feat: add pixi build options

.github/workflows/python-request.yml

@@ -30,31 +30,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up mamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        micromamba-version: 'latest'
-        environment-file: environment.yml
-        init-shell: bash
-        environment-name: timescale
-        cache-environment: true
-        post-cleanup: 'all'
-        create-args: >-
-          python=${{ matrix.python-version }}
-          flake8
-          pytest
-          pytest-cov
-          pytest-xdist
+    - 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 -n 0 --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 }}
     - name: Archive code coverage results

.gitignore

@@ -41,7 +41,10 @@ wheels/
 .installed.cfg
 *.egg
 .pytest_cache
+.coverage
 pythonenv*/
+venv/
+*build-commands.txt
 setup-miniconda-patched-environment.yml
 # OS generated files #
 ######################
@@ -66,6 +69,7 @@ Thumbs.db
 *.ilg
 *.ind
 *.ist
+*.jats
 *.lof
 *.lot
 *.nav
@@ -92,3 +96,7 @@ None*.png
 #######################
 .ipynb_checkpoints
 Untitled.ipynb
+core.*
+# pixi environments
+.pixi/*
+!.pixi/config.toml

MANIFEST.in

@@ -1,8 +1,7 @@
 graft timescale/data
 prune .github*
 prune doc*
+prune run*
 prune test*
 exclude *.cfg
 exclude *.yml
-include requirements.txt
-include version.txt

README.md

@@ -35,6 +35,29 @@ Development version from GitHub:
 python3 -m pip install git+https://github.com/pyTMD/timescale.git
 ```
 
+### Running with Pixi
+
+Alternatively, you can use [Pixi](https://pixi.sh/) for a streamlined workspace environment:
+
+1. Install Pixi following the [installation instructions](https://pixi.sh/latest/#installation)
+2. Clone the project repository:
+
+```bash
+git clone https://github.com/pyTMD/timescale.git
+```
+
+3. Move into the `timescale` directory
+
+```bash
+cd timescale
+```
+
+4. Install dependencies and start a shell to run programs:
+
+```bash
+pixi shell
+```
+
 ## Dependencies
 
 - [dateutil: powerful extensions to datetime](https://dateutil.readthedocs.io/en/stable/)

doc/source/conf.py

@@ -10,14 +10,16 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
+import os
 # import sys
 import datetime
+import warnings
 # sys.path.insert(0, os.path.abspath('.'))
 import importlib.metadata
 
 
 # -- Project information -----------------------------------------------------
+on_rtd = os.environ.get('READTHEDOCS') == 'True'
 
 # package metadata
 metadata = importlib.metadata.metadata("timescale")
@@ -31,6 +33,10 @@
 # append "v" before the version
 release = f"v{version}"
 
+# suppress warnings in examples and documentation
+if on_rtd:
+    warnings.filterwarnings("ignore")
+
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be

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 timescale
 
+Development Install
+###################
+
 To use the development repository, please fork ``timescale`` into your own account and then clone onto your system:
 
 .. code-block:: bash
@@ -36,3 +39,32 @@ The development version of ``timescale`` can also be installed directly from Git
 .. code-block:: bash
 
     python3 -m pip install --user git+https://github.com/pyTMD/timescale.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
+``timescale`` 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 ``timescale`` workspace:
+
+.. code-block:: bash
+
+    pixi task list
+
+.. note::
+
+    ``pixi`` is under active development and may change in future releases

doc/source/project/Testing.rst

@@ -16,7 +16,13 @@ Using the ``pytest`` command:
 
 .. code-block:: bash
 
-    pytest --directory <path_to_tide_models> test/
+    pytest test/
+
+Using ``pixi``:
+
+.. code-block:: bash
+
+    pixi run test 
 
 The test suite is run in verbose mode as a default.
 
@@ -29,6 +35,10 @@ Coverage reports can be generated using the ``pytest-cov`` plugin (which is inst
 
     pytest --cov timescale --cov-report=term 
 
+.. code-block:: bash
+
+    pixi run test "--cov ../timescale --cov-report=term"
+
 Parallelization
 ^^^^^^^^^^^^^^^
 
@@ -37,17 +47,20 @@ To run in series and disable parallelization, set the number of processes to 0:
 
 .. code-block:: bash
 
-    pytest --n 0
+    pytest -n 0
+
+.. code-block:: bash
+
+    pixi run test "-n 0"
 
 Continuous Integration
 ^^^^^^^^^^^^^^^^^^^^^^
-We use `GitHub Actions <https://github.com/pyTMD/timescale/actions>`_ continuous integration (CI) services to build and test the project on Linux (Ubuntu) and Mac Operating Systems.
+We use `GitHub Actions <https://github.com/pyTMD/timescale/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/pyTMD/timescale/tree/main/.github/workflows>`_ directory.
-The workflows use ``mamba`` and the `environment.yml <https://github.com/pyTMD/timescale/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:
 
-* Updating `leap second <https://github.com/pyTMD/timescale/blob/main/timescale/data/leap-seconds.list>`_ and `delta time  <https://github.com/pyTMD/timescale/blob/main/timescale/data/merged_deltat.list>`_ files
 * Running `flake8 <https://flake8.pycqa.org/en/latest/>`_ to check the code for style and compilation errors
 * Running the test suite on multiple combinations of OS and Python version
 * Uploading source and wheel distributions to `PyPI <https://pypi.org/project/timescale/>`_ (on releases)