Merge pull request #11 from jpvantassel/dev

v0.5.1

.circleci/config.yml

@@ -1,16 +1,32 @@
-version: 2
+version: 2.1
+
+orbs:
+  coverage-reporter: codacy/[email protected]
+  codecov: codecov/[email protected]
+
 workflows:
-  version: 2
-  test:
+  build:
     jobs:
-      - test-3.6
-      - test-3.7
-      - test-3.8
-      # - test-3.9
+      - test-36:
+          context:
+            - docker          
+      - test-37:
+          context:
+            - docker
+      - test-38:
+          context:
+            - docker
+      # - test-39:
+      #     context:
+      #       - docker
+
 jobs:
-  test-3.6: &test-template
+  test-36: &test-template
     docker:
       - image: circleci/python:3.6.9
+        auth:
+          username: jpvantassel
+          password: $DOCKER_PASS
     working_directory: ~/repo
     steps:
       - checkout
@@ -26,7 +42,7 @@ jobs:
             . venv/bin/activate
             pip install numpy==1.18.5
       - run:
-          name: Install SigProPy
+          name: Install sigpropy from source
           command: |
             . venv/bin/activate
             pip install git+ssh://[email protected]/jpvantassel/sigpropy.git
@@ -47,27 +63,35 @@ jobs:
             . venv/bin/activate
             mv test/.coverage test-results
             cd test-results
-            coverage xml -o coverage.xml
+            coverage xml -o cobertura.xml
       - store_test_results:
           path: test-results
       - store_artifacts:
           path: test-results
-      - run:
-          name: Call Codecov
-          command: |
-            . venv/bin/activate
-            pip install codecov
-            codecov
+      - codecov/upload:
+          file: test-results/cobertura.xml
+      - coverage-reporter/send_report
 
-  test-3.7:
+  test-37:
     <<: *test-template
     docker:
       - image: circleci/python:3.7.5
-  test-3.8:
+        auth:
+          username: jpvantassel
+          password: $DOCKER_PASS
+
+  test-38:
     <<: *test-template
     docker:
       - image: circleci/python:3.8.0
-  # test-3.9:
+        auth:
+          username: jpvantassel
+          password: $DOCKER_PASS
+
+  # test-39:
   #   <<: *test-template
   #   docker:
   #     - image: circleci/python:3.9.0
+  #       auth:
+  #         username: jpvantassel
+  #         password: $DOCKER_PASS

.gitattributes

@@ -0,0 +1,2 @@
+docs/* linguist-documentation
+*.ipynb linguist-documentation

README.md

@@ -7,8 +7,8 @@
 [![CircleCI](https://circleci.com/gh/jpvantassel/hvsrpy.svg?style=svg)](https://circleci.com/gh/jpvantassel/hvsrpy)
 [![Documentation Status](https://readthedocs.org/projects/hvsrpy/badge/?version=latest)](https://hvsrpy.readthedocs.io/en/latest/?badge=latest)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/jpvantassel/hvsrpy.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/jpvantassel/hvsrpy/context:python)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/528737ade629492e8652be369528c756)](https://www.codacy.com/manual/jpvantassel/hvsrpy?utm_source=github.com&utm_medium=referral&utm_content=jpvantassel/hvsrpy&utm_campaign=Badge_Grade)
-[![codecov](https://codecov.io/gh/jpvantassel/hvsrpy/branch/master/graph/badge.svg)](https://codecov.io/gh/jpvantassel/hvsrpy)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/528737ade629492e8652be369528c756)](https://www.codacy.com/gh/jpvantassel/hvsrpy/dashboard?utm_source=github.com&utm_medium=referral&utm_content=jpvantassel/hvsrpy&utm_campaign=Badge_Grade)
+[![codecov](https://codecov.io/gh/jpvantassel/hvsrpy/branch/master/graph/badge.svg?token=MJ3WDNRIM0)](https://codecov.io/gh/jpvantassel/hvsrpy)
 
 ## Table of Contents
 

hvsrpy/__init__.py

@@ -17,9 +17,13 @@
 
 """Import modules into the hvsrpy namespace."""
 
+import logging
+
 from .meta import __version__
 from .hvsr import Hvsr
 from .hvsr_rotated import HvsrRotated
 from .sensor3c import Sensor3c
 from .plottools import quick_plot
 from .hvsr_spatial import HvsrVault, montecarlo_f0
+
+logging.getLogger('swprocess').addHandler(logging.NullHandler())

hvsrpy/hvsr.py

@@ -26,8 +26,9 @@
 
 from .meta import __version__
 
-logger = logging.getLogger(name=__name__)
+logger = logging.getLogger("swprocess.hvsr")
 
+__all__ = ["Hvsr"]
 
 class Hvsr():
     """Class for creating and manipulating HVSR objects.

hvsrpy/hvsr_rotated.py

@@ -24,7 +24,7 @@
 
 from hvsrpy import Hvsr, __version__
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger("swprocess.hvsr_rotated")
 
 __all__ = ["HvsrRotated"]
 
@@ -378,7 +378,8 @@ def mc_peak_amp(self, distribution='lognormal'):
         """
         mc = self.mean_curve(distribution)
         mc = mc.reshape((1, mc.size))
-        return np.max(mc[0, Hvsr.find_peaks(mc)[0]])
+        i_low, i_high = self.hvsrs[0].i_low, self.hvsrs[0].i_high
+        return np.max(mc[0, Hvsr.find_peaks(mc[:, i_low:i_high], starting_index=i_low)[0]])
 
     def mc_peak_frq(self, distribution='lognormal'):
         """Frequency of the peak of the mean HVSR curve.
@@ -396,7 +397,8 @@ def mc_peak_frq(self, distribution='lognormal'):
         """
         mc = self.mean_curve(distribution)
         mc = mc.reshape((1, mc.size))
-        return float(self.frq[np.where(mc[0] == np.max(mc[0, Hvsr.find_peaks(mc)[0]]))])
+        i_low, i_high = self.hvsrs[0].i_low, self.hvsrs[0].i_high
+        return self.frq[i_low + int(np.where(mc[0, i_low:i_high] == np.max(mc[0, Hvsr.find_peaks(mc[:, i_low:i_high], starting_index=i_low)[0]]))[0])]
 
     def _stats(self, distribution_f0):
         distribution_f0 = Hvsr.correct_distribution(distribution_f0)

hvsrpy/hvsr_spatial.py

@@ -24,7 +24,7 @@
 from scipy.spatial import Voronoi
 from shapely.geometry import MultiPoint, Point, Polygon
 
-logger = logging.getLogger(name=__name__)
+logger = logging.getLogger("swprocess.hvsr_rotated")
 
 __all__ = ["montecarlo_f0", "HvsrVault"]
 

hvsrpy/meta.py

@@ -17,4 +17,4 @@
 
 """Metadata for hvsrpy."""
 
-__version__ = "0.5.0"
+__version__ = "0.5.1"

hvsrpy/plottools.py

@@ -24,6 +24,8 @@
 
 import hvsrpy
 
+__all__ = ["quick_plot", "quick_voronoi_plot"]
+
 
 def quick_plot(file_name, windowlength=60, width=0.1, bandwidth=40,
                minf=0.2, maxf=20, nf=128, res_type="log",