Merge pull request #4 from U-S-NRL-Marine-Meteorology-Division/3-uplo…

…ad-package-to-pypi

3 upload package to pypi

Closes #3 #5 #6

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,31 @@
+name: Publish to PyPI
+
+on:
+  push:
+    #On any tag
+    tags:
+      - "*"
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+
+    name: Build
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10' 
+    - run: |
+        python -m pip install --upgrade pip
+        python setup.py sdist
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_TOKEN }}
+    # - name: Publish package to TestPyPI
+    #   uses: pypa/gh-action-pypi-publish@release/v1
+    #   with:
+    #     verbose: true
+    #     password: ${{ secrets.TEST_PYPI_TOKEN }}
+    #     repository_url: https://test.pypi.org/legacy/             

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.formatting.provider": "black"
+}

MANIFEST

@@ -0,0 +1,22 @@
+# file GENERATED by distutils, do NOT edit
+setup.cfg
+setup.py
+xnrl\__init__.py
+xnrl\cli.py
+xnrl\compute.py
+xnrl\constant.py
+xnrl\flatfile.py
+xnrl\generic.py
+xnrl\grads.py
+xnrl\grib.py
+xnrl\hdf5.py
+xnrl\internal.py
+xnrl\io.py
+xnrl\main.py
+xnrl\netcdf.py
+xnrl\packages.py
+xnrl\plot.py
+xnrl\select.py
+xnrl\tutorial.py
+xnrl\util.py
+xnrl\visual.py

MANIFEST.in

@@ -0,0 +1,15 @@
+# Things to always exclude
+global-exclude .git*
+global-exclude .ipynb_checkpoints
+global-exclude *.py[co]
+global-exclude __pycache__/**
+
+# Top-level Config
+include DISTRIBUTION
+include LICENSE
+include README.md
+include VERSION
+include MANIFEST.in
+include setup.cfg
+include environment.yml
+include environment_xnrl.yml

README.md

@@ -20,11 +20,11 @@
   align="center"
 >
 
-# <p style="text-align:center"><img src="images/logo.png" width=250>
+# <p style="text-align:center"><img src="https://github.com/U-S-NRL-Marine-Meteorology-Division/xnrl/blob/main/images/logo.png?raw=true" width=250>
 
 <!-- Badges -->
 
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) ![PyPI](https://img.shields.io/pypi/v/xnrl) [![Publish to PyPI](https://github.com/U-S-NRL-Marine-Meteorology-Division/xnrl/actions/workflows/publish-to-pypi.yml/badge.svg)](https://github.com/U-S-NRL-Marine-Meteorology-Division/xnrl/actions/workflows/publish-to-pypi.yml)
 
 <!-- (Badges) -->
 </div>
@@ -34,6 +34,11 @@
 # Install
 xNRL requires numpy, pandas, and xarray.
 
+## Install with pip
+```bash
+pip install xnrl
+```
+
 ## Clone and install with pip
 ```bash
 git clone https://github.com/U-S-NRL-Marine-Meteorology-Division/xnrl.git

VERSION

@@ -1 +1 @@
-2022.06.13
+2022.09.29

setup.py

@@ -17,19 +17,22 @@
 
 '''Python setup script for xnrl package'''
 
-from os.path import realpath, join, dirname
 from setuptools import setup
+from pathlib import Path
 
-with open(join(dirname(realpath(__file__)), 'VERSION'), encoding='utf-8') as version_file:
-    version = version_file.read().strip()
+this_directory = Path(__file__).parent
+long_description = (this_directory / "README.md").read_text()
+version = (this_directory / "VERSION").read_text()
 
 setup(
     name="xnrl",
     version=version,
     description="xNRL - Read NRL files into xarray Datasets nested within pandas DataFrames",
+    long_description=long_description,
+    long_description_content_type='text/markdown',
     packages=["xnrl"],
     include_package_data=True,
-    install_requires=["numpy", "xarray==0.16.2", "dask[delayed]", "metpy"],
+    install_requires=[ "xarray", "numpy", "dask[delayed]", "metpy"],    
     keywords=["flatfile", "nrl", "xarray", "dataset", "binary", "hdf5", "grib"],
     entry_points={
         "console_scripts": [

xnrl/internal.py

@@ -1,15 +1,15 @@
 # # Distribution Statement A. Approved for public release. Distribution unlimited.
-# # 
+# #
 # # Author:
 # # Naval Research Laboratory, Marine Meteorology Division
-# # 
+# #
 # # This program is free software:
 # # you can redistribute it and/or modify it under the terms
 # # of the NRLMMD License included with this program.
 # # If you did not receive the license, see
 # # https://github.com/U-S-NRL-Marine-Meteorology-Division/
 # # for more information.
-# # 
+# #
 # # This program is distributed WITHOUT ANY WARRANTY;
 # # without even the implied warranty of MERCHANTABILITY
 # # or FITNESS FOR A PARTICULAR PURPOSE.
@@ -957,8 +957,12 @@ def open_dataset(self, paths):
                     f"Sub-selected for {self._lev_type} "
                     f"{self._grid_dim} successfully!"
                 )
-                ds = ds.transpose(*C.BASE_DIMS + [...])
-
+                if "missing_dims" in xr.Dataset.transpose.__code__.co_varnames:
+                    # Xarray 0.16 ignored by default. New versions raise exception by default.
+                    ds = ds.transpose(*C.BASE_DIMS + [...], missing_dims="ignore")
+                else:
+                    # Backwards Compatible for transpose.
+                    ds = ds.transpose(*C.BASE_DIMS + [...])
                 num_groups = selc_groupby.ngroups
                 if self.max_groups is not None and self.max_groups < num_groups:
                     num_groups = self.max_groups

xnrl/io.py

@@ -1,15 +1,15 @@
 # # Distribution Statement A. Approved for public release. Distribution unlimited.
-# # 
+# #
 # # Author:
 # # Naval Research Laboratory, Marine Meteorology Division
-# # 
+# #
 # # This program is free software:
 # # you can redistribute it and/or modify it under the terms
 # # of the NRLMMD License included with this program.
 # # If you did not receive the license, see
 # # https://github.com/U-S-NRL-Marine-Meteorology-Division/
 # # for more information.
-# # 
+# #
 # # This program is distributed WITHOUT ANY WARRANTY;
 # # without even the implied warranty of MERCHANTABILITY
 # # or FITNESS FOR A PARTICULAR PURPOSE.
@@ -295,26 +295,49 @@ def export_flatfile(df, out_dir=C.WORK_DIR, show=False, fmt=None, sigma=False):
             else:
                 metadata["grid_dim"] = f"glob{num_x:03d}x{num_y:03d}"
 
-        ds_pre = (
-            ds.expand_dims(expand_dims)
-            .drop(["sig_w", "sig_m"], errors="ignore")
-            .stack(**{"dims_": stack_dims})
-            .transpose("dims_", *grid_dims)
-        )
+        if "missing_dims" in xr.Dataset.transpose.__code__.co_varnames:
+            # Xarray 0.16 ignored by default. New versions raise exception by default.
+            ds_pre = (
+                ds.expand_dims(expand_dims)
+                .drop_vars(["sig_w", "sig_m"], errors="ignore")
+                .stack(**{"dims_": stack_dims})
+                .transpose("dims_", *grid_dims, missing_dims="ignore")
+            )
+        else:
+            # Backwards Compatible for transpose.
+            ds_pre = (
+                ds.expand_dims(expand_dims)
+                .drop_vars(["sig_w", "sig_m"], errors="ignore")
+                .stack(**{"dims_": stack_dims})
+                .transpose("dims_", *grid_dims)
+            )
 
         out_fps = set([])
         missing_fps = set([])
         for field in ds_pre.data_vars:
             field_name = field.replace("_", "")
             metadata.update(**{"field": field_name})
             for slice_ in ds_pre[field]:
-                slice_ = slice_.transpose(
-                    *[
-                        dim
-                        for dim in C.BASE_DIMS + C.GRID_DIMS + C.XY_DIMS
-                        if dim in slice_.dims
-                    ]
-                )
+                if "missing_dims" in xr.Dataset.transpose.__code__.co_varnames:
+                    # Xarray 0.16 ignored by default. New versions raise exception by default.
+                    slice_ = slice_.transpose(
+                        *[
+                            dim
+                            for dim in C.BASE_DIMS + C.GRID_DIMS + C.XY_DIMS
+                            if dim in slice_.dims
+                        ],
+                        missing_dims="ignore",
+                    )
+                else:
+                    # Backwards Compatible for transpose.
+                    slice_ = slice_.transpose(
+                        *[
+                            dim
+                            for dim in C.BASE_DIMS + C.GRID_DIMS + C.XY_DIMS
+                            if dim in slice_.dims
+                        ]
+                    )
+
                 try:
                     exp, mbr, ini, tau, lev = np.atleast_1d(slice_["dims_"].values)[0]
                 except ValueError:
@@ -326,8 +349,7 @@ def export_flatfile(df, out_dir=C.WORK_DIR, show=False, fmt=None, sigma=False):
                     seconds = tau
                 mm, ss = divmod(seconds, 60)
                 hh, mm = divmod(mm, 60)
-
-                mbr = mbr if mbr != C.MASK_VALUE else 0
+                mbr = mbr if mbr != C.MASK_VALUE and np.isnan(mbr) == False else 0
                 metadata.update(
                     **{"mbr": mbr, "ini": ini, "hh": hh, "mm": mm, "ss": ss, "lev": lev}
                 )

xnrl/plot.py

@@ -1,15 +1,15 @@
 # # Distribution Statement A. Approved for public release. Distribution unlimited.
-# # 
+# #
 # # Author:
 # # Naval Research Laboratory, Marine Meteorology Division
-# # 
+# #
 # # This program is free software:
 # # you can redistribute it and/or modify it under the terms
 # # of the NRLMMD License included with this program.
 # # If you did not receive the license, see
 # # https://github.com/U-S-NRL-Marine-Meteorology-Division/
 # # for more information.
-# # 
+# #
 # # This program is distributed WITHOUT ANY WARRANTY;
 # # without even the implied warranty of MERCHANTABILITY
 # # or FITNESS FOR A PARTICULAR PURPOSE.
@@ -24,6 +24,7 @@
 import numpy as np
 import pandas as pd
 import xnrl.constant as C
+import xarray as xr
 from mpl_toolkits.axes_grid1 import make_axes_locatable
 from xnrl import compute, util
 
@@ -222,7 +223,12 @@ def _plot(
                 ax.grid(color="gray", alpha=0.3)
             else:
                 if y in da_ovl.dims and x in da_ovl.dims:
-                    da_ovl = da_ovl.transpose(y, x)
+                    if("missing_dims" in xr.Dataset.transpose.__code__.co_varnames):
+                        # Xarray 0.16 ignored by default. New versions raise exception by default.
+                        da_ovl = da_ovl.transpose(y, x, missing_dims="ignore")
+                    else:
+                        #Backwards Compatible for transpose.
+                        da_ovl = da_ovl.transpose(y, x)
 
                 plot_args = (da_ovl[x], da_ovl[y], da_ovl.values)
                 plot_kwds = dict(transform=transform, shading="auto")
@@ -508,4 +514,4 @@ def visualize(
                 ds, da.sel(**{sep: val}), *plot_args, sep=sep, val=val, **plot_kwds
             )
     else:
-        return _plot(ds, da, *plot_args, **plot_kwds)
+        return _plot(ds, da, *plot_args, **plot_kwds)

xnrl/util.py

@@ -1,15 +1,15 @@
 # # Distribution Statement A. Approved for public release. Distribution unlimited.
-# # 
+# #
 # # Author:
 # # Naval Research Laboratory, Marine Meteorology Division
-# # 
+# #
 # # This program is free software:
 # # you can redistribute it and/or modify it under the terms
 # # of the NRLMMD License included with this program.
 # # If you did not receive the license, see
 # # https://github.com/U-S-NRL-Marine-Meteorology-Division/
 # # for more information.
-# # 
+# #
 # # This program is distributed WITHOUT ANY WARRANTY;
 # # without even the implied warranty of MERCHANTABILITY
 # # or FITNESS FOR A PARTICULAR PURPOSE.
@@ -516,8 +516,14 @@ def regrid(
     if "idx" in ds1.dims:
         ds1 = ds1.dropna("idx")
 
-    ds1 = ds1.transpose(*[..., "lat", "lon"])
-    ds2 = ds2.transpose(*[..., "lat", "lon"])
+    if "missing_dims" in xr.Dataset.transpose.__code__.co_varnames:
+        # Xarray 0.16 ignored by default. New versions raise exception by default.
+        ds1 = ds1.transpose(*[..., "lat", "lon"], missing_dims="ignore")
+        ds2 = ds2.transpose(*[..., "lat", "lon"], missing_dims="ignore")
+    else:
+        # Backwards Compatible for transpose.
+        ds1 = ds1.transpose(*[..., "lat", "lon"])
+        ds2 = ds2.transpose(*[..., "lat", "lon"])
 
     if locstream_in and method in ["bilinear", "nearest"]:
         method = "nearest_s2d"
@@ -646,10 +652,21 @@ def _interp_rebuild(da, var_y, var_x, data_list, dims, coords, to_irregular=Fals
         base_dims = ["tmp_dim", var_y, var_x]
 
     da_interp = xr.DataArray(
-        data_list, coords=coords, dims=base_dims, name=da.name, attrs=da.attrs,
+        data_list,
+        coords=coords,
+        dims=base_dims,
+        name=da.name,
+        attrs=da.attrs,
     )
     if len(dims) > 0:
-        da_interp = da_interp.unstack("tmp_dim").transpose(*dims + base_dims[1:])
+        if "missing_dims" in xr.Dataset.transpose.__code__.co_varnames:
+            # Xarray 0.16 ignored by default. New versions raise exception by default.
+            da_interp = da_interp.unstack("tmp_dim").transpose(
+                *dims + base_dims[1:], missing_dims="ignore"
+            )
+        else:
+            # Backwards Compatible for transpose.
+            da_interp = da_interp.unstack("tmp_dim").transpose(*dims + base_dims[1:])
     else:
         da_interp = da_interp.squeeze("tmp_dim")
     return da_interp
@@ -711,7 +728,11 @@ def _cross_section_2d(ds, var_y, var_x, ys, xs, method, num_steps):
 
     coords = np.concatenate((ys, xs))
     ds_cross = interpolate.cross_section(
-        ds, coords[:, 0], coords[:, 1], steps=num_steps, interp_type=method,
+        ds,
+        coords[:, 0],
+        coords[:, 1],
+        steps=num_steps,
+        interp_type=method,
     ).rename({"index": "idx"})
     remove_nan_list = [
         idx for idx in ds_cross["idx"].values if not np.isnan(ds_cross[var_y][idx])