Refactor/tests

.github/workflows/github-pages-mkdocs.yml

@@ -30,7 +30,7 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-    - uses: Serapieum-of-alex/github-actions/actions/mkdocs-deploy@mkdocs/v1
+    - uses: serapeum-org/github-actions/actions/mkdocs-deploy@mkdocs/v1
       with:
         trigger: 'pull_request'
         package-manager: 'pixi'
@@ -44,7 +44,7 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-    - uses: Serapieum-of-alex/github-actions/actions/mkdocs-deploy@mkdocs/v1
+    - uses: serapeum-org/github-actions/actions/mkdocs-deploy@mkdocs/v1
       with:
         trigger: 'main'
         package-manager: 'pixi'
@@ -60,7 +60,7 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-    - uses: Serapieum-of-alex/github-actions/actions/mkdocs-deploy@mkdocs/v1
+    - uses: serapeum-org/github-actions/actions/mkdocs-deploy@mkdocs/v1
       with:
         trigger: 'release'
         package-manager: 'pixi'

.github/workflows/github-release.yml

@@ -57,7 +57,7 @@ jobs:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Create GitHub Release with Commitizen
-        uses: Serapieum-of-alex/github-actions/actions/release/github@github-release/v1
+        uses: serapeum-org/github-actions/actions/release/github@github-release/v1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           increment: ${{ github.event.inputs.increment }}

.github/workflows/pypi-release.yml

@@ -22,7 +22,7 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.event.workflow_run.head_sha || github.sha }}
       - name: Build and publish to PyPI
-        uses: Serapieum-of-alex/github-actions/actions/release/pypi@pypi-release/v1
+        uses: serapeum-org/github-actions/actions/release/pypi@pypi-release/v1
         with:
           pypi-username: __token__
           pypi-password: ${{ secrets.PYPI_PUBLISH }}

.github/workflows/tests.yml

@@ -25,7 +25,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up Python
-        uses: Serapieum-of-alex/github-actions/actions/python-setup/pixi@pixi/v1
+        uses: serapeum-org/github-actions/actions/python-setup/pixi@pixi/v1
         with:
           environments: ${{ matrix.environment }}
           activate-environment: ${{ matrix.environment }}
@@ -35,7 +35,7 @@ jobs:
         run: |
           pixi run -e ${{ matrix.environment }} test-all
         env:
-          HAPI_DATA_DIR: ${{ github.workspace }}/src/Hapi/parameters
+          HAPI_DATA_DIR: ${{ github.workspace }}/src/hapi/parameters
 
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v5

README.md

@@ -24,7 +24,7 @@ Current build status
 </table>
 
 [![Build status](https://ci.appveyor.com/api/projects/status/rys2u0l1nbmfjuww?svg=true)](https://ci.appveyor.com/project/MAfarrag/hapi)
-[![codecov](https://codecov.io/gh/Serapieum-of-alex/Hapi/branch/main/graph/badge.svg?token=EMQSR7K2YV)](https://codecov.io/gh/Serapieum-of-alex/Hapi)
+[![codecov](https://codecov.io/gh/serapeum-org/Hapi/branch/main/graph/badge.svg?token=EMQSR7K2YV)](https://codecov.io/gh/serapeum-org/Hapi)
 ![GitHub last commit](https://img.shields.io/github/last-commit/MAfarrag/Hapi)
 ![GitHub forks](https://img.shields.io/github/forks/MAfarrag/hapi?style=social)
 ![GitHub Repo stars](https://img.shields.io/github/stars/MAfarrag/Hapi?style=social)

docs/api/calibration.md

@@ -1,4 +1,4 @@
 # Calibration
 
 ## Calibration
-::: Hapi.calibration.Calibration
+::: hapi.calibration.Calibration

docs/api/catchment.md

@@ -1,4 +1,4 @@
 # Catchment
 
 ## Catchment
-::: Hapi.catchment.Catchment
+::: hapi.catchment.Catchment

docs/api/dem.md

@@ -1,4 +1,4 @@
 # DEM
 
 ## DEM
-::: Hapi.dem.DEM
+::: hapi.dem.DEM

docs/api/hbv-bergestrom92.md

@@ -1,4 +1,4 @@
 # HBV rainfall runoff model
 
 ## HBVBergestrom92
-::: Hapi.rrm.hbv_bergestrom92.HBVBergestrom92
+::: hapi.rrm.hbv_bergestrom92.HBVBergestrom92

docs/api/hbv-lake.md

@@ -1,4 +1,4 @@
 # HBV rainfall runoff model
 
 ## HBVLake
-::: Hapi.rrm.hbv_lake.HBVLake
+::: hapi.rrm.hbv_lake.HBVLake

docs/api/hbv.md

@@ -1,4 +1,4 @@
 # HBV rainfall runoff model
 
 ## HBV
-::: Hapi.rrm.hbv.HBV
+::: hapi.rrm.hbv.HBV

docs/api/inputs.md

@@ -1,4 +1,4 @@
 # Inputs
 
 ## Inputs
-::: Hapi.inputs.Inputs
+::: hapi.inputs.Inputs

docs/api/routing.md

@@ -1,4 +1,4 @@
 # Routing
 
 ## Routing
-::: Hapi.routing.Routing
+::: hapi.routing.Routing

docs/api/rrm-parameters.md

@@ -1,4 +1,4 @@
 # Parameters
 
 ## Parameters
-::: Hapi.rrm.parameters.Parameters
+::: hapi.rrm.parameters.Parameters

docs/api/run.md

@@ -1,4 +1,4 @@
 # Run
 
 ## Run
-::: Hapi.run.Run
+::: hapi.run.Run

docs/api/wrapper.md

@@ -1,4 +1,4 @@
 # Wrapper
 
 ## Wrapper
-::: Hapi.wrapper.Wrapper
+::: hapi.wrapper.Wrapper

docs/change-log.md

@@ -74,4 +74,4 @@
 ## 1.3.2 (2022-12-26)
 
 - Remove parameters from the package and retrieve them with the
-  parameter package.
+  parameter package.

docs/dev/Installation.md

@@ -61,17 +61,17 @@ pip install HAPI-Nile=={release}
 ## From sources
 
 The sources for HapiSM can be downloaded from the
-[Github repo](https://github.com/Serapieum-of-alex/Hapi).
+[Github repo](https://github.com/serapeum-org/Hapi).
 
 You can either clone the public repository:
 
 ```shell
-$ git clone git://github.com/Serapieum-of-alex/Hapi
+$ git clone git://github.com/serapeum-org/Hapi
 ```
-Or download the [tarball](https://github.com/Serapieum-of-alex/Hapi/tarball/master):
+Or download the [tarball](https://github.com/serapeum-org/Hapi/tarball/master):
 
 ```shell
-$ curl -OJL https://github.com/Serapieum-of-alex/Hapi/tarball/master
+$ curl -OJL https://github.com/serapeum-org/Hapi/tarball/master
 ```
 Once you have a copy of the source, you can install it with:
 
@@ -82,11 +82,11 @@ $ python setup.py install
 
 To install directly from GitHub (from the HEAD of the master branch):
 
-+ `pip install git+https://github.com/Serapieum-of-alex/Hapi.git`
++ `pip install git+https://github.com/serapeum-org/Hapi.git`
 
 or from Github from a specific release:
 
-+ `pip install git+https://github.com/Serapieum-of-alex/Hapi.git@{release}`
++ `pip install git+https://github.com/serapeum-org/Hapi.git@{release}`
 
 Now you should be able to start this environment's Python with `python`, try
 `import Hapi` to see if the package is installed.
@@ -102,15 +102,15 @@ of you clone. This will not move a copy to your Python installation directory, b
 instead create a link in your Python installation pointing to the folder you installed
 it from, such that any changes you make there are directly reflected in your install.
 
-+ `git clone https://github.com/Serapieum-of-alex/Hapi.git`
++ `git clone https://github.com/serapeum-org/Hapi.git`
 + `cd Hapi`
 + `activate Hapi`
 + `pip install -e .`
 
 Alternatively, if you want to avoid using `git` and simply want to test the latest
 version from the `master` branch, you can replace the first line with downloading
-a zip archive from GitHub: https://github.com/Serapieum-of-alex/Hapi/archive/master.zip
-[libraries.io](https://libraries.io/github/Serapieum-of-alex/Hapi).
+a zip archive from GitHub: https://github.com/serapeum-org/Hapi/archive/master.zip
+[libraries.io](https://libraries.io/github/serapeum-org/Hapi).
 
 ## Install using pip
 
@@ -122,7 +122,7 @@ use the conda package manager:
 conda install numpy scipy gdal netcdf4 pyproj
 ```
 
-you can check [libraries.io](https://libraries.io/github/Serapieum-of-alex/Hapi). to check versions of the libraries
+you can check [libraries.io](https://libraries.io/github/serapeum-org/Hapi). to check versions of the libraries
 
 
 Then install a release {release} of Hapi (available from release 2018.1) with pip:
@@ -150,4 +150,4 @@ This should run without errors.
       https://Hapi.readthedocs.org/en/latest/
 
       Documentation for the stable version:
-      https://Hapi.readthedocs.org/en/stable/
+      https://Hapi.readthedocs.org/en/stable/

docs/examples/distributed-model-calib.md

@@ -300,4 +300,4 @@ EndDate = "2010-04-20"
 Prefix = 'Qtot_'
 
 Coello.saveResults(FlowAccPath, Result=1, StartDate=StartDate, EndDate=EndDate, Path="F:/02Case studies/Coello/Hapi/Model/results/", Prefix=Prefix)
-```
+```

docs/examples/distributed-model-run.md

@@ -129,4 +129,4 @@ cal_parameters = Coello.runCalibration(SpatialVarFun, OptimizationArgs,printErro
 ```python
 SpatialVarFun.Function(Coello.Parameters, kub=SpatialVarFun.Kub, klb=SpatialVarFun.Klb)
 SpatialVarFun.saveParameters(SaveTo)
-```
+```

docs/examples/gis-inputs.md

@@ -66,4 +66,4 @@ the following steps are done in QGIS
 
 	this step we will multiply the DEM (5km) with the `Standardized_Burn.tif` raster
 
-	output will be the raster `DEM_Burn.tif`
+	output will be the raster `DEM_Burn.tif`

docs/examples/hbv.md

@@ -93,4 +93,4 @@ Lakes have a significant impact on the dynamics of runoff process and the routin
 
 # References
 
-		Bergström, Sten. 1992. “The HBV Model - Its Structure and Applications.” Smhi Rh 4(4): 35.
+		Bergström, Sten. 1992. “The HBV Model - Its Structure and Applications.” Smhi Rh 4(4): 35.

docs/examples/lumped-model-calibration.md

@@ -46,7 +46,7 @@ To calibrate the HBV lumped model inside Hapi you need to follow the same steps
 	parameters = []
 	# Routing
 	Route = 1
-	RoutingFn = Routing.TriangularRouting1
+	RoutingFn = Routing.triangular_routing_1
 
 	Basic_inputs = dict(Route=Route, RoutingFn=RoutingFn, InitialValues = parameters)
 
@@ -84,4 +84,4 @@ To calibrate the HBV lumped model inside Hapi you need to follow the same steps
 	print("Objective Function = " + str(round(cal_parameters[0],2)))
 	print("Parameters are " + str(cal_parameters[1]))
 	print("Time = " + str(round(cal_parameters[2]['time']/60,2)) + " min")
-```
+```

docs/examples/lumped-model-run.md

@@ -53,8 +53,8 @@ Coello.readParameters(Parameterpath, Snow)
 - Prepare the routing options.
 
 ```python
-# RoutingFn = Routing.TriangularRouting2
-RoutingFn = Routing.Muskingum_V
+# RoutingFn = Routing.triangular_routing_2
+RoutingFn = Routing.muskingum_v
 Route = 1
 ```
 - now all the data required for the model are prepared in the right form, now you can call the `runLumped` wrapper to initiate the calculation
@@ -104,4 +104,4 @@ EndDate = "2010-04-20"
 
 Path = SaveTo + "Results-Lumped-Model" + str(dt.datetime.now())[0:10] + ".txt"
 Coello.saveResults(Result=5, StartDate=StartDate, EndDate=EndDate, Path=Path)
-```
+```

docs/examples/meteo-inputs.md

@@ -110,4 +110,4 @@ Coello = RS(StartDate=StartDate, EndDate=EndDate, Time=Time,
 	latlim=lat , lonlim=lon, Path=Path, Vars=variables)
 
 Coello.ECMWF(Waitbar=1)
-```
+```

docs/examples/parameters.md

@@ -57,4 +57,4 @@ To extract the parameters from one of the ten scenarios developed to derive the
 # extract parameters in a specific scenarion from the 10 scenarios
 Par['1'] = IN.extractParameters(Basin,"01")
 ```
-the extracted parameters needs to be modified incase you are not considering the snow bucket the first 5 parameters are disregarded
+the extracted parameters needs to be modified incase you are not considering the snow bucket the first 5 parameters are disregarded