Merge pull request #115 from Serapieum-of-alex/hm-analysis

Hydraulic model analysis scripts

.github/workflows/pypi.yml

@@ -0,0 +1,30 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: pypi-package
+
+on:
+    release:
+        types: [created]
+
+jobs:
+    deploy:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v3
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.x"
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install setuptools wheel twine
+            - name: Build and publish
+              env:
+                  TWINE_USERNAME: ${{ secrets.PYPI_USERS }}
+                  TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+              run: |
+                  python setup.py sdist bdist_wheel
+                  twine upload dist/*

.github/workflows/ubuntu.yml

@@ -33,18 +33,16 @@ jobs:
         run: |
             python -c "from osgeo import gdal"
             gdalinfo --version
-      - name: libgeo and cartopy
+      - name: libgeos and cartopy
         run: |
             sudo apt -y install libgeos-dev
             pip install cartopy
       - name: Install dependencies
         run: |
+            #$CONDA/bin/mamba env update --file environment.yml --name base
             pip install -r requirements.txt -r requirements-dev.txt
             python setup.py install
-#      - name: Install dependencies
-#        run: |
-#          $CONDA/bin/mamba env update --file environment.yml --name base
-#          python setup.py install
+
 #    - name: Lint with flake8
 #      run: |
 #        # add CONDA/bin/ in front of everything
@@ -53,11 +51,13 @@ jobs:
 #        $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
 #        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
 #        $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
       - name: Generate coverage report
-#        working-directory: ../
+        #working-directory: ../
         run: |
           pwd
-          python -m pytest -vvv --cov=hapi --cov-report=xml
+          ls
+          python -m pytest -vvv --cov=Hapi --cov-report=xml
 
 #      - name: Upload coverage to Codecov
 #        uses: codecov/codecov-action@v1

.gitignore

@@ -185,3 +185,4 @@ examples/Hydrodynamic models/test_case/results/USbnd/right_results/*
 examples/Hydrodynamic models/test_case/results/q/New folder/*
 examples/Hydrodynamic models/test_case/results/h/New folder/*
 examples/Hydrodynamic models/test_case/results/USbnd/New folder/*
+tests/mo/*

HISTORY.rst

@@ -25,3 +25,13 @@ History
 * fix pypi package names in the requirements.txt file for all internal packages
 * fix python version number
 * tests are all passing
+
+1.4.0 (2022-12-27)
+------------------
+
+* remove fiona and the reading file exception using fion
+* unify reading results of rainfall-runoff model in the readRRMResults, ReadLaterals, ReadUSHydrographs
+* refactor code and change methods to camelcase
+* add hydrodynamic model 1d config file read function
+* simplify functions with too many parameters using decorator
+* add automatic pypi build and publish github actions

Hapi/hm/calibration.py

@@ -1,8 +1,7 @@
 """Hydaulic model calibration related function module."""
 import datetime as dt
-from typing import Any, Union  # , Optional,Tuple,
+from typing import Any, Union
 
-import fiona
 import geopandas as gpd
 import matplotlib.pyplot as plt
 import numpy as np
@@ -167,8 +166,12 @@ def readGaugesTable(self, path: str):
         """
         try:
             self.hm_gauges = gpd.read_file(path, driver="GeoJSON")
-        except fiona.errors.DriverError:
+        except Exception as e:
+            logger.warning(
+                f"the {path} could not be opened with geopandas and will be opened with pandas instead"
+            )
             self.hm_gauges = pd.read_csv(path)
+
         # sort the gauges table based on the segment
         self.hm_gauges.sort_values(by="id", inplace=True, ignore_index=True)
 
@@ -514,7 +517,7 @@ def readRRM(
             for i in range(len(gauges)):
                 station_id = gauges[i]
                 try:
-                    self.q_rrm[station_id] = self.readRRMResults(
+                    self.q_rrm[station_id] = self._readRRMResults(
                         self.version,
                         self.rrmreferenceindex,
                         path,
@@ -533,7 +536,7 @@ def readRRM(
             for i in range(len(gauges)):
                 station_id = gauges[i]
                 try:
-                    self.q_rrm[station_id] = self.readRRMResults(
+                    self.q_rrm[station_id] = self._readRRMResults(
                         self.version,
                         self.rrmreferenceindex,
                         path,
@@ -542,7 +545,7 @@ def readRRM(
                         today,
                         date_format=fmt,
                     )[station_id].tolist()
-                    self.QRRM2[station_id] = self.readRRMResults(
+                    self.QRRM2[station_id] = self._readRRMResults(
                         self.version,
                         self.rrmreferenceindex,
                         path2,
@@ -639,7 +642,7 @@ def readHMQ(
         # fill non modelled time steps with zeros
         for i in range(len(gauges)):
             nodeid = gauges[i]
-            self.q_hm[nodeid] = self.readRRMResults(
+            self.q_hm[nodeid] = self._readRRMResults(
                 self.version,
                 self.ReferenceIndex,
                 path,
@@ -738,7 +741,7 @@ def ReadHMWL(
         self.WLHM = pd.DataFrame()
         for i in range(len(gauges)):
             nodeid = gauges[i]
-            self.WLHM[nodeid] = self.readRRMResults(
+            self.WLHM[nodeid] = self._readRRMResults(
                 self.version,
                 self.ReferenceIndex,
                 path,
@@ -1559,8 +1562,8 @@ def Metrics(
         for i in range(len(gauges)):
             start_date = Metrics.loc[gauges[i], "start"]
             end_date = Metrics.loc[gauges[i], "end"]
-            obs = df1.loc[start_date : end_date, gauges[i]].values.tolist()
-            sim = df2.loc[start_date : end_date, gauges[i]].values.tolist()
+            obs = df1.loc[start_date:end_date, gauges[i]].values.tolist()
+            sim = df2.loc[start_date:end_date, gauges[i]].values.tolist()
 
             # shift hm result
             sim[shift:-shift] = sim[0 : -shift * 2]
@@ -1629,7 +1632,7 @@ def HMvsRRM(
             right_index=True,
             how="left",
             sort=False,
-        )#.set_geometry("geometry")
+        )
         self.MetricsHMvsRRM.index = self.MetricsHMvsRRM[self.gauge_id_col]
         self.MetricsHMvsRRM.index.name = "index"
         if isinstance(self.hm_gauges, GeoDataFrame):

Hapi/hm/inputs.py

@@ -21,9 +21,10 @@
 
 
 class Inputs(River):
-    """Inputs.
+    """Hydraulic model Inputs class.
 
     Methods
+    -------
         1- ExtractHydrologicalInputs
         2- StatisticalProperties
         3- WriteHQFile

Hapi/hm/interface.py

@@ -117,8 +117,8 @@ def readLateralsTable(
     def _readRRMwrapper(
         self,
         table: DataFrame,
-        fromday: Union[str, int] = "",
-        today: Union[str, int] = "",
+        fromday: int = None,
+        today: int = None,
         path: str = "",
         date_format: str = "'%Y-%m-%d'",
         prefix: str = "lf_xsid",
@@ -160,7 +160,7 @@ def _readRRMwrapper(
 
             node_ids = table.loc[:, "xsid"].to_list()
             fnames = [f"{prefix}{NodeID}" for NodeID in node_ids]
-            func = self.readRRMResults
+            func = self._readRRMResults
             results = Parallel(n_jobs=cores)(
                 delayed(func)(
                     self.version,
@@ -183,7 +183,7 @@ def _readRRMwrapper(
                 node_id = table.loc[i, "xsid"]
                 fname = f"{prefix}{node_id}"
 
-                rrm_ts[node_id] = self.readRRMResults(
+                rrm_ts[node_id] = self._readRRMResults(
                     self.version,
                     self.ReferenceIndex,
                     path,
@@ -195,9 +195,9 @@ def _readRRMwrapper(
                 logger.info(f"Lateral file {fname} is read")
 
         rrm_ts["total"] = rrm_ts.sum(axis=1)
-        if fromday == "":
+        if not fromday:
             fromday = 1
-        if today == "":
+        if not today:
             today = len(rrm_ts[rrm_ts.columns[0]])
 
         start = self.ReferenceIndex.loc[fromday, "date"]
@@ -208,8 +208,8 @@ def _readRRMwrapper(
 
     def readLaterals(
         self,
-        fromday: Union[str, int] = "",
-        today: Union[str, int] = "",
+        fromday: int = None,
+        today: int = None,
         path: str = "",
         date_format: str = "'%Y-%m-%d'",
         cores: Optional[Union[int, bool]] = None,