chores: dependencies and tests (#96)

* fixing tests

* ci: upd dependecies

* update README

Co-authored-by: Marius Isken <[email protected]>

.github/workflows/build-wheels.yaml

@@ -21,7 +21,7 @@ jobs:
 
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.8.1
+        uses: pypa/cibuildwheel@v2.11.4
         # to supply options, put them in 'env', like:
         env:
           CIBW_ARCHS_MACOS: x86_64 universal2
@@ -60,7 +60,7 @@ jobs:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.5.0
+      - uses: pypa/gh-action-pypi-publish@v1.6.2
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -1,23 +1,25 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.3.0
+  rev: v4.3.0
   hooks:
   - id: check-added-large-files
   - id: check-yaml
+  - id: check-toml
+  - id: check-json
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.1.0
+  rev: v2.2.2
   hooks:
   - id: codespell
-    args: [--write-changes, "-L ure,nd,ue,parms,Ue"]
+    args: [--write-changes, "-L ure,nd,ue,parms,Ue,lamda"]
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.11.4
   hooks:
   - id: isort
     name: isort (python)
     args: [--profile, black]
 - repo: https://github.com/psf/black
-  rev: 22.6.0
+  rev: 22.12.0
   hooks:
   - id: black

README.md

@@ -15,7 +15,15 @@ Install from pip:
 ```sh
 pip install kite
 ```
+
+With additional gdal dependency, used for GeoTIFF (GACOS and LiCSAR):
+
+```sh
+pip install kite[gdal]
+```
+
 ## Introduction
+
 This framework is streamlining InSAR displacement processing routines for earthquake inversion through [Pyrocko](https://www.pyrocko.org) and Grond.
 
 Kite features simple and efficient handling of displacement data:
@@ -27,16 +35,19 @@ Kite features simple and efficient handling of displacement data:
 * **APS removal** from [GACOS](http://ceg-research.ncl.ac.uk/v2/gacos/) atmoshperic models and empirical elevation correlation
 
 ## Citation
+
 Recommended citation for Kite
 
-> Isken, Marius; Sudhaus, Henriette; Heimann, Sebastian; Steinberg, Andreas; Daout, Simon; Vasyura-Bathke, Hannes (2017): Kite - Software for Rapid Earthquake Source Optimisation from InSAR Surface Displacement. V. 0.1. GFZ Data Services. http://doi.org/10.5880/GFZ.2.1.2017.002
+> Isken, Marius; Sudhaus, Henriette; Heimann, Sebastian; Steinberg, Andreas; Daout, Simon; Vasyura-Bathke, Hannes (2017): Kite - Software for Rapid Earthquake Source Optimisation from InSAR Surface Displacement. V. 0.1. GFZ Data Services. <http://doi.org/10.5880/GFZ.2.1.2017.002>
 
 [![DOI](https://img.shields.io/badge/DOI-10.5880%2FGFZ.2.1.2017.002-blue.svg)](http://doi.org/10.5880/GFZ.2.1.2017.002)
 
 # Documentation
-Find the documentation at https://pyrocko.org/kite/docs/current/.
+
+Find the documentation at <https://pyrocko.org/kite/docs/current/>.
 
 ## Short Example
+
 ```python
 from kite import Scene
 

docs/source/tools/talpa.rst

@@ -13,7 +13,7 @@ Examples for a programmatic interaction with the sandbox can be found :doc:`/exa
 Available Static Displacement Sources
 -------------------------------------
 
-The :mod:`~kite.SandboxScene` can hosts different types of displacement source by levering different processing engines, analytical and numerical. The different types of dispalcement source can be mixed within a single sandbox
+The :mod:`~kite.SandboxScene` can hosts different types of displacement source by levering different processing engines, analytical and numerical. The different types of displacement source can be mixed within a single sandbox
 
 1. Okada Source
 ~~~~~~~~~~~~~~~~

kite/aps.py

@@ -1,4 +1,4 @@
-import numpy as num
+import numpy as np
 from pyrocko.guts import Tuple
 from scipy import stats
 
@@ -26,7 +26,7 @@ def get_patch_coords(self):
         if self.config.patch_coords is None:
             frame = self.scene.frame
             scene = self.scene
-            rstate = num.random.RandomState(123)
+            rstate = np.random.RandomState(123)
 
             while True:
                 llE = rstate.uniform(0, frame.lengthE * (4 / 5))
@@ -38,7 +38,7 @@ def get_patch_coords(self):
                 rowmin, rowmax = frame.mapENMatrix(llN, llN + urN)
 
                 displacement = scene._displacement[rowmin:rowmax, colmin:colmax]
-                if num.any(displacement):
+                if np.any(displacement):
                     return llE, llN, urE, urN
 
         return self.config.patch_coords
@@ -55,7 +55,7 @@ def get_data(self):
         displacement = scene._displacement[rowmin:rowmax, colmin:colmax]
         elevation = self.get_elevation()[rowmin:rowmax, colmin:colmax]
 
-        mask = num.isfinite(displacement)
+        mask = np.isfinite(displacement)
         elevation = elevation[mask]
         displacement = displacement[mask]