make style

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401, E402
+max-line-length = 88
+max-complexity = 60
+select = B,C,E,F,W,T4,B9

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,67 @@
+name: Publish to PyPI
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.9', '3.10', '3.11']
+        include:
+          - os: ubuntu-latest
+            cc: gcc
+            cxx: g++
+            label: linux-64
+          - os: macos-latest
+            cc: clang
+            cxx: clang++
+            label: osx-64
+          - os: windows-latest
+            cc: cl
+            cxx: cl
+            label: win-64
+
+    name: ${{ matrix.label }}-Python-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup Poetry in Conda Environment
+        uses: snok/install-poetry@v1
+        with:
+          version: latest
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      - name: Cache Poetry Env
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: poetry-${{ runner.os }}-python${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install Poetry Dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction
+
+      - name: Build and Publish
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" && "${{ matrix.python-version }}" == "3.11" ]]; then
+            poetry build
+          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+            poetry build -f wheel
+          elif [[ "${{ matrix.os }}" == "windows-latest" ]]; then
+            poetry build -f wheel
+          fi
+          poetry config pypi-token.pypi ${{ secrets.PYPI_TOKEN_SEISOPT }}
+          poetry publish

.github/workflows/publish-to-test-pypi.yml

@@ -0,0 +1,69 @@
+name: Publish to Test PyPI
+
+on:
+  push:
+    branches:
+      - 'test/**'
+
+jobs:
+  testpypi:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.9', '3.10', '3.11']
+        include:
+          - os: ubuntu-latest
+            cc: gcc
+            cxx: g++
+            label: linux-64
+          - os: macos-latest
+            cc: clang
+            cxx: clang++
+            label: osx-64
+          - os: windows-latest
+            cc: cl
+            cxx: cl
+            label: win-64
+
+    name: ${{ matrix.label }}-Python-${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup Poetry in Conda Environment
+        uses: snok/install-poetry@v1
+        with:
+          version: latest
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      - name: Cache Poetry Env
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: poetry-${{ runner.os }}-python${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install Poetry Dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction
+
+      - name: Build and Publish
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" && "${{ matrix.python-version }}" == "3.11" ]]; then
+            poetry build
+          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+            poetry build -f wheel
+          elif [[ "${{ matrix.os }}" == "windows-latest" ]]; then
+            poetry build -f wheel
+          fi
+          poetry config repositories.test-pypi https://test.pypi.org/legacy/
+          poetry publish --repository test-pypi --username __token__ --password ${{ secrets.TEST_PYPI_TOKEN_SEISOPT }}

.github/workflows/sphinx.yml

@@ -0,0 +1,32 @@
+name: Sphinx
+on:
+  push:
+    branches:
+      - main
+jobs:
+  sphinx:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+      - name: run doc
+        run: |
+          pip install poetry-core@https://github.com/python-poetry/poetry-core/archive/refs/tags/1.6.1.zip
+          pip install numpy obspy scipy matplotlib
+          pip install . --no-build-isolation
+          pip install sphinx pydata-sphinx-theme sphinx-autoapi jupyter-sphinx sphinx-copybutton
+          cd docs
+          make html
+          echo "yinfu.info" > _build/html/CNAME
+          cd ..
+      - name: push to github page
+        if: ${{ !env.ACT }}
+        uses: peaceiris/actions-gh-pages@v3.9.3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./docs/_build/html
+          user_name: "github-actions[bot]"
+          user_email: "github-actions[bot]@users.noreply.github.com"

.github/workflows/workflow.yml

@@ -0,0 +1,54 @@
+name: seisopt
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  code-coverage:
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          version: latest
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      - name: Load Cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+
+      - name: Install Dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+
+      - name: build and publish
+        run: poetry build
+
+      - name: Generate Coverage Report
+        run: |
+          pip install pytest
+          pip install pytest-cov
+          pytest --cov=./seisopt --cov-report=xml
+
+      - name: Upload Coverage Reports to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN_SEISOPT }}
+          env_vars: OS
+          fail_ci_if_error: false
+          verbose: true

.gitignore

@@ -1,3 +1,8 @@
+# ShakeFlow
+.DS_Store
+.vscode/*
+setup.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: mixed-line-ending
+        args: ['--fix=lf']
+-   repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+    -   id: black
+-   repo: https://github.com/PyCQA/flake8
+    rev: 3.8.3
+    hooks:
+    -   id: flake8
+        additional_dependencies:
+          - flake8-black
+          - flake8-breakpoint
+          - flake8-docstrings
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        args: ["--profile", "black"]
+      - id: isort
+        name: isort (cython)
+        types: [cython]
+      - id: isort
+        name: isort (pyi)
+        types: [pyi]
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.6.1
+  hooks:
+    - id: nbstripout

README.md

@@ -1,2 +1,12 @@
 # seisopt
-Seismology optimize approaches
+
+[![Actions Status](https://github.com/shakeflow/seisopt/actions/workflows/workflow.yml/badge.svg)](https://github.com/shakeflow/seisopt/actions)
+[![coverage](https://codecov.io/gh/shakeflow/seisopt/branch/main/graph/badge.svg)](https://codecov.io/gh/shakeflow/seisopt)
+[![docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://shakeflow.github.io/seisopt/)
+[![supported versions](https://img.shields.io/pypi/pyversions/seisopt.svg?label=python_versions)](https://pypi.python.org/pypi/seisopt)
+[![docs](https://badge.fury.io/py/seisopt.svg)](https://badge.fury.io/py/seisopt)
+
+
+Seismology optimize approaches.
+
+## License

benchmarks/run.py

@@ -0,0 +1 @@
+import numpy as np

codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  status:
+    project: off
+    patch: off
+
+ignore:
+  - "seisopt/tests/*"
+
+comment: true