modernize repo

.github/workflows/ci.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/doc.yml

@@ -0,0 +1,35 @@
+name: Build documentation
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  docs:
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: nschloe/action-cached-lfs-checkout@v1
+      - uses: actions/setup-python@v4
+        with:
+            python-version: '3.9'
+      - name: Install toughio
+        run: |
+          git lfs pull
+          pip install -e .[full]
+      - name: Install dependencies
+        run: |
+          pip install -r doc/requirements.txt
+      - name: Sphinx build
+        run: |
+          sphinx-build -b html doc/source doc/build
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: doc/build/
+          force_orphan: true

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "esbonio.sphinx.confDir": ""
+}

doc/requirements.txt

@@ -4,4 +4,4 @@ sphinx-argparse
 sphinx-gallery
 pydata-sphinx-theme
 sphinxcontrib-bibtex
--e git://github.com/Naeka/pybtex-apa-style.git#egg=pybtex-apa-style
+pybtex-apa-style

evodcinv/VERSION

@@ -0,0 +1 @@
+2.1.0

evodcinv/__about__.py

@@ -1,9 +1,9 @@
-try:
-    from importlib import metadata
-except ImportError:
-    import importlib_metadata as metadata
+import pathlib
 
-try:
-    __version__ = metadata.version("evodcinv")
-except Exception:
-    __version__ = "unknown"
+__all__ = [
+    "__version__",
+]
+
+
+with open(f"{pathlib.Path(__file__).parent}/VERSION") as f:
+    __version__ = f.readline().strip()

evodcinv/_io/h5/_h5.py

@@ -42,7 +42,11 @@ def write(filename, result, compression_opts=4):
     with h5py.File(filename, "w") as f:
         for k, v in result.items():
             if np.ndim(v) == 0:
-                f.create_dataset(k, data=(v,), compression="gzip", compression_opts=compression_opts)
+                f.create_dataset(
+                    k, data=(v,), compression="gzip", compression_opts=compression_opts
+                )
 
             else:
-                f.create_dataset(k, data=v, compression="gzip", compression_opts=compression_opts)
+                f.create_dataset(
+                    k, data=v, compression="gzip", compression_opts=compression_opts
+                )

evodcinv/_model.py

@@ -369,7 +369,11 @@ def _misfit_function(self, x, curves):
 
                 else:
                     ell = Ellipticity(
-                        thickness, velocity_p, velocity_s, density, dc=dc,
+                        thickness,
+                        velocity_p,
+                        velocity_s,
+                        density,
+                        dc=dc,
                     )
                     rel = ell(curve.period, mode=curve.mode)
                     dcalc = np.abs(rel.ellipticity)

evodcinv/_result.py

@@ -230,7 +230,12 @@ def get_y(thickness, velocity_p, velocity_s, density):
 
             def get_y(thickness, velocity_p, velocity_s, density):
                 ell = Ellipticity(
-                    thickness, velocity_p, velocity_s, density, "dunkin", dc,
+                    thickness,
+                    velocity_p,
+                    velocity_s,
+                    density,
+                    "dunkin",
+                    dc,
                 )
                 rel = ell(period, mode)
 

requirements-dev.txt

@@ -1,6 +1,8 @@
 black
+build
 docformatter
 invoke
 isort
 pytest
-pytest-cov
+pytest-cov
+twine

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = evodcinv
-version = 2.0.1
+version = file: evodcinv/VERSION
 author = Keurfon Luu
 email = keurfonluu@outlook.com
 description = Inversion of dispersion curves using Evolutionary Algorithms
@@ -19,10 +19,11 @@ classifiers =
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Physics
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
 
 [options]
 packages = find:
@@ -34,8 +35,12 @@ install_requires =
     h5py
     progress
     disba >= 0.6.1
-    stochopy >= 2.2.0
-python_requires = >= 3.6
+    stochopy >= 2.3.0
+python_requires = >= 3.7
 setup_requires =
     setuptools >= 42
-    wheel
+    wheel
+
+[options.package_data]
+evodcinv =
+    VERSION

tasks.py

@@ -13,6 +13,11 @@ def build(c):
     c.run("python -m build --sdist --wheel .")
 
 
+@task
+def html(c):
+    c.run("sphinx-build -b html doc/source doc/build")
+
+
 @task
 def tag(c):
     c.run("git tag v{}".format(evodcinv.__version__))
@@ -30,6 +35,8 @@ def clean(c, bytecode=False):
         "build",
         "dist",
         "evodcinv.egg-info",
+        "doc/build",
+        "doc/source/examples",
     ]
 
     if bytecode:
@@ -45,8 +52,8 @@ def clean(c, bytecode=False):
 
 @task
 def black(c):
-    c.run("black -t py36 evodcinv")
-    c.run("black -t py36 test")
+    c.run("black -t py38 evodcinv")
+    c.run("black -t py38 tests")
 
 
 @task
@@ -57,7 +64,7 @@ def docstring(c):
 @task
 def isort(c):
     c.run("isort evodcinv")
-    c.run("isort test")
+    c.run("isort tests")
 
 
 @task

test/helpers.py → tests/helpers.py

@@ -35,5 +35,9 @@
     optimizer="cpso",
     misfit="rmse",
     density="nafe-drake",
-    optimizer_args={"popsize": 5, "maxiter": 5, "seed": 0,},
+    optimizer_args={
+        "popsize": 5,
+        "maxiter": 5,
+        "seed": 0,
+    },
 )