Move to single python package "hsp2"

* Moved the HSP2, HSP2IO, and HSP2tools top level packages to
  hsp2.hsp2, hsp2.hsp2io, and hsp2.hsp2tools respectively.
* Corrected the imports in python and Jupyter notebooks to use
  the new locations.
* HSP2 can be run in all of the CompareHSP2.ipynb in tests/,
  however some do not have the HSPF results to compare to.
* The Jupyter notebooks in examples/ need some work to find
  input data and where to write output.

HSP2_Driver.py

@@ -32,21 +32,21 @@
 
 if file_ext.upper() == "UCI":
     h5_name = filename[:-3] + "h5"
-    from HSP2tools.readUCI import readUCI
+    from hsp2.hsp2tools.readUCI import readUCI
     readUCI(filename, h5_name)
     # readUCI('HSPF.uci', 'test.h5')
 
 if file_ext.upper() == "WDM":
     h5_name = filename[:-3] + "h5"
-    from HSP2tools.readWDM import readWDM
+    from hsp2.hsp2tools.readWDM import readWDM
     readWDM(filename, h5_name)
     # readWDM('GRICM.wdm', 'test.h5')
     # readWDM('ZUMBROSCEN.WDM', 'test.h5')
 
 if file_ext.upper() == ".H5":
-    from HSP2.main import main
-    from HSP2IO.hdf import HDF5
-    from HSP2IO.io import IOManager
+    from hsp2.hsp2.main import main
+    from hsp2.hsp2io.hdf import HDF5
+    from hsp2.hsp2io.io import IOManager
 
     hdf5_instance = HDF5(filename)
     io_manager = IOManager(hdf5_instance)

examples/2_ExploreResultsHDF5.ipynb

@@ -45,10 +45,9 @@
     "import os\n",
     "from pathlib import Path\n",
     "\n",
-    "import tables  # PyTables\n",
     "import h5py\n",
-    "\n",
-    "import pandas as pd"
+    "import pandas as pd\n",
+    "import tables  # PyTables"
    ]
   },
   {
@@ -70,7 +69,7 @@
    ],
    "source": [
     "# Confirm that your active environment for this notebook is the one you created for HSP2.\n",
-    "os.environ['CONDA_DEFAULT_ENV']"
+    "os.environ[\"CONDA_DEFAULT_ENV\"]"
    ]
   },
   {
@@ -113,7 +112,7 @@
    "outputs": [],
    "source": [
     "# Set your project directory to your local folder for your clone of the HSPsquared repository\n",
-    "project_folder = Path('/Users/aaufdenkampe/Documents/Python/respec.HSPsquared/')"
+    "project_folder = Path(\"/Users/aaufdenkampe/Documents/Python/respec.HSPsquared/\")"
    ]
   },
   {
@@ -132,16 +131,18 @@
     }
    ],
    "source": [
-    "# use the Path module to construct file path \n",
+    "# use the Path module to construct file path\n",
     "\n",
-    "output_data_folder = Path('examples/_TutorialData')\n",
+    "output_data_folder = Path(\"examples/_TutorialData\")\n",
     "\n",
-    "output_file = 'test10.h5' # HSP2 data HDF5 binary file, for all inputs and outputs\n",
+    "output_file = \"test10.h5\"  # HSP2 data HDF5 binary file, for all inputs and outputs\n",
     "\n",
-    "output_hdf5_path = project_folder / output_data_folder / output_file  # pathlib concatenation\n",
+    "output_hdf5_path = (\n",
+    "    project_folder / output_data_folder / output_file\n",
+    ")  # pathlib concatenation\n",
     "\n",
     "print(output_hdf5_path)\n",
-    "print('File exists? ' + str(output_hdf5_path.exists()) )\n",
+    "print(\"File exists? \" + str(output_hdf5_path.exists()))\n",
     "# The file path should not yet exist. If it does, delete it for this tutorial."
    ]
   },
@@ -489,7 +490,7 @@
    ],
    "source": [
     "# If you know what table you want, you can easily retrieve it with the `pd.read_hdf()` function\n",
-    "pd.read_hdf(output_hdf5_path, '/TIMESERIES/SUMMARY')"
+    "pd.read_hdf(output_hdf5_path, \"/TIMESERIES/SUMMARY\")"
    ]
   },
   {
@@ -557,7 +558,7 @@
     }
    ],
    "source": [
-    "pd.read_hdf(output_hdf5_path, '/CONTROL/GLOBAL')"
+    "pd.read_hdf(output_hdf5_path, \"/CONTROL/GLOBAL\")"
    ]
   },
   {
@@ -567,7 +568,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ts_hydrology = pd.read_hdf(output_hdf5_path, '/RESULTS/RCHRES_R005/HYDR')"
+    "ts_hydrology = pd.read_hdf(output_hdf5_path, \"/RESULTS/RCHRES_R005/HYDR\")"
    ]
   },
   {
@@ -10197,7 +10198,7 @@
    ],
    "source": [
     "for key in h5py_file.keys():\n",
-    "  print(key)"
+    "    print(key)"
    ]
   },
   {
@@ -10218,7 +10219,7 @@
     }
    ],
    "source": [
-    "h5py_file['CONTROL'].keys()"
+    "h5py_file[\"CONTROL\"].keys()"
    ]
   },
   {
@@ -10239,7 +10240,7 @@
     }
    ],
    "source": [
-    "h5py_file['CONTROL']['GLOBAL'].keys()"
+    "h5py_file[\"CONTROL\"][\"GLOBAL\"].keys()"
    ]
   },
   {
@@ -10353,7 +10354,7 @@
    "source": [
     "for name in h5py_file:\n",
     "    for subname in h5py_file[name]:\n",
-    "        print(name+r'\\ '+subname)\n",
+    "        print(name + r\"\\ \" + subname)\n",
     "#         print(r'')\n",
     "#         for subsubname in h5py_file[name][subname]:\n",
     "#             print(name+r'\\ '+subname+r'\\ '+subsubname)"
@@ -10446,7 +10447,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.8.12 ('hsp2_py38')",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -10460,7 +10461,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.14"
   },
   "toc-autonumbering": true,
   "vscode": {

examples/__init__.py

@@ -1,2 +1,2 @@
-import HSP2
-__version__ = HSP2.__version__
+from hsp2 import hsp2
+__version__ = hsp2.__version__

pyproject.toml

@@ -52,7 +52,7 @@ test = ["pytest", "pytest-cov"]
 dev = ["hsp2[test]"]
 
 [project.scripts]
-hsp2 = "HSP2tools.HSP2_CLI:main"
+hsp2 = "hsp2.hsp2tools.HSP2_CLI:main"
 
 [project.urls]
 documentation = "http://www.respec.com/product/hydrologic-simulation-program-python-hsp%C2%B2/"
@@ -67,7 +67,7 @@ readme = {file = "README.rst"}
 version = {file = "VERSION"}
 
 [tool.setuptools.packages.find]
-include = ["HSP2*"]
+where = ["src"]
 
 [tool.setuptools.package-data]
-"HSP2tools.data" = ["*"]
+"hsp2.hsp2tools.data" = ["*"]

HSP2/ADCALC.py → src/hsp2/hsp2/ADCALC.py

@@ -5,7 +5,7 @@
 
 from numpy import zeros, array
 from numba import njit
-from HSP2.utilities import make_numba_dict
+from hsp2.hsp2.utilities import make_numba_dict
 
 # The clean way to get calculated data from adcalc() into advert() is to use a closure. 
 # This is not currently supported by Numba.

HSP2/ATEMP.py → src/hsp2/hsp2/ATEMP.py

@@ -6,9 +6,9 @@
 
 from numba import njit
 from numpy import empty, zeros, int64
-from HSP2.utilities import hoursval, make_numba_dict, LAPSE
+from hsp2.hsp2.utilities import hoursval, make_numba_dict, LAPSE
 
-from HSP2IO.protocols import SupportsReadTS, Category
+from hsp2.hsp2io.protocols import SupportsReadTS, Category
 
 ERRMSGS = ()
 

HSP2/CONS.py → src/hsp2/hsp2/CONS.py

@@ -23,9 +23,9 @@
 '''
 
 from numpy import zeros
-from HSP2.ADCALC import advect
+from hsp2.hsp2.ADCALC import advect
 from numba import njit
-from HSP2.utilities  import make_numba_dict, initm
+from hsp2.hsp2.utilities  import make_numba_dict, initm
 
 ERRMSG = []
 

HSP2/COPY.py → src/hsp2/hsp2/COPY.py

@@ -1,8 +1,8 @@
-from HSP2.utilities import get_timeseries
+from hsp2.hsp2.utilities import get_timeseries
 import pandas as pd
 from typing import List, Dict
 
-from HSP2IO.protocols import SupportsReadTS
+from hsp2.hsp2io.protocols import SupportsReadTS
 
 class Copy():
     """

HSP2/GQUAL.py → src/hsp2/hsp2/GQUAL.py

@@ -6,8 +6,8 @@
 from numpy import array, zeros, int64
 from numba import njit
 from math import exp
-from HSP2.utilities import initm, make_numba_dict, hoursval, dayval
-from HSP2.ADCALC import advect, oxrea
+from hsp2.hsp2.utilities import initm, make_numba_dict, hoursval, dayval
+from hsp2.hsp2.ADCALC import advect, oxrea
 
 ERRMSGS =('GQUAL: one or more gquals are sediment-associated, but section sedtrn not active',             #ERRMSG0
           'GQUAL: simulation of photolysis requires aux1fg to be on to calculate average depth',          #ERRMSG1

HSP2/HTRCH.py → src/hsp2/hsp2/HTRCH.py

@@ -23,10 +23,10 @@
         END IF
 '''
 
-from HSP2.ADCALC import advect
+from hsp2.hsp2.ADCALC import advect
 from numpy import zeros, full, float64, int64
 from numba import njit
-from HSP2.utilities  import make_numba_dict, hourflag, hoursval, initm
+from hsp2.hsp2.utilities  import make_numba_dict, hourflag, hoursval, initm
 
 
 # METRIC LAPSE DATA

HSP2/HYDR.py → src/hsp2/hsp2/HYDR.py

@@ -17,11 +17,11 @@
 from math import sqrt, log10
 from numba import njit, types
 from numba.typed import List
-from HSP2.utilities import initm, make_numba_dict
+from hsp2.hsp2.utilities import initm, make_numba_dict
 
 # the following imports added by rb to handle dynamic code and special actions
-from HSP2.state import hydr_get_ix, hydr_init_ix
-from HSP2.om import pre_step_model, step_model, model_domain_dependencies
+from hsp2.hsp2.state import hydr_get_ix, hydr_init_ix
+from hsp2.hsp2.om import pre_step_model, step_model, model_domain_dependencies
 from numba.typed import Dict
 
 
@@ -140,7 +140,7 @@ def hydr(io_manager, siminfo, uci, ts, ftables, state):
     if (hsp2_local_py != False):
         from hsp2_local_py import state_step_hydr
     else:
-        from HSP2.state_fn_defaults import state_step_hydr
+        from hsp2.hsp2.state_fn_defaults import state_step_hydr
     # initialize the hydr paths in case they don't already reside here
     hydr_init_ix(state, state['domain'])
     # must split dicts out of state Dict since numba cannot handle mixed-type nested Dicts

HSP2/IQUAL.py → src/hsp2/hsp2/IQUAL.py

@@ -7,7 +7,7 @@
 from math import exp
 from numpy import zeros, where, full, float64, int64
 from numba import njit
-from HSP2.utilities import initm, make_numba_dict, hourflag, initmdiv
+from hsp2.hsp2.utilities import initm, make_numba_dict, hourflag, initmdiv
 
 
 ''' DESIGN NOTES

HSP2/IWATER.py → src/hsp2/hsp2/IWATER.py

@@ -7,7 +7,7 @@
 from numpy import zeros, ones, full, nan, int64, float64
 from math import sqrt
 from numba import njit
-from HSP2.utilities import hourflag, hoursval, initm, make_numba_dict
+from hsp2.hsp2.utilities import hourflag, hoursval, initm, make_numba_dict
 
 MAXLOOPS  = 100      # newton method max steps
 TOLERANCE = 0.01     # newton method exit tolerance

HSP2/IWTGAS.py → src/hsp2/hsp2/IWTGAS.py

@@ -6,7 +6,7 @@
 
 from numpy import zeros, where, full, float64, int64
 from numba import njit
-from HSP2.utilities import initm, make_numba_dict, hourflag
+from hsp2.hsp2.utilities import initm, make_numba_dict, hourflag
 
 ERRMSG = []
 

HSP2/NUTRX_Class.py → src/hsp2/hsp2/NUTRX_Class.py

@@ -4,10 +4,10 @@
 import numba as nb
 from numba.experimental import jitclass
 
-from HSP2.ADCALC import advect
-from HSP2.RQUTIL import sink, decbal, benth
-from HSP2.OXRX_Class import OXRX_Class
-from HSP2.utilities  import make_numba_dict, initm
+from hsp2.hsp2.ADCALC import advect
+from hsp2.hsp2.RQUTIL import sink, decbal, benth
+from hsp2.hsp2.OXRX_Class import OXRX_Class
+from hsp2.hsp2.utilities  import make_numba_dict, initm
 
 spec = [
 	('adnh4', nb.float64[:]),

HSP2/OXRX_Class.py → src/hsp2/hsp2/OXRX_Class.py

@@ -5,9 +5,9 @@
 from numba.experimental import jitclass
 from math import exp
 
-from HSP2.ADCALC import advect, oxrea
-from HSP2.RQUTIL import sink
-from HSP2.utilities	 import make_numba_dict
+from hsp2.hsp2.ADCALC import advect, oxrea
+from hsp2.hsp2.RQUTIL import sink
+from hsp2.hsp2.utilities	 import make_numba_dict
 
 spec = [
 	('AFACT', nb.float64),

HSP2/PHCARB_Class.py → src/hsp2/hsp2/PHCARB_Class.py

@@ -5,8 +5,8 @@
 from numba.experimental import jitclass
 from math import log10
 
-from HSP2.ADCALC import advect
-from HSP2.RQUTIL import benth
+from hsp2.hsp2.ADCALC import advect
+from hsp2.hsp2.RQUTIL import benth
 
 spec = [
     ('alk', nb.float64),

HSP2/PLANK_Class.py → src/hsp2/hsp2/PLANK_Class.py

@@ -6,11 +6,11 @@
 import numba as nb
 from numba.experimental import jitclass
 
-from HSP2.ADCALC import advect
-from HSP2.OXRX_Class import OXRX_Class
-from HSP2.NUTRX_Class import NUTRX_Class
-from HSP2.RQUTIL import sink, decbal
-from HSP2.utilities  import make_numba_dict, initm
+from hsp2.hsp2.ADCALC import advect
+from hsp2.hsp2.OXRX_Class import OXRX_Class
+from hsp2.hsp2.NUTRX_Class import NUTRX_Class
+from hsp2.hsp2.RQUTIL import sink, decbal
+from hsp2.hsp2.utilities  import make_numba_dict, initm
 
 if os.environ.get("NUMBA_DISABLE_JIT", 0): # jit should be on by default.
 	OXRX_Class_ = OXRX_Class

HSP2/PQUAL.py → src/hsp2/hsp2/PQUAL.py

@@ -7,7 +7,7 @@
 from math import exp
 from numpy import zeros, where, full, float64, int64
 from numba import njit
-from HSP2.utilities import initm, make_numba_dict, hourflag, initmdiv
+from hsp2.hsp2.utilities import initm, make_numba_dict, hourflag, initmdiv
 
 ''' DESIGN NOTES
 Each constituent will be in its own subdirectory in the HDF5 file.

HSP2/PSTEMP.py → src/hsp2/hsp2/PSTEMP.py

@@ -7,7 +7,7 @@
 
 from numpy import zeros, where, ones, float64, full, int64
 from numba import njit
-from HSP2.utilities  import hoursval, initm, make_numba_dict
+from hsp2.hsp2.utilities  import hoursval, initm, make_numba_dict
 
 
 ERRMSG = ['SLTMP temperature less than -100C',   # MSG0