From e6d9c0835f3d46fb3d695cbeba97898f9fdeb0f7 Mon Sep 17 00:00:00 2001
From: Yijian ZHOU <34815814+YijianZhou@users.noreply.github.com>
Date: Sat, 26 Aug 2023 20:39:26 -0700
Subject: [PATCH] rm env & modify readme

---
 README.md    |  14 ++--
 env/mess.yml | 210 ---------------------------------------------------
 2 files changed, 7 insertions(+), 217 deletions(-)
 delete mode 100644 env/mess.yml

diff --git a/README.md b/README.md
index 02392e8..cd36262 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,13 @@
-# MESS
-MESS is a matched filter earthquake detector  <br>
+# MESS  
+MESS is a matched filter earthquake detector  
   
 - **MESS Workflow**  
-1. **M**atch: calculate CC trace on every station (matched filter)
-2. **E**xpand: expand peak values on CC traces
+1. **M**atch: calculate CC trace on every station (matched filter)  
+2. **E**xpand: expand peak values on CC traces  
 3. **S**hift: time shift to origin times for all CC traces  
 4. **S**tack: stack CC traces of different stations & detect events on the stacked trace  
 5. *dt_p* and *dt_s* are picked by cross-correlation  
-![Zhou et al., (2021)](./doc/PALM_workflow.jpg)
+![Zhou et al., (2021)](./doc/PALM_workflow.jpg)  
 
 - **Usage** (see *example_mess_workdir*)  
 1. Prepare template phase file (e.g. run [PAL](https://github.com/YijianZhou/PAL)) & cut template waveform  
@@ -17,10 +17,10 @@ MESS is a matched filter earthquake detector  <br>
 2021/10 Online training in Chinese: vedio recording on [KouShare](https://www.koushare.com/lives/room/549779)  
 2022/08 Online training in Chinese: vedio recording on [KouShare](https://www.koushare.com/video/videodetail/31656)  
 
-## Installation <br>
+## Installation  
 MESS is a set of codes. All you need is to setup proper Python environment. This can be accomplished easily by installing [Anaconda](https://www.anaconda.com/products/individual#Downloads), [Obspy](https://github.com/obspy/obspy/wiki/Installation-via-Anaconda), and [Pytorch](https://pytorch.org/) sequentially. Or you can use the *env/mess.yml* file with *conda*. 
 
-## References
+## References  
 
 - **Zhou, Y.**, H. Yue, S. Zhou, L. Fang, Y. Zhou, L. Xu, Z. Liu, T. Wang, L. Zhao, & A. Ghosh (2022). Microseismicity along Xiaojiang Fault Zone (Southeastern Tibetan Plateau) and the Characterization of Interseismic Fault Behavior. *Tectonophysics*; 833: 229364. doi: [10.1016/j.tecto.2022.229364](https://doi.org/10.1016/j.tecto.2022.229364)  
 
diff --git a/env/mess.yml b/env/mess.yml
deleted file mode 100644
index 40a35ba..0000000
--- a/env/mess.yml
+++ /dev/null
@@ -1,210 +0,0 @@
-name: obspy
-channels:
-  - pytorch
-  - conda-forge
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=1_llvm
-  - absl-py=0.11.0=py37h89c1867_0
-  - aiohttp=3.7.4=py37h5e8e339_0
-  - asciitree=0.3.3=py_2
-  - async-timeout=3.0.1=py_1000
-  - async_generator=1.10=py_0
-  - attrs=20.3.0=pyhd3deb0d_0
-  - backcall=0.2.0=pyh9f0ad1d_0
-  - backports=1.0=py_2
-  - backports.functools_lru_cache=1.6.1=py_0
-  - bleach=3.3.0=pyh44b312d_0
-  - blinker=1.4=py_1
-  - brotlipy=0.7.0=py37h5e8e339_1001
-  - bzip2=1.0.8=h7f98852_4
-  - c-ares=1.17.1=h7f98852_1
-  - ca-certificates=2021.5.30=ha878542_0
-  - cachetools=4.2.1=pyhd8ed1ab_0
-  - certifi=2021.5.30=py37h89c1867_0
-  - cffi=1.14.4=py37h11fe52a_0
-  - chardet=4.0.0=py37h89c1867_1
-  - click=7.1.2=pyh9f0ad1d_0
-  - cryptography=3.4.5=py37h5d9358c_1
-  - cudatoolkit=10.1.243=h6bb024c_0
-  - cudnn=7.6.5=cuda10.1_0
-  - cycler=0.10.0=py_2
-  - dbus=1.13.6=he372182_0
-  - decorator=4.4.2=py_0
-  - defusedxml=0.7.1=pyhd8ed1ab_0
-  - entrypoints=0.3=pyhd8ed1ab_1003
-  - expat=2.2.10=h9c3ff4c_0
-  - fasteners=0.14.1=py_3
-  - fontconfig=2.13.1=he4413a7_1000
-  - freetype=2.10.4=h0708190_1
-  - future=0.18.2=py37h89c1867_3
-  - gettext=0.19.8.1=hf34092f_1004
-  - glib=2.66.1=h680cd38_0
-  - gmp=6.2.1=h58526e2_0
-  - gmpy2=2.1.0b1=py37hcb968a4_1
-  - google-auth=1.24.0=pyhd3deb0d_0
-  - google-auth-oauthlib=0.4.1=py_2
-  - grpcio=1.36.1=py37hb27c1af_0
-  - gst-plugins-base=1.14.5=h0935bb2_2
-  - gstreamer=1.14.5=h36ae1b5_2
-  - h5py=2.10.0=nompi_py37h513d04c_101
-  - hdf5=1.10.5=nompi_h7c3c948_1111
-  - icu=58.2=hf484d3e_1000
-  - idna=2.10=pyh9f0ad1d_0
-  - importlib-metadata=3.7.2=py37h89c1867_0
-  - ipykernel=5.5.0=py37h888b3d9_1
-  - ipython=7.21.0=py37h888b3d9_0
-  - ipython_genutils=0.2.0=py_1
-  - ipywidgets=7.6.3=pyhd3deb0d_0
-  - jedi=0.18.0=py37h89c1867_2
-  - jinja2=2.11.3=pyh44b312d_0
-  - jpeg=9d=h36c2ea0_0
-  - jsonschema=3.2.0=pyhd8ed1ab_3
-  - jupyter=1.0.0=py_2
-  - jupyter_client=6.1.11=pyhd8ed1ab_1
-  - jupyter_console=6.2.0=py_0
-  - jupyter_core=4.7.1=py37h89c1867_0
-  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
-  - jupyterlab_widgets=1.0.0=pyhd8ed1ab_1
-  - kiwisolver=1.3.1=py37h2527ec5_1
-  - krb5=1.17.2=h926e7f8_0
-  - lcms2=2.12=hddcbb42_0
-  - libblas=3.9.0=8_openblas
-  - libcblas=3.9.0=8_openblas
-  - libcurl=7.75.0=hc4aaa36_0
-  - libedit=3.1.20191231=he28a2e2_2
-  - libev=4.33=h516909a_1
-  - libffi=3.2.1=he1b5a44_1007
-  - libgcc-ng=9.3.0=h2828fa1_18
-  - libgfortran-ng=7.5.0=h14aa051_18
-  - libgfortran4=7.5.0=h14aa051_18
-  - libiconv=1.16=h516909a_0
-  - liblapack=3.9.0=8_openblas
-  - libnghttp2=1.43.0=h812cca2_0
-  - libopenblas=0.3.12=pthreads_hb3c22a3_1
-  - libpng=1.6.37=h21135ba_2
-  - libprotobuf=3.15.5=h780b84a_0
-  - libsodium=1.0.18=h36c2ea0_1
-  - libssh2=1.9.0=ha56f1ee_6
-  - libstdcxx-ng=9.3.0=h6de172a_18
-  - libtiff=4.2.0=hdc55705_0
-  - libuuid=2.32.1=h7f98852_1000
-  - libwebp-base=1.2.0=h7f98852_0
-  - libxcb=1.13=h7f98852_1003
-  - libxml2=2.9.9=h13577e0_2
-  - libxslt=1.1.32=hae48121_1003
-  - llvm-openmp=11.0.1=h4bd325d_0
-  - llvmlite=0.29.0=py37hfd453ef_1
-  - lxml=4.4.1=py37h7ec2d77_0
-  - lz4-c=1.9.3=h9c3ff4c_0
-  - markdown=3.3.4=pyhd8ed1ab_0
-  - markupsafe=1.1.1=py37h5e8e339_3
-  - matplotlib-base=3.3.4=py37h0c9df89_0
-  - mistune=0.8.4=py37h5e8e339_1003
-  - mkl=2020.4=h726a3e6_304
-  - monotonic=1.5=py_0
-  - mpc=1.1.0=h04dde30_1009
-  - mpfr=4.0.2=he80fd80_1
-  - mpmath=1.2.1=pyhd8ed1ab_0
-  - msgpack-python=1.0.2=py37h2527ec5_1
-  - mtspec=0.3.2=py37h7eb8c7e_4
-  - multidict=5.1.0=py37h5e8e339_1
-  - nbclient=0.5.3=pyhd8ed1ab_0
-  - nbconvert=6.0.7=py37h89c1867_3
-  - nbformat=5.1.2=pyhd8ed1ab_1
-  - ncurses=6.2=h58526e2_4
-  - nest-asyncio=1.4.3=pyhd8ed1ab_0
-  - ninja=1.10.2=h4bd325d_0
-  - notebook=6.0.3=py37hc8dfbb8_0
-  - numba=0.45.1=py37hb3f55d8_0
-  - numcodecs=0.7.3=py37hcd2ae1e_0
-  - numpy=1.20.1=py37haa41c4c_0
-  - oauthlib=3.0.1=py_0
-  - obspy=1.2.2=py37h03ebfcd_0
-  - olefile=0.46=pyh9f0ad1d_1
-  - openssl=1.1.1k=h7f98852_0
-  - packaging=20.9=pyh44b312d_0
-  - pandoc=2.12=h7f98852_0
-  - pandocfilters=1.4.2=py_1
-  - parso=0.8.1=pyhd8ed1ab_0
-  - pcre=8.44=he1b5a44_0
-  - pexpect=4.8.0=pyh9f0ad1d_2
-  - pickleshare=0.7.5=py_1003
-  - pillow=8.1.2=py37h4600e1f_0
-  - pip=21.0.1=pyhd8ed1ab_0
-  - prometheus_client=0.9.0=pyhd3deb0d_0
-  - prompt-toolkit=3.0.16=pyha770c72_0
-  - prompt_toolkit=3.0.16=hd8ed1ab_0
-  - protobuf=3.15.5=py37hcd2ae1e_0
-  - pthread-stubs=0.4=h36c2ea0_1001
-  - ptyprocess=0.7.0=pyhd3deb0d_0
-  - pyasn1=0.4.8=py_0
-  - pyasn1-modules=0.2.7=py_0
-  - pycparser=2.20=pyh9f0ad1d_2
-  - pygments=2.8.1=pyhd8ed1ab_0
-  - pyjwt=2.0.1=pyhd8ed1ab_0
-  - pyopenssl=20.0.1=pyhd8ed1ab_0
-  - pyparsing=2.4.7=pyh9f0ad1d_0
-  - pyqt=5.9.2=py37hcca6a23_4
-  - pyrsistent=0.17.3=py37h5e8e339_2
-  - pysocks=1.7.1=py37h89c1867_3
-  - python=3.7.1=h381d211_1002
-  - python-dateutil=2.8.1=py_0
-  - python_abi=3.7=1_cp37m
-  - pytorch=1.4.0=py3.7_cuda10.1.243_cudnn7.6.3_0
-  - pyzmq=22.0.3=py37h336d617_1
-  - qt=5.9.7=h52cfd70_2
-  - qtconsole=5.0.2=pyhd8ed1ab_0
-  - qtpy=1.9.0=py_0
-  - readline=7.0=hf8c457e_1001
-  - requests=2.25.1=pyhd3deb0d_0
-  - requests-oauthlib=1.3.0=pyh9f0ad1d_0
-  - rsa=4.7.2=pyh44b312d_0
-  - scipy=1.5.3=py37h8911b10_0
-  - send2trash=1.5.0=py_0
-  - setuptools=49.6.0=py37h89c1867_3
-  - sip=4.19.8=py37hf484d3e_1000
-  - six=1.15.0=pyh9f0ad1d_0
-  - sqlalchemy=1.3.23=py37h5e8e339_0
-  - sqlite=3.28.0=h8b20d00_0
-  - sympy=1.7.1=py37h89c1867_1
-  - tensorboard=2.4.1=pyhd8ed1ab_0
-  - tensorboard-plugin-wit=1.8.0=pyh44b312d_0
-  - tensorboardx=2.2=pyhd8ed1ab_0
-  - terminado=0.9.2=py37h89c1867_0
-  - testpath=0.4.4=py_0
-  - tk=8.6.10=h21135ba_1
-  - torchvision=0.5.0=py37_cu101
-  - tornado=6.1=py37h5e8e339_1
-  - tqdm=4.53.0=pyhd3deb0d_0
-  - traitlets=5.0.5=py_0
-  - typing-extensions=3.7.4.3=0
-  - typing_extensions=3.7.4.3=py_0
-  - urllib3=1.26.3=pyhd8ed1ab_0
-  - wcwidth=0.2.5=pyh9f0ad1d_2
-  - webencodings=0.5.1=py_1
-  - werkzeug=1.0.1=pyh9f0ad1d_0
-  - wheel=0.36.2=pyhd3deb0d_0
-  - widgetsnbextension=3.5.1=py37h89c1867_4
-  - xorg-libxau=1.0.9=h7f98852_0
-  - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xz=5.2.5=h516909a_1
-  - yarl=1.6.3=py37h5e8e339_1
-  - zarr=2.6.1=pyhd8ed1ab_0
-  - zeromq=4.3.4=h9c3ff4c_0
-  - zipp=3.4.1=pyhd8ed1ab_0
-  - zlib=1.2.11=h516909a_1010
-  - zstd=1.4.9=ha95c52a_0
-  - pip:
-    - blessings==1.7
-    - gpustat==0.6.0
-    - hinetpy==0.6.5
-    - nvidia-ml-py3==7.352.0
-    - pandas==0.24.2
-    - patsy==0.5.1
-    - psutil==5.6.7
-    - pytz==2018.9
-    - seaborn==0.9.0
-    - statsmodels==0.9.0
-prefix: /usr/local/anaconda3/envs/obspy