
     # Add `osgeo` for gdal (not listed in pip requirements)
-    deps += ["osgeo.gdal"]
+    deps += ["gdal"]
     return {name: _get_version(name) for name in deps}
 
 
-def _get_gpu_info() -> dict[str, Optional[str]]:
+def _get_gpu_info() -> dict[str, str | None]:
     """Overview of the optional GPU packages.
 
     Returns
@@ -100,7 +92,10 @@ def _get_gpu_info() -> dict[str, Optional[str]]:
     """
     from dolphin.utils import gpu_is_available
 
-    return {"jax": _get_version("jax"), "gpu_is_available": str(gpu_is_available())}
+    return {
+        "jax": _get_version("jax"),
+        "gpu_is_available": str(gpu_is_available()),
+    }
 
 
 def _print_info_dict(info_dict: dict) -> None:

tests/test_show_versions.py

@@ -26,7 +26,7 @@ def test_get_sys_info():
 def test_get_deps_info():
     deps_info = _get_deps_info()
 
-    assert "osgeo.gdal" in deps_info
+    assert "gdal" in deps_info
     assert "numpy" in deps_info
     assert "pydantic" in deps_info
     assert "h5py" in deps_info