diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml new file mode 100644 index 0000000000000000000000000000000000000000..b7fce1df816ffebda85ab1e34394271080b31404 --- /dev/null +++ b/.github/workflows/python-publish.yml @@ -0,0 +1,37 @@ +# This workflow will upload a Python Package using Twine when a release is created +# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries + +# This workflow uses actions that are not certified by GitHub. +# They are provided by a third-party and are governed by +# separate terms of service, privacy policy, and support +# documentation. + +name: Upload Python Package + +on: + pull_request: + branches: + - master + +jobs: + deploy: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.x' + - name: Install dependencies + run: | + python -m pip install --upgrade pip + sudo pip install twine + - name: Build package + run: python setup.py sdist build + - name: Publish package + uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + with: + user: __token__ + password: ${{ secrets.PYPI_TOKEN }} diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 81e2de1541d6a106f93e290c608d7d3604bf3f80..0000000000000000000000000000000000000000 --- a/.travis.yml +++ /dev/null @@ -1,42 +0,0 @@ -language: python - -install: -- pip install . - - -jobs: - include: - - stage: test - python: '3.7' - - - stage: test - python: '3.8' - - - - stage: test - python: '3.9' - - - - stage: doc - script: bash -c "$(curl -fsSL https://git.nju.edu.cn/xumi1993/source/-/raw/master/trigger.sh)" - - - stage: deploy - python: 3.8 - script: skip - deploy: - provider: pypi - username: "__token__" - password: - secure: "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" - on: - branch: master - - -script: - - git clone https://github.com/xumi1993/seispy-test test - - cd test && bash run.sh - - - - - diff --git a/README.md b/README.md index a1c2a4618da28bbcf39a343e0334025826343d5a..a6965fbd3a2016b9ce33dd649cd9c28d093e5fe7 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,12 @@ -# Seispy +# -[![pipeline status](https://img.shields.io/travis/com/xumi1993/seispy)](https://travis-ci.com/xumi1993/seispy) -[![Build Status](https://img.shields.io/travis/com/xumi1993/seispy-doc.post?label=doc)](https://seispy.xumijian.me) +[![Upload Python Package](https://github.com/xumi1993/seispy/actions/workflows/python-publish.yml/badge.svg)](https://github.com/xumi1993/seispy/actions/workflows/python-publish.yml) +[![Deploy Seispy Docs](https://github.com/xumi1993/seispy-doc.post/actions/workflows/deploy.yml/badge.svg)](https://github.com/xumi1993/seispy-doc.post/actions/workflows/deploy.yml) + + + + +[![Conda Version](https://img.shields.io/conda/vn/conda-forge/seispy.svg)](https://anaconda.org/conda-forge/seispy) [![PyPI](https://img.shields.io/pypi/v/python-seispy)](https://pypi.org/project/python-seispy/) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/python-seispy)](https://pypi.org/project/python-seispy/) [![GitHub](https://img.shields.io/github/license/xumi1993/seispy)]() @@ -26,7 +31,7 @@ Seispy is a Python module for processing seismological data and calculating Rece * [NumPy](http://www.numpy.org/) >= 1.16 * [SciPy](http://www.scipy.org/) >= 1.2.0 * [matplotlib](https://matplotlib.org/) >= 3.0.0 - * [PyQt5](https://www.riverbankcomputing.com/software/pyqt/) >= 5.15.0 + * [PyQt5](https://www.riverbankcomputing.com/software/pyqt/) >= 5.12.0 ## Installation ``` @@ -36,23 +41,49 @@ python setup.py install # Inclusion ## Libraries - * `seispy.distaz`: Calculate distance and azimuth (by [the lithospheric seismology program at USC](http://www.seis.sc.edu/software/distaz/)).
- * `seispy.geo`: Tiny codes of geophysics. - * `seispy.bootstrap`: Bootstrap confidence interval estimation (by [scikits-bootstrap](https://github.com/cgevans/scikits-bootstrap)) - * `seispy.decon`: Iterative time domain deconvolution method (Ligorria and Ammon's 1999 BSSA) - * `seispy.rfcorrect`: Subsequent process of PRFs includeing moveout correct and time to depth conversion (1D and 3D) (see [Mijian Xu et al., 2018 EPSL](https://www.sciencedirect.com/science/article/pii/S0012821X17306921?via%3Dihub)) - * `seispy.ccp`: CCP stacking along a profile. + +- `seispy.distaz`: Calculate distance and azimuth (by the + [lithospheric seismology program at USC][]). +- `seispy.geo`: Tiny codes of geophysics. +- `seispy.bootstrap`: Bootstrap confidence interval estimation (by + [scikits-bootstrap][]) +- `seispy.decon`: Functions of deconvolution transferred from + [iwbailey/processRFmatlab][] including + - Iterative time domain deconvolution method (Ligorría and Ammon + 1999 BSSA). + - Water level frequency domain deconvolution method (CJ. Ammon + 1991 BSSA) +- `seispy.rf`: Procedure for RF calculation. The functions of + `match_eq`, `search_eq` invoked `obspy.core.UTCDateTime` and + `obspy.clients` from the [Obspy][]. +- `seispy.eq`: RF processing for each event, which invoked + `obspy.io.sac`, `obspy.signal`, `obspy.taup` and `obspy.core.Stream` + from the [Obspy][]. +- `seispy.rfcorrect`: Subsequent process of RFs including moveout + correction and time to depth conversion (1D and 3D) (see [Xu et al., + 2018 EPSL][]) +- `seispy.ccpprofile`: CCP stacking along a profile. +- `seispy.ccp3d`: 3-D CCP stacking with extracting depth D410 and + D660. + + [lithospheric seismology program at USC]: http://www.seis.sc.edu/software/distaz/ + [scikits-bootstrap]: https://github.com/cgevans/scikits-bootstrap + [iwbailey/processRFmatlab]: https://github.com/iwbailey/processRFmatlab + [Obspy]: https://docs.obspy.org/ + [Xu et al., 2018 EPSL]: https://www.sciencedirect.com/science/article/pii/S0012821X17306921?via%3Dihub ## Commands ### Receiver Functions * `prf`: Calculate PRFs for a station. * `pickrf`: Pick PRFs with virtual quality control after the calculation. - * `plotrt`: Plot PRFs in R and T components order by back-azimuth. - * `plotr`: Plot PRFs in R component order by back-azimuth. - * `hk`: H-Kappa stacking. + * `plotrt`: Plot PRFs with R and T components order by back-azimuth. + * `plotr`: Plot PRFs with R component order by back-azimuth. + * `hk`: H-Kappa stacking for estimating Moho depth and crustal Vp/Vs. * `rf2depth`: Convert PRFs to depth axis. * `ccp_profile`: Stack PRFs along a profile with a CCP stacking method. + * `ccp3d`: Stack PRFs with spaced bins. + * `rfani`: Estimating crustal anisotropy with a joint method. ### Others * `ndk2dat`: Convert the GCMT catalog file ("ndk" format) to the list file for the `prf` command. diff --git a/seispy/hk.py b/seispy/hk.py index 1dd68390053a87127c27a909344d4a19e920c9a7..2b3959d35df2df3974cd3eafb81a93554ede4b67 100644 --- a/seispy/hk.py +++ b/seispy/hk.py @@ -129,7 +129,7 @@ def plot(stack, allstack, h, kappa, besth, bestk, cvalue, cmap=load_cyan_map(), if path is None: plt.show() else: - f.savefig(path, format='pdf', bbox_inches='tight') + f.savefig(path, format='png', dpi=400, bbox_inches='tight') def ci(allstack, h, kappa, ev_num): @@ -178,7 +178,7 @@ def hksta(hpara, isplot=False, isdisplay=False): if isdisplay: print_result(besth, bestk, maxhsig, maxksig, print_comment=True) if isplot: - img_path = join(hpara.hkpath, station+'_Hk.pdf') + img_path = join(hpara.hkpath, station+'_Hk.png') plot(stack, allstack, hpara.hrange, hpara.krange, besth, bestk, cvalue, title=title, path=img_path) else: plot(stack, allstack, hpara.hrange, hpara.krange, besth, bestk, cvalue, title=title) diff --git a/seispy/plotR.py b/seispy/plotR.py index b672fd8071667a4a0823168fa412fdf5d3934086..6f3f5ae04d2e26c409afc2c2d78f539a3d716938 100644 --- a/seispy/plotR.py +++ b/seispy/plotR.py @@ -81,23 +81,20 @@ def plotr(rfpath, outpath='./', xlim=[-2, 80], enf=6, format='pdf'): def main(): parser = argparse.ArgumentParser(description="Plot R&T receiver functions") parser.add_argument('rfpath', help='Path to PRFs with a \'finallist.dat\' in it', type=str) - parser.add_argument('-w', help="Time window from t1 to t2, defaults to -2/80", type=str, default='-2/80', metavar='t1/t2') parser.add_argument('-e', help='Enlargement factor, defaults to 6', dest='enf', type=float, default=6, metavar='enf') parser.add_argument('-o', help='Output path without file name, defaults to current path', dest='output', default='./', type=str, metavar='outpath') parser.add_argument('-t', help='Specify figure format. f = \'.pdf\', g = \'.png\', defaults to \'g\'', dest='format', default='g', type=str, metavar='f|g') + parser.add_argument('-x', help='The max time scale in sec, defaults to 85s', default=85, type=float, metavar='max_time') + arg = parser.parse_args() - try: - xlim = [float(v) for v in arg.w.split('/')] - except: - raise ValueError("Error format in time window") if arg.format not in ('f', 'g'): raise ValueError('Error: The format must be in \'f\' and \'g\'') elif arg.format == 'g': fmt = 'png' elif arg.format == 'f': fmt = 'pdf' - plotr(arg.rfpath, arg.output, enf=arg.enf, xlim=xlim, format=fmt) + plotr(arg.rfpath, arg.output, enf=arg.enf, xlim=[-2, arg.x], format=fmt) diff --git a/seispy/plotRT.py b/seispy/plotRT.py index 628dcaf19c63233f28475c5193f8f0586fa73c0e..485f0f7f4f78acd5596e8f5eb3869cf0600c5fae 100644 --- a/seispy/plotRT.py +++ b/seispy/plotRT.py @@ -123,7 +123,7 @@ def set_fig(axr, axt, axb, axr_sum, axt_sum, stadata, station, xmin=-2, xmax=30, axb.set_xlabel(r'Back-azimuth ($\circ$)', fontsize=13) -def plotrt(rfpath, enf=3, out_path='./', outformat='g'): +def plotrt(rfpath, enf=3, out_path='./', outformat='g', xmax=30): """[summary] :param rfpath: [description] @@ -146,11 +146,11 @@ def plotrt(rfpath, enf=3, out_path='./', outformat='g'): h, axr, axt, axb, axr_sum, axt_sum = init_figure() stadata = read_process_data(rfpath) plot_waves(axr, axt, axb, axr_sum, axt_sum, stadata, enf=enf) - set_fig(axr, axt, axb, axr_sum, axt_sum, stadata, station) + set_fig(axr, axt, axb, axr_sum, axt_sum, stadata, station, xmax=xmax, comp=stadata.comp) if outformat == 'g': - h.savefig(join(out_path, station+'_RT_bazorder_{:.1f}.png'.format(stadata.f0[0])), dpi=200) + h.savefig(join(out_path, station+'_RT_bazorder_{:.1f}.png'.format(stadata.f0[0])), dpi=400, bbox_inches='tight') elif outformat == 'f': - h.savefig(join(out_path, station+'_RT_bazorder_{:.1f}.pdf'.format(stadata.f0[0])), format='pdf') + h.savefig(join(out_path, station+'_RT_bazorder_{:.1f}.pdf'.format(stadata.f0[0])), format='pdf', bbox_inches='tight') def main(): @@ -160,12 +160,11 @@ def main(): parser.add_argument('-o', help='Output path without file name, defaults to current path', dest='output', default='./', type=str, metavar='outpath') parser.add_argument('-t', help='Specify figure format. f = \'.pdf\', g = \'.png\', defaults to \'g\'', dest='format', default='g', type=str, metavar='f|g') + parser.add_argument('-x', help='The max time scale in sec, defaults to 30s', default=30, type=float, metavar='max_time') arg = parser.parse_args() if arg.format not in ('f', 'g'): - print('Errpr: The format must be in \'f\' and \'g\'') - parser.print_help() - sys.exit(1) - plotrt(rfpath=arg.path, enf=arg.enf, out_path=arg.output, outformat=arg.format) + raise ValueError('Error: The format must be in \'f\' and \'g\'') + plotrt(rfpath=arg.rfpath, enf=arg.enf, out_path=arg.output, outformat=arg.format, xmax=arg.x) if __name__ == '__main__': diff --git a/seispy/rfani.py b/seispy/rfani.py index a53aaec60c07868f69bdba7f37a90a175c2b5e88..e91faf8df59a6ae21250ce64c4242b154eb6a341 100644 --- a/seispy/rfani.py +++ b/seispy/rfani.py @@ -260,7 +260,7 @@ class RFAni(): if show: plt.show() else: - fig.savefig(join(outpath, 'joint_ani_'+self.sacdatar.staname+'.png'), dpi=400, bbox_inches='tight') + fig.savefig(join(outpath, self.sacdatar.staname+'_joint_ani.png'), dpi=400, bbox_inches='tight') if __name__ == "__main__": diff --git a/seispy/scripts.py b/seispy/scripts.py index aed253d1ea33755990a694a15e5cc2e37298589d..09f862a35e4459e252730360854c98c208896c06 100644 --- a/seispy/scripts.py +++ b/seispy/scripts.py @@ -11,9 +11,9 @@ def rfani(): parser = argparse.ArgumentParser(description="Estimate crustal anisotropy with a Joint inversion method. See Liu and Niu (2012) in detail.") parser.add_argument('rfpath', type=str, help="Path to PRFs") parser.add_argument('-t', help="Time window cut from tb to te", metavar='tb/te', required=True) - parser.add_argument('-c', help="List file in text format for saving results, defaults to rfani.dat", + parser.add_argument('-c', help="List file in text format for saving results, defaults to ./rfani.dat", default="rfani.dat", metavar="list_file_name") - parser.add_argument('-l', help="Half length of time window when cut out Pms phases", + parser.add_argument('-l', help="Half length of time window when cut out Pms phases, defaults to 3s", default=3, metavar="half_time_length", type=float) parser.add_argument('-o', dest='outpath', help="Directory to the image, defaults to current directory.", default='./') parser.add_argument('-p', help="If plot RFs stacked by back-azimuth, defaults to \'False\'", @@ -27,7 +27,7 @@ def rfani(): bf, bt = rfsta.jointani(timewin[0], timewin[1], tlen=arg.l, weight=weights) with open(arg.c, 'a+') as fid: for f, t in zip(bf, bt): - fid.write('{}\t{:.3f}\t{:.3f}\t{:.2f}\t{:.2f}'.format(rfsta.staname, rfsta.stla, rfsta.stlo, f, t)) + fid.write('{}\t{:.3f}\t{:.3f}\t{:.2f}\t{:.2f}\n'.format(rfsta.staname, rfsta.stla, rfsta.stlo, f, t)) if arg.isplot: rfsta.ani.plot_stack_baz(outpath=arg.outpath) rfsta.ani.plot_polar(outpath=arg.outpath) diff --git a/setup.py b/setup.py index b4d35a8ffdeaa87ed1d4b8709f4772669fc1a215..1bbc29cfd6c72929e77f20121a8ddb48ebfb8f15 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ packages = find_packages() with open("README.md", "r") as fh: long_description = fh.read() -VERSION = "1.2.1" +VERSION = "1.2.3" setup(name='python-seispy', version=VERSION, author='Mijian Xu', @@ -39,7 +39,7 @@ setup(name='python-seispy', 'rfani=seispy.scripts:rfani', 'ccp3d=seispy.scripts:ccp3d', 'get_pierce_points=seispy.scripts:get_pierce_points']}, - include_package_data=True, + # include_package_data=True, zip_safe=False, classifiers=['Programming Language :: Python', 'Programming Language :: Python :: 3.7',