Bug: readUCI() renames columns before setting defaults, which creates duplicate columns

@timcera

Status: This bug is currently active, and awaiting the completion of @timcera iomanager branch to be fully functional - see code here
Location: See Add update_uci mode in CLI and test UCI files #200
Problem: readUCI() renames columns before setting defaults, but does not flush to hdf5, which creates duplicate columns
Outcome:
- if calling "readUCI()" with the 3rd parameter overwrite=False duplicate columns get written to the hdf5
- This seems to have the result of causing an index error when doing multiple UCI re-reads with overwrite=False
Use case: this is important as the import_uci step can be very time consuming if you have large WDM inputs, and so I am working on a command line function to allow one to only re-import UCI parameters, and leaving WDM/timeseries things untouched in the original h5 file.

Testing:

Get Branch branch:

First Import and Run

cd tests/testcbp/HSP2Results
hsp2 import_uci PL3_5250_0001eq.uci PL3_5250_0001eq.h5
hsp2 run PL3_5250_0001eq.h5

2026-01-02 20:35:10.69   Simulation Start: 2001-01-01 00:00:00, Stop: 2002-01-01 00:00:00
2026-01-02 20:35:10.69      RCHRES R001 DELT(minutes): 60
2026-01-02 20:35:18.66         HYDR
2026-01-02 20:35:58.46         ADCALC
2026-01-02 20:35:59.41   Done; Run time is about 01:37.8 (mm:ss)

First Update with longer sim and Run

2026-01-02 20:39:48.09   Simulation Start: 1984-01-01 00:00:00, Stop: 2020-01-01 00:00:00
2026-01-02 20:39:48.09      RCHRES R001 DELT(minutes): 60
2026-01-02 20:39:55.57         HYDR
2026-01-02 20:42:14.50         ADCALC
2026-01-02 20:42:17.27   Done; Run time is about 03:24.5 (mm:ss)

2nd Update (back to shorter duration) and Run

hsp2 update_uci PL3_5250_0001eq.uci PL3_5250_0001eq.h5

Traceback (most recent call last):
  File "/usr/local/share/venv/hsp2dev_py10/bin/hsp2", line 7, in <module>
    sys.exit(main())
<snip>
File "/usr/local/share/venv/hsp2dev_py10/lib/python3.10/site-packages/hsp2/hsp2tools/readUCI.py", line 318, in readUCI
    df.to_hdf(store, key=path, data_columns=True)
<snip>
ValueError: cannot reindex on an axis with duplicate labels

Analysis

Line 318 is a renaming of columns in the PERLND/SNOW space.
I suspect that the cause of this is the renaming of PERLND SNOW parameters due to duplicate columns {"PKSNOW": "PACKF", "PKICE": "PACKI", "PKWATR": "PACKW"}

import h5py
import pandas as pd

store = pd.HDFStore(str("./tests/testcbp/HSP2results/PL3_5250_0001eq.h5"), mode='r')
pd.read_hdf(store, "/PERLND/SNOW/STATES")
Traceback (most recent call last):
  File "/usr/local/share/venv/hsp2dev_py10/lib/python3.10/site-packages/pandas/io/pytables.py", line 1819, in _create_storer
    cls = _TABLE_MAP[tt]
KeyError: None

But the h5 is valid, as is evidenced by other tables being read just fine:

pd.read_hdf(store, "/RCHRES/ACIDPH/STATES")

     OPNID  ACCONC1  ACCONC2  ACCONC3  ACCONC4  ACCONC5  ACCONC6  ACCONC7
R001   NaN      0.0      0.0      0.0      0.0      0.0      0.0      0.0

Lines 312-318 in readUCI.py rename some columns in the /PERLND/SNOW/STATES table
In Line 466, each existing hsp path in the hdf is loaded in the var df
In line 477, the defaults for that matching table are loaded into dct_params
- But for at least some, like /PERLND/SNOW/STATES the default columns still have their old names
In Line 470-483 any missing default columns are added to an updated df for that table then pushed back to the hdf5
For some, like the /PERLND/SNOW/STATES table, this adds deprecated column names back into the df, in addition to the recently renamed versions of those old columns.
Then, the next time readUCI() is run with overwrite = False, the renaming line adds duplicate copies of the renamed columns.
I think this is the issue, or at last 1 issue.
Below is some slightly edited code from readUCI() that allows one to step through this, not as efficient as a command line debugger, but my VSCode is partially broken since a recent update and I can't step into code for the time being on Windows.

The Entire Code as command line runnable test

"""
Read data from a UCI file and create an HDF file with the data.

Parameters
----------
uciname : str
    The name of the UCI file to read.
hdfname : str
    The name of the HDF file to store the data.
overwrite : bool, optional
    Whether to overwrite existing data in the HDF file. Defaults to True.

Returns
-------
None
"""
import h5py
import pandas as pd
from hsp2.hsp2tools.readUCI import *
from hsp2.hsp2io import *


# Hard code inputs for example testing
uciname = "./tests/testcbp/HSP2results/PL3_5250_0001eq.uci"
hdfname = "./tests/testcbp/HSP2results/PL3_5250_0001eq.h5"
overwrite = False

# Load needed functions
convert = {"C": str, "I": int, "R": float}


if overwrite is True and os.path.exists(hdfname):
    os.remove(hdfname)

# create lookup dictionaries from 'ParseTable.csv' and 'rename.csv'
parse = defaultdict(list)
defaults = {}
cat = {}
path = {}
hsp_paths = {}
datapath = os.path.join(hsp2tools.__path__[0], "data", "ParseTable.csv")
for row in pd.read_csv(datapath).itertuples():
    parse[row.OP, row.TABLE].append(
        (row.NAME, row.TYPE, row.START, row.STOP, row.DEFAULT)
    )
    defaults[row.OP, row.SAVE, row.NAME] = convert[row.TYPE](row.DEFAULT)
    cat[row.OP, row.TABLE] = row.CAT
    path[row.OP, row.TABLE] = row.SAVE
    # store paths for checking defaults:
    hsp_path = f"/{row.OP}/{row.SAVE}/{row.CAT}"
    if not hsp_path in hsp_paths:
        hsp_paths[hsp_path] = {}
    hsp_paths[hsp_path][row.NAME] = defaults[row.OP, row.SAVE, row.NAME]

rename = {}
extendlen = {}
datapath = os.path.join(hsp2tools.__path__[0], "data", "rename.csv")
for row in pd.read_csv(datapath).itertuples():
    if row.LENGTH != 1:
        extendlen[row.OPERATION, row.TABLE] = row.LENGTH
    rename[row.OPERATION, row.TABLE] = row.RENAME

net = None
sc = None
store = pd.HDFStore(hdfname, mode="a")
info = (store, parse, path, defaults, cat, rename, extendlen)
f = reader(uciname)
for line in f:
    if line.startswith("GLOBAL"):
        global_(info, getlines(f))
    elif line.startswith("OPN"):
        opn(info, getlines(f))
    elif line.startswith("NETWORK"):
        net = network(info, getlines(f))
    elif line.startswith("SCHEMATIC"):
        sc = schematic(info, getlines(f))
    elif line.startswith("MASS-LINK"):
        masslink(info, getlines(f))
    elif line.startswith("FTABLES"):
        ftables(info, getlines(f))
    elif line.startswith("EXT"):
        ext(info, getlines(f))
    elif line.startswith("GENER"):
        gener(info, getlines(f))
    elif line.startswith("PERLND"):
        operation(info, getlines(f), "PERLND")
    elif line.startswith("IMPLND"):
        operation(info, getlines(f), "IMPLND")
    elif line.startswith("RCHRES"):
        operation(info, getlines(f), "RCHRES")
    elif line.startswith("MONTH-DATA"):
        monthdata(info, getlines(f))
    elif line.startswith("SPEC-ACTIONS"):
        specactions(info, getlines(f))

colnames = (
    "AFACTR",
    "MFACTOR",
    "MLNO",
    "SGRPN",
    "SMEMN",
    "SMEMSB",
    "SVOL",
    "SVOLNO",
    "TGRPN",
    "TMEMN",
    "TMEMSB",
    "TRAN",
    "TVOL",
    "TVOLNO",
    "COMMENTS",
)
if not ((net is None) and (sc is None)):
    linkage = pd.concat((net, sc), ignore_index=True, sort=True)
    for cname in colnames:
        if cname not in linkage.columns:
            linkage[cname] = ""
    linkage = linkage.sort_values(by=["TVOLNO"]).replace("na", "")
    linkage.to_hdf(store, key="/CONTROL/LINKS", data_columns=True)

Lapse.to_hdf(store, key="TIMESERIES/LAPSE_Table")
Seasons.to_hdf(store, key="TIMESERIES/SEASONS_Table")
Svp.to_hdf(store, key="TIMESERIES/Saturated_Vapor_Pressure_Table")
keys = set(store.keys())
# rename needed for restart. NOTE issue with line 157 in PERLND SNOW HSPF
# where PKSNOW = PKSNOW + PKICE at start - ONLY
path = "/PERLND/SNOW/STATES"
if path in keys:
    df = pd.read_hdf(store, path)
    df = df.rename(
        columns={"PKSNOW": "PACKF", "PKICE": "PACKI", "PKWATR": "PACKW"}
    )
    df.to_hdf(store, key=path, data_columns=True)

path = "/IMPLND/SNOW/STATES"
if path in keys:
    df = pd.read_hdf(store, path)
    df = df.rename(
        columns={"PKSNOW": "PACKF", "PKICE": "PACKI", "PKWATR": "PACKW"}
    )
    df.to_hdf(store, key=path, data_columns=True)

path = "/PERLND/SNOW/FLAGS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "SNOPFG" not in df.columns:  # didn't read SNOW-FLAGS table
        df["SNOPFG"] = 0
        df.to_hdf(store, key=path, data_columns=True)

path = "/IMPLND/SNOW/FLAGS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "SNOPFG" not in df.columns:  # didn't read SNOW-FLAGS table
        df["SNOPFG"] = 0
        df.to_hdf(store, key=path, data_columns=True)

# Need to fixup missing data
path = "/IMPLND/IWATER/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "PETMIN" not in df.columns:  # didn't read IWAT-PARM2 table
        df["PETMIN"] = 0.35
        df["PETMAX"] = 40.0
        df.to_hdf(store, key=path, data_columns=True)

path = "/IMPLND/IWTGAS/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "SDLFAC" not in df.columns:  # didn't read LAT-FACTOR table
        df["SDLFAC"] = 0.0
        df["SLIFAC"] = 0.0
        df.to_hdf(store, key=path, data_columns=True)

path = "/IMPLND/IQUAL/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "SDLFAC" not in df.columns:  # didn't read LAT-FACTOR table
        df["SDLFAC"] = 0.0
        df["SLIFAC"] = 0.0
        df.to_hdf(store, key=path, data_columns=True)

path = "/PERLND/PWTGAS/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "SDLFAC" not in df.columns:  # didn't read LAT-FACTOR table
        df["SDLFAC"] = 0.0
        df["SLIFAC"] = 0.0
        df["ILIFAC"] = 0.0
        df["ALIFAC"] = 0.0
        df.to_hdf(store, key=path, data_columns=True)
    if "SOTMP" not in df.columns:  # didn't read PWT-TEMPS table
        df["SOTMP"] = 60.0
        df["IOTMP"] = 60.0
        df["AOTMP"] = 60.0
        df.to_hdf(store, key=path, data_columns=True)
    if "SODOX" not in df.columns:  # didn't read PWT-GASES table
        df["SODOX"] = 0.0
        df["SOCO2"] = 0.0
        df["IODOX"] = 0.0
        df["IOCO2"] = 0.0
        df["AODOX"] = 0.0
        df["AOCO2"] = 0.0
        df.to_hdf(store, key=path, data_columns=True)

path = "/PERLND/PWATER/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "FZG" not in df.columns:  # didn't read PWAT-PARM5 table
        df["FZG"] = 1.0
        df["FZGL"] = 0.1
        df.to_hdf(store, key=path, data_columns=True)

path = "/PERLND/PQUAL/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "SDLFAC" not in df.columns:  # didn't read LAT-FACTOR table
        df["SDLFAC"] = 0.0
        df["SLIFAC"] = 0.0
        df["ILIFAC"] = 0.0
        df["ALIFAC"] = 0.0
        df.to_hdf(store, key=path, data_columns=True)

path = "/RCHRES/GENERAL/INFO"
if path in keys:
    dfinfo = pd.read_hdf(store, path)
    path = "/RCHRES/HYDR/PARAMETERS"
    if path in keys:
        df = pd.read_hdf(store, path)
        df["NEXITS"] = dfinfo["NEXITS"]
        df["LKFG"] = dfinfo["LKFG"]
        if "IREXIT" not in df.columns:  # didn't read HYDR-IRRIG table
            df["IREXIT"] = 0
            df["IRMINV"] = 0.0
        df["FTBUCI"] = df["FTBUCI"].map(lambda x: f"FT{int(x):03d}")
        df.to_hdf(store, key=path, data_columns=True)
    del dfinfo["NEXITS"]
    del dfinfo["LKFG"]
    dfinfo.to_hdf(store, key="RCHRES/GENERAL/INFO", data_columns=True)

path = "/RCHRES/HTRCH/FLAGS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "BEDFLG" not in df.columns:  # didn't read HT-BED-FLAGS table
        df["BEDFLG"] = 0
        df["TGFLG"] = 2
        df["TSTOP"] = 55
        df.to_hdf(store, key=path, data_columns=True)

path = "/RCHRES/HTRCH/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "ELEV" not in df.columns:  # didn't read HEAT-PARM table
        df["ELEV"] = 0.0
        df["ELDAT"] = 0.0
        df["CFSAEX"] = 1.0
        df["KATRAD"] = 9.37
        df["KCOND"] = 6.12
        df["KEVAP"] = 2.24
        df.to_hdf(store, key=path, data_columns=True)

path = "/RCHRES/HTRCH/PARAMETERS"
if path in keys:
    df = pd.read_hdf(store, path)
    if "MUDDEP" not in df.columns:  # didn't read HT-BED-PARM table
        df["MUDDEP"] = 0.33
        df["TGRND"] = 59.0
        df["KMUD"] = 50.0
        df["KGRND"] = 1.4
        df.to_hdf(store, key=path, data_columns=True)

path = "/RCHRES/HTRCH/STATES"
if path in keys:
    df = pd.read_hdf(store, path)
    # if 'TW' not in df.columns:  # didn't read HEAT-INIT table
    #    df['TW']    = 60.0
    #    df['AIRTMP']= 60.0

# apply defaults:
# JUST FOR TESTING WE OVERWRITE hsp_paths to ONLY CONTAIN the SNOW PERLND
path = '/PERLND/SNOW/STATES'
hsp_paths = {path:hsp_paths[path]}

for path in hsp_paths:
    if path in keys:
        df = pd.read_hdf(store, path)
        dct_params = hsp_paths[path]
        
        new_columns = {}
        for par_name in dct_params:
            if par_name == "CFOREA":
                ichk = 0
            
            if par_name not in df.columns:  # missing value in HDF5 path
                def_val = dct_params[par_name]
                if def_val != "None":
                    # df[par_name] = def_val
                    new_columns[par_name] = def_val
        
        new_columns = pd.DataFrame(new_columns, index=df.index)
        df1 = pd.concat([df, new_columns], axis=1)
        
        df1.to_hdf(store, key=path, data_columns=True)
    else:
        if path[-6:] == "STATES":
            # need to add states if it doesn't already exist to save initial state variables
            # such as the case where entire IWAT-STATE1 table is being defaulted
            if not "df" in locals():
                x = 1  # sometimes when debugging keys gets creamed, seems like an IDE bug
            for column in df.columns:  # clear out existing data frame columns
                df = df.drop([column], axis=1)
            dct_params = hsp_paths[path]
            for par_name in dct_params:
                def_val = dct_params[par_name]
                if def_val != "None":
                    df[par_name] = def_val
            df.to_hdf(store, key=path, data_columns=True)

# now see what the hdf has in it
pd.read_hdf(store, path)
store.close()

@timcera

@timcera - FYI - there is many different instances of things being renamed and so forth in this routine, and while I traced the majority of that code to waaaaaayyyy back in the first versions of this file, I figured I would tag you as you had more recently gotten your hands dirty here.

My sense is that:

It may be as simple as a check to see if a column already exists before trying to add default columns, and re-rename them?
Or, it may be worth going back into the parameter setup CSV files and figuring out why the heck these things need to be renamed in the first place? Like, that seems like some sort of hacky code that was in there to get something to work, and it's just been carried over.

List of renaming code functions/locations:

in readUCI() on line 244 there is a function that does a mass renaming based on mappings defined in the file rename.csv
in readUCI() lines [312-326]
- To me, this is an appealing place to have ALL renaming if possible.
- Personally I would prefer that this renaming be put into a separate function with a big warning about future deprecation, unless for some reason it is always going to be needed? (https://github.com/HARPgroup/HSPsquared/blob/f1103a929f96c6f77c0dc112878a77bcdeb46a74/src/hsp2/hsp2tools/readUCI.py#L312)
in operation() beginning on lines 770, 812 & 840

@PaulDudaRESPEC

Hey @PaulDudaRESPEC tagging you here since I know that you've worked on the model parameter defaults code a bit. At first glance (and I truly just looked at this code for the first time last week), there appears to be multiple locations for model parameter defaults, and in some cases they are not identical. So, I think this is an opportunity to clean stuff up, and I'll take some time to do so if I can get some guidance.

Primary location for parameter names and defaults: https://github.com/HARPgroup/HSPsquared/blob/develop-state-class/src/hsp2/hsp2tools/data/ParseTable.csv
- Personally, I conceptually prefer this location of defaults and names since it is a single location, and NOT in code.
- Second benefit of this file, is that it provides a template for other CSV/pandas based model parameterization. I wonder what @austinorr thinks about this, but seems to me that it suits that pandas objective, i.e., load a CSV into your pandas to insure that you have a working base case to build off.
Secondary locations for parameterization is within the readUCI() function, see lines with annotation "Fix missing data" beginning here
- So, the big need here IMO is to put defaults into a single place, and as noted I would prefer to remove the code blocks that provide hard-wired defaults, and replace with entries in the CSV.
- Note: the default for PETMIN = 0.35 in code, and 35.0 in the CSV. Someone please advise on this.
Renaming: see also my comments above to @timcera -- I think there are opportunities to consolidate code into a single place here and that would be very good.

I obviously bit off more than I can chew, and I kept on expanding the scope (especially after learning a little bit about IOManager), but a lot of stuff is already coded up and mostly working in timcera@62003c0

The new src/hsp2/data/Parameters.csv and src/hsp2/data/Tables.csv were created from the HSPF *.seq files. The Parameters.csv holds metric and english defaults and min/max for each parameter along with the fixed width columns that should be read. For reading the UCI file I use pd.read_fwf with the columns from Parameters.csv.

There is other stuff in there also including a new idea for processing the SPECIAL-ACTIONS block.

@timcera

Hey @timcera -- OK, I propose that I will simply accept that the update_uci() function works once only for the time being, under the assumption that your new UCI code will sort out the redundant renaming issue, and I will verify that when you put up a completely working branch. I'll keep this issue open in the meantime and reference your branch in the top of the issue.

But for my edification, what is the fate of all this renaming in the current code, and how does your code handle this going forward?

Also, the PETMIN is 35 in your Parameters.CSV, and as I noted above in the comment to @PaulDudaRESPEC there is a disagreement in code where PETMIN is set to 0.35 (in current develop branch). Just thinking through this, the PETMIN is described in the manual as Temperature at and below which ET will be zero (deg F)... Use the default of 35 as an initial value..., so 35 seems to be right, so consider yours as fixing that bug :). https://www.epa.gov/sites/default/files/2015-08/documents/2000_08_14_basins_tecnote6.pdf

Taking on the simplest answer first, yes, 35.0 is the correct default for PETMIN. I can only guess that this was a typo in the python from the beginning and hasn't been caught since hitting that line of the code would only happen if that input table is left out of a UCI.

I believe those python-coded defaults are needed in instances where the entire corresponding table is left out of the UCI, as opposed to the instances where a particular parameter value is left blank in a UCI table (which is the case covered by the values in parameters.csv).... and where the values are needed based on some other conditional flag somewhere. We wouldn't want to instantiate every possible HSPF parameter value from every table because the majority of the parameters are unused in any given HSPF model for features that are not being used in that model. So there's some logic needed somewhere to determine if the default values for a parameter need to be set. There may be a better way to do that, and I'm sure expediency was part of why it was done in python that way.

With regard to all the renaming, I can think of a couple of design decisions that at least partially explain all that.

PKSNOW refers to the initial condition, the initial quantity of snow in the pack. PACKF is the output timeseries of snow in the pack. An early HSP2 design decision must have been see how those names (in most cases the HSPF variable names) are related, see that the initial value of PACKF is PKSNOW, and decide to name them the same thing.

Other instances of the renaming have to do with the feature of HSP2 that allows for pretty much any input parameter to be a timeseries. Instead of 12 monthly NSURM values in table MON-MANNINGS for instance, HSP2 creates a full timeseries of NSUR values; if a user wants to input a different NSUR value for each timestep of the simulation they have the power to do that in HSP2. So where HSPF had parameters representing NSUR as a constant and NSURM as 12 monthly values, HSP2 calls them all NSUR as a timeseries.

This is a far ranging discussion, but I think most of these issues are resolved in #225.

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Bug: readUCI() renames columns before setting defaults, which creates duplicate columns #201

Testing:

Get Branch branch:

First Import and Run

First Update with longer sim and Run

2nd Update (back to shorter duration) and Run

Analysis

The Entire Code as command line runnable test

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Bug: readUCI() renames columns before setting defaults, which creates duplicate columns #201

Description

Testing:

Get Branch branch:

First Import and Run

First Update with longer sim and Run

2nd Update (back to shorter duration) and Run

Analysis

The Entire Code as command line runnable test

Activity

rburghol commented on Jan 2, 2026

rburghol commented on Jan 5, 2026

timcera commented on Jan 5, 2026

rburghol commented on Jan 5, 2026

PaulDudaRESPEC commented on Jan 7, 2026

PaulDudaRESPEC commented on Jan 7, 2026

timcera commented on Jul 8, 2026

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