Merge pull request #50 from paudetseis/updates

- Minor update to fix numpy deprecation of np.float() to float
- Updated documentation for installation with python<=3.10
- Fixed GH actions for deployment
- New version v0.2.2

Author: paudetseis

.github/test_conda_env.yml

@@ -7,4 +7,5 @@ dependencies:
   - fortran-compiler
   # see obspy issue #2912, can be removed after obspy release 1.3.0
   - 'numpy<1.22'
+  - 'setuptools=60'
 

.github/workflows/tests.yml

@@ -1,28 +1,33 @@
 name: tests
+
+# Controls when the action will run. 
 on:
   push:
+    branches: [ master ]
   pull_request:
-    branches:
-      # only branches from forks which have the form 'user:branch-name'
-      - '**:**'
+    branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
 jobs:
   run_tests:
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ['3.7', '3.8', '3.9', '3.10']
-        include:
-          - os: macos-latest
-            python: '3.10'
+        python: ['3.10']
+        # include:
+        #   - os: macos-latest
+        #     python: '3.10'
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           python-version: ${{ matrix.python }}
           environment-file: .github/test_conda_env.yml
@@ -32,6 +37,7 @@ jobs:
           conda list
       - name: install package
         run: |
+          conda install libstdcxx-ng
           pip install -v --no-deps .
       - name: run test suite
         run: |
@@ -40,3 +46,21 @@ jobs:
           coverage xml -o ../coverage.xml
       - name: upload coverage
         uses: codecov/codecov-action@v1
+      - name: Make docs
+        if: matrix.python == '3.10' 
+        shell: bash -l {0}
+        run: |
+          cd docs
+          pip install sphinx
+          pip install sphinx_rtd_theme
+          make html
+          touch _build/html/.nojekyll
+          cd ..
+      - name: Deploy 🚀
+        if: matrix.python == '3.10' 
+        uses: JamesIves/github-pages-deploy-action@3.7.1
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages # The branch the action should deploy to.
+          FOLDER: docs/_build/html # The folder the action should deploy.
+          CLEAN: true # Automatically remove deleted files from the deploy branch

docs/conf.py

@@ -10,9 +10,9 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../.'))
 
 
 # -- Project information -----------------------------------------------------

telewavesim/__init__.py

@@ -52,18 +52,6 @@
 Installation
 ------------
 
-Dependencies
-++++++++++++
-
-The current version works well with **Python>3.5**.
-Also, the following packages are required:
-
-- `gfortran <https://gcc.gnu.org/wiki/GFortran>`_ (or any Fortran compiler)
-- `obspy <https://github.com/obspy/obspy/wiki>`_
-
-By  default, both ``numpy`` and ``matplotlib`` are installed as dependencies
-of ``obspy``.
-
 Conda environment
 +++++++++++++++++
 
@@ -73,46 +61,22 @@
 
 .. sourcecode:: bash
 
-   conda create -n tws python=3.7 obspy -c conda-forge
+   conda create -n tws -c conda-forge "python=3.10" "numpy<1.22" "setuptools=60" obspy fortran-compiler
 
 Activate the newly created environment:
 
 .. sourcecode:: bash
 
    conda activate tws
 
-Installing latest version from PyPi
-+++++++++++++++++++++++++++++++++++
-
-Install the latest version from PyPi with the following command:
-
-.. sourcecode:: bash
-
-    pip install telewavesim
-
-Installing development version from source
-++++++++++++++++++++++++++++++++++++++++++
-
-- Clone the repository:
-
-.. sourcecode:: bash
-
-   git clone https://github.com/paudetseis/Telewavesim.git
-   cd Telewavesim
+Installing development branch from GitHub
++++++++++++++++++++++++++++++++++++++++++
 
-- Install using ``pip``:
+Install the latest version from the GitHub repository with the following command:
 
 .. sourcecode:: bash
 
-   pip install .
-
-Possible installation pitfalls with conda
-+++++++++++++++++++++++++++++++++++++++++
-
-Using ``conda`` it might be necessary to use the fortran compiler provided with
-conda-forge. Add ``fortran-compiler`` package to the
-above ``conda`` environment calls.
-On Linux it might further be necessary to install the ``lapack`` conda package.
+    pip install telewavesim@git+https://github.com/paudetseis/telewavesim
 
 Testing
 +++++++
@@ -404,20 +368,20 @@
 
 """
 
-try:
-    from . import rmat_f
-except:
-    from numpy.distutils.system_info import get_info as _get_info
-    import os as _os
-    from ctypes import cdll as _cdll
+# try:
+#     from . import rmat_f
+# except:
+#     from numpy.distutils.system_info import get_info as _get_info
+#     import os as _os
+#     from ctypes import cdll as _cdll
 
-    _shared_libraries = []
+#     _shared_libraries = []
 
-    for path in _get_info('lapack')['library_dirs']:
-        for lib in _os.listdir(path):
-            if lib.startswith('lib'):
-                _slib = _cdll.LoadLibrary("{}/{}".format(path, lib))
-                _shared_libraries.append(_slib)
+#     for path in _get_info('lapack')['library_dirs']:
+#         for lib in _os.listdir(path):
+#             if lib.startswith('lib'):
+#                 _slib = _cdll.LoadLibrary("{}/{}".format(path, lib))
+#                 _shared_libraries.append(_slib)
 
 
-__version__ = '0.2.1'
+__version__ = '0.2.2'

telewavesim/utils.py

@@ -534,13 +534,13 @@ def stack_all(st1, st2, pws=False):
         weight2 += np.exp(1j*phase2)
 
     # Normalize
-    tmp1 = tmp1/np.float(len(st1))
-    tmp2 = tmp2/np.float(len(st2))
+    tmp1 = tmp1/float(len(st1))
+    tmp2 = tmp2/float(len(st2))
 
     # Phase-weighting
     if pws:
-        weight1 = weight1/np.float(len(st1))
-        weight2 = weight2/np.float(len(st2))
+        weight1 = weight1/float(len(st1))
+        weight2 = weight2/float(len(st2))
         weight1 = np.real(abs(weight1))
         weight2 = np.real(abs(weight2))
     else: