Merge pull request #118 from Serapieum-of-alex/refactor-rename

Clean up

Author: MAfarrag

.coveralls.yml

@@ -1,5 +1,5 @@
 [flake8]
-ignore = E203, E266, E501, W503, C901, E722, E731, W605, E712, F841, D202
+ignore = E203, E266, E501, W503, C901, E722, E731, W605, E712, F841, D202, D203
 max-line-length = 88
 max-complexity = 18
 select = B,C,E,F,W,T4

.flake8

@@ -55,6 +55,6 @@ jobs:
       - name: Generate coverage report
         run: |
           python -m pytest -vvv --cov=Hapi --cov-report=xml
-          
+
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v3

.github/workflows/ubuntu.yml

@@ -1,85 +1,114 @@
+fail_fast: true
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v2.3.0
-  hooks:
-    - id: end-of-file-fixer
-      name: "[py -  check] validate yaml"
-    - id: trailing-whitespace
-      name: "[file - format] trim trailing whitespace"
-      args: [ --markdown-linebreak-ext=md ]
-    -   id: check-added-large-files
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: end-of-file-fixer
+        name: "[py -  check] validate yaml"
+      - id: trailing-whitespace
+        name: "[file - format] trim trailing whitespace"
+        args: [ --markdown-linebreak-ext=md ]
+      - id: check-added-large-files
         name: "[file -  check] large file"
         args: [ --maxkb=5000 ]
-    -   id: check-docstring-first
+      - id: check-docstring-first
         name: "[py   -  check] docstring first"
         files: /examples
         types : [file, python ]
-    -   id: check-json
+      - id: check-json
         name: "[json -  check] validate json"
-    -   id: check-merge-conflict
+      - id: check-merge-conflict
         name: "[git  -  check] merge conflict"
-    -   id: debug-statements
+      - id: debug-statements
         name: "[py   -  check] debug statements"
-    -   id: detect-private-key
+      - id: detect-private-key
         name: "[cred -  check] private keys"
-    -   id: fix-encoding-pragma
+      - id: fix-encoding-pragma
         name: "[file - format] coding pragma"
         args: [ --remove ]
-    -   id: mixed-line-ending
+      - id: mixed-line-ending
         name: "[file - format] mixed line ending"
         args: [ --fix=auto ]
-    -   id: pretty-format-json
+      - id: pretty-format-json
         name: "[json - format] pretty json"
         args: [ --autofix,
                 --indent=4,
                 --no-sort-keys ]
-    -   id: requirements-txt-fixer
+      - id: requirements-txt-fixer
         name: "[reqs - format] fix requirements.txt"
-    -   id: check-yaml
+      - id: check-yaml
         name: "[yaml -  check] validate yaml"
-- repo: https://github.com/PyCQA/docformatter
-  rev: v1.4
-  hooks:
-    - id: docformatter
-      name: "[py   - format] docformatter"
-      args: [ -i, --wrap-summaries, "0" ]
+#  - repo: https://github.com/pre-commit/mirrors-isort
+#    rev: v5.10.1
+#    hooks:
+#      - id: isort
+#        name: "[py   - format] isort"
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.4
+    hooks:
+      - id: docformatter
+        name: "[py   - format] docformatter"
+        args: [ -i, --wrap-summaries, "0" ]
 
-- repo: https://github.com/PyCQA/pydocstyle
-  rev: 6.1.1
-  hooks:
-    - id: pydocstyle
-      name: "[py   - check] pydocstyle"
-      files: ^Hapi/
+  - repo: https://github.com/PyCQA/pydocstyle
+    rev: 6.1.1
+    hooks:
+      - id: pydocstyle
+        name: "[py   - check] pydocstyle"
+        files: ^Hapi/
 
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.4
-  hooks:
-    - id: flake8
-      name: "[py   - check] flake8"
-      language_version: python3.9
-      exclude: ^(examples/|tests/)
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        name: "[py   - check] flake8"
+        language_version: python3.9
+        exclude: ^(examples/|tests/)
 
-- repo: https://github.com/psf/black
-  rev: 22.8.0
-  hooks:
-    - id: black
-- repo: https://github.com/pre-commit/mirrors-isort
-  rev: v5.7.0
-  hooks:
-    - id: isort
-      name: "[py   - format] isort"
-- repo: https://github.com/ambv/black
-  rev: 22.8.0
-  hooks:
-    - id: black
-      name: "[py   - format] black"
-      language_version: python3.9
+  #- repo: https://github.com/psf/black
+  #  rev: 22.8.0
+  #  hooks:
+  #    - id: black
+  - repo: https://github.com/ambv/black
+    rev: 22.8.0
+    hooks:
+      - id: black
+        name: "[py   - format] black"
+        language_version: python3.9
+  - repo: https://github.com/lovesegfault/beautysh
+    rev: v6.2.1
+    hooks:
+      - id: beautysh
+        name: "[bash - format] beautysh"
 
-- repo: local
-  hooks:
-    - id: pytest-check
-      name: pytest-check
-      entry: pytest -vvv --cov=Hapi
-      language: system
-      pass_filenames: false
-      always_run: true
+  # pre-commit-shell: Checks shell scripts against shellcheck.
+  - repo: https://github.com/detailyang/pre-commit-shell
+    rev: v1.0.6
+    hooks:
+      - id: shell-lint
+        name: "[bash -   lint] shell-lint"
+
+  - repo: https://github.com/rlindsgaard/pre-commit-commit-msg-hooks
+    rev: 0.1.0
+    hooks:
+      - id: check-description-max-length
+        name: "[bash -   format] check-description-max-length"
+      - id: check-second-line-empty
+        name: "[bash -   format] check-second-line-empty"
+      - id: check-summary-capitalized
+        name: "[bash -   format] check-summary-capitalized"
+      - id: check-summary-imperative
+        name: "[bash -   format] check-summary-imperative"
+      - id: check-summary-max-length
+        name: "[bash -   format] check-summary-max-length"
+      - id: check-summary-punctuation
+        name: "[bash -   format] check-summary-punctuation"
+
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: pytest-check
+        entry: pytest -vvv --cov=Hapi
+        language: system
+        pass_filenames: false
+        always_run: true

.pre-commit-config.yaml

@@ -1,2 +1,2 @@
 [pydocstyle]
-ignore = D202, D413, D417, D107, D213
+ignore = D202, D413, D417, D107, D213, D203

.pydocstyle

@@ -40,4 +40,12 @@ History
 ------------------
 * hydraulic model can read chunked big zip file
 * fix CI
-* fix missing module (saint venant script and module)
+* fix missing module (saint venant script and module)
+
+1.6.0 (2023-02-03)
+------------------
+* all attributes follows snake case naming convention
+* refactor all modules with pre-commit
+* add smoothDikeLevel, getReach and updateReach
+* bump up denpendencies versions
+* move un-necessary functions to serapeum-utils

HISTORY.rst

@@ -3,9 +3,11 @@
 @author: Mostafa
 """
 try:
-    from importlib.metadata import PackageNotFoundError, version  # type: ignore
+    from importlib.metadata import PackageNotFoundError  # type: ignore
+    from importlib.metadata import version
 except ImportError:  # pragma: no cover
-    from importlib_metadata import PackageNotFoundError, version  # type: ignore
+    from importlib_metadata import PackageNotFoundError  # type: ignore
+    from importlib_metadata import version
 
 
 try:
@@ -37,6 +39,7 @@
 
 
 def configuration(parent_package="", top_path=None):
+    """configure."""
     from numpy.distutils.misc_util import Configuration
 
     config = Configuration(None, parent_package, top_path)

Hapi/__init__.py

@@ -27,9 +27,14 @@
 
 
 class Catchment:
-    """Catchment. The class include methods to read the meteorological and Spatial inputs of the distributed hydrological model. Catchment class also reads the data of the gauges, it is a super class that has the run subclass, so you need to build the catchment object and hand it as an inpit to the Run class to run the model.
+    """Catchment.
 
-    methods:
+        The class include methods to read the meteorological and Spatial inputs of the distributed hydrological model.
+        Catchment class also reads the data of the gauges, it is a super class that has the run subclass,
+        so you need to build the catchment object and hand it as an inpit to the Run class to run the model.
+
+    Methods
+    -------
         1-readRainfall
         2-readTemperature
         3-readET
@@ -375,7 +380,9 @@ def readFlowAcc(self, Path: str):
         logger.debug("Flow Accmulation input is read successfully")
 
     def readFlowDir(self, Path: str):
-        """readFlowDir method reads the flow direction raster.
+        """Read Flow Direction.
+
+            reads the flow direction raster.
 
         Parameters
         ----------
@@ -428,7 +435,9 @@ def readFlowDir(self, Path: str):
         logger.debug("Flow Direction input is read successfully")
 
     def ReadFlowPathLength(self, Path: str):
-        """ReadFlowPathLength method reads the flow path length.
+        """Read Flow Path Length method.
+
+            reads the flow path length.
 
         Parameters
         ----------
@@ -981,7 +990,9 @@ def plotHydrograph(
         label: str = "",
         fmt: str = "%Y-%m-%d",
     ):
-        """plotHydrograph. plot the simulated and gauge hydrograph.
+        r"""Plot Hydrograph.
+
+            plot the simulated and gauge hydrograph.
 
         Parameters
         ----------
@@ -1143,7 +1154,7 @@ def plotDistributedResults(
                 size of the numbers plotted intop of each cells. The default is 8.
             Title : [str], optional
                 title of the plot. The default is 'Total Discharge'.
-            titlesize : [integer], optional
+            title_size : [integer], optional
                 title size. The default is 15.
             Backgroundcolorthreshold : [float/integer], optional
                 threshold value if the value of the cell is greater, the plotted
@@ -1427,9 +1438,15 @@ def ListAttributes(self):
 
 
 class Lake:
-    """Lake. Lake class reads the meteorological inputs, and the module to simulate a lake as a lumped model, using a rating curve, the lake and the upstream sub-catchments are going to be considered as one lumped model than result in a discharge input to the lake, the discharge input is going to change the volume of the water in the lake, and from the volume-outflow curve the outflow can be obtained.
+    """Lake.
+
+        Lake class reads the meteorological inputs, and the module to simulate a lake as a lumped model, using a
+        rating curve, the lake and the upstream sub-catchments are going to be considered as one lumped model than
+        result in a discharge input to the lake, the discharge input is going to change the volume of the water in
+        the lake, and from the volume-outflow curve the outflow can be obtained.
 
-    methods:
+    Methods
+    -------
         1- readMeteoData
         2- readParameters
         3- readLumpedModel

Hapi/catchment.py

@@ -1,7 +1,6 @@
+"""Custom warning and silencing warnings."""
 import warnings
 
-import numpy as np
-
 
 class InstabilityWarning(UserWarning):
     """Issued when results may be unstable."""
@@ -13,9 +12,11 @@ class InstabilityWarning(UserWarning):
 warnings.simplefilter("always", UserWarning)
 
 
-def SilenceNumpyWarning():
-    np.warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning)
+def SilencePandasWarning():
+    """Silence pandas future warning."""
+    warnings.simplefilter(action="ignore", category=FutureWarning)
 
 
 def SilenceShapelyWarning():
+    """Silence Shapely deprecation warning."""
     warnings.filterwarnings("ignore", category=DeprecationWarning)