PySEP v0.5.0

.readthedocs.yaml

@@ -1,8 +1,13 @@
 version: 2
 
+build:
+    os: "ubuntu-22.04"
+    tools:
+        python: "mambaforge-22.9"
+
 sphinx:
     builder: html
-    configuration: ./docs/conf.py
+    configuration: docs/conf.py
 
 conda:
-    environment: ./docs/environment.yml
+    environment: docs/environment.yml

CHANGELOG.md

@@ -64,7 +64,47 @@
   - PySEP warns when config parameters are not used by the program
 
 
-## Version 0.4.1 (Master/Devel)
+## Version 0.4.1 
 - Adds Tutorial documentation following GEOS626 lab (thanks, Aakash!)
 - Adds version release documentation
 - Slightly modifies pysep-docs conda environment to accomodate converted nbooks
+
+## Version 0.5.0 (Master)
+- Improves functions 'read_forcesolution' and 'read_source', which now return
+  `obspy.core.event.Event` objects, rather than the makeshift Source objects 
+- 'read_forcesolution' can now handle FORCESOLUTION files from both SPECFEM3D
+  and SPECFEM3D_GLOBE
+- Added function `read_events_plus` that provides additional support to 
+  Obspys `read_events` function by allowing for support of FORCESOLUTION and
+  SOURCE files from SPECFEM2D/3D/3D_GLOBE
+- Remove the `Source` class from `Pysep.utils.io.mt`. This was a remnant of the
+  old Pyatoa approach to building an Obspy Event-like object to mimic certain
+  behaviors. This has been replaced by read functions which simply return Events
+- #117: New quality control function that removes Traces with array length <= 1,
+  which would cause preprocessing to fail
+- #116: RecSec now logs absmax amplitudes and absmax amplitude ratios IFF both
+  `st` and `st_syn` are provided
+- #120: Version number is now only sourced from `pyproject.toml`, other 
+  locations now reference this file to determine version number
+- #124:
+  - API Change: RecordSection parameter `cmtsolution` has been **renamed** to 
+	`source`. 
+  - RecordSection now only expects readable files in  --pysep_path or 
+	--syn_path.
+	- New `RecordSection.read_data()`function which handles data reading logic 
+	and can read both obs data (.SAC from PySEP) and syn data 
+	(SPECFEM ASCII files or SAC files)
+	- Bugfix: Added an exit catch in RecordSection to stop the workflow if no 
+	data is available
+- Bugfix: RecSec unable to read different `source` file formats. New parameter
+  'srcfmt' allows User to set this manually. If not given, RecSec will attempt
+  to guess the file format based on the name of the file.
+- Bugfix: `read_specfem3d_cmtsolution_cartesian` was unable to handle 
+	Flinn-Engdahl regions that had spaces in them. Also it was unable to 
+	handle extra lines in the file. 
+- Bugfix #126: Fixed some incorrect parameters in example config files
+- PySEP variable namechange: `_legacy_naming` -> 'legacy_naming`
+- New RecSec Parameters `wildcard` and `syn_wildcard` to specify how to 
+	search for data to plot with RecSec
+- Removed unnused parameters 'legacy_naming' and 'log_level' from 
+	`Pysep.write_config`

docs/conf.py

@@ -18,7 +18,12 @@ def setup(app):
 copyright = '2023, adjTomo Dev Team'
 author = 'adjTomo Dev Team'
 release = ''
-version = '0.4.1'
+# Grab version number from 'pyproject.toml'
+with open("../pyproject.toml", "r") as f:
+    _lines = f.readlines()
+for _line in _lines:
+    if _line.startswith("version"):
+        version = _line.split('"')[1].strip()
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/how_to_version_release.md

@@ -8,8 +8,6 @@ patch), or provide reason in PR for why certain points are not checked.
 ## Prior to PR merge:
 - [ ] Merge `devel` -> `master`
 - [ ] Bump version number `pyproject.toml`
-- [ ] Bump version number `docs/conf.py`
-- [ ] Bump version number `pysep/__init__.py`
 - [ ] Ensure all tests still pass, fix broken tests
 - [ ] Update `CHANGELOG` to include all major changes since last version
 

docs/recsec.rst

@@ -158,13 +158,13 @@ structure:
 
 .. code:: bash
 
-    recsec --syn_path OUTPUT_FILES/ --cmtsolution DATA/CMTSOLUTION --stations DATA/STATIONS
+    recsec --syn_path OUTPUT_FILES/ --source DATA/CMTSOLUTION --stations DATA/STATIONS
 
 Or when scripting,
 
 .. code:: python
 
-    plotw_rs(syn_path="OUTPUT_FILES", cmtsolution="DATA/CMTSOLUTION",
+    plotw_rs(syn_path="OUTPUT_FILES", source="DATA/CMTSOLUTION",
              stations="DATA/STATIONS")
 
 You can also directly feed in an ObsPy stream containing your synthetic data
@@ -188,7 +188,7 @@ and tell RecSec to preprocess both data streams identically
 
 .. code:: bash
 
-    recsec --pysep_path ./SAC --syn_path OUTPUT_FILES/ --cmtsolution DATA/CMTSOLUTION --stations DATA/STATIONS --preprocess both
+    recsec --pysep_path ./SAC --syn_path OUTPUT_FILES/ --source DATA/CMTSOLUTION --stations DATA/STATIONS --preprocess both
 
 Preprocessing flags can be applied to the observed data only (`st`), synthetic
 data only (`st_syn`) or both (`both`). See the `preprocess` parameter in the
@@ -220,15 +220,15 @@ For SPECFEM3D_Cartesian this would look like
 
 .. code:: bash
 
-    recsec --syn_path OUTPUT_FILES --cmtsolution DATA/CMTSOLUTION --stations DATA/STATIONS --cartesian
+    recsec --syn_path OUTPUT_FILES --source DATA/CMTSOLUTION --stations DATA/STATIONS --cartesian
 
 
 For SPECFEM2D, the source file may not be a CMTSOLUTION. Additionally, the 
 default seismogram components may not be defined in ZNE
 
 .. code:: bash
 
-    recsec --syn_path OUTPUT_FILES --cmtsolution DATA/SOURCE --stations DATA/STATIONS --components Y --cartesian
+    recsec --syn_path OUTPUT_FILES --source DATA/SOURCE --stations DATA/STATIONS --components Y --cartesian
 
 
 While scripting, the input parameter `cartesian` can be used:
@@ -252,14 +252,14 @@ and provide paths to both `--pysep_path` and `--syn_path`.
 .. note::
 
     RecSec makes the assumption that both sets of synthetics share the
-    same metadata provided in the `--cmtsolution` and `--stations` flags.
+    same metadata provided in the `--source` and `--stations` flags.
 
 Let's say you've stored your 'data' in a directory called 'observed/' and your
 synthetics in a directory called 'synthetic/'
 
 .. code:: bash
 
-    recsec --pysep_path observed/ --syn_path synthetic/ --cmtsolution DATA/CMTSOLUTION --stations DATA/STATIONS --synsyn
+    recsec --pysep_path observed/ --syn_path synthetic/ --source DATA/CMTSOLUTION --stations DATA/STATIONS --synsyn
 
 
 

pyproject.toml

@@ -4,10 +4,10 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pysep-adjtomo"
-version = "0.4.1"
+version = "0.5.0"
 description = "Python Seismogram Extraction and Processing"
 readme = "README.md"
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 license = {file = "LICENSE.txt"}
 authors = [
     {name = "adjTomo Dev Team"},

pysep/__init__.py

@@ -1,6 +1,8 @@
 import logging
+from importlib.metadata import version
 
-__version__ = "0.4.1"
+# Defines version number from 'pyproject.toml'
+__version__ = version("pysep-adjtomo")
 
 logger = logging.getLogger("pysep")
 logger.setLevel("INFO")
@@ -15,3 +17,4 @@
 from pysep.pysep import Pysep, get_data  # NOQA
 from pysep.recsec import RecordSection, plotw_rs  # NOQA
 from pysep.declust import Declust  # NOQA
+from pysep.utils.io import read_sem, read_stations, read_events_plus  # NOQA

pysep/configs/alvizuri_tape_2018/2006-10-09T013528_NORTH_KOREA.yaml

@@ -47,4 +47,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/misc_events/1988-02-15T181000_KERNVILLE_EXPLOSION.yaml

@@ -46,4 +46,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/misc_events/2015-10-18T051831_TAAN_FJORD_LANDSLIDE.yaml

@@ -50,4 +50,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/misc_events/2016-01-24T103037_INISKIN.yaml

@@ -47,4 +47,3 @@ remove_insufficient_length: true
 remove_masked_data: true
 fill_data_gaps: false
 gap_fraction: 1.0
-log_level: DEBUG

pysep/configs/mtuq_workshop_2022/2014-08-25T161903_ICELAND.yaml

@@ -11,7 +11,7 @@ seconds_before_event: 20
 seconds_after_event: 20
 event_latitude: 64.612
 event_longitude: -17.472
-event_depth_km: 50.0
+event_depth_km: 5.0
 event_magnitude: 4.6
 networks: Z7
 stations: RODG,DYSA,LIND,LOKT,LAUF,KALF,HELI,FAG,SVIN,K250

pysep/configs/mtuq_workshop_2022/2017-09-03T033001_NORTH_KOREA.yaml

@@ -19,7 +19,7 @@ channels: BH?
 locations: '00'
 reference_time: '2017-09-03T03:30:01.760000Z'
 seconds_before_ref: 100
-seconds_after_ref: 300
+seconds_after_ref: 1000
 phase_list:
 - ttall
 mindistance_km: 0

pysep/configs/template_config.yaml

@@ -1,48 +1,48 @@
-# PYSEP Config file - Template v0.1.0
+# PySEP Template config v0.5.0
+event_tag: null
 config_file: null
 client: IRIS
 client_debug: false
 timeout: 600
+taup_model: ak135
+use_mass_download: false
 event_selection: default
-origin_time: 2009-04-07T20:12:55.351
+origin_time: null
 seconds_before_event: 20
 seconds_after_event: 20
-event_latitude: 61.45420
-event_longitude: -149.7428
-event_depth_km: 33.033
-event_magnitude: 4.6
-networks: 'AK,YV,AV,AT,XZ,PN'
+event_latitude: null
+event_longitude: null
+event_depth_km: null
+event_magnitude: null
+networks: '*'
 stations: '*'
-channels: 'BH?'
+channels: '*'
 locations: '*'
 reference_time: null
 seconds_before_ref: 100
 seconds_after_ref: 300
-phase_list: null
-llnl_db_path: /store/raw/LLNL/UCRL-MI-222502/westernus.wfdisc
-min_dist: 0
-max_dist: 300.0
-min_az: 0
-max_az: 360
-min_lat: null
-max_lat: null
-min_lon: null
-max_lon: null
+phase_list:
+- ttall
+mindistance_km: 0
+maxdistance_km: 20000.0
+minazimuth: 0
+maxazimuth: 360
+minlatitude: null
+maxlatitude: null
+minlongitude: null
+maxlongitude: null
 demean: true
 detrend: true
-taper_percentage: 0
+taper_percentage: 0.0
 rotate: null
 remove_response: true
 output_unit: VEL
 water_level: 60
 pre_filt: default
-scale_factor: 100.0
-resample_freq: 50
-remove_clipped: false
-output_dir: ./
-write_files: !!set
-  all: null
-plot_files: !!set
-  all: null
-log_level: DEBUG
-event_tag: null
+scale_factor: 1
+resample_freq: null
+remove_clipped: true
+remove_insufficient_length: true
+remove_masked_data: true
+fill_data_gaps: false
+gap_fraction: 1.0

pysep/pysep.py

@@ -532,7 +532,7 @@ def __init__(self, config_file=None, event_selection="default",
         self.write_files = write_files
         self.plot_files = plot_files
         self.log_level = log_level
-        self._legacy_naming = legacy_naming
+        self.legacy_naming = legacy_naming
         self._overwrite = overwrite
         self._overwrite_event_tag = overwrite_event_tag
 
@@ -1580,7 +1580,7 @@ def write(self, write_files=None, _return_filenames=False, _subset=None,
                 self.st.write(fid, format="MSEED")
 
         # Used for determining where to save SAC files
-        if self._legacy_naming:
+        if self.legacy_naming:
             _output_dir = self.output_dir
         else:
             _output_dir = os.path.join(self.output_dir, sac_subdir)
@@ -1632,7 +1632,7 @@ def _write_sac(self, st, output_dir=os.getcwd(), components=None):
         for tr in st:
             if components and tr.stats.component not in components:
                 continue
-            if self._legacy_naming:
+            if self.legacy_naming:
                 # Legacy: e.g., 20000101000000.NN.SSS.LL.CC.c
                 _trace_id = f"{tr.get_id()[:-1]}.{tr.get_id()[-1].lower()}"
                 if self.event_tag:
@@ -1680,10 +1680,9 @@ def write_config(self, fid=None, overwrite=False):
                     if not key.startswith("_")}
         # Internal attributes that don't need to go into the written config
         attr_remove_list = ["st", "st_raw", "event", "inv", "c", "write_files",
-                            "plot_files", "output_dir", "station_ids", "kwargs"]
+                            "plot_files", "output_dir", "station_ids", "kwargs",
+                            "llnl_db_path", "log_level", "legacy_naming"]
 
-        if self.client.upper() != "LLNL":
-            attr_remove_list.append("llnl_db_path")  # not important unless LLNL
         for key in attr_remove_list:
             del(dict_out[key])
         # Write times in as strings not UTCDateTime
@@ -1736,7 +1735,7 @@ def _event_tag_and_output_dir(self):
         # Default behavior, auto-generate event tag
         if self._overwrite_event_tag is None:
             # Options for choosing how to name things. Legacy or new-style
-            if self._legacy_naming:
+            if self.legacy_naming:
                 logger.debug("reverting to legacy style file naming")
                 event_tag = format_event_tag_legacy(self.event)
             else: