ci: use pixi for builds

.gitattributes

@@ -1 +1,3 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
 gravity_toolkit/data/*.nc filter=lfs diff=lfs merge=lfs -text

.github/workflows/python-publish.yml

@@ -23,12 +23,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install build setuptools wheel twine
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
+        python -m build
         twine upload dist/*
-

.github/workflows/python-request.yml

@@ -20,11 +20,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.12]
+        os: [ubuntu-latest, macos-latest, windows-latest]
     env:
       OS: ${{ matrix.os }}
-      PYTHON: ${{ matrix.python-version }}
     defaults:
       run:
         shell: bash -l {0}
@@ -33,34 +31,21 @@ jobs:
     - uses: actions/checkout@v4
       with:
         lfs: true
-    - name: Set up mamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        micromamba-version: 'latest'
-        environment-file: .binder/environment.yml
-        init-shell: bash
-        environment-name: gravity_toolkit
-        cache-environment: true
-        post-cleanup: 'all'
-        create-args: >-
-          python=${{ matrix.python-version }}
-          flake8
-          pytest
-          pytest-cov
-          cython
+    - name: Set up pixi environment
+      uses: prefix-dev/setup-pixi@v0.9.1
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        pixi run lint
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        pixi run lint "--exit-zero --max-complexity=10 --max-line-length=127"
     - name: Test with pytest
       run: |
-        pip install --no-deps .
-        pytest --verbose --capture=no --cov=./ --cov-report=xml \
+        # install the package in editable mode
+        pip install --no-deps --editable .
+        pixi run --environment dev pytest -n 0 --cov=./ --cov-report=xml \
             --username=${{ secrets.EARTHDATA_USERNAME }} \
-            --password=${{ secrets.EARTHDATA_PASSWORD }} \
-            --webdav=${{ secrets.PODAAC_PASSWORD }}
+            --password=${{ secrets.EARTHDATA_PASSWORD }}
     - name: Archive code coverage results
       uses: actions/upload-artifact@v4
       with:

.gitignore

@@ -28,6 +28,7 @@
 *.gmtdefaults4
 .RData
 .Rhistory
+octave-workspace
 __pycache__
 build/
 _build/
@@ -40,7 +41,11 @@ wheels/
 .installed.cfg
 *.egg
 .pytest_cache
+.coverage
 pythonenv*/
+venv/
+*build-commands.txt
+setup-miniconda-patched-environment.yml
 # OS generated files #
 ######################
 .DS_Store
@@ -64,6 +69,7 @@ Thumbs.db
 *.ilg
 *.ind
 *.ist
+*.jats
 *.lof
 *.lot
 *.nav
@@ -87,6 +93,11 @@ None*.png
 #######################
 .ipynb_checkpoints
 Untitled.ipynb
+core.*
 # Large data files #
 ####################
 *-complete.dat
+# pixi environments #
+#####################
+.pixi/*
+!.pixi/config.toml

MANIFEST.in

@@ -2,7 +2,7 @@ graft gravity_toolkit/data
 prune .github*
 prune doc*
 prune notebooks*
+prune run*
+prune test*
 exclude *.cfg
 exclude *.yml
-include requirements.txt
-include version.txt

doc/source/api_reference/utilities.rst

@@ -6,7 +6,6 @@ Download and management utilities for syncing time and auxiliary files
 
  - Can list a directory on a ftp host
  - Can download a file from a ftp or http host
- - Can download a file from PO.DAAC via https when WebDAV credentials are supplied
  - Checks ``MD5`` or ``sha1`` hashes between local and remote files
 
 `Source code`__

doc/source/getting_started/Install.rst

@@ -19,6 +19,9 @@ The simplest installation for most users will likely be using ``conda`` or ``mam
 
     conda update gravity-toolkit
 
+Development Install
+###################
+
 To use the development repository, please fork ``gravity-toolkit`` into your own account and then clone onto your system:
 
 .. code-block:: bash
@@ -31,8 +34,43 @@ To use the development repository, please fork ``gravity-toolkit`` into your own
 
     python3 -m pip install --user .
 
+To include all optional dependencies:
+
+.. code-block:: bash
+
+   python3 -m pip install --user .[all]
+
 The development version of ``gravity-toolkit`` can also be installed directly from GitHub using ``pip``:
 
 .. code-block:: bash
 
     python3 -m pip install --user git+https://github.com/tsutterley/gravity-toolkit.git
+
+Package Management with ``pixi``
+################################
+
+Alternatively ``pixi`` can be used to create a `streamlined environment <https://pixi.sh/>`_ after cloning the repository:
+
+.. code-block:: bash
+
+    pixi install
+
+``pixi`` maintains isolated environments for each project, allowing for different versions of
+``gravity-toolkit`` and its dependencies to be used without conflict. The ``pixi.lock`` file within the
+repository defines the required packages and versions for the environment.
+
+``pixi`` can also create shells for running programs within the environment:
+
+.. code-block:: bash
+
+    pixi shell
+
+To see the available tasks within the ``gravity-toolkit`` workspace:
+
+.. code-block:: bash
+
+    pixi task list
+
+.. note::
+
+    ``pixi`` is under active development and may change in future releases

doc/source/project/Citations.rst

@@ -54,6 +54,7 @@ This software is also dependent on other commonly used Python packages:
 Disclaimer
 ##########
 
+This work is currently supported by the NASA GRACE-FO Science Team (Grant Number 80NSSC24K1153).
 This program is not sponsored or maintained by the Universities Space Research Association (USRA),
 the Center for Space Research at the University of Texas (UTCSR),
 the Jet Propulsion Laboratory (JPL),

doc/source/project/Testing.rst

@@ -3,21 +3,61 @@ Testing
 =======
 
 ``gravity-toolkit`` uses the ``pytest`` framework to run tests and verify outputs.
+Running the test suite requires a `dev installation <../getting_started/Install.html>`_ of the ``gravity-toolkit`` package to include all of the optional dependencies.
+
+.. code-block:: bash
+
+    python -m pip install --editable '.[dev]'
 
 Running the Test Suite
 ^^^^^^^^^^^^^^^^^^^^^^
 
+Using the ``pytest`` command:
+
 .. code-block:: bash
 
     pytest --directory <path_to_tide_models> test/
 
+Using ``pixi``:
+
+.. code-block:: bash
+
+    pixi run test "--directory <path_to_tide_models>"
+
 The test suite is run in verbose mode as a default.
 
+Coverage Reports
+^^^^^^^^^^^^^^^^
+
+Coverage reports can be generated using the ``pytest-cov`` plugin (which is installed with the dev installation).
+
+.. code-block:: bash
+
+    pytest --cov pyTMD --cov-report=term 
+
+.. code-block:: bash
+
+    pixi run test "--cov ../gravity-toolkit --cov-report=term"
+
+Parallelization
+^^^^^^^^^^^^^^^
+
+As a default, the ``pytest`` suite is run in parallel using the ``pytest-xdist`` plugin (which is also installed with the dev installation).
+To run in series and disable parallelization, set the number of processes to 0:
+
+.. code-block:: bash
+
+    pytest -n 0
+
+.. code-block:: bash
+
+    pixi run test "-n 0"
+
 Continuous Integration
 ^^^^^^^^^^^^^^^^^^^^^^
 We use `GitHub Actions <https://github.com/tsutterley/gravity-toolkit/actions>`_ continuous integration (CI) services to build and test the project on Linux (``ubuntu-latest``), Mac (``macos-latest``) and Windows (``windows-latest``) Operating Systems.
 The configuration files for this service are in the `GitHub workflows <https://github.com/tsutterley/gravity-toolkit/tree/main/.github/workflows>`_ directory.
-The workflows use ``mamba`` and the `environment.yml <https://github.com/tsutterley/gravity-toolkit/blob/main/environment.yml>`_ file to install the required dependencies and build the environment.
+The workflows use ``pixi`` to install the required dependencies and build the custom environment.
 
 The GitHub Actions jobs include:
 

gravity_toolkit/utilities.py

@@ -1036,7 +1036,7 @@ def get_token(
     password: str or NoneType, default None
         NASA Earthdata password
     build: bool, default True
-        Build opener and check WebDAV credentials
+        Build opener and check credentials
     timeout: int or NoneType, default None
         timeout in seconds for blocking operations
     context: obj, default gravity_toolkit.utilities._default_ssl_context
@@ -1093,7 +1093,7 @@ def list_tokens(
     password: str or NoneType, default None
         NASA Earthdata password
     build: bool, default True
-        Build opener and check WebDAV credentials
+        Build opener and check credentials
     timeout: int or NoneType, default None
         timeout in seconds for blocking operations
     context: obj, default gravity_toolkit.utilities._default_ssl_context
@@ -1153,7 +1153,7 @@ def revoke_token(
     password: str or NoneType, default None
         NASA Earthdata password
     build: bool, default True
-        Build opener and check WebDAV credentials
+        Build opener and check credentials
     timeout: int or NoneType, default None
         timeout in seconds for blocking operations
     context: obj, default gravity_toolkit.utilities._default_ssl_context