Merge pull request #159 from GeoStat-Framework/pylint_fixes

Pylint fixes

.github/workflows/main.yml

@@ -14,8 +14,8 @@ on:
   workflow_dispatch:
 
 jobs:
-  format_check:
-    name: format check
+  source_check:
+    name: source check
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -31,12 +31,17 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black
+          pip install black pylint
+          pip install --editable .
 
       - name: black check
         run: |
           python -m black --check .
 
+      - name: pylint check
+        run: |
+          python -m pylint gstools/
+
   build_wheels:
     name: wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}

CHANGELOG.md

@@ -39,7 +39,7 @@ All notable changes to **GSTools** will be documented in this file.
 #### Directional Variograms and Auto-binning ([#87](https://github.com/GeoStat-Framework/GSTools/issues/87), [#106](https://github.com/GeoStat-Framework/GSTools/issues/106), [#131](https://github.com/GeoStat-Framework/GSTools/issues/131))
 - new routine name `vario_estimate` instead of `vario_estimate_unstructured` (old kept for legacy code) for simplicity
 - new routine name `vario_estimate_axis` instead of `vario_estimate_structured` (old kept for legacy code) for simplicity
-- **`vario_estimate`**
+- **vario_estimate**
   - added simple automatic binning routine to determine bins from given data (one third of box diameter as max bin distance, sturges rule for number of bins)
   - allow to pass multiple fields for joint variogram estimation (e.g. for daily precipitation) on same mesh
   - `no_data` option added to allow missing values
@@ -53,7 +53,7 @@ All notable changes to **GSTools** will be documented in this file.
     - prepared for nD
   - structured fields (pos tuple describes axes) can now be passed to estimate an isotropic or directional variogram
   - distance calculation in cython routines in now independent of dimension
-- **`vario_estimate_axis`**
+- **vario_estimate_axis**
   - estimation along array axis now possible in arbitrary dimensions
   - `no_data` option added to allow missing values (sovles [#83](https://github.com/GeoStat-Framework/GSTools/issues/83))
   - axis can be given by name (`"x"`, `"y"`, `"z"`) or axis number (`0`, `1`, `2`, `3`, ...)
@@ -141,6 +141,7 @@ All notable changes to **GSTools** will be documented in this file.
 - isotropic rotation of SRF was not possible [#100](https://github.com/GeoStat-Framework/GSTools/issues/100)
 - `CovModel.opt_arg` now sorted [#103](https://github.com/GeoStat-Framework/GSTools/issues/103)
 - CovModel.fit: check if weights are given as a string (numpy comparison error) [#111](https://github.com/GeoStat-Framework/GSTools/issues/111)
+- several pylint fixes ([#159](https://github.com/GeoStat-Framework/GSTools/pull/159))
 
 ## [1.2.1] - Volatile Violet - 2020-04-14
 
@@ -180,13 +181,13 @@ All notable changes to **GSTools** will be documented in this file.
 ## [1.1.1] - Reverberating Red - 2019-11-08
 
 ### Enhancements
-- added a changelog. See: [commit](https://github.com/GeoStat-Framework/GSTools/commit/fbea88300d0862393e52f4b7c3d2b15c2039498b)
+- added a changelog. See: [commit fbea883](https://github.com/GeoStat-Framework/GSTools/commit/fbea88300d0862393e52f4b7c3d2b15c2039498b)
 
 ### Changes
 - deprecation warnings are now printed if Python versions 2.7 or 3.4 are used #40 #41
 
 ### Bugfixes
-- define spectral_density instead of spectrum in covariance models since Cov-base derives spectrum. See: [commit](https://github.com/GeoStat-Framework/GSTools/commit/00f2747fd0503ff8806f2eebfba36acff813416b)
+- define spectral_density instead of spectrum in covariance models since Cov-base derives spectrum. See: [commit 00f2747](https://github.com/GeoStat-Framework/GSTools/commit/00f2747fd0503ff8806f2eebfba36acff813416b)
 - better boundaries for CovModel parameters. See: https://github.com/GeoStat-Framework/GSTools/issues/37
 
 
@@ -201,8 +202,8 @@ All notable changes to **GSTools** will be documented in this file.
 - incompressible flow fields can now be generated #14
 - new submodule providing several field transformations like: Zinn&Harvey, log-normal, bimodal, ... #13
 - Python 3.4 and 3.7 wheel support #19
-- field can now be generated directly on meshes from [meshio](https://github.com/nschloe/meshio) and [ogs5py](https://github.com/GeoStat-Framework/ogs5py), see: [commit](https://github.com/GeoStat-Framework/GSTools/commit/f4a3439400b81d8d9db81a5f7fbf6435f603cf05)
-- the srf and kriging classes now store the last ``pos``, ``mesh_type`` and ``field`` values to keep them accessible, see: [commit](https://github.com/GeoStat-Framework/GSTools/commit/29f7f1b029866379ce881f44765f72534d757fae)
+- field can now be generated directly on meshes from [meshio](https://github.com/nschloe/meshio) and [ogs5py](https://github.com/GeoStat-Framework/ogs5py), see: [commit f4a3439](https://github.com/GeoStat-Framework/GSTools/commit/f4a3439400b81d8d9db81a5f7fbf6435f603cf05)
+- the srf and kriging classes now store the last ``pos``, ``mesh_type`` and ``field`` values to keep them accessible, see: [commit 29f7f1b](https://github.com/GeoStat-Framework/GSTools/commit/29f7f1b029866379ce881f44765f72534d757fae)
 - tutorials on all important features of GSTools have been written for you guys #20
 - a new interface to pyvista is provided to export fields to python vtk representation, which can be used for plotting, exploring and exporting fields #29
 
@@ -211,8 +212,8 @@ All notable changes to **GSTools** will be documented in this file.
 - the rotation angles are now interpreted in positive direction (counter clock wise)
 - the ``force_moments`` keyword was removed from the SRF call method, it is now in provided as a field transformation #13
 - drop support of python implementations of the variogram estimators #18
-- the ``variogram_normed`` method was removed from the ``CovModel`` class due to redundance [commit](https://github.com/GeoStat-Framework/GSTools/commit/25b164722ac6744ebc7e03f3c0bf1c30be1eba89)
-- the position vector of 1D fields does not have to be provided in a list-like object with length 1 [commit](https://github.com/GeoStat-Framework/GSTools/commit/a6f5be8bfd2db1f002e7889ecb8e9a037ea08886)
+- the ``variogram_normed`` method was removed from the ``CovModel`` class due to redundance [commit 25b1647](https://github.com/GeoStat-Framework/GSTools/commit/25b164722ac6744ebc7e03f3c0bf1c30be1eba89)
+- the position vector of 1D fields does not have to be provided in a list-like object with length 1 [commit a6f5be8](https://github.com/GeoStat-Framework/GSTools/commit/a6f5be8bfd2db1f002e7889ecb8e9a037ea08886)
 
 ### Bugfixes
 - several minor bugfixes

CONTRIBUTING.md

@@ -29,8 +29,66 @@ with your idea or suggestion and we'd love to discuss about it.
 
 - Fork the repo on [GitHub](https://github.com/GeoStat-Framework/GSTools) from the [develop branch](https://github.com/GeoStat-Framework/GSTools/tree/develop).
 - Add yourself to AUTHORS.md (if you want to).
-- We use the black code format, please use the script `black --line-length 79 gstools/` after you have written your code.
+- We use the black code format, please use the script `black .` after you have written your code.
 - Add some tests if possible.
 - Add an example showing your new feature in one of the examples sub-folders if possible.
   Follow this [Sphinx-Gallary guide](https://sphinx-gallery.github.io/stable/syntax.html#embed-rst-in-your-example-python-files)
 - Push to your fork and submit a pull request.
+
+### PyLint Settings
+
+Your code will be checked by [Pylint](https://github.com/PyCQA/pylint/)
+with `pylint gstools` in the CI.
+We made some generous default settings in `pyproject.toml` for the linter:
+
+- max-args = 20
+- max-locals = 50
+- max-branches = 30
+- max-statements = 80
+- max-attributes = 25
+- max-public-methods = 75
+
+Since some classes in GSTools are quite huge and some function signatures are
+somewhat longish.
+
+By default [R0801](https://vald-phoenix.github.io/pylint-errors/plerr/errors/similarities/R0801)
+(duplicate-code) is disabled, since it produces a lot of false positive errors
+for docstrings and `__init__.py` settings.
+
+We also disabled some pylint checks for some files by setting
+comments like these at the beginning:
+```python
+# pylint: disable=C0103
+```
+
+Here is a list of the occurring disabled errors:
+- [C0103](https://vald-phoenix.github.io/pylint-errors/plerr/errors/basic/C0103)
+  (invalid-name) - `ax`, `r` etc. are marked as no valid names
+- [C0302](https://vald-phoenix.github.io/pylint-errors/plerr/errors/format/C0302)
+  (too-many-lines) - namely the `CovModel` definition has more than 1000 lines
+- [C0415](https://vald-phoenix.github.io/pylint-errors/plerr/errors/imports/C0415)
+  (import-outside-toplevel) - needed sometimes for deferred imports of optional
+  dependencies like `matplotlib`
+- [R0201](https://vald-phoenix.github.io/pylint-errors/plerr/errors/classes/R0201)
+  (no-self-use) - methods with no `self` calls in some base-classes
+- [W0212](https://vald-phoenix.github.io/pylint-errors/plerr/errors/classes/W0212)
+  (protected-access) - we didn't want to draw attention to `CovModel._prec`
+- [W0221](https://vald-phoenix.github.io/pylint-errors/plerr/errors/classes/W0221)
+  (arguments-differ) - the `__call__` methods of `SRF` and `Krige` differ from `Field`
+- [W0222](https://vald-phoenix.github.io/pylint-errors/plerr/errors/classes/W0222)
+  (signature-differ) - the `__call__` methods of `SRF` and `Krige` differ from `Field`
+- [W0231](https://vald-phoenix.github.io/pylint-errors/plerr/errors/classes/W0231)
+  (super-init-not-called) - some child classes have their specialized `__init__`
+- [W0613](https://vald-phoenix.github.io/pylint-errors/plerr/errors/variables/W0613)
+  (unused-argument) - needed sometimes to match required call signatures
+- [W0632](https://vald-phoenix.github.io/pylint-errors/plerr/errors/variables/W0632)
+  (unbalanced-tuple-unpacking) - false positive for some call returns
+- [E1101](https://vald-phoenix.github.io/pylint-errors/plerr/errors/typecheck/E1101)
+  (no-member) - some times false positive
+- [E1102](https://vald-phoenix.github.io/pylint-errors/plerr/errors/typecheck/E1102)
+  (not-callable) - this is a false-positive result form some called properties
+- [E1130](https://vald-phoenix.github.io/pylint-errors/plerr/errors/typecheck/E1130)
+  (invalid-unary-operand-type) - false positive at some points
+
+Although we disabled these errors at some points, we encourage you to prevent
+disabling errors when it is possible.

gstools/covmodel/base.py

@@ -9,8 +9,7 @@
 .. autosummary::
    CovModel
 """
-# pylint: disable=C0103, R0201, E1101
-
+# pylint: disable=C0103, R0201, E1101, C0302, W0613
 import copy
 import numpy as np
 from scipy.integrate import quad as integral
@@ -212,14 +211,12 @@ def __init_subclass__(cls):
             cls.__doc__ = "User defined GSTools Covariance-Model."
         cls.__doc__ += CovModel.__doc__[45:]
         # overridden functions get standard doc if no new doc was created
-        ignore = ["__", "variogram", "covariance", "cor"]
-        for attr in cls.__dict__:
-            if any(
-                [attr.startswith(ign) for ign in ignore]
-            ) or attr not in dir(CovModel):
+        ign = ["__", "variogram", "covariance", "cor"]
+        for att in cls.__dict__:
+            if any(att.startswith(i) for i in ign) or att not in dir(CovModel):
                 continue
-            attr_doc = getattr(CovModel, attr).__doc__
-            attr_cls = cls.__dict__[attr]
+            attr_doc = getattr(CovModel, att).__doc__
+            attr_cls = cls.__dict__[att]
             if attr_cls.__doc__ is None:
                 attr_cls.__doc__ = attr_doc
 

gstools/covmodel/fit.py

@@ -9,8 +9,7 @@
 .. autosummary::
    fit_variogram
 """
-
-# pylint: disable=C0103
+# pylint: disable=C0103, W0632
 import numpy as np
 from scipy.optimize import curve_fit
 from gstools.covmodel.tools import check_arg_in_bounds, default_arg_from_bounds
@@ -341,7 +340,7 @@ def _check_vario(model, x_data, y_data):
         raise ValueError(
             "CovModel.fit_variogram: lat-lon models don't support anisotropy."
         )
-    elif model.latlon:
+    if model.latlon:
         # convert to yadrenko model
         x_data = 2 * np.sin(x_data / 2)
     return x_data, y_data, is_dir_vario

gstools/covmodel/models.py

@@ -20,13 +20,12 @@
    SuperSpherical
    JBessel
 """
-# pylint: disable=C0103, E1101, E1137, R0201
-
+# pylint: disable=C0103, E1101, R0201
 import warnings
 import numpy as np
 from scipy import special as sps
 from gstools.covmodel.tools import AttributeWarning
-from gstools.covmodel import CovModel
+from gstools.covmodel.base import CovModel
 
 __all__ = [
     "Gaussian",