Hotfix: CAP weight file sorting (#145)

* removed pypi version documentation, moved to adjdocs
bump patch version number
remove annoying warning log when specfem source does not have origin time

* added docstring for recsec taper parameter

* fixed sorting issue related to #144 and extended test to cover this function

* update changelog

Author: bch0w

CHANGELOG.md

@@ -122,3 +122,10 @@
 - #137: More control over RecSec kwargs and better warning messages
 - #138: Improved SAC header creation for SPECFEM synthetics
 - #139: Improved RecSec preprocessing setup, more manual control for the User 
+
+## Version 0.6.1
+
+- Change log level from warning -> info for empty origin time when reading SPECFEM sources
+- Remove README doc page about publishing to PyPi, moved this to adjDocs
+- Hotfix: incorrect sorting in CAP weights file related to #144
+- Added some more to the RecSec docstring

docs/README.md

@@ -26,28 +26,3 @@ make html
 
 See your locally built documentation by opening *_build/html/index.html*
 
-## Publishing Package on PyPi 
-*Useful link: https://realpython.com/pypi-publish-python-package/*
-
-1. Ensure your `pyproject.toml` file is set up properly; required fields are name and version
-2. Set dependencies, do **not(( pin exact versions but allow for upper and lower bounds; only list direct dependencies
-3. Include `tests/`, `docs/`, license, and MANIFEST files (MANIFIST used for including non-source code material
-4. Ensure you have an account on PyPi and TestPyPi (for testing publishing)
-5. Install `twine` and `build` which are used to build and push packages to PyPi
-6. Build your packages locally, which creates the `.tar.gz` and `.whl` dist files
-```bash
-python -m build
-```
-6. Check that files in your .whl (zip file) are as expected (including everything in 3)
-7. Check dist files with:
-```bash
-twine check dist/*
-```
-8. Upload test package (note: requires TestPyPi account)
-```bash
-twine upload -r testpypi dist/*
-```
-9. Upload real package (note: requires PyPi account)
-```bash
-twine upload dist/*
-```

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pysep-adjtomo"
-version = "0.6.0"
+version = "0.6.1"
 description = "Python Seismogram Extraction and Processing"
 readme = "README.md"
 requires-python = ">=3.8"

pysep/recsec.py

@@ -340,6 +340,12 @@ def __init__(
         :type trim: bool
         :param trim: trim waveforms to the same length, and if any data gaps
             are present, fill with mean values by default
+        :type taper: bool
+        :param taper: if True, taper ends of waveform during preprocessing. Uses
+            keyword arguments `max_percentage` (float) to define the percentage
+            to taper, and `taper_type` (str) to define shape of the taper. See
+            ObsPy's stream.taper() function for acceptable values for these
+            arguments.
         :type integrate: int
         :param integrate: apply integration `integrate` times on all traces.
             acceptable values [-inf, inf], where positive values are integration

pysep/tests/test_utils.py

@@ -11,7 +11,8 @@
 from obspy import read, read_events, read_inventory, Stream
 from obspy.io.sac.sactrace import SACTrace
 from pysep.utils.cap_sac import (append_sac_headers,
-                                 format_sac_header_w_taup_traveltimes)
+                                 format_sac_header_w_taup_traveltimes,
+                                 write_cap_weights_files)
 from pysep.utils.curtail import (remove_for_clipped_amplitudes, rename_channels,
                                  remove_stations_for_missing_channels,
                                  remove_stations_for_insufficient_length,
@@ -101,6 +102,32 @@ def test_sac_header_correct_origin_time(tmpdir, test_st, test_inv, test_event):
     assert(sac.reftime == test_event.preferred_origin().time)
 
 
+def test_write_cap_weights_files(tmpdir, test_st, test_inv, test_event):
+    """
+    Test writing out CAP weight files and make sure sorting works for distance
+    and code works as advertised. No testing for az sorting
+    """
+    st = append_sac_headers(st=test_st, inv=test_inv, event=test_event)
+
+    # Check sorting by dist
+    write_cap_weights_files(st=st, path_out=tmpdir, order_by="dist")
+    assert(os.path.exists(os.path.join(tmpdir, "weights.dat")))
+    dists = np.loadtxt(os.path.join(tmpdir, "weights.dat"), usecols=1)
+    # Check that distances are in ascending order
+    assert(np.all(np.diff(dists) >= 0))
+
+    # Remove so we know that new files are being made each time
+    os.remove(os.path.join(tmpdir, "weights.dat"))
+
+    # Check sorting by code
+    write_cap_weights_files(st=st, path_out=tmpdir, order_by="code")
+    assert(os.path.exists(os.path.join(tmpdir, "weights.dat")))
+    codes = np.loadtxt(os.path.join(tmpdir, "weights.dat"), usecols=0, 
+                       dtype=str)
+    # Check that distances are in ascending order
+    assert(np.all(codes == np.sort(codes)))
+
+
 def test_rename_channels(test_st):
     """
     Edit some waveforms to be obviously bad and make sure we can catch it

pysep/utils/cap_sac.py

@@ -98,7 +98,7 @@ def write_cap_weights_files(st, path_out="./", order_by="dist"):
 
     # Order codes based on distance, name or azimuth
     idx = ["code", "dist", "az"].index(order_by)
-    code_list = np.array(code_list)
+    code_list = np.array(code_list, dtype="object")
     ordered_codes = code_list[code_list[:, idx].argsort()]
 
     logger.info("writing CAP weight files")

pysep/utils/io.py

@@ -269,7 +269,7 @@ def read_specfem2d_source(path_to_source, origin_time=None):
     # First set dummy origin time
     if origin_time is None:
         origin_time = "1970-01-01T00:00:00"
-        logger.warning("no origin time set for SPECFEM2D source, setting "
+        logger.info("no origin time set for SPECFEM2D source, setting "
                        f"dummy value: {origin_time}")
 
     with open(path_to_source, "r") as f: