Merge pull request #87 from xumi1993/dev

Dev

.github/workflows/doc_build.yml

@@ -5,34 +5,36 @@ name: Seispy docs
 
 on:
   push:
-    branches: [ docs ]
+    branches: [ docs, dev ]
   pull_request:
     branches: [ master ]
-  workflow_call:
-    inputs:
-      config-path:
-        required: true
-        type: string
-    secrets:
-      token:
-        required: true
 
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  deploy:
+  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
 
@@ -41,20 +43,60 @@ jobs:
         with:
           activate-environment: docs
           environment-file: environment.yml
-          miniforge-variant: Mambaforge
-          use-mamba: true
-
+          # 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
           user_name: 'github-actions[bot]'
-          user_email: 'github-actions[bot]@users.noreply.github.com'
+          user_email: 'github-actions[bot]@users.noreply.github.com'

seispy/ccpprofile.py

@@ -24,6 +24,7 @@ def _prof_range(lat, lon):
 
 def create_center_bin_profile(stations, val=5, method='linear'):
     """Create bins along a profile with given stations
+
     :param stations: Stations along a profile
     :type stations: :class:`seispy.rf2depth_makedata.Station`
     :param val: The interval between two points in km
@@ -109,6 +110,7 @@ def init_profile(lat1, lon1, lat2, lon2, val):
 class CCPProfile():
     def __init__(self, cfg_file=None, log:SetupLog=SetupLog()):
         """CCPProfile class for CCP stacking along a profile
+
         :param cfg_file: Configure file for CCP stacking
         :type cfg_file: str
         :param log: Log class for logging
@@ -118,12 +120,12 @@ def __init__(self, cfg_file=None, log:SetupLog=SetupLog()):
         if cfg_file is None:
             self.cpara = CCPPara()
         elif isinstance(cfg_file, str):
-            self.load_para(cfg_file)
+            self._load_para(cfg_file)
         else:
             raise ValueError('cfg_file must be str format.')
         self.stack_data = []
 
-    def load_para(self, cfg_file):
+    def _load_para(self, cfg_file):
         try:
             self.cpara = ccppara(cfg_file)
         except Exception as e:
@@ -277,12 +279,19 @@ def stack(self):
             self.stack_data.append(boot_stack)   
 
     def save_stack_data(self, format='npz'):
-        """If format is \'npz\', saving stacked data and parameters to local as a npz file. To load the file, please use data = np.load(fname, allow_pickle=True).
-        data['cpara'] is the parameters when CCP stacking.
-        data['stack_data'] is the result of stacked data.
+        """If format is ``npz``, saving stacked data and parameters to local as a npz file. To load the file, please use data = np.load(fname, allow_pickle=True).
+        ``data['cpara']`` is the parameters when CCP stacking.
+        ``data['stack_data']`` is the result of stacked data.
 
-        If format is \'dat\' the stacked data will be save into a txt file with 8 columns, including bin_lat, bin_lon, profile_dis, depth, amp, ci_low, ci_high and count.
-        where bin_lat and bin_lon represent the position of each bin; profile_dis represents the distance in km between each bin and the start point of the profile; depth represents depth of each bin; amp means the stacked amplitude; ci_low and ci_high mean confidence interval with bootstrap method; count represents stacking number of each bin.
+        If format is ``dat`` the stacked data will be save into a txt file with 8 columns,
+        including ``bin_lat``, ``bin_lon``, ``profile_dis``, ``depth``, ``amp``, ``ci_low``, ``ci_high`` and ``count``.
+        
+        - ``bin_lat`` and ``bin_lon`` represent the position of each bin; 
+        - ``profile_dis`` represents the distance in km between each bin and the start point of the profile;
+        - ``depth`` represents depth of each bin;
+        - ``amp`` means the stacked amplitude; 
+        - ``ci_low`` and ``ci_high`` mean confidence interval with bootstrap method;
+        - ``count`` represents stacking number of each bin.
 
         :param format: Format for stacked data
         :type format: str

seispy/core/RFStation.py

@@ -25,6 +25,9 @@
 class Trace_Clust(UserList):
     """
     user can accese traces from self.data or like a default list
+
+    .. rubric:: Example
+    
     >>> st= obspy.read();tt=Trace_Clust()
     >>> for _i in st:
     ...   _i.stats.sac ={};