Feature/adcircmeshupgrade (#67)

* Refactor of mesh package + bugfixes

* Testing auto-badge capability

* Updated test, added auto-coverage badging

* correction to init file

* Added directory for badges

* Add/Update badge

* Test auto-badging

* test auto-badging

* Test auto-bdge

* autobadging debug

* test auto-badging

* Add/Update badge

* Update README.md

* auto-badge debug

* Add/Update badge

* readme fix

* remove badge

* Add/Update badge

* Disabled auto-badging

* Removed unnecessary files

Co-authored-by: jreniel <jreniel@gmail.com>

Author: JaimeCalzadaNOAA

.github/badges/.keep

@@ -0,0 +1,55 @@
+name: tests
+
+on: [ push ]
+
+jobs:
+  tests:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: [ 3.8 ]
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Restore cached dependencies
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('setup.py') }}
+          restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}-
+      - name: Install dependencies
+        run: |
+          apt-get update -y && apt-get install -y libnetcdf-dev libnetcdff-dev
+          pip install wheel
+          pip install -e .[development]
+      - name: Test with coverage
+        run: coverage run --source adcircpy -m nose --nologcapture --verbose
+      - name: Generate coverage report
+        run: coverage report -m
+      - name: Generate coverage badge
+        run: coverage-badge -f -o .github/badges/badge.svg
+      - name: Extract branch name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        id: extract_branch
+      - name: Commit badge
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add .github/badges/badge.svg
+          git commit -m "Add/Update badge"
+      - name: Push badge commit
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ steps.extract_branch.outputs.branch }}
+
+# https://stackoverflow.com/questions/59203704/how-create-a-badge-with-test-coverage-jacoco-on-github-actions
+# 

tests/coverage.svg renamed to .github/badges/badge.svg

@@ -38,4 +38,4 @@ jobs:
       - name: Test with coverage
         run: coverage run --source adcircpy -m nose --nologcapture --verbose
       - name: Generate coverage report
-        run: coverage report -m
+        run: coverage report -m

.github/workflows/badge.yml.disabled

@@ -2,7 +2,7 @@
 ## Python library for automating ADCIRC model runs.
 [![tests](https://github.com/JaimeCalzadaNOAA/adcircpy/workflows/tests/badge.svg)](https://github.com/JaimeCalzadaNOAA/adcircpy/actions?query=workflow%3Atests)
 [![build](https://github.com/JaimeCalzadaNOAA/adcircpy/workflows/build/badge.svg)](https://github.com/JaimeCalzadaNOAA/adcircpy/actions?query=workflow%3Abuild)
-[![coverage](tests/coverage.svg)](https://github.com/JaimeCalzadaNOAA/adcircpy/actions)
+![coverage](.github/badges/badge.svg)
 [![version](https://img.shields.io/pypi/v/adcircpy)](https://pypi.org/project/adcircpy)
 [![license](https://img.shields.io/github/license/JaimeCalzadaNOAA/adcircpy)](https://opensource.org/licenses/gpl-license)
 

.github/workflows/tests.yml

@@ -3,7 +3,7 @@
 import matplotlib as mpl
 from pandas.plotting import register_matplotlib_converters
 
-from adcircpy.driver import AdcircRun
+from adcircpy.driver.driver import AdcircRun
 from adcircpy.forcing import Tides
 from adcircpy.mesh import AdcircMesh
 from adcircpy.fort15 import Fort15
@@ -20,5 +20,4 @@
 
 if util.find_spec("colored_traceback") is not None:
     import colored_traceback
-
     colored_traceback.add_hook(always=True)

MANIFEST.in

@@ -1,5 +1,4 @@
 import argparse
-import logging
 import sys
 
 
@@ -36,22 +35,11 @@ def generate_only(parser):
 
 
 def log_level(parser):
-    log_level = parser.add_mutually_exclusive_group()
-    log_level.add_argument(
-        '--log-level-info',
-        nargs='?',
-        const=logging.INFO,
-        dest="log_level")
-    log_level.add_argument(
-        '--log-level-debug',
-        nargs='?',
-        const=logging.DEBUG,
-        dest="log_level")
-    log_level.add_argument(
-        '--log-level-warning',
-        nargs='?',
-        const=logging.WARNING,
-        dest="log_level")
+    parser.add_argument(
+        "--log-level",
+        choices=['info', 'warning', 'debug'],
+        default='warning'
+    )
 
 
 def server(parser):
@@ -68,8 +56,8 @@ def server(parser):
     parser.add_argument("--additional-mpi-options")
 
     # make nproc required when using ssh
-    args = parser.parse_known_args()[0]
-    if args.hostname is not None:
+    # args = parser.parse_known_args()[0]
+    if '--hostname' in sys.argv:
         parser.add_argument("--nproc", "--ncpu", type=int, required=True)
     else:
         parser.add_argument("--nproc", "--ncpu", type=int, default=-1)
@@ -169,7 +157,7 @@ def best_track(parser):
     msg += " Examples: AL132012 for Sandy2012 or AL152017 for Maria2017."
     parser.add_argument('storm_id', help=msg)
     parser.add_argument('--start-date')
-    parser.add_argument('--end-date')
+    parser.add_argument('--run-days', type=float)
     parser.add_argument('--spinup-days', type=float, required=True)