feat: add changes for uploading to pypi (#75)

tsutterley · web-flow · commit 79effcf54519 · 2022-06-15T13:46:36.000-07:00
diff --git a/.binder/environment.yml b/.binder/environment.yml
@@ -1,4 +1,4 @@
-name: read-GRACE-harmonics
+name: gravity_toolkit 
 channels:
   - conda-forge
 dependencies:
@@ -23,5 +23,4 @@ dependencies:
   - tk
   - pip
   - pip:
-     - git+https://github.com/tsutterley/read-GRACE-geocenter.git
      - git+https://github.com/tsutterley/geoid-toolkit.git
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -0,0 +1,32 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install 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
+        twine upload dist/*
+
diff --git a/.github/workflows/python-request.yml b/.github/workflows/python-request.yml
@@ -33,6 +33,7 @@ jobs:
     - name: Create conda Test Environment
       run: |
         conda install flake8 pytest pytest-cov cython
+        pip install git+https://github.com/tsutterley/read-GRACE-geocenter.git
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
diff --git a/.gitignore b/.gitignore
@@ -30,12 +30,16 @@
 .Rhistory
 __pycache__
 build/
-run/
+dist/
 develop-eggs/
+run/
 wheels/
+.eggs/
 *.egg-info/
 .installed.cfg
 *.egg
+.pytest_cache
+pythonenv*/
 # OS generated files #
 ######################
 .DS_Store
@@ -77,6 +81,7 @@ Thumbs.db
 *.sw*
 *.hidden
 None*.png
+*.gfc
 # Jupyter Checkpoints #
 #######################
 .ipynb_checkpoints
diff --git a/Dockerfile b/Dockerfile
@@ -34,7 +34,6 @@ RUN pip3 install --no-cache-dir --no-binary=cartopy \
         python-dateutil \
         pyyaml \
         scipy && \
-    pip3 install --no-cache-dir --no-deps git+https://github.com/tsutterley/read-GRACE-geocenter.git && \
     pip3 install --no-cache-dir --no-deps git+https://github.com/tsutterley/geoid-toolkit.git
 
 COPY . .
diff --git a/README.rst b/README.rst
@@ -15,6 +15,9 @@ read-GRACE-harmonics
 .. |License| image:: https://img.shields.io/github/license/tsutterley/read-grace-harmonics
    :target: https://github.com/tsutterley/read-GRACE-harmonics/blob/main/LICENSE
 
+.. |PyPI Version| image:: https://img.shields.io/pypi/v/gravity-toolkit.svg
+   :target: https://pypi.python.org/pypi/gravity-toolkit/
+
 .. |Documentation Status| image:: https://readthedocs.org/projects/read-grace-harmonics/badge/?version=latest
    :target: https://read-grace-harmonics.readthedocs.io/en/latest/?badge=latest
 
@@ -53,7 +56,6 @@ Dependencies
 - `cartopy: Python package designed for geospatial data processing <https://scitools.org.uk/cartopy/docs/latest/>`_
 - `netCDF4: Python interface to the netCDF C library <https://unidata.github.io/netcdf4-python/>`_
 - `h5py: Python interface for Hierarchal Data Format 5 (HDF5) <https://www.h5py.org/>`_
-- `read-GRACE-geocenter: Python reader for GRACE/GRACE-FO geocenter data <https://github.com/tsutterley/read-GRACE-geocenter/>`_
 - `geoid-toolkit: Python utilities for calculating geoid heights from static gravity field coefficients <https://github.com/tsutterley/geoid-toolkit/>`_
 
 References
diff --git a/doc/environment.yml b/doc/environment.yml
@@ -33,6 +33,5 @@ dependencies:
   - texlive-core
   - tk
   - pip:
-     - git+https://github.com/tsutterley/read-GRACE-geocenter.git
      - git+https://github.com/tsutterley/geoid-toolkit.git
      - ..
diff --git a/doc/source/getting_started/Examples.rst b/doc/source/getting_started/Examples.rst
@@ -7,7 +7,9 @@ Examples
 Jupyter Notebooks providing demonstrations of the functionality within ``read-GRACE-harmonics``:
 
 - Creating Spatial Maps |github spatial| |nbviewer spatial|
-    Creates an animation of spatial maps on a global Equirectangular projection using data derived from the monthly GRACE/GRACE-FO Level-2 spherical harmonic product
+    Creates an animation of spatial maps using data derived from the monthly GRACE/GRACE-FO Level-2 spherical harmonic product
+- Creating Spatial Error Maps |github error| |nbviewer error|
+    Creates spatial maps of estimated GRACE/GRACE-FO errors derived from the monthly Level-2 spherical harmonic product
 - Creating Harmonic Plots |github harmonic| |nbviewer harmonic|
     Creates an animation of triangle plots that visualize the GRACE/GRACE-FO Level-2 spherical harmonic product
 
@@ -17,6 +19,12 @@ Jupyter Notebooks providing demonstrations of the functionality within ``read-GR
 .. |nbviewer spatial| image:: https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg
    :target: https://nbviewer.jupyter.org/github/tsutterley/read-GRACE-harmonics/blob/main/notebooks/GRACE-Spatial-Maps.ipynb
 
+.. |github error| image:: https://img.shields.io/badge/GitHub-view-6f42c1?style=flat&logo=Github
+  :target: https://github.com/tsutterley/read-GRACE-harmonics/blob/main/notebooks/GRACE-Spatial-Error.ipynb
+
+.. |nbviewer error| image:: https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg
+  :target: https://nbviewer.jupyter.org/github/tsutterley/read-GRACE-harmonics/blob/main/notebooks/GRACE-Spatial-Error.ipynb
+
 .. |github harmonic| image:: https://img.shields.io/badge/GitHub-view-6f42c1?style=flat&logo=Github
    :target: https://github.com/tsutterley/read-GRACE-harmonics/blob/main/notebooks/GRACE-Harmonic-Plots.ipynb
 
diff --git a/doc/source/getting_started/Install.rst b/doc/source/getting_started/Install.rst
@@ -2,7 +2,8 @@
 Installation
 ============
 
-Presently ``read-GRACE-harmonics`` is only available for use as a `GitHub repository <https://github.com/tsutterley/read-GRACE-harmonics>`_.
+``read-GRACE-harmonics`` is available for download from the `GitHub repository <https://github.com/tsutterley/read-GRACE-harmonics>`_,
+and the `Python Package Index (pypi) <https://pypi.org/project/gravity-toolkit/>`_,
 The contents of the repository can be download as a `zipped file <https://github.com/tsutterley/read-GRACE-harmonics/archive/main.zip>`_  or cloned.
 
 To use this repository, please fork into your own account and then clone onto your system:
@@ -29,6 +30,11 @@ Alternatively can install the ``gravity_toolkit`` utilities directly from GitHub
 
     python3 -m pip install --user git+https://github.com/tsutterley/read-GRACE-harmonics.git
 
-Executable versions of this repository can also be tested using
-`Binder <https://mybinder.org/v2/gh/tsutterley/read-GRACE-harmonics/main>`_ or
-`Pangeo <https://aws-uswest2-binder.pangeo.io/v2/gh/tsutterley/read-GRACE-harmonics/main?urlpath=lab>`_.
+| This repository can be also tested using `BinderHub <https://github.com/jupyterhub/binderhub>`_ platforms:
+| |Binder| |Pangeo|
+
+.. |Binder| image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/tsutterley/read-GRACE-harmonics/main
+
+.. |Pangeo| image:: https://img.shields.io/static/v1.svg?logo=Jupyter&label=PangeoBinderAWS&message=us-west-2&color=orange
+   :target: https://aws-uswest2-binder.pangeo.io/v2/gh/tsutterley/read-GRACE-harmonics/main?urlpath=lab
diff --git a/doc/source/getting_started/NASA-Earthdata.rst b/doc/source/getting_started/NASA-Earthdata.rst
@@ -20,6 +20,12 @@ The `Physical Oceanography Distributed Active Archive Center (PO.DAAC) <https://
 provides data and related information pertaining to the physical processes and conditions of the global oceans,
 including measurements of ocean winds, temperature, topography, salinity, circulation and currents, and sea ice.
 PO.DAAC hosts
+
+PO.DAAC is `migrating its data archive to the Earthdata Cloud <https://podaac.jpl.nasa.gov/cloud-datasets/migration>`_,
+which is hosted in Amazon Web Services (AWS).
+GRACE/GRACE-FO spherical harmonic data is currently scheduled to be "cloud enabled"
+during Phase 4 and Phase 5 of the transition, slated for April and July 2022 respectively.
+
 If any problems contact JPL PO.DAAC support at `podaac@podaac.jpl.nasa.gov <mailto:podaac@podaac.jpl.nasa.gov>`_
 or the NASA EOSDIS support team `support@earthdata.nasa.gov <mailto:support@earthdata.nasa.gov>`_.
 
diff --git a/gravity_toolkit/geocenter.py b/gravity_toolkit/geocenter.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 geocenter.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (06/2022)
 Data class for reading and processing geocenter data
 
 PYTHON DEPENDENCIES:
@@ -15,6 +15,7 @@
         https://github.com/yaml/pyyaml
 
 UPDATE HISTORY:
+    Updated 06/2022: drop external reader dependency for UCI format
     Updated 04/2022: updated docstrings to numpy documentation format
         include utf-8 encoding in reads to be windows compliant
     Updated 03/2022: add try/except for read_GRACE_geocenter
@@ -36,16 +37,11 @@
 import gzip
 import time
 import uuid
+import yaml
 import logging
 import netCDF4
-import warnings
 import numpy as np
 import gravity_toolkit.time
-try:
-    from read_GRACE_geocenter.read_GRACE_geocenter import read_GRACE_geocenter
-except ModuleNotFoundError:
-    warnings.filterwarnings("always")
-    warnings.warn("read_GRACE_geocenter not available")
 
 class geocenter(object):
     """
@@ -176,7 +172,8 @@ def from_gravis(self, geocenter_file, **kwargs):
         """
         Reads monthly geocenter spherical harmonic data files from
         `GFZ GravIS calculated using GRACE/GRACE-FO measurements
-        and Ocean Models of degree 1 <ftp://isdcftp.gfz-potsdam.de/grace/GravIS/GFZ/Level-2B/aux_data/GRAVIS-2B_GFZOP_GEOCENTER_0002.dat>`_
+        and Ocean Models of degree 1
+        <ftp://isdcftp.gfz-potsdam.de/grace/GravIS/GFZ/Level-2B/aux_data/GRAVIS-2B_GFZOP_GEOCENTER_0002.dat>`_
 
 
         Parameters
@@ -431,12 +428,13 @@ def from_SLR(self, geocenter_file, **kwargs):
 
     def from_UCI(self, geocenter_file, **kwargs):
         """
-        Reads geocenter file and extracts dates and spherical harmonic data
+        Reads monthly geocenter files computed using GRACE/GRACE-FO
+        measurements and ocean models [Swenson2008]_ [Sutterley2019]_
 
         Parameters
         ----------
         geocenter_file: str
-            degree 1 file
+            input datafile with geocenter coefficients
 
         References
         ----------
@@ -452,7 +450,78 @@ def from_UCI(self, geocenter_file, **kwargs):
         """
         #-- set filename
         self.case_insensitive_filename(geocenter_file)
-        DEG1 = read_GRACE_geocenter(self.filename)
+        #-- read geocenter file and get contents
+        with open(os.path.expanduser(geocenter_file), mode='r', encoding='utf8') as f:
+            file_contents = f.read().splitlines()
+        #-- number of lines contained in the file
+        file_lines = len(file_contents)
+
+        #-- counts the number of lines in the header
+        HEADER = False
+        count = 0
+        #-- Reading over header text
+        while (HEADER is False) and (count < file_lines):
+            #-- file line at count
+            line = file_contents[count]
+            #--if End of YAML Header is found: set HEADER flag
+            HEADER = bool(re.search("\# End of YAML header",line))
+            #-- add 1 to counter
+            count += 1
+
+        #-- verify HEADER flag was set
+        if not HEADER:
+            raise IOError('Data not found in file:\n\t{0}'.format(geocenter_file))
+
+        #-- number of months within the file
+        n_mon = np.int64(file_lines - count)
+        #-- output time variables
+        DEG1 = {}
+        DEG1['time'] = np.zeros((n_mon))
+        DEG1['JD'] = np.zeros((n_mon))
+        DEG1['month'] = np.zeros((n_mon), dtype=np.int64)
+        #-- parse the YAML header (specifying yaml loader)
+        DEG1.update(yaml.load('\n'.join(file_contents[:count]),
+            Loader=yaml.BaseLoader))
+
+        #-- compile numerical expression operator
+        regex_pattern = '[-+]?(?:(?:\d*\.\d+)|(?:\d+\.?))(?:[Ee][+-]?\d+)?'
+        rx = re.compile(regex_pattern, re.VERBOSE)
+
+        #-- get names and columns of input variables
+        variables = copy.copy(DEG1['header']['variables'])
+        variables.pop('mid-epoch_time')
+        variables.pop('month')
+        columns = {}
+        #-- for each output data variable
+        for key in variables:
+            DEG1[key] = np.zeros((n_mon))
+            comment_text, = rx.findall(variables[key]['comment'])
+            columns[key] = int(comment_text) - 1
+
+        #-- for every other line:
+        for t, line in enumerate(file_contents[count:]):
+            #-- find numerical instances in line including integers, exponents,
+            #-- decimal points and negatives
+            line_contents = rx.findall(line)
+            #-- extacting mid-date time and GRACE/GRACE-FO "month"
+            DEG1['time'][t] = np.float64(line_contents[0])
+            DEG1['month'][t] = np.int64(line_contents[-1])
+            #-- calculate mid-date as Julian dates
+            #-- calendar year of date
+            year = np.floor(DEG1['time'][t])
+            #-- check if year is a leap year
+            days_per_year = np.sum(gravity_toolkit.time.calendar_days(year))
+            #-- calculation of day of the year
+            day_of_the_year = days_per_year*(DEG1['time'][t] % 1)
+            #-- calculate Julian day
+            DEG1['JD'][t] = np.float64(367.0*year - np.floor(7.0*(year)/4.0) -
+                np.floor(3.0*(np.floor((year - 8.0/7.0)/100.0) + 1.0)/4.0) +
+                np.floor(275.0/9.0) + day_of_the_year + 1721028.5)
+            #-- extract fully-normalized degree one spherical harmonics
+            for key,val in columns.items():
+                DEG1[key][t] = np.float64(line_contents[val])
+
+        #-- return the geocenter harmonics
         return self.from_dict(DEG1)
 
     def from_swenson(self, geocenter_file, **kwargs):
diff --git a/gravity_toolkit/tools.py b/gravity_toolkit/tools.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 tools.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (05/2022)
 Jupyter notebook, user interface and plotting tools
 
 PYTHON DEPENDENCIES:
@@ -27,6 +27,7 @@
     utilities.py: download and management utilities for files
 
 UPDATE HISTORY:
+    Updated 05/2022: adjusted mask oceans function to be able to output mask
     Updated 04/2022: updated docstrings to numpy documentation format
     Updated 12/2021: added custom colormap function for some common scales
     Written 09/2021
@@ -1114,7 +1115,7 @@ def interp_grid(data, xin, yin, xout, yout, order=0):
 
 # PURPOSE: parallels the matplotlib basemap maskoceans function but with
 # updated Greenland coastlines (G250) and Rignot (2017) Antarctic grounded ice
-def mask_oceans(datain, xin, yin, order=0, lakes=False,
+def mask_oceans(xin, yin, data=None, order=0, lakes=False,
     iceshelves=True, resolution='qd'):
     """
     Mask a data grid over global ocean and water points
@@ -1123,12 +1124,12 @@ def mask_oceans(datain, xin, yin, order=0, lakes=False,
 
     Parameters
     ----------
-    datain: float
-        input data grid to be interpolated
     xin: float
         input x-coordinate array (monotonically increasing)
     yin: float
         input y-coordinate array (monotonically increasing)
+    data: float or NoneType
+        input data grid to be masked
     order: int, default 0
         interpolation order
 
@@ -1147,6 +1148,8 @@ def mask_oceans(datain, xin, yin, order=0, lakes=False,
 
     Returns
     -------
+    mask: bool
+        mask grid
     datain: float
         masked data grid
     """
@@ -1170,9 +1173,15 @@ def mask_oceans(datain, xin, yin, order=0, lakes=False,
     #-- find Greenland and Antarctic ice shelf values (4)
     if iceshelves:
         land_function |= (landsea.data == 4)
-    # interpolation to output grid
-    datain.mask |= interp_grid(land_function.astype(np.int32),
-        landsea.lon, landsea.lat, xin, yin, order).astype(bool)
-    # replace data with updated mask
-    datain.data[datain.mask] = datain.fill_value
-    return datain
+    #-- interpolate to output grid
+    mask = interp_grid(land_function.astype(np.int32),
+        landsea.lon, landsea.lat, xin, yin, order)
+    #-- mask input data or return the interpolated mask
+    if data is not None:
+        # update data mask with interpolated mask
+        data.mask |= mask.astype(bool)
+        # replace data with fill values where invalid
+        data.data[data.mask] = data.fill_value
+        return data
+    else:
+        return mask.astype(bool)
diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,7 @@
 boto3
 cartopy --no-binary=cartopy
 future
+geoid-toolkit
 h5py
 lxml
 matplotlib
diff --git a/setup.py b/setup.py
