Merge branch 'docs' of https://github.com/xumi1993/seispy into docs

.github/workflows/doc_build.yml

@@ -5,26 +5,36 @@ name: Seispy docs
 
 on:
   push:
-    branches: [ docs ]
+    branches: [ docs, dev ]
   pull_request:
     branches: [ master ]
 
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  deploy:
-    runs-on: macos-latest
+  build_deploy:
+    runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
+      - name: Set branch name
+        id: vars
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" ]]; then
+            echo ::set-output name=branch::${{ github.event.pull_request.head.ref }}
+          else
+            echo ::set-output name=branch::dev
+          fi
+          echo ${{ steps.vars.outputs.branch }}
+  
       - name: Cancel Previous Runs
         uses: styfle/[email protected]
 
-      - name: Checkout
-        uses: actions/checkout@v2.4.0
+      - name: Checkout to docs branch
+        uses: actions/checkout@v4
         with:
           ref: docs
 
@@ -35,16 +45,56 @@ jobs:
           environment-file: environment.yml
           # miniforge-variant: Mambaforge
           # use-mamba: true
-
+
+      - name: Checkout to source branch
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ steps.vars.outputs.branch }}
+          path: seispy_source
+          fetch-depth: 0
+
+      - name: Install Seispy
+        run: |
+          cd seispy_source
+          pip install .
+          cd ..
+
       - name: Build documentation
         run: |
           make html
+      
+      - name: Checkout the gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+          # Checkout to this folder instead of the current one
+          path: deploy
+          # Download the entire history
+          fetch-depth: 0
+
+      - name: Copy documentation
+        run: |
+          cd seispy_source
+          if [[ ${{ steps.vars.outputs.branch }} == "dev" ]]; then
+            version=“$(python setup.py --version)_$(git rev-parse --short HEAD)”
+          else
+            version=$(python setup.py --version)
+          fi
+          cd ../deploy
+          touch .nojekyll
+          echo -e "\nRemoving old files from previous builds of ${version}:"
+          rm -rvf dev_* ${version}
+          echo -e "\nCopying new files from ${version}:"
+          cp -rvf ../build/html ${version}
+          rm -rfv latest
+          ln -sfv ${version} latest
+          cd ..
         
       - name: Deploy documentation
         uses: peaceiris/actions-gh-pages@068dc23d9710f1ba62e86896f84735d869951305
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./build/html
+          publish_dir: deploy
           # Only keep the latest commit to avoid bloating the repository
           force_orphan: true
           cname: seispy.xumijian.me

environment.yml

@@ -3,14 +3,12 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python=3.10
-  - seispy
   - pip
   - sphinx
   - sphinx-copybutton
   - sphinx-design
   - myst-nb
-  - pydata-sphinx-theme=0.8.1
+  - furo
   - obspy
   - numpydoc
   - pip:

source/conf.py

@@ -15,20 +15,21 @@
 
 import os
 import sys
-sys.path.insert(0, os.path.abspath('./seispy/seispy'))
+from importlib.metadata import version as get_version
+# sys.path.insert(0, os.path.abspath('./seispy/seispy'))
 # sys.path.insert(0, os.path.abspath('/Users/xumj/Codes/seispy/seispy'))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'seispy'
+project = 'Seispy'
 copyright = '2020, Mijian Xu'
 author = 'Mijian Xu'
 
 # The short X.Y version
-version = ''
+version = f"v{get_version('python-seispy')}"
 # The full version, including alpha/beta/rc tags
-release = 'latest'
+release = version
 
 
 # -- General configuration ---------------------------------------------------
@@ -90,7 +91,7 @@
 exclude_patterns = []
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+# pygments_style = 'sphinx'
 
 myst_heading_anchors = 3
 
@@ -101,16 +102,14 @@
 #
 
 html_baseurl = "seispy.xumijian.me"
-# html_theme = 'classic'
-html_theme = 'pydata_sphinx_theme'
+html_theme = 'furo'
+# html_theme = 'pydata_sphinx_theme'
 # html_theme_path = [lsst_dd_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
-# html_theme_options = {}
-
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
@@ -126,19 +125,24 @@
 # default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
 # 'searchbox.html']``.
 html_theme_options = {
-    "icon_links": [
-        {
-            # Label for this link
-            "name": "GitHub",
-            # URL where the link will redirect
-            "url": "https://github.com/xumi1993/seispy",  # required
-            # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
-            "icon": "fab fa-github-square",
-            # Whether icon should be a FontAwesome class, or a local file
-            # "type": "fontawesome OR local",  # Default is fontawesome
-        }
-   ]
+#     "icon_links": [
+#         {
+#             # Label for this link
+#             "name": "GitHub",
+#             # URL where the link will redirect
+#             "url": "https://github.com/xumi1993/seispy",  # required
+#             # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local")
+#             "icon": "fab fa-github-square",
+#             # Whether icon should be a FontAwesome class, or a local file
+#             # "type": "fontawesome OR local",  # Default is fontawesome
+#         }
+#    ],
+    "light_css_variables": {
+        "color-brand-primary": "#0080C4",
+        "color-brand-content": "#0080C4",
+    },
 }
+
 #
 # html_sidebars = {}
 html_favicon = os.path.abspath(os.path.join('.', '_static', 'seispy_100.png'))

source/examples/ex-harmo.md

@@ -3,7 +3,7 @@
 ## Background
 Harmonic decomposition is an effective technique to separate anisotropic and dipping components from radius and transverse RFs ([Bianchi et al., 2010](https://doi.org/10.1029/2009JB007061])). This technique not only used to estimate azimuthal crustal anisotropy and crustal layer dipping , but used to extract isotropic component of RF for 1D RF inversion. In the Seispy, the command `rfharmo` is accessible for computing the harmonic decomposition, plotting different components after the decomposition, and save the isotropic component to a local SAC file.
 
-```Code
+```
 usage: Harmonic decomposition for extracting anisotropic and isotropic features from the radial and transverse RFs [-h] [-t tb/te] [-s dt] [-o outpath] [-e enf] [-p figure_path] rfpath
 
 positional arguments:

source/index.md

@@ -5,11 +5,10 @@
 
 # Seispy Documentation
 
-[![License](https://img.shields.io/github/license/xumi1993/seispy)]()
-[![](https://img.shields.io/github/last-commit/xumi1993/seispy)]()
-[![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/xumi1993/seispy)]()
-[![GitHub repo size](https://img.shields.io/github/repo-size/xumi1993/seispy)]()
-[![DOI](https://zenodo.org/badge/41006349.svg)](https://zenodo.org/badge/latestdoi/41006349)
+![License](https://img.shields.io/github/license/xumi1993/seispy)
+![Last commit](https://img.shields.io/github/last-commit/xumi1993/seispy)
+![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/xumi1993/seispy)
+![GitHub repo size](https://img.shields.io/github/repo-size/xumi1993/seispy)
 
 [![CRV test](https://github.com/xumi1993/seispy/actions/workflows/test.yml/badge.svg?branch=dev)](https://github.com/xumi1993/seispy/actions/workflows/test.yml)
 [![codecov](https://codecov.io/gh/xumi1993/seispy/branch/dev/graph/badge.svg?token=XN3E3N6S3V)](https://codecov.io/gh/xumi1993/seispy)
@@ -26,8 +25,11 @@
 [![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 stars](https://img.shields.io/github/stars/xumi1993/seispy?style=social)]()
-[![](https://img.shields.io/github/forks/xumi1993/seispy?style=social)]()
+[![Static Badge](https://img.shields.io/badge/DOI-10.1785%2F0220220288-pink)](https://doi.org/10.1785/0220220288)
+
+[![GitHub stars](https://img.shields.io/github/stars/xumi1993/seispy?style=social)](https://github.com/xumi1993/seispy)
+[![](https://img.shields.io/github/forks/xumi1993/seispy?style=social)](https://github.com/xumi1993/seispy)
+
 
 Seispy is a graphical interface Python module for receiver function (RF) calculation and post-processing in seismological research. Automated workflows of RF calculations facilitate processing large volumes of different types of seismic data. The graphic user interface enables an intuitive and straightforward evaluation of RF quality control. Seispy contains the basic RF-based methods. Five main modules for the post-processing of RF are H-k stacking, crustal anisotropic estimation, harmonic decomposition, 2D and 3D common conversion point (CCP) stacking. The CCP staking in the different application scenarios can be handled by rich modules, such as time-to-depth conversion, 2D or 3D CCP stacking, and adaptive station or bin selection for CCP stacking profiles in a dense seismic array or a linear seismic array. As a Python module, functions in the Seispy can be called easily in python scripts for other purposes. The modular design allows new functionality to be added in a collaborative development environment. Seispy licensed under GPLv3 can be open accessed on [Github repository](https://github.com/xumi1993/seispy).
 
@@ -56,7 +58,8 @@ Further details are available in the [Installation Guide](installation).
 Users using Seispy in their research please cite our peer-reviewed journal article in manuscripts
 
 ```{admonition} Reference
-Mijian Xu, Jing He; Seispy: Python Module for Batch Calculation and Postprocessing of Receiver Functions. *Seismological Research Letters* 2022; doi: [https://doi.org/10.1785/0220220288](https://doi.org/10.1785/0220220288)
+Mijian Xu, Jing He; Seispy: Python Module for Batch Calculation and Postprocessing of Receiver Functions. *Seismological Research Letters* 2022; [![Static Badge](https://img.shields.io/badge/DOI-10.1785%2F0220220288-pink)](https://doi.org/10.1785/0220220288)
+
 ```
 
 
@@ -115,6 +118,15 @@ notes/index
 modules
 :::
 
+```{toctree}
+:caption: Project Links
+:hidden:
+
+GitHub <https://github.com/xumi1993/seispy>
+GitLab <https://gitlab.com/xumi1993/seispy>
+Anaconda <https://anaconda.org/conda-forge/seispy>
+PyPI <https://pypi.org/project/python-seispy/>
+```
 
 ## References
 

source/modules.rst

@@ -1,11 +1,9 @@
 Module Index
-======
+============
 
 .. toctree::
    :maxdepth: 2
 
    rf
    post
    ccp
-   .. gui
-   .. seispy

source/post.rst

@@ -1,6 +1,14 @@
 Post-processing package
 ====================
 
+seispy.core.depmodel module
+---------------------------
+
+.. automodule:: seispy.core.depmodel
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 seispy.hk module
 ----------------
 

source/usage/ccp.rst

@@ -165,7 +165,7 @@ The output structure would be saved as a ``.npy`` file, which can be read with `
 
 .. note::
 
-  The layer_num was determined by field ``[depth]`` in parameter file.
+  The ``layer_num`` was determined by field ``[depth]`` in parameter file.
 
 CCP Stack PRFs along a profile
 ================================

source/usage/pickrf.md

@@ -42,7 +42,9 @@ When you have selected all PRFs, please click `finish` button to delete all 'poo
 - Magnitude
 - Gaussian factor
 
+```{note}
 This list file is **very important** for derived method such as H-k stacking and CCP stacking.
+```
 
 ## Other functions