Creation of ION Functions Documentation Pages

.github/workflows/docs-preview.yml

@@ -0,0 +1,34 @@
+name: Deploy docs preview to GitHub Pages
+
+on:
+  push:
+    branches:
+      - documentation
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: pip install numpy scipy gsw ppigrf numexpr mkdocs-material mkdocstrings[python]
+
+      - name: Add package to PYTHONPATH
+        run: echo "PYTHONPATH=$PYTHONPATH:$(pwd)" >> $GITHUB_ENV
+
+      - name: Set fork site_url
+        run: |
+          sed -i "s|site_url:.*|site_url: https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/|" mkdocs.yml
+
+      - name: Deploy
+        run: mkdocs gh-deploy --force

.github/workflows/docs.yml

@@ -0,0 +1,30 @@
+name: Deploy docs to GitHub Pages
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: pip install numpy scipy gsw ppigrf numexpr mkdocs-material mkdocstrings[python]
+
+      - name: Add package to PYTHONPATH
+        run: echo "PYTHONPATH=$PYTHONPATH:$(pwd)" >> $GITHUB_ENV
+
+      - name: Deploy
+        run: mkdocs gh-deploy --force

.gitignore

@@ -1,18 +1,21 @@
-*pyc
-*.swp
-bin
-eggs
-develop-eggs
-ion_functions.egg-info
-parts
-.installed.cfg
-ion_functions/data/tmp/
-build
-*.egg
-*.o
-*.c
-!extensions/*.c
-extensions/test
-*.so
-notebooks/
-.idea
+*pyc
+*.swp
+bin
+eggs
+develop-eggs
+ion_functions.egg-info
+parts
+.installed.cfg
+ion_functions/data/tmp/
+build
+*.egg
+*.o
+*.c
+!extensions/*.c
+extensions/test
+*.so
+notebooks/
+.idea
+
+.claude
+CLAUDE.md

README.md

@@ -1,146 +1,35 @@
-ION Functions
-==============
+# ion-functions
 
-Functions for utilization in the ION Parameter Function framework
+Python library of oceanographic data processing functions for the
+[Ocean Observatories Initiative (OOI)](https://oceanobservatories.org/).
 
-Reference Information:  *add link*
+ion-functions transforms raw instrument data (L0) into calibrated scientific
+data products at L1 and L2 levels, covering CTD, ADCP, velocity, dissolved
+oxygen, CO2, fluorometry, pH, pressure, meteorology, and more.
 
+**Documentation:** https://oceanobservatories.github.io/ion-functions/
 
-#Prerequisites
+## Installation
 
-This assumes basic development environment setup (git, directory structure). Please follow the
-"New Developers Tutorial" for basic steps.
+```bash
+conda env create -f conda_env.yml
+conda activate ion
+python setup.py develop
+```
 
+## Running tests
 
-**Install the following if not yet present:**
+```bash
+pytest
+```
 
-**Install** git 1.7.7:
-*Download the Mac or Linux installer and run it*
+## Running C-extension tests
 
-*OS Packages and package management:*
-For Mac, use homebrew
+```bash
+make
+extensions/test
+```
 
-    /usr/bin/ruby -e "$(curl -fsSL https://raw.github.com/gist/323731)"
+## License
 
-  * python 2.7
-
-**Install** python, hdf5 and netcdf with Homebrew
-
-    brew install python
-
-You can even reinstall git using brew to clean up your /usr/local directory
-Be sure to read the pyon README for platform specific guidance to installing
-dependent libraries and packages.
-Linux: Note that many installs have much older versions installed by default.
-You will need to upgrade couchdb to at least 1.1.0.
-
-##libgswteos Dependency
-
-A very important component is the libgswteos-10 library.  Installation is quite straightforward on Mac OSX and a little more hairy on Linux.
-
-**On OSX**  
-
-The libgswteos dependency is brew installable:
-
-    brew tap lukecampbell/homebrew-libgswteos
-    brew install libgswteos-10
-    brew test -v libgswteos-10
-
-**On Linux**
-
-The dependencies for building/installing the library are:  **autoconf**, **automake**, & **libtool**
-
-1. Obtain the tarball from:  https://github.com/lukecampbell/gsw-teos/tarball/v3.0r4
-    * sha1: 6ae190b7da78d6aff7859e7d1a3bb027ce6cc5f3
-
-1. Build Procedure
-
-        bash ./autogen.sh  
-        ./configure --prefix=/usr/local/libgswteos-10  
-        make  
-        sudo make install  
-
-1. Linking Procedure:
-
-        sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.la /usr/local/lib/  
-        sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.so.3 /usr/local/lib/  
-        sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.so.3.0.0 /usr/local/lib/  
-        sudo ln -s /usr/local/libgswteos-10/lib/libgswteos-10.so /usr/local/lib/  
-        sudo ln -s /usr/local/libgswteos-10/include/gswteos-10.h /usr/local/include/  
-
-1. Ensure that the global `C_INCLUDE_PATH` and `LD_LIBRARY_PATH` includes /usr/local/lib in all profiles otherwise python won't run correctly:
-
-        export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib  
-        export C_INCLUDE_PATH=$C_INCLUDE_PATH:/usr/local/include  
-
-**Python packages and environment management:**
-
-**Install** pip
-
-    easy_install pip
-
-**Install** virtualenv and virtualenvwrapper modules for your python 2.7 installation
-*Note: This may require Mac's XCode (use XCode 3.3 free version*
-
-    easy_install --upgrade virtualenv
-    easy_install --upgrade virtualenvwrapper
-
-
-Setup a virtualenv to run ion-functions (use any name you like):
-
-    mkvirtualenv --python=python2.7 ion_functions
-    workon ion_functions
-    pip install numpy==1.6.2
-    pip install -r requirements.txt
-
-#Source
-
-To obtain the ion-functions project, begin by [forking the GitHub repository](https://github.com/ooici/ion-functions/).  Next, clone your fork of the repository to your local machine (replace **your_name** with the name of your github account:
-
-    git clone git@github.com:your_name/ion-functions.git
-    cd ion-functions
-
-#Installation
-**Ensure you are in a virtualenv prior to running the steps below**
-
-From the *ion-functions* directory, run the following commands:
-
-    python bootstrap.py -v 1.7
-    bin/buildout
-
-Once those steps complete, you should be able to run the unit tests
-
-#Running unit tests (via [nose](https://nose.readthedocs.org/en/latest/))
-
-From the *coverage-model* directory, run the following command:
-
-    bin/nosetests -v
-
-This will run all tests in the ion-functions repository.  The **-v** flag denotes verbose output (the name of each test prints as it runs).  For more *nose* options, refer to the [nose documentation](https://nose.readthedocs.org/en/latest/man.html)
-
-# Running C-Extension Unit Tests
-
-From the *ion-functions* directory, run the following command:
-
-    make
-
-This will compile the C-extension unit tests. To run the tests:
-
-    extensions/test
-
-You should see something of the like:
-
-    test_spike_simple... ok
-    test_spike_l simple... ok
-    test_spike_long... ok
-
-#Libraries Currently Included
-* [Numpy](http://www.scipy.org/Tentative_NumPy_Tutorial) – array manipulation
-    * import numpy as np
-* [Numexpr](https://code.google.com/p/numexpr/) – relatively trivial "one line" expressions
-    * import numexpr
-        * vals = umexpr.evaluate('sin(x)**10 – y', local\_dict={'x': x\_vals, 'y': y\_vals})
-* [Gibbs Seawater equations – from TEOS-10](https://pypi.python.org/pypi/pygsw) _(Contact Luke Campbell if you notice something's missing)_
-    * from pygsw import vectors as gsw
-        * vals = gsw.sp_from_sa(input_1, …)
-* [GeoMag python library](https://pypi.python.org/pypi/geomag/)
+See [LICENSE.txt](LICENSE.txt).

conda_env.yml

@@ -1,17 +1,15 @@
 name: ion
 channels:
-- defaults
-- ooi
-- conda-forge
+  - conda-forge
+  - defaults
 dependencies:
-- cython=0.25.2
-- ipython=5.3.0
-- matplotlib
-- nose=1.3.7
-- numexpr=2.6.2
-- numpy=1.16
-- python=2.7
-- scipy=1.2.1
-- geomag=0.9.2015
-- pygsw=0.0.11
-prefix: ion
+  - python>=3.13
+  - cython
+  - numpy>=2.4
+  - scipy>=1.17
+  - matplotlib>=3.10
+  - gsw>=3.6
+  - ppigrf>=2.0
+  - mkdocstrings
+  - mkdocstrings-python
+  - mkdocs-material