Merge pull request #289 from noisepy/noisepy/ishika

Added a dependency on the new noisepy-seis-io and fixed the import statements

.github/workflows/test.yaml

@@ -20,7 +20,7 @@ jobs:
         python-version: ${{env.python_version}}
         mpi: 'true'
     - name: pytest
-      run: PYTHONPATH=src pytest tests/. integration_tests/. --cov
+      run: pytest tests/. integration_tests/. --cov=noisepy.seis --cov=noisepy.monitoring
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:

integration_tests/cc_stack_test.py

@@ -8,17 +8,17 @@
     cross_correlate,
     stack_cross_correlations,
 )
-from noisepy.seis.channel_filter_store import channel_filter
-from noisepy.seis.channelcatalog import (
+from noisepy.seis.io.channel_filter_store import channel_filter
+from noisepy.seis.io.channelcatalog import (
     XMLStationChannelCatalog,  # Required stationXML handling object
 )
-from noisepy.seis.datatypes import (  # Main configuration object
+from noisepy.seis.io.datatypes import (  # Main configuration object
     CCMethod,
     ConfigParameters,
     StackMethod,
 )
-from noisepy.seis.numpystore import NumpyCCStore, NumpyStackStore
-from noisepy.seis.scedc_s3store import (  # Object to query SCEDC data from on S3
+from noisepy.seis.io.numpystore import NumpyCCStore, NumpyStackStore
+from noisepy.seis.io.scedc_s3store import (  # Object to query SCEDC data from on S3
     SCEDCS3DataStore,
 )
 

pyproject.toml

@@ -50,6 +50,7 @@ dependencies = [
     "PyYAML==6.0",
     "pydantic-yaml==1.0",
     "psutil>=5.9.5,<6.0.0",
+    "noisepy-seis-io>=0.1.11",
 ]
 
 

script/test_whiten.py

@@ -3,7 +3,7 @@
 import scipy
 from scipy.fftpack import next_fast_len
 
-from noisepy.seis.datatypes import FreqNorm
+from noisepy.seis.io.datatypes import FreqNorm
 from noisepy.seis.noise_module import moving_ave, whiten
 
 

script/write_speed/write.py

@@ -13,8 +13,8 @@
 import pyasdf
 import zarr
 
-from noisepy.seis.tiledb import _TileDBHelper
-from noisepy.seis.utils import fs_join, get_filesystem
+from noisepy.seis.io.tiledb import _TileDBHelper
+from noisepy.seis.io.utils import fs_join, get_filesystem
 
 logger = logging.getLogger(__name__)
 s3_path = "s3://<bucket>/write_speed/"

src/noisepy/functions_2019/S0B_to_ASDF_2019.py

@@ -9,8 +9,9 @@
 import pyasdf
 from mpi4py import MPI
 
+from noisepy.seis.io.datatypes import RmResp
+
 from . import noise_module
-from .datatypes import RmResp
 
 if not sys.warnoptions:
     import warnings

src/noisepy/seis/__init__.py

@@ -24,7 +24,6 @@
                     Used to assemble and/or stack all cross-correlation functions computed for the staion
                     pairs in the cross_correlate step
 - noise_module:     Collection of functions used in the cross_correlate and stacking steps
-- plotting_modules: Utility functions for plotting the data
 """
 
 logging.basicConfig(