requake 0.5__tar.gz → 0.7__tar.gz

requake-0.7/CHANGELOG.md

@@ -0,0 +1,128 @@
+# Requake Changelog
+
+Copyright (c) 2021-2026 Claudio Satriano <satriano@ipgp.fr>
+
+## unreleased
+
+## v0.7 - 2026-04-10
+
+This version requires at least Python 3.9.
+
+Note: you might want to run `requake update_config` to update your config file
+to the latest version.
+
+- New option `--shorterthan` to select families with a duration shorter than a
+  given value. For this option and for `--longerthan` it is now possible to
+  specify the duration in seconds, minutes, hours, or months, in addition to
+  days and years.
+- New option `--colorby` for many plot commands, to color families by a
+  specific attribute other than the family number
+- New option `--colormap` for many plot commands, to select a colormap
+  for coloring families. If not specified, a default colormap for each
+  attribute specified in `--colorby` is used.
+- New option `--range` to manually specify the range of values for the color
+  scale
+- New option `--force` for commands that write files, to overwrite existing
+  files without asking
+- New option `--freq_band` for trace plotting commands, to override the
+  frequency band specified in the config file
+- New option `--detailed` for `print_families`, to print more detailed
+  information about each family, including the list of events
+- New option `--output` to save plots to files instead of showing them on
+  screen
+- Config option `waveform_data_path` renamed to `sds_data_path`
+- New config option `event_data_path` to specify the path to a local directory
+  with waveform files organized per event
+- Add missing `street` map style for `map_families`
+- Catalog scan: when more than a station is provided and the closest station
+  to the event is not available, use the next closest station instead.
+- Catalog scan: accurate estimation of the number of event pairs to process
+- Initial support for plotting families found with template scan
+- Improved reading of CSV catalog files:
+  - avoid duplicated column guessing
+  - ensure that prefectly matching column field names are correctly guessed
+  - warn if an invalid time format is found
+- Colored terminal output for warnings and errors
+
+## v0.6 - 2024-05-04
+
+Note: you might want to run `requake update_config` to update your config file
+to the latest version.
+
+- Verb `plot_slip` renamed to `plot_cumulative`. This new verb has new options
+  to plot cumulative slip, cumulative moment, and cumulative number of events,
+  and to make the plot logarithmic.
+- New verb `print_catalog`: print the event catalog to screen
+- New verb `print_pairs`: print the event pairs to screen
+- `print_families`: also print minimum and maximum family magnitudes
+- Additional models to convert magnitude to slip. Currently supported models
+  are: Nadeau and Johnson (1998), Beeler et al. (2001), Eshelby (1957).
+  Model selection is done using the `mag_to_slip_model` config parameter.
+- New verb `update_config`: update an existing config file to the latest
+  version
+
+## v0.5 - 2024-04-23
+
+- New config options: `station_metadata_path` and `waveform_data_path` to
+  read station metadata and waveform data from files. Supports any metadata
+  format supported by ObsPy and SDS (SeisComp Data Structure) waveform
+  archives.
+- Filter catalog files on reading using the criteria in the config file
+- Improved time axes in `plot_timespans` and `plot_slip` for short time
+  intervals
+- `print_families`: autoset duration units based on the average duration
+- `plot_timespans`: default sorting changed to `family_number`
+
+## v0.4.1 - 2024-03-11
+
+- Bugfix: `requake` executable was not installed
+
+## v0.4 - 2024-03-11
+
+- Package license changed to GPL-3.0 or later
+- New verb: `read_catalog`: read a catalog from web services or from a file
+  (FDSN text, QuakeML, or CSV)
+- New verb: `scan_templates`: scan a continuous waveform stream using one
+  or more templates. Templates can be from families or from file
+- New verb: `print_families`: print families to screen
+- New verb: `plot_slip`: plot cumulative slip for one or more families
+- New config parameter: `clustering_algorithm` to select the algorithm
+  for building event families. Currently supported options are `shared` and
+  `UPGMA` (default: `shared`)
+- `family_numbers` argument is no more mandatory (default: `all`)
+  - argument added to `map_families` and `plot_timespans`
+- Config parameter `trace_average_from_normalized_traces` renamed to
+  `normalize_traces_before_averaging`
+- `plot_timespans`: possibility to sort by `family_number`
+- New options for `map_families` to select a map style and a zoom level for the
+  map tiles
+- New option `--minevents` (`-m`) for many verbs, to select families with a
+  minimum number of events
+- Support for events with no location
+- Bugfix: `plot_timespans`: correctly plot x time axis when sort by `time`
+
+## v0.3 - 2021-11-08
+
+- New verb: `build_templates`
+- New option: `cc_allow_negative` to search for anticorrelated events
+- New progressbar, using `tqdm`
+- `plot_families`:
+  - show average trace
+  - pan/zoom traces using arrows
+  - show/hide theoretical arrivals using 'a' (command line option removed)
+  - show event origin time as y-label
+  - show trace mean CC
+  - also shift theoretical arrivals when aligning traces
+- Bugfix: last family was not read from family file
+
+## v0.2 - 2021-09-24
+
+Mostly a bugfix release with a slightly improved trace plotting.
+
+- Bugfix: `scan_catalog` could not run properly due to missing variable
+- Bugfix: detrend traces before filtering
+- `plot_families`: print number of events and station-event distance
+
+## v0.1 - 2021-09-16
+
+- Initial release, not yet feature complete

{requake-0.5 → requake-0.7}/PKG-INFO

@@ -1,39 +1,43 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: requake
-Version: 0.5
+Version: 0.7
 Summary: Repeating earthquakes search and analysis
-Home-page: https://requake.seismicsource.org
-Author: Claudio Satriano
-Author-email: satriano@ipgp.fr
-License: GNU General Public License v3 or later (GPLv3+)
+Author-email: Claudio Satriano <satriano@ipgp.fr>
+License-Expression: GPL-3.0-or-later
 Project-URL: Homepage, https://requake.seismicsource.org
 Project-URL: Source, https://github.com/SeismicSource/requake
 Project-URL: Documentation, https://requake.readthedocs.io
-Platform: OS Independent
+Platform: OS
+Platform: Independent
 Classifier: Development Status :: 4 - Beta
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering
 Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: >3.7
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
 Requires-Dist: scipy>=1.5.0
 Requires-Dist: obspy>=1.2.0
+Requires-Dist: cartopy
 Requires-Dist: argcomplete
 Requires-Dist: tqdm
 Requires-Dist: tabulate
+Requires-Dist: pygments
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: license-file
 
-<img src="imgs/Requake_logo.svg" width="400">
+<img src="https://cdn.jsdelivr.net/gh/SeismicSource/requake@5f302920590ec696d958625433fbad76c9820f5c/imgs/Requake_logo.svg" width="400">
 
 # Requake
 
@@ -45,7 +49,7 @@ Repeating earthquakes search and analysis.
 [![docs-badge]][docs-link]
 [![DOI-badge]][DOI-link]
 
-Copyright (c) 2021-2024 Claudio Satriano <satriano@ipgp.fr>
+Copyright (c) 2021-2026 Claudio Satriano <satriano@ipgp.fr>
 
 ## Description
 
@@ -55,18 +59,43 @@ It can either scan an existing earthquake catalog to search for similar events,
 or perform template matching on a continuous waveform stream.
 
 Catalogs and waveforms can be read from local files or downloaded using
-standard [FDSN web services](https://www.fdsn.org/webservices/).
+standard [FDSN web services].
 
-Requake is written in Python and uses [ObsPy](https://obspy.org) as backend.
+Requake is written in Python and uses [ObsPy] as backend.
 
 ## Installation
 
 ### Installing the latest release
 
-#### Using pip and PyPI (preferred method)
+#### Using Anaconda
 
-The latest release of Requake is available on the
-[Python Package Index](https://pypi.org/project/requake/).
+The following command will automatically create an [Anaconda] environment
+named `requake`, install the required packages and install the latest
+version of SourceSpec via `pip`:
+
+    conda env create --file https://raw.githubusercontent.com/SeismicSource/requake/main/requake_conda_env.yml
+
+If you want a different name for your environment, use:
+
+    conda env create -n YOUR_ENV_NAME --file https://raw.githubusercontent.com/SeismicSource/requake/main/requake_conda_env.yml
+
+Activate the environment with:
+
+    conda activate requake
+
+(or `conda activate YOUR_ENV_NAME`)
+
+To keep Requake updated run the following command from within the environment:
+
+    pip install --upgrade requake
+
+Or, to switch to a development snapshot, run:
+
+    pip install git+https://github.com/SeismicSource/requake.git
+
+#### Using pip and PyPI
+
+The latest release of Requake is available on the [Python Package Index].
 
 You can install it easily through `pip`:
 
@@ -75,9 +104,8 @@ You can install it easily through `pip`:
 ### Installing a development snapshot
 
 If you need a recent feature that is not in the latest release (see the
-`unreleased` section in [CHANGELOG](CHANGELOG.md)), you want to use the more
-recent development snapshot from the
-[Requake GitHub repository](https://github.com/SeismicSource/requake).
+`unreleased` section in [CHANGELOG][changelog-link]), you want to use the more
+recent development snapshot from the [Requake GitHub repository].
 
 #### Using pip
 
@@ -122,35 +150,41 @@ To get help, use:
 
     requake -h
 
-The different running modes are specified as "verbs" (positional arguments).
-Currently supported verbs are:
+Different commands are available:
 
     sample_config       write sample config file to current directory and exit
+    update_config       update an existing config file to the latest version
     read_catalog        read an event catalog from web services or from a file
+    print_catalog       print the event catalog to screen
     scan_catalog        scan an existing catalog for earthquake pairs
+    print_pairs         print pairs to screen
     plot_pair           plot traces for a given event pair
     build_families      build families of repeating earthquakes from a catalog
                         of pairs
     print_families      print families to screen
     plot_families       plot traces for one ore more event families
     plot_timespans      plot family timespans
-    plot_slip           plot cumulative slip for one or more families
+    plot_cumulative     cumulative plot for one or more families
     map_families        plot families on a map
     flag_family         flag a family of repeating earthquakes as valid or not
-                        valid. Note that all families are valid by default
-                        when first created
+                        valid.
     build_templates     build waveform templates for one or more event
                         families
     scan_templates      scan a continuous waveform stream using one or more
                         templates
 
-Certain running modes (e.g., `plot_pair`) require further arguments (use, e.g.,
+Certain commands (e.g., `plot_pair`) require further arguments (use, e.g.,
 `requake plot_pair -h` to get help).
 
-Requake supports command line tab completion for arguments, thanks to
-[argcomplete](https://kislyuk.github.io/argcomplete/).
-To enable command line tab completion, add the following line to your `.bashrc`
-or `.zshrc`:
+Requake supports command line tab completion for commands and arguments, thanks
+to [argcomplete].
+To enable command line tab completion run:
+
+    activate-global-python-argcomplete
+
+(This is a one-time command that needs to be run only once).
+
+Or, alternatively, add the following line to your `.bashrc` or `.zshrc`:
 
     eval "$(register-python-argcomplete requake)"
 
@@ -192,8 +226,8 @@ parallelization will be implemented.
 
 If you used Requake for a scientific paper, please cite it as:
 
-> Satriano, C. (2024). Requake: Repeating earthquakes search and analysis (X.Y).
-> [doi: 10.5281/ZENODO.10832204]
+> Satriano, C. (2026). Requake: Repeating earthquakes search and analysis (X.Y).
+> [doi: 10.5281/ZENODO.10832203]
 
 Please replace `X.Y` with the Requake version number you used.
 
@@ -214,9 +248,17 @@ You can also cite the following abstract presented at the
 [docs-link]: https://requake.readthedocs.io/en/latest/?badge=latest
 [changelog-badge]: https://img.shields.io/badge/Changelog-136CB6.svg
 [changelog-link]: https://github.com/SeismicSource/requake/blob/main/CHANGELOG.md
-[DOI-badge]: https://zenodo.org/badge/DOI/10.5281/zenodo.10832204.svg
-[DOI-link]: https://doi.org/10.5281/zenodo.10832204
+[DOI-badge]: https://zenodo.org/badge/DOI/10.5281/zenodo.10832203.svg
+[DOI-link]: https://doi.org/10.5281/zenodo.10832203
+[Requake GitHub repository]: https://github.com/SeismicSource/requake
+
+<!-- External links -->
+[FDSN web services]: https://www.fdsn.org/webservices/
+[ObsPy]: https://obspy.org
+[Anaconda]: https://www.anaconda.com/download
+[Python Package Index]: https://pypi.org/project/requake/
+[argcomplete]: https://kislyuk.github.io/argcomplete/
 
 <!-- References -->
-[doi: 10.5281/ZENODO.10832204]: https://doi.org/10.5281/ZENODO.10832204
+[doi: 10.5281/ZENODO.10832203]: https://doi.org/10.5281/ZENODO.10832203
 [bibcode: 2021AGUFM.T25A0167S]: https://ui.adsabs.harvard.edu/abs/2021AGUFM.T25A0167S

{requake-0.5 → requake-0.7}/README.md

@@ -10,7 +10,7 @@ Repeating earthquakes search and analysis.
 [![docs-badge]][docs-link]
 [![DOI-badge]][DOI-link]
 
-Copyright (c) 2021-2024 Claudio Satriano <satriano@ipgp.fr>
+Copyright (c) 2021-2026 Claudio Satriano <satriano@ipgp.fr>
 
 ## Description
 
@@ -20,18 +20,43 @@ It can either scan an existing earthquake catalog to search for similar events,
 or perform template matching on a continuous waveform stream.
 
 Catalogs and waveforms can be read from local files or downloaded using
-standard [FDSN web services](https://www.fdsn.org/webservices/).
+standard [FDSN web services].
 
-Requake is written in Python and uses [ObsPy](https://obspy.org) as backend.
+Requake is written in Python and uses [ObsPy] as backend.
 
 ## Installation
 
 ### Installing the latest release
 
-#### Using pip and PyPI (preferred method)
+#### Using Anaconda
 
-The latest release of Requake is available on the
-[Python Package Index](https://pypi.org/project/requake/).
+The following command will automatically create an [Anaconda] environment
+named `requake`, install the required packages and install the latest
+version of SourceSpec via `pip`:
+
+    conda env create --file https://raw.githubusercontent.com/SeismicSource/requake/main/requake_conda_env.yml
+
+If you want a different name for your environment, use:
+
+    conda env create -n YOUR_ENV_NAME --file https://raw.githubusercontent.com/SeismicSource/requake/main/requake_conda_env.yml
+
+Activate the environment with:
+
+    conda activate requake
+
+(or `conda activate YOUR_ENV_NAME`)
+
+To keep Requake updated run the following command from within the environment:
+
+    pip install --upgrade requake
+
+Or, to switch to a development snapshot, run:
+
+    pip install git+https://github.com/SeismicSource/requake.git
+
+#### Using pip and PyPI
+
+The latest release of Requake is available on the [Python Package Index].
 
 You can install it easily through `pip`:
 
@@ -40,9 +65,8 @@ You can install it easily through `pip`:
 ### Installing a development snapshot
 
 If you need a recent feature that is not in the latest release (see the
-`unreleased` section in [CHANGELOG](CHANGELOG.md)), you want to use the more
-recent development snapshot from the
-[Requake GitHub repository](https://github.com/SeismicSource/requake).
+`unreleased` section in [CHANGELOG][changelog-link]), you want to use the more
+recent development snapshot from the [Requake GitHub repository].
 
 #### Using pip
 
@@ -87,35 +111,41 @@ To get help, use:
 
     requake -h
 
-The different running modes are specified as "verbs" (positional arguments).
-Currently supported verbs are:
+Different commands are available:
 
     sample_config       write sample config file to current directory and exit
+    update_config       update an existing config file to the latest version
     read_catalog        read an event catalog from web services or from a file
+    print_catalog       print the event catalog to screen
     scan_catalog        scan an existing catalog for earthquake pairs
+    print_pairs         print pairs to screen
     plot_pair           plot traces for a given event pair
     build_families      build families of repeating earthquakes from a catalog
                         of pairs
     print_families      print families to screen
     plot_families       plot traces for one ore more event families
     plot_timespans      plot family timespans
-    plot_slip           plot cumulative slip for one or more families
+    plot_cumulative     cumulative plot for one or more families
     map_families        plot families on a map
     flag_family         flag a family of repeating earthquakes as valid or not
-                        valid. Note that all families are valid by default
-                        when first created
+                        valid.
     build_templates     build waveform templates for one or more event
                         families
     scan_templates      scan a continuous waveform stream using one or more
                         templates
 
-Certain running modes (e.g., `plot_pair`) require further arguments (use, e.g.,
+Certain commands (e.g., `plot_pair`) require further arguments (use, e.g.,
 `requake plot_pair -h` to get help).
 
-Requake supports command line tab completion for arguments, thanks to
-[argcomplete](https://kislyuk.github.io/argcomplete/).
-To enable command line tab completion, add the following line to your `.bashrc`
-or `.zshrc`:
+Requake supports command line tab completion for commands and arguments, thanks
+to [argcomplete].
+To enable command line tab completion run:
+
+    activate-global-python-argcomplete
+
+(This is a one-time command that needs to be run only once).
+
+Or, alternatively, add the following line to your `.bashrc` or `.zshrc`:
 
     eval "$(register-python-argcomplete requake)"
 
@@ -157,8 +187,8 @@ parallelization will be implemented.
 
 If you used Requake for a scientific paper, please cite it as:
 
-> Satriano, C. (2024). Requake: Repeating earthquakes search and analysis (X.Y).
-> [doi: 10.5281/ZENODO.10832204]
+> Satriano, C. (2026). Requake: Repeating earthquakes search and analysis (X.Y).
+> [doi: 10.5281/ZENODO.10832203]
 
 Please replace `X.Y` with the Requake version number you used.
 
@@ -179,9 +209,17 @@ You can also cite the following abstract presented at the
 [docs-link]: https://requake.readthedocs.io/en/latest/?badge=latest
 [changelog-badge]: https://img.shields.io/badge/Changelog-136CB6.svg
 [changelog-link]: https://github.com/SeismicSource/requake/blob/main/CHANGELOG.md
-[DOI-badge]: https://zenodo.org/badge/DOI/10.5281/zenodo.10832204.svg
-[DOI-link]: https://doi.org/10.5281/zenodo.10832204
+[DOI-badge]: https://zenodo.org/badge/DOI/10.5281/zenodo.10832203.svg
+[DOI-link]: https://doi.org/10.5281/zenodo.10832203
+[Requake GitHub repository]: https://github.com/SeismicSource/requake
+
+<!-- External links -->
+[FDSN web services]: https://www.fdsn.org/webservices/
+[ObsPy]: https://obspy.org
+[Anaconda]: https://www.anaconda.com/download
+[Python Package Index]: https://pypi.org/project/requake/
+[argcomplete]: https://kislyuk.github.io/argcomplete/
 
 <!-- References -->
-[doi: 10.5281/ZENODO.10832204]: https://doi.org/10.5281/ZENODO.10832204
-[bibcode: 2021AGUFM.T25A0167S]: https://ui.adsabs.harvard.edu/abs/2021AGUFM.T25A0167S
+[doi: 10.5281/ZENODO.10832203]: https://doi.org/10.5281/ZENODO.10832203
+[bibcode: 2021AGUFM.T25A0167S]: https://ui.adsabs.harvard.edu/abs/2021AGUFM.T25A0167S

requake-0.7/pyproject.toml

@@ -0,0 +1,72 @@
+[build-system]
+requires = ["setuptools>=77", "versioneer[toml]"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "requake"
+dynamic = ["version", "readme"]
+authors = [
+    { name = "Claudio Satriano", email = "satriano@ipgp.fr" },
+]
+description = "Repeating earthquakes search and analysis"
+license = "GPL-3.0-or-later"
+license-files = ["LICENSE.txt"]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+requires-python = ">=3.9"
+dependencies = [
+    "scipy>=1.5.0",
+    "obspy>=1.2.0",
+    "cartopy",
+    "argcomplete",
+    "tqdm",
+    "tabulate",
+    "pygments",
+]
+
+[project.urls]
+Homepage = "https://requake.seismicsource.org"
+Source = "https://github.com/SeismicSource/requake"
+Documentation = "https://requake.readthedocs.io"
+
+[project.scripts]
+requake = "requake.main:main"
+
+[tool.setuptools]
+include-package-data = true
+platforms = [
+    "OS",
+    "Independent",
+]
+
+[tool.setuptools.packages.find]
+include = ["requake", "requake.*"]
+
+[tool.setuptools.package-data]
+"*" = ["LICENSE"]
+"requake.config" = ["*.conf"]
+
+[tool.setuptools.dynamic]
+version = {attr = "requake.__version__"}
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "requake/_version.py"
+versionfile_build = "requake/_version.py"
+tag_prefix = "v"
+parentdir_prefix = "requake-"

{requake-0.5 → requake-0.7}/requake/__init__.py

@@ -4,11 +4,10 @@
 Initialize requake package.
 
 :copyright:
-    2021-2024 Claudio Satriano <satriano@ipgp.fr>
+    2021-2026 Claudio Satriano <satriano@ipgp.fr>
 :license:
     GNU General Public License v3.0 or later
     (https://www.gnu.org/licenses/gpl-3.0-standalone.html)
 """
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']

{requake-0.5 → requake-0.7}/requake/_version.py

@@ -1,5 +1,5 @@
 
-# This file was generated by 'versioneer.py' (0.19) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2024-04-23T09:52:34+0200",
+ "date": "2026-04-10T18:38:40+0200",
  "dirty": false,
  "error": null,
- "full-revisionid": "5223a069ca428a69bba654b59dc8bc7b8860cbdd",
- "version": "0.5"
+ "full-revisionid": "5f302920590ec696d958625433fbad76c9820f5c",
+ "version": "0.7"
 }
 '''  # END VERSION_JSON
 

{requake-0.5 → requake-0.7}/requake/catalog/__init__.py

@@ -4,9 +4,14 @@
 Functions and data structures for managing earthquake catalogs.
 
 :copyright:
-    2021-2024 Claudio Satriano <satriano@ipgp.fr>
+    2021-2026 Claudio Satriano <satriano@ipgp.fr>
 :license:
     GNU General Public License v3.0 or later
     (https://www.gnu.org/licenses/gpl-3.0-standalone.html)
 """
+from .catalog import (  # noqa
+    RequakeCatalog, RequakeEvent, generate_evid,
+    fix_non_locatable_events, read_stored_catalog
+)
 from .read_catalog import read_catalog  # noqa
+from .print_catalog import print_catalog  # noqa