Merge pull request #50 from phobson/more-gh-actions-part2

More GH  actions part2

.github/workflows/check-test-coverage.yml

@@ -0,0 +1,32 @@
+name: Coverage via codecov
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Generate coverage report
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pytest-cov pytest-mpl coverage docopt
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install scipy
+        export MPL_IMGCOMP_TOLERANCE=35
+        coverage run --source cloudside check_cloudside.py --doctest-modules --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        # directory: ./coverage/reports/
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: true
+        path_to_write_report: ./codecov_report.gz

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# 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 to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    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.PMH_PYPI_USER }}
+        TWINE_PASSWORD: ${{ secrets.PMH_PYPI_PASS }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/python-package.yml → .github/workflows/python-runlinter.yml

@@ -1,7 +1,7 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
+name: Lint with flake8
 
 on:
   push:
@@ -13,27 +13,21 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.6, 3.7, 3.8]
-
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install flake8 pytest
-        if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - 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
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude .git,docs/*
         # 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
-    - name: Test with pytest
-      run: |
-        python check_cloudside.py --runslow
+

.github/workflows/python-runtests-basic.yml

@@ -0,0 +1,33 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Run basic unit tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi
+    - name: Test with pytest
+      run: |
+        python check_cloudside.py --runslow

.github/workflows/python-runtests-img-comp.yml

@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Image comparison tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pytest-mpl docopt
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Test with pytest
+      run: |
+        export MPL_IMGCOMP_TOLERANCE=37
+        python check_cloudside.py --mpl

README.rst

@@ -3,8 +3,8 @@ cloudside: download, assess, and visualize weather data
 .. image:: https://travis-ci.org/Geosyntec/cloudside.svg?branch=master
     :target: https://travis-ci.org/Geosyntec/cloudside
 
-.. image:: https://coveralls.io/repos/phobson/cloudside/badge.svg?branch=master&service=github
-  :target: https://coveralls.io/github/phobson/cloudside?branch=master
+.. image:: https://codecov.io/gh/Geosyntec/cloudside/branch/master/graph/badge.svg?token=02qkR2vPrK
+    :target: https://codecov.io/gh/Geosyntec/cloudside
 
 
 The problem this is solving

cloudside/asos.py

@@ -1,5 +1,4 @@
 # std lib stuff
-import datetime
 import logging
 import warnings
 from ftplib import FTP, error_perm
@@ -8,7 +7,7 @@
 
 import numpy
 import pandas
-from metar import Metar, Datatypes
+from metar import Metar
 
 from . import validate
 
@@ -118,7 +117,7 @@ def _fetch_file(
     past_attempts=0,
     max_attempts=10,
 ):
-    """ Fetches a single file from the ASOS ftp and returns its pathh on the
+    """Fetches a single file from the ASOS ftp and returns its pathh on the
     local file system
 
     Parameters
@@ -192,7 +191,7 @@ def fetch_files(
     force_download=False,
     pbar_fxn=None,
 ):
-    """ Fetches a single file from the ASOS ftp and returns its path on the
+    """Fetches a single file from the ASOS ftp and returns its path on the
     local file system
 
     Parameters
@@ -234,7 +233,7 @@ def fetch_files(
 
 
 def _find_reset_time(precip_ts):
-    """ Determines the precipitation gauge's accumulation reset time.
+    """Determines the precipitation gauge's accumulation reset time.
 
     Parameters
     ----------
@@ -265,7 +264,7 @@ def get_idxmin(g):
 
 
 def _process_precip(data, rt, raw_precipcol):
-    """ Processes precip data that accumulates hourly into raw minute
+    """Processes precip data that accumulates hourly into raw minute
     intensities.
 
     Parameters
@@ -300,7 +299,7 @@ def _process_precip(data, rt, raw_precipcol):
 
 
 def parse_file(filepath, new_precipcol="precipitation"):
-    """ Parses a raw ASOS/METAR file into a pandas.DataFrame
+    """Parses a raw ASOS/METAR file into a pandas.DataFrame
 
     Parameters
     ----------
@@ -342,7 +341,7 @@ def get_data(
     force_download=False,
     pbar_fxn=None,
 ):
-    """ Download and process a range of FAA/ASOS data files for a given station
+    """Download and process a range of FAA/ASOS data files for a given station
 
     Parameters
     ----------
@@ -373,7 +372,7 @@ def get_data(
     --------
     >>> from cloudside import asos
     >>> from tqdm import tqdm
-    >>> pdx = asos.get_data('KPDX', '2010-10-01', '2013-10-31', my_email,
+    >>> pdx = asos.get_data('KPDX', '2013-09-01', '2013-10-31', '[email protected]',
     ...                     folder='Portland_weather', raw_folder='asos_files',
     ...                     force_download=False, pbar_fxn=tqdm)
     """

cloudside/exporters.py

@@ -239,6 +239,22 @@ def _write_obs(rowheader, year, month, day, obs):
 
 
 def _obs_from_row(row):
+    """
+    Parses the NCDC format illustrated below:
+    HPD04511406HPCPHI19480700010040100000000 1300000000M 2400000000M 2500000000I
+    AAABBBBBBCCCCCCDDEEEEFFGGGGHHHIIJJJJJJJJ IIJJJJJJJJK IIJJJJJJJJK IIJJJJJJJJK
+
+    Group A - the Record Type
+    Group B - the station COOPID
+    Group C - the element (i.e., parameter; e.g., precip)
+    Group D - units (HI = hundreths of an inch)
+    Group E - year
+    Group F - month
+    Group H - day
+    Group I - hour
+    Group J - observed value
+    Group K - qualifier
+    """
     values = row.strip().split()
     header = list(values.pop(0))
     recordtype = _pop_many(header, 3)
@@ -249,7 +265,8 @@ def _obs_from_row(row):
     month = int(_pop_many(header, 2))
     day = int(_pop_many(header, 4))
 
-    _count = int(_pop_many(header, 3))
+    # strip the the row's count of observations from the header
+    int(_pop_many(header, 3))
 
     observations = ["".join(header)]
     observations.extend(values)

cloudside/hydra.py

@@ -15,7 +15,7 @@ def _fetch_file(station_id, raw_folder, force_download=False):
 
 
 def parse_file(filepath):
-    """ Parses a rain file downloaded from the Portland Hydra Network
+    """Parses a rain file downloaded from the Portland Hydra Network
 
     Parameters
     ----------
@@ -61,7 +61,7 @@ def parse_file(filepath):
 
 
 def get_data(station_id, folder=".", raw_folder="01-raw", force_download=False):
-    """ Download and parse full records from Portland's Hydra Network
+    """Download and parse full records from Portland's Hydra Network
 
     Parameters
     ----------

cloudside/ncdc.py

@@ -16,7 +16,7 @@ def date_parser(x):
 
 
 def remove_bad_rain_values(df, raincol="hpcp", threshold=500):
-    """ Filters invalid rainfall values and returns a new series.
+    """Filters invalid rainfall values and returns a new series.
 
     NCDC use 99999 1/100th of inch for invalid/missing values.
     We downloaded the data in mm so NCDC coverted that value to
@@ -114,8 +114,6 @@ def setup_station_data(
     # sort the now chaotic index
     station_data.sort_index(inplace=True)
 
-    cooptxt = coopid.replace(":", "")
-
     # generate the full index (every hour, ever day)
     fulldates = pandas.date_range(
         start=origin_date, end=future_date, freq=pandas.offsets.Hour(1)
@@ -186,7 +184,6 @@ def timediff(row, t2, t1, asdays=False):
     )
 
     if summary.shape[0] > 1:
-        secperhr = 60.0 * 60.0
         # compute storm durations
         summary["Duration Hours"] = summary.apply(
             lambda row: timediff(row, "End Date", "Start Date", asdays=False), axis=1
@@ -236,8 +233,6 @@ def availabilityByStation(
         for status, pct in zip(_statuses, _avail_pct.values)
     ]
 
-    cooptxt = coopid.replace(":", "")
-
     # reset in the index and compute year and month-day-hour representations of the date
     stationdata = stationdata.reset_index()[["index", "status"]]
     stationdata["Yr"] = stationdata["index"].apply(lambda d: d.strftime("%Y"))
@@ -271,7 +266,7 @@ def availabilityByStation(
     bounds = [-0.5, 0.5, 1.5, 2.5, 3.5]
     norm = colors.BoundaryNorm(bounds, cmap.N)
 
-    img = ax.pcolorfast(grid, cmap=cmap, norm=norm)
+    ax.pcolorfast(grid, cmap=cmap, norm=norm)
     ax.set_aspect(grid.shape[1] / grid.shape[0])
 
     ax.set_yticks(numpy.arange(grid.shape[0]) + 0.5)
@@ -328,7 +323,7 @@ def dataAvailabilityHeatmap(data, figsize=None):
     mdata = numpy.ma.masked_less(data.values, 1)
 
     ax = fig.add_subplot(gs[1])
-    img = ax.pcolorfast(mdata, cmap=cmap)
+    ax.pcolorfast(mdata, cmap=cmap)
     ax.set_xlabel("Year")
     ax.set_ylabel("Precipitation Gauge")
     ax.xaxis.tick_bottom()
@@ -350,7 +345,7 @@ def dataAvailabilityHeatmap(data, figsize=None):
     )
 
     cax = fig.add_subplot(gs[0])
-    cbar = colorbar.ColorbarBase(
+    colorbar.ColorbarBase(
         cax, cmap=cmap, norm=norm, orientation="horizontal", extend="min"
     )
     cax.invert_xaxis()

cloudside/storms.py

@@ -1,5 +1,3 @@
-import warnings
-
 import numpy
 import pandas
 

cloudside/tests/__init__.py

@@ -2,7 +2,6 @@
 from functools import wraps
 from contextlib import contextmanager
 
-import cloudside
 
 try:
     import pytest

cloudside/tests/test_asos.py

@@ -1,4 +1,3 @@
-from datetime import datetime
 import pathlib
 import tempfile
 import ftplib