Merge pull request #44 from nfsi-canada/v014

New version 0.1.5

Added ability to specify ZComp name (instead of just "Z"), to handle CH[123] data from NFSI.

Added ability to specify a local base_url for the fdsnws data_select.

Fixed all scripts and corresponding docs

Author: paudetseis

.github/workflows/deploy.yml

@@ -17,20 +17,19 @@ on:
 jobs:
   # This workflow contains a single job called "build"
   build:
-    name: Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }}
     # The type of runner that the job will run on
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
-        python-version: ['3.7', '3.8', '3.9']
+        os: ["ubuntu-latest"]
+        python-version: ["3.10"]
 
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
-          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           activate-environment: test
           auto-activate-base: false
@@ -40,22 +39,22 @@ jobs:
         run: |
           conda info
           conda config --add channels conda-forge
-          conda install obspy pandas
+          conda install obspy pandas libstdcxx-ng
           pip install stdb
-          pip install -e .
+          pip install .
 
-      - name: Tests
-        shell: bash -l {0}
-        run: |
-          export MPLBACKEND=Agg
-          mkdir empty
-          cd empty
-          conda install pytest-cov
-          pytest -v --cov=obstools ../obstools/tests/
-          bash <(curl -s https://codecov.io/bash)
+      # - name: Tests
+      #   shell: bash -l {0}
+      #   run: |
+      #     export MPLBACKEND=Agg
+      #     mkdir empty
+      #     cd empty
+      #     conda install pytest-cov
+      #     pytest -v --cov=obstools ../obstools/tests/
+      #     bash <(curl -s https://codecov.io/bash)
 
       - name: Make docs
-        if: matrix.python-version == '3.8' 
+        if: matrix.python-version == '3.10' 
         shell: bash -l {0}
         run: |
           cd docs
@@ -66,7 +65,7 @@ jobs:
           cd ..
 
       - name: Deploy 🚀
-        if: matrix.python-version == '3.8' 
+        if: matrix.python-version == '3.10' 
         uses: JamesIves/[email protected]
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

docs/atacr.rst

@@ -243,20 +243,26 @@ Usage
                             correction. [Default looks for both horizontal and
                             pressure and allows for both tilt AND compliance
                             corrections]
+      --zcomp ZCOMP         Specify the Vertical Component Channel Identifier.
+                            [Default Z].
       -O, --overwrite       Force the overwriting of pre-existing data. [Default
                             False]
 
     Server Settings:
       Settings associated with which datacenter to log into.
 
-      -S SERVER, --Server SERVER
+      -S SERVER, --server SERVER
                             Specify the server to connect to. Options include:
                             BGR, ETH, GEONET, GFZ, INGV, IPGP, IRIS, KOERI, LMU,
                             NCEDC, NEIP, NERIES, ODC, ORFEUS, RESIF, SCEDC, USGS,
                             USP. [Default IRIS]
-      -U USERAUTH, --User-Auth USERAUTH
-                            Enter your IRIS Authentification Username and Password
-                            (--User-Auth='username:authpassword') to access and
+      --server-url SERVER_URL
+                            Specify the obspy base_url server address (and port if
+                            needed) to open for the fdsn client. Overrides any
+                            settings to '--server'. [Default None]
+      -U USERAUTH, --user-auth USERAUTH
+                            Enter your Authentification Username and Password
+                            (--user-auth='username:authpassword') to access and
                             download restricted data. [Default no user and
                             password]
 
@@ -572,20 +578,26 @@ Usage
                             correction. [Default looks for both horizontal and
                             pressure and allows for both tilt AND compliance
                             corrections]
+      --zcomp ZCOMP         Specify the Vertical Component Channel Identifier.
+                            [Default Z].
       -O, --overwrite       Force the overwriting of pre-existing data. [Default
                             False]
 
     Server Settings:
       Settings associated with which datacenter to log into.
 
-      -S SERVER, --Server SERVER
+      -S SERVER, --server SERVER
                             Specify the server to connect to. Options include:
                             BGR, ETH, GEONET, GFZ, INGV, IPGP, IRIS, KOERI, LMU,
                             NCEDC, NEIP, NERIES, ODC, ORFEUS, RESIF, SCEDC, USGS,
                             USP. [Default IRIS]
-      -U USERAUTH, --User-Auth USERAUTH
-                            Enter your IRIS Authentification Username and Password
-                            (--User-Auth='username:authpassword') to access and
+      --server-url SERVER_URL
+                            Specify the obspy base_url server address (and port if
+                            needed) to open for the fdsn client. Overrides any
+                            settings to '--server'. [Default None]
+      -U USERAUTH, --user-auth USERAUTH
+                            Enter your Authentification Username and Password
+                            (--user-auth='username:authpassword') to access and
                             download restricted data. [Default no user and
                             password]
 
@@ -599,6 +611,10 @@ Usage
       --pre-filt PRE_FILT   Specify four comma-separated corner frequencies
                             (float, in Hz) for deconvolution pre-filter. [Default
                             0.001,0.005,45.,50.]
+      --window WINDOW       Specify window length in seconds. Default value is
+                            highly recommended. Program may not be stable for
+                            large deviations from default value. [Default 7200.
+                            (or 2 hours)]
 
     Event Settings:
       Settings associated with refining the events to include in matching

obstools/__init__.py

@@ -109,7 +109,7 @@
 
 """
 
-__version__ = '0.1.4'
+__version__ = '0.1.5'
 
 __author__ = 'Pascal Audet & Helen Janiszewski'
 

obstools/atacr/classes.py

@@ -642,13 +642,11 @@ def average_daily_spectra(self, calc_rotation=True, fig_average=False,
 
         Attributes
         ----------
-        f : :class:`~numpy.ndarray`
-            Positive frequency axis for corresponding window parameters
         power : :class:`~obstools.atacr.classes.Power`
             Container for the Power spectra
         cross : :class:`~obstools.atacr.classes.Cross`
             Container for the Cross power spectra
-        rotation : :class:`~obstools.atacr.classes.Cross`, optional
+        rotation : :class:`~obstools.atacr.classes.Rotation`, optional
             Container for the Rotated power and cross spectra
 
         Examples

obstools/comply/classes.py

@@ -55,9 +55,6 @@ class Comply(object):
         components (obtained from the
         :class:`~obstools.atacr.classes.DayNoise` or the
         :class:`~obstools.atacr.classes.StaNoise` noise objects)
-    complyfunc : Dict
-        Dictionary of compliance and coherence functions given the available
-        components.
 
     """
 

obstools/scripts/atacr_download_data.py

@@ -88,6 +88,13 @@ def get_daylong_arguments(argv=None):
         "for tilt correction. Specifying 'P' allows for compliance " +
         "correction. [Default '12,P' looks for both horizontal and " +
         "pressure and allows for both tilt AND compliance corrections]")
+    parser.add_argument(
+        "--zcomp", 
+        dest="zcomp",
+        type=str,
+        default="Z",
+        help="Specify the Vertical Component Channel Identifier. "+
+        "[Default Z].")
     parser.add_argument(
         "-O", "--overwrite",
         action="store_true",
@@ -102,23 +109,32 @@ def get_daylong_arguments(argv=None):
         description="Settings associated with which "
         "datacenter to log into.")
     ServerGroup.add_argument(
-        "-S", "--Server",
+        "-S", "--server",
         action="store",
         type=str,
-        dest="Server",
+        dest="server",
         default="IRIS",
         help="Specify the server to connect to. Options include: " +
         "BGR, ETH, GEONET, GFZ, INGV, IPGP, IRIS, KOERI, LMU, NCEDC, " +
         "NEIP, NERIES, ODC, ORFEUS, RESIF, SCEDC, USGS, USP. " +
         "[Default IRIS]")
     ServerGroup.add_argument(
-        "-U", "--User-Auth",
+        "--server-url",
+        action="store",
+        type=str,
+        dest="server_url",
+        default=None,
+        help="Specify the obspy base_url server address (and port if needed) " +
+         "to open for the fdsn client. Overrides any settings to '--server'. " +
+         "[Default None]")
+    ServerGroup.add_argument(
+        "-U", "--user-auth",
         action="store",
         type=str,
-        dest="UserAuth",
+        dest="userauth",
         default="",
-        help="Enter your IRIS Authentification Username and Password " +
-        "(--User-Auth='username:authpassword') to access and download " +
+        help="Enter your Authentification Username and Password " +
+        "(--user-auth='username:authpassword') to access and download " +
         "restricted data. [Default no user and password]")
 
     """
@@ -243,16 +259,16 @@ def get_daylong_arguments(argv=None):
         args.endT = None
 
     # Parse User Authentification
-    if not len(args.UserAuth) == 0:
-        tt = args.UserAuth.split(':')
+    if not len(args.userauth) == 0:
+        tt = args.userauth.split(':')
         if not len(tt) == 2:
             parser.error(
                 "Error: Incorrect Username and Password Strings for " +
                 "User Authentification")
         else:
-            args.UserAuth = tt
+            args.userauth = tt
     else:
-        args.UserAuth = []
+        args.userauth = []
 
     # # Parse Local Data directories
     # if args.localdata is not None:
@@ -323,11 +339,24 @@ def main(args=None):
             datapath.mkdir(parents=True)
 
         # Establish client
-        if len(args.UserAuth) == 0:
-            client = Client(args.Server)
+        if len(args.userauth) == 0:
+            if args.server_url is not None:
+                client = Client(
+                    base_url=args.server_url)
+            else:
+                client = Client(
+                    args.server)
         else:
-            client = Client(
-                args.Server, user=args.UserAuth[0], password=args.UserAuth[1])
+            if args.server_url is not None:
+                client = Client(
+                    base_url=args.server_url,
+                    user=args.userauth[0], 
+                    password=args.userauth[1])
+            else:
+                client = Client(
+                    args.server, 
+                    user=args.userauth[0], 
+                    password=args.userauth[1])
 
         # Get catalogue search start time
         if args.startT is None:
@@ -420,7 +449,7 @@ def main(args=None):
                         continue
 
                 channels = sta.channel.upper()+'1,'+sta.channel.upper() + \
-                    '2,'+sta.channel.upper()+'Z'
+                    '2,'+sta.channel.upper()+args.zcomp
 
                 # Get waveforms from client
                 try:
@@ -455,7 +484,7 @@ def main(args=None):
                         t2 += dt
                         continue
 
-                channels = sta.channel.upper() + 'Z'
+                channels = sta.channel.upper() + args.zcomp
 
                 # Get waveforms from client
                 try:
@@ -517,7 +546,7 @@ def main(args=None):
                         continue
 
                 channels = sta.channel.upper()+'1,'+sta.channel.upper() + \
-                    '2,'+sta.channel.upper()+'Z'
+                    '2,'+sta.channel.upper()+args.zcomp
 
                 # Get waveforms from client
                 try:
@@ -580,14 +609,14 @@ def main(args=None):
                 continue
 
             sth = st.select(component='1') + st.select(component='2') + \
-                st.select(component='Z')
+                st.select(component=args.zcomp)
 
             # Remove responses
             print("*   -> Removing responses - Seismic data")
             sth.remove_response(pre_filt=args.pre_filt, output=args.units)
 
-            # Extract traces - Z
-            trZ = sth.select(component='Z')[0]
+            # Extract traces - Z 
+            trZ = sth.select(component=args.zcomp)[0]
             trZ = utils.update_stats(
                 trZ, sta.latitude, sta.longitude, sta.elevation,
                 sta.channel+'Z')