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fix(createpackages): avoid creating invalid escape characters (#1055) 

* Fix latex escape characters in description processing with math
* Replace latex characters to plaintext for Python
* Replace several other latex items involving \citep and \ref
  that are specific to mfio.pdf
develop
Mike Taves 2021-02-18 13:12:26 +13:00 committed by GitHub
parent f633012d77
commit 8a2cffb052
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GPG Key ID: 4AEE18F83AFDEB23
14 changed files with 109 additions and 98 deletions
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3
.flake8
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@ -31,7 +31,6 @@ ignore =
W293, # blank line contains whitespace
W391, # blank line at end of file
W503, # line break before binary operator
W504, # line break after binary operator
W605 # invalid escape sequence
W504 # line break after binary operator
statistics = True

20
flopy/mf6/data/mfstructure.py
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@ -1037,10 +1037,24 @@ class MFDataItemStructure(object):
self.description = " ".join(arr_line[1:])
# clean self.description
self.description = self.description.replace("``", '"')
self.description = self.description.replace("''", '"')
replace_pairs = [
("``", '"'), # double quotes
("''", '"'),
("`", "'"), # single quotes
("~", " "), # non-breaking space
(r"\mf", "MODFLOW 6"),
(r"\citep{konikow2009}", "(Konikow et al., 2009)"),
(r"\citep{hill1990preconditioned}", "(Hill, 1990)"),
(r"\ref{table:ftype}", "in mf6io.pdf"),
(r"\ref{table:gwf-obstypetable}", "in mf6io.pdf"),
]
for s1, s2 in replace_pairs:
if s1 in self.description:
self.description = self.description.replace(s1, s2)
# massage latex equations
self.description = self.description.replace("$<$", "<")
self.description = self.description.replace("$>$", ">")
if "$" in self.description:
descsplit = self.description.split("$")
mylist = [
@ -1050,7 +1064,7 @@ class MFDataItemStructure(object):
+ "`"
for i, j in zip(descsplit[::2], descsplit[1::2])
]
mylist.append(descsplit[-1])
mylist.append(descsplit[-1].replace("\\", ""))
self.description = "".join(mylist)
else:
self.description = self.description.replace("\\", "")

4
flopy/mf6/modflow/mfgwf.py
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@ -51,8 +51,8 @@ class ModflowGwf(mfmodel.MFModel):
Newton-Raphson UNDER_RELAXATION is not applied.
packages : [ftype, fname, pname]
* ftype (string) is the file type, which must be one of the following
character values shown in table~ref{table:ftype}. Ftype may be
entered in any combination of uppercase and lowercase.
character values shown in table in mf6io.pdf. Ftype may be entered in
any combination of uppercase and lowercase.
* fname (string) is the name of the file containing the package input.
The path to the file should be included if the file is not located in
the folder where the program was run.

5
flopy/mf6/modflow/mfgwfgwf.py
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@ -131,9 +131,8 @@ class ModflowGwfgwf(mfpackage.MFPackage):
* cl2 (double) is the distance between the center of cell 2 and the its
shared face with cell 1.
* hwva (double) is the horizontal width of the flow connection between
cell 1 and cell 2 if IHC :math:`>` 0, or it is the area perpendicular
to flow of the vertical connection between cell 1 and cell 2 if IHC =
0.
cell 1 and cell 2 if IHC > 0, or it is the area perpendicular to flow
of the vertical connection between cell 1 and cell 2 if IHC = 0.
* aux (double) represents the values of the auxiliary variables for
each GWFGWF Exchange. The values of auxiliary variables must be
present for each exchange. The values must be specified in the order

14
flopy/mf6/modflow/mfgwflak.py
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@ -353,13 +353,13 @@ class ModflowGwflak(mfpackage.MFPackage):
* rate (string) real or character value that defines the
extraction rate for the lake outflow. A positive value
indicates inflow and a negative value indicates outflow from
the lake. RATE only applies to active (IBOUND :math:`>` 0)
lakes. A specified RATE is only applied if COUTTYPE for the
OUTLETNO is SPECIFIED. If the Options block includes a
TIMESERIESFILE entry (see the "Time-Variable Input" section),
values can be obtained from a time series by entering the
time-series name in place of a numeric value. By default, the
RATE for each SPECIFIED lake outlet is zero.
the lake. RATE only applies to active (IBOUND > 0) lakes. A
specified RATE is only applied if COUTTYPE for the OUTLETNO
is SPECIFIED. If the Options block includes a TIMESERIESFILE
entry (see the "Time-Variable Input" section), values can be
obtained from a time series by entering the time-series name
in place of a numeric value. By default, the RATE for each
SPECIFIED lake outlet is zero.
invert : [string]
* invert (string) real or character value that defines the
invert elevation for the lake outlet. A specified INVERT

30
flopy/mf6/modflow/mfgwfmaw.py
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@ -281,12 +281,12 @@ class ModflowGwfmaw(mfpackage.MFPackage):
* rate (double) is the volumetric pumping rate for the multi-
aquifer well. A positive value indicates recharge and a
negative value indicates discharge (pumping). RATE only
applies to active (IBOUND :math:`>` 0) multi-aquifer wells.
If the Options block includes a TIMESERIESFILE entry (see the
"Time-Variable Input" section), values can be obtained from a
time series by entering the time-series name in place of a
numeric value. By default, the RATE for each multi-aquifer
well is zero.
applies to active (IBOUND > 0) multi-aquifer wells. If the
Options block includes a TIMESERIESFILE entry (see the "Time-
Variable Input" section), values can be obtained from a time
series by entering the time-series name in place of a numeric
value. By default, the RATE for each multi-aquifer well is
zero.
well_head : [double]
* well_head (double) is the head in the multi-aquifer well.
WELL_HEAD is only applied to constant head (STATUS is
@ -300,15 +300,15 @@ class ModflowGwfmaw(mfpackage.MFPackage):
* head_limit (string) is the limiting water level (head) in the
well, which is the minimum of the well RATE or the well
inflow rate from the aquifer. HEAD_LIMIT can be applied to
extraction wells (RATE :math:`<` 0) or injection wells (RATE
:math:`>` 0). HEAD\_LIMIT can be deactivated by specifying
the text string `OFF'. The HEAD\_LIMIT option is based on the
HEAD\_LIMIT functionality available in the
MNW2~\citep{konikow2009} package for MODFLOW-2005. The
HEAD\_LIMIT option has been included to facilitate backward
compatibility with previous versions of MODFLOW but use of
the RATE\_SCALING option instead of the HEAD\_LIMIT option is
recommended. By default, HEAD\_LIMIT is `OFF'.
extraction wells (RATE < 0) or injection wells (RATE > 0).
HEAD_LIMIT can be deactivated by specifying the text string
'OFF'. The HEAD_LIMIT option is based on the HEAD_LIMIT
functionality available in the MNW2 (Konikow et al., 2009)
package for MODFLOW-2005. The HEAD_LIMIT option has been
included to facilitate backward compatibility with previous
versions of MODFLOW but use of the RATE_SCALING option
instead of the HEAD_LIMIT option is recommended. By default,
HEAD_LIMIT is 'OFF'.
shutoffrecord : [minrate, maxrate]
* minrate (double) is the minimum rate that a well must exceed
to shutoff a well during a stress period. The well will shut

4
flopy/mf6/modflow/mfgwfnam.py
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@ -44,8 +44,8 @@ class ModflowGwfnam(mfpackage.MFPackage):
Newton-Raphson UNDER_RELAXATION is not applied.
packages : [ftype, fname, pname]
* ftype (string) is the file type, which must be one of the following
character values shown in table~ref{table:ftype}. Ftype may be
entered in any combination of uppercase and lowercase.
character values shown in table in mf6io.pdf. Ftype may be entered in
any combination of uppercase and lowercase.
* fname (string) is the name of the file containing the package input.
The path to the file should be included if the file is not located in
the folder where the program was run.

43
flopy/mf6/modflow/mfgwfnpf.py
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@ -94,12 +94,11 @@ class ModflowGwfnpf(mfpackage.MFPackage):
icelltype : [integer]
* icelltype (integer) flag for each cell that specifies how saturated
thickness is treated. 0 means saturated thickness is held constant;
:math:`>`0 means saturated thickness varies with computed head when
head is below the cell top; :math:`<`0 means saturated thickness
varies with computed head unless the THICKSTRT option is in effect.
When THICKSTRT is in effect, a negative value of icelltype indicates
that saturated thickness will be computed as STRT-BOT and held
constant.
>0 means saturated thickness varies with computed head when head is
below the cell top; <0 means saturated thickness varies with computed
head unless the THICKSTRT option is in effect. When THICKSTRT is in
effect, a negative value of icelltype indicates that saturated
thickness will be computed as STRT-BOT and held constant.
k : [double]
* k (double) is the hydraulic conductivity. For the common case in
which the user would like to specify the horizontal hydraulic
@ -108,8 +107,8 @@ class ModflowGwfnpf(mfpackage.MFPackage):
assigned as the vertical hydraulic conductivity, and K22 and the
three rotation angles should not be specified. When more
sophisticated anisotropy is required, then K corresponds to the K11
hydraulic conductivity axis. All included cells (IDOMAIN :math:`>` 0)
must have a K value greater than zero.
hydraulic conductivity axis. All included cells (IDOMAIN > 0) must
have a K value greater than zero.
k22 : [double]
* k22 (double) is the hydraulic conductivity of the second ellipsoid
axis (or the ratio of K22/K if the K22OVERK option is specified); for
@ -120,15 +119,15 @@ class ModflowGwfnpf(mfpackage.MFPackage):
conductivity along columns in the y direction. For an unstructured
DISU grid, the user must assign principal x and y axes and provide
the angle for each cell face relative to the assigned x direction.
All included cells (IDOMAIN :math:`>` 0) must have a K22 value
greater than zero.
All included cells (IDOMAIN > 0) must have a K22 value greater than
zero.
k33 : [double]
* k33 (double) is the hydraulic conductivity of the third ellipsoid
axis (or the ratio of K33/K if the K33OVERK option is specified); for
an unrotated case, this is the vertical hydraulic conductivity. When
anisotropy is applied, K33 corresponds to the K33 tensor component.
All included cells (IDOMAIN :math:`>` 0) must have a K33 value
greater than zero.
All included cells (IDOMAIN > 0) must have a K33 value greater than
zero.
angle1 : [double]
* angle1 (double) is a rotation angle of the hydraulic conductivity
tensor in degrees. The angle represents the first of three sequential
@ -172,16 +171,16 @@ class ModflowGwfnpf(mfpackage.MFPackage):
wetdry : [double]
* wetdry (double) is a combination of the wetting threshold and a flag
to indicate which neighboring cells can cause a cell to become wet.
If WETDRY :math:`<` 0, only a cell below a dry cell can cause the
cell to become wet. If WETDRY :math:`>` 0, the cell below a dry cell
and horizontally adjacent cells can cause a cell to become wet. If
WETDRY is 0, the cell cannot be wetted. The absolute value of WETDRY
is the wetting threshold. When the sum of BOT and the absolute value
of WETDRY at a dry cell is equaled or exceeded by the head at an
adjacent cell, the cell is wetted. WETDRY must be specified if
"REWET" is specified in the OPTIONS block. If "REWET" is not
specified in the options block, then WETDRY can be entered, and
memory will be allocated for it, even though it is not used.
If WETDRY < 0, only a cell below a dry cell can cause the cell to
become wet. If WETDRY > 0, the cell below a dry cell and horizontally
adjacent cells can cause a cell to become wet. If WETDRY is 0, the
cell cannot be wetted. The absolute value of WETDRY is the wetting
threshold. When the sum of BOT and the absolute value of WETDRY at a
dry cell is equaled or exceeded by the head at an adjacent cell, the
cell is wetted. WETDRY must be specified if "REWET" is specified in
the OPTIONS block. If "REWET" is not specified in the options block,
then WETDRY can be entered, and memory will be allocated for it, even
though it is not used.
filename : String
File name for this package.
pname : String

20
flopy/mf6/modflow/mfgwfsfr.py
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@ -114,11 +114,11 @@ class ModflowGwfsfr(mfpackage.MFPackage):
working with FloPy and Python. Flopy will automatically subtract one
when loading index variables and add one when writing index
variables.
* cellid ((integer, ...)) The keyword `NONE' must be specified for
* cellid ((integer, ...)) The keyword 'NONE' must be specified for
reaches that are not connected to an underlying GWF cell. The keyword
`NONE' is used for reaches that are in cells that have IDOMAIN values
'NONE' is used for reaches that are in cells that have IDOMAIN values
less than one or are in areas not covered by the GWF model grid.
Reach-aquifer flow is not calculated if the keyword `NONE' is
Reach-aquifer flow is not calculated if the keyword 'NONE' is
specified. This argument is an index variable, which means that it
should be treated as zero-based when working with FloPy and Python.
Flopy will automatically subtract one when loading index variables
@ -132,11 +132,11 @@ class ModflowGwfsfr(mfpackage.MFPackage):
* rtp (double) real value that defines the top elevation of the reach
streambed.
* rbth (double) real value that defines the thickness of the reach
streambed. RBTH can be any value if CELLID is `NONE'. Otherwise, RBTH
streambed. RBTH can be any value if CELLID is 'NONE'. Otherwise, RBTH
must be greater than zero.
* rhk (double) real value that defines the hydraulic conductivity of
the reach streambed. RHK can be any positive value if CELLID is
`NONE'. Otherwise, RHK must be greater than zero.
'NONE'. Otherwise, RHK must be greater than zero.
* man (string) real or character value that defines the Manning's
roughness coefficient for the reach. MAN must be greater than zero.
If the Options block includes a TIMESERIESFILE entry (see the "Time-
@ -223,23 +223,23 @@ class ModflowGwfsfr(mfpackage.MFPackage):
water is available to meet all diversion stipulations, and is used in
conjunction with the value of FLOW value specified in the
STRESS_PERIOD_DATA section. Available diversion options include: (1)
CPRIOR = `FRACTION', then the amount of the diversion is computed as
CPRIOR = 'FRACTION', then the amount of the diversion is computed as
a fraction of the streamflow leaving reach RNO (:math:`Q_{DS}`); in
this case, 0.0 :math:`\\le` DIVFLOW :math:`\\le` 1.0. (2) CPRIOR =
`EXCESS', a diversion is made only if :math:`Q_{DS}` for reach RNO
'EXCESS', a diversion is made only if :math:`Q_{DS}` for reach RNO
exceeds the value of DIVFLOW. If this occurs, then the quantity of
water diverted is the excess flow (:math:`Q_{DS} -` DIVFLOW) and
:math:`Q_{DS}` from reach RNO is set equal to DIVFLOW. This
represents a flood-control type of diversion, as described by Danskin
and Hanson (2002). (3) CPRIOR = `THRESHOLD', then if :math:`Q_{DS}`
and Hanson (2002). (3) CPRIOR = 'THRESHOLD', then if :math:`Q_{DS}`
in reach RNO is less than the specified diversion flow (DIVFLOW), no
water is diverted from reach RNO. If :math:`Q_{DS}` in reach RNO is
greater than or equal to (DIVFLOW), (DIVFLOW) is diverted and
:math:`Q_{DS}` is set to the remainder (:math:`Q_{DS} -` DIVFLOW)).
This approach assumes that once flow in the stream is sufficiently
low, diversions from the stream cease, and is the `priority'
low, diversions from the stream cease, and is the 'priority'
algorithm that originally was programmed into the STR1 Package
(Prudic, 1989). (4) CPRIOR = `UPTO' -- if :math:`Q_{DS}` in reach RNO
(Prudic, 1989). (4) CPRIOR = 'UPTO' -- if :math:`Q_{DS}` in reach RNO
is greater than or equal to the specified diversion flow (DIVFLOW),
:math:`Q_{DS}` is reduced by DIVFLOW. If :math:`Q_{DS}` in reach RNO
is less than (DIVFLOW), DIVFLOW is set to :math:`Q_{DS}` and there

6
flopy/mf6/modflow/mfgwfsto.py
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@ -26,9 +26,9 @@ class ModflowGwfsto(mfpackage.MFPackage):
iconvert : [integer]
* iconvert (integer) is a flag for each cell that specifies whether or
not a cell is convertible for the storage calculation. 0 indicates
confined storage is used. :math:`>`0 indicates confined storage is
used when head is above cell top and a mixed formulation of
unconfined and confined storage is used when head is below cell top.
confined storage is used. >0 indicates confined storage is used when
head is above cell top and a mixed formulation of unconfined and
confined storage is used when head is below cell top.
ss : [double]
* ss (double) is specific storage (or the storage coefficient if
STORAGECOEFFICIENT is specified as an option). Specific storage

4
flopy/mf6/modflow/mfgwfuzf.py
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@ -217,8 +217,8 @@ class ModflowGwfuzf(mfpackage.MFPackage):
a given volume of soil divided by that volume. Values range from 0 to
about 3 :math:`cm^{-2}`, depending on the plant community and its
stage of development. ROOTACT is always specified, but is only used
if SIMULATE\_ET and UNSAT\_ETAE are specified in the OPTIONS block.
If the Options block includes a TIMESERIESFILE entry (see the "Time-
if SIMULATE_ET and UNSAT_ETAE are specified in the OPTIONS block. If
the Options block includes a TIMESERIESFILE entry (see the "Time-
Variable Input" section), values can be obtained from a time series
by entering the time-series name in place of a numeric value.
* aux (double) represents the values of the auxiliary variables for

4
flopy/mf6/modflow/mfgwt.py
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@ -46,8 +46,8 @@ class ModflowGwt(mfmodel.MFModel):
Output Control.
packages : [ftype, fname, pname]
* ftype (string) is the file type, which must be one of the following
character values shown in table~ref{table:ftype}. Ftype may be
entered in any combination of uppercase and lowercase.
character values shown in table in mf6io.pdf. Ftype may be entered in
any combination of uppercase and lowercase.
* fname (string) is the name of the file containing the package input.
The path to the file should be included if the file is not located in
the folder where the program was run.

4
flopy/mf6/modflow/mfgwtnam.py
View File

@ -39,8 +39,8 @@ class ModflowGwtnam(mfpackage.MFPackage):
Output Control.
packages : [ftype, fname, pname]
* ftype (string) is the file type, which must be one of the following
character values shown in table~ref{table:ftype}. Ftype may be
entered in any combination of uppercase and lowercase.
character values shown in table in mf6io.pdf. Ftype may be entered in
any combination of uppercase and lowercase.
* fname (string) is the name of the file containing the package input.
The path to the file should be included if the file is not located in
the folder where the program was run.

46
flopy/mf6/modflow/mfims.py
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@ -201,8 +201,8 @@ class ModflowIms(mfpackage.MFPackage):
residual increases, while a low value serves to control step size
more severely. The value usually ranges from 1.0 to 10:math:`^6`; a
value of 10:math:`^4` works well for most problems but lower values
like 1.1 may be required for harder problems. BACKTRACKING\_TOLERANCE
only needs to be specified if BACKTRACKING\_NUMBER is greater than
like 1.1 may be required for harder problems. BACKTRACKING_TOLERANCE
only needs to be specified if BACKTRACKING_NUMBER is greater than
zero.
backtracking_reduction_factor : double
* backtracking_reduction_factor (double) real value defining the
@ -254,32 +254,32 @@ class ModflowIms(mfpackage.MFPackage):
tolerance for convergence of the IMS linear solver and specific flow
residual criteria used. This value represents the maximum allowable
residual at any single node. Value is in units of length cubed per
time, and must be consistent with mf length and time units. Usually a
value of :math:`1.0 \\times 10^{-1}` is sufficient for the flow-
residual criteria when meters and seconds are the defined \mf length
and time.
time, and must be consistent with MODFLOW 6 length and time units.
Usually a value of :math:`1.0 \\times 10^{-1}` is sufficient for the
flow-residual criteria when meters and seconds are the defined
MODFLOW 6 length and time.
* rclose_option (string) an optional keyword that defines the specific
flow residual criterion used. STRICT--an optional keyword that is
used to specify that INNER_RCLOSE represents a infinity-Norm
(absolute convergence criteria) and that the dependent-variable (for
example, head) and flow convergence criteria must be met on the first
inner iteration (this criteria is equivalent to the criteria used by
the MODFLOW-2005 PCG package~citep{hill1990preconditioned}).
L2NORM_RCLOSE--an optional keyword that is used to specify that
INNER_RCLOSE represents a L-2 Norm closure criteria instead of a
infinity-Norm (absolute convergence criteria). When L2NORM_RCLOSE is
specified, a reasonable initial INNER_RCLOSE value is 0.1 times the
number of active cells when meters and seconds are the defined mf
length and time. RELATIVE_RCLOSE--an optional keyword that is used to
specify that INNER_RCLOSE represents a relative L-2 Norm reduction
closure criteria instead of a infinity-Norm (absolute convergence
criteria). When RELATIVE_RCLOSE is specified, a reasonable initial
INNER_RCLOSE value is :math:`1.0 \\times 10^{-4}` and convergence is
achieved for a given inner (linear) iteration when :math:`\\Delta h
\\le` INNER_DVCLOSE and the current L-2 Norm is :math:`\\le` the
product of the RELATIVE\_RCLOSE and the initial L-2 Norm for the
current inner (linear) iteration. If RCLOSE\_OPTION is not specified,
an absolute residual (infinity-norm) criterion is used.
the MODFLOW-2005 PCG package (Hill, 1990)). L2NORM_RCLOSE--an
optional keyword that is used to specify that INNER_RCLOSE represents
a L-2 Norm closure criteria instead of a infinity-Norm (absolute
convergence criteria). When L2NORM_RCLOSE is specified, a reasonable
initial INNER_RCLOSE value is 0.1 times the number of active cells
when meters and seconds are the defined MODFLOW 6 length and time.
RELATIVE_RCLOSE--an optional keyword that is used to specify that
INNER_RCLOSE represents a relative L-2 Norm reduction closure
criteria instead of a infinity-Norm (absolute convergence criteria).
When RELATIVE_RCLOSE is specified, a reasonable initial INNER_RCLOSE
value is :math:`1.0 \\times 10^{-4}` and convergence is achieved for
a given inner (linear) iteration when :math:`\\Delta h \\le`
INNER_DVCLOSE and the current L-2 Norm is :math:`\\le` the product of
the RELATIVE_RCLOSE and the initial L-2 Norm for the current inner
(linear) iteration. If RCLOSE_OPTION is not specified, an absolute
residual (infinity-norm) criterion is used.
linear_acceleration : string
* linear_acceleration (string) a keyword that defines the linear
acceleration method used by the default IMS linear solvers. CG -
@ -312,7 +312,7 @@ class ModflowIms(mfpackage.MFPackage):
defines the drop tolerance used to drop preconditioner terms based on
the magnitude of matrix entries in the ILUT and MILUT
preconditioners. A value of :math:`10^{-4}` works well for most
problems. By default, PRECONDITIONER\_DROP\_TOLERANCE is zero and the
problems. By default, PRECONDITIONER_DROP_TOLERANCE is zero and the
zero-fill incomplete LU factorization preconditioners (ILU(0) and
MILU(0)) are used.
number_orthogonalizations : integer