pymake Documentation¶

This is a python package for compiling MODFLOW-based and other Fortran, C, and C++ programs. The package determines the build order using a directed acyclic graph and then compiles the source files using GNU compilers (gcc, g++, gfortran) or Intel compilers (ifort, icc).

pymake can be run from the command line or it can be called from within python. By default, pymake sets the optimization level, Fortran flags, C/C++ flags, and linker flags that are consistent with those used to compile MODFLOW-based programs released by the USGS.

pymake includes example scripts for building MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, MODFLOW-LGR, MODFLOW-2000, MODPATH 6, MODPATH 7, GSFLOW, VS2DT, MT3DMS, MT3D-USGS, SEAWAT, and SUTRA. Example scripts for creating the utility programs CRT, Triangle, and GRIDGEN are also included. The scripts download the distribution file from the USGS (and other organizations) and compile the source into a binary executable.

The main documentation for the site is organized into the following sections:

Getting Started¶

Pymake can be used directly from the command line and within a python script. Examples of both use cases are given below.

Command Line Usage¶

pymake can be used to compile MODFLOW 6 directly from the command line using the Intel Fortran compiler ifort from a subdirectory at the same level as the src subdirectory by specifying:

python -m pymake ../src/ ../bin/mf6 -mc --subdirs -fc ifort

To see help for running from command line, use the following statement.

python -m pymake -h

The help message identifies required positional arguments and optional arguments that can be provided to overide default values.

usage: __main__.py [-h] [-fc {ifort,mpiifort,gfortran,ftn,none}] [-cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}] [-ar {ia32,ia32_intel64,intel64}] [-mc] [-dbl] [-dbg] [-e] [-dr] [-sd] [-ff FFLAGS] [-cf CFLAGS] [-sl {-lc,-lm}] [-mf] [-md] [-cs COMMONSRC] [-ef EXTRAFILES] [-exf EXCLUDEFILES] [-so]
                   [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--inplace] [--networkx] [--mb] [-mbd]
                   srcdir target

This is the pymake program for compiling fortran, c, and c++ source files, such as the source files that come with MODFLOW. The program works by building a directed acyclic graph of the module dependencies and then compiling the source files in the proper order.

positional arguments:
  srcdir                Path source directory.
  target                Name of target to create. (can include path)

optional arguments:
  -h, --help            show this help message and exit
  -fc {ifort,mpiifort,gfortran,ftn,none}
                        Fortran compiler to use. (default is gfortran)
  -cc {gcc,clang,clang++,icc,icl,mpiicc,g++,cl,none}
                        C/C++ compiler to use. (default is gcc)
  -ar {ia32,ia32_intel64,intel64}, --arch {ia32,ia32_intel64,intel64}
                        Architecture to use for Intel and Microsoft compilers on Windows. (default is intel64)
  -mc, --makeclean      Clean temporary object, module, and source files when done. (default is False)
  -dbl, --double        Force double precision. (default is False)
  -dbg, --debug         Create debug version. (default is False)
  -e, --expedite        Only compile out of date source files. Clean must not have been used on previous build. (default is False)
  -dr, --dryrun         Do not actually compile. Files will be deleted, if --makeclean is used. Does not work yet for ifort. (default is False)
  -sd, --subdirs        Include source files in srcdir subdirectories. (default is None)
  -ff FFLAGS, --fflags FFLAGS
                        Additional Fortran compiler flags. Fortran compiler flags should be enclosed in quotes and start with a blank space or separated from the name (-ff or --fflags) with a equal sign (-ff='-O3'). (default is None)
  -cf CFLAGS, --cflags CFLAGS
                        Additional C/C++ compiler flags. C/C++ compiler flags should be enclosed in quotes and start with a blank space or separated from the name (-cf or --cflags) with a equal sign (-cf='-O3'). (default is None)
  -sl {-lc,-lm}, --syslibs {-lc,-lm}
                        Linker system libraries. Linker libraries should be enclosed in quotes and start with a blank space or separated from the name (-sl or --syslibs) with a equal sign (-sl='-libgcc'). (default is None)
  -mf, --makefile       Create a GNU make makefile. (default is False)
  -md, --makefile-dir   GNU make makefile directory. (default is '.')
  -cs COMMONSRC, --commonsrc COMMONSRC
                        Additional directory with common source files. (default is None)
  -ef EXTRAFILES, --extrafiles EXTRAFILES
                        List of extra source files to include in the compilation. extrafiles can be either a list of files or the name of a text file that contains a list of files. (default is None)
  -exf EXCLUDEFILES, --excludefiles EXCLUDEFILES
                        List of extra source files to exclude from the compilation. excludefiles can be either a list of files or the name of a text file that contains a list of files. (default is None)
  -so, --sharedobject   Create shared object or dll on Windows. (default is False)
  -ad APPDIR, --appdir APPDIR
                        Target path that overides path defined target path (default is None)
  -v, --verbose         Verbose output to terminal. (default is False)
  --keep                Keep existing executable. (default is False)
  --zip ZIP             Zip built executable. (default is False)
  --inplace             Source files in srcdir are used directly. (default is False)
  --networkx            Use networkx package to build Directed Acyclic Graph use to determine the order source files are compiled in. (default is False)
  --mb, --meson-build   Use meson to build executable. (default is False)
  -mbd, --mesonbuild-dir
                        meson directory. (default is '.')

Note that the source directory should not contain any bad or duplicate source files as all source files in the source directory, the common source file directory (srcdir2), and the extra files (extrafiles) will be built and linked. Files can be excluded by using the excludefiles command line switch.

Note that command line arguments for Fortran flags, C/C++ flags, and syslib libraries should be enclosed in quotes and start with a space prior to the first value (-ff ' -O3') or use an equal sign separating the command line argument and the values (-ff='-O3'). The command line argument to use an -O3 optimization level when compiling MODFLOW 6 with the ifort compiler would be:

python -m pymake ../src/ ../bin/mf6 -mc --subdirs -fc ifort -ff='-O3'

From Python¶

Script to compile MODFLOW 6¶

When using the pymake object (Pymake()) only the positional arguments (srcdir, target) need to be specified in the script.

import pymake
pm = pymake.Pymake()
pm.srcdir = '../src'
pm.target = 'mf6'
pm.include_subdirs = True
pm.build()

It is suggested that optional variables required for successful compiling and linking be manually specified in the script to mininimize the potential for unsuccessful builds. For MODFLOW 6, subdirectories in the src subdirectory need to be included and ‘pm.include_subdirs = True’ has been specified in the script. Custom optimization levels and compiler flags could be specified to get consistent builds.

Non-default values for the optional arguments can specified as command line arguments. For example, MODFLOW 6 could be compiled using Intel compilers instead of the default GNU compilers with the script listed above by specifying:

python mymf6script.py -fc ifort -cc icc

Notes¶

If gfortran is used to compile MODFLOW-based codes, the openspec.f and FILESPEC.inc (MT3DMS) files will automatically be changed to the following so that binary files are created properly using standard Fortran:

c -- created by pymake.py
CHARACTER*20 ACCESS,FORM,ACTION(2)
DATA ACCESS/'STREAM'/
DATA FORM/'UNFORMATTED'/
DATA (ACTION(I),I=1,2)/'READ','READWRITE'/
c -- end of include file

Use of STREAM access does not delete an existing unformatted file before opening it for writing. As a result, data from previous runs may exist in the file if the model is run for a shorter period of time. This does not apply to MODFLOW 6 simulations.

pymake Installation¶

To install a stable version from PyPI:

pip install mfpymake

To install pymake directly from the git repository type:

pip install https://github.com/modflowpy/pymake/zipball/master

To update your version of pymake with the latest from the git repository type:

pip install https://github.com/modflowpy/pymake/zipball/master --upgrade

Building Applications¶

The following scripts can be run directly from the command line to build MODFLOW 6, MODFLOW-2005, MODFLOW-NWT, MODFLOW-USG, MODFLOW-LGR, MODFLOW-2000, MODPATH 6, MODPATH 7, MT3DMS, MT3D-USGS, and SEAWAT binaries on Linux, Mac, and Windows. The scripts will download the distribution file from the USGS (requires internet connection), unzip the file, and compile the source.MT3DMS will be downloaded from the University of Alabama and Triangle will be downloaded from netlib.org. The scripts use the pymake.build_apps() method which download and unzip the distribution files and set all of the pymake settings required to build the program. Available example scripts include:

make_modflow6.py
make_mf2005.py
make_mfnwt.py
make_mfusg.py
make_mflgr.py
make_mf2000.py
make_modpath6.py
make_modpath7.py
make_gsflow.py
make_vs2dt.py
make_mt3d.py
make_mt3dusgs.py
make_swtv4.py
make_crt.py
make_gridgen.py
make_triangle.py

Optional command line arguments can be used to customize the build (-fc, -cc, --fflags, etc.). MODFLOW 6 could be built using intel compilers and an O3 optimation level by specifying:

python make_mf6.py -fc=ifort --fflags='-O3'

API-docs¶

This section contains the Documentation of the Application Programming Interface (API) of pymake. The information in this section is automatically created from the documentation strings in original Python code. In the left-hand menu you will find the different categories of the API documentation.

pymake.pymake module¶

Pymake() class to make a binary executable for a FORTRAN, C, or C++ program, such as MODFLOW 6.

An example of how to build MODFLOW-2005 from source files in the official release downloaded from the USGS using Intel compilers is:

import pymake

# create an instance of the Pymake object
pm = pymake.Pymake(verbose=True)

# reset select pymake settings
pm.target = "mf2005"
pm.appdir = "../bin"
pm.fc = "ifort"
pm.cc = "icc"
pm.fflags = "-O3 -fbacktrace"
pm.cflags = "-O3"

# download the target
pm.download_target(pm.target, download_path="temp")

# build the target
pm.build()

# clean up downloaded files
pm.finalize()

All other settings not specified in the script would be based on command line arguments or default values. The same Pymake() object could be used to compile MODFLOW 6 by appending the following code to the previous code block:

# reset the target
pm.target = "mf6"

# download the target
pm.download_target(pm.target, download_path="temp")

# build the target
pm.build()

# clean up downloaded files
pm.finalize()

The Intel compilers and fortran flags defined previously would be used when MODFLOW 6 was built.

class Pymake(name='pymake', verbose=None)[source]¶

Bases: object

Pymake class for interacting with pymake functionality. This is essentially a wrapper for all of the pymake functions needed to download and build a target.

argv_reset_settings(args)[source]¶

Reset settings using command line arguments

Parameters: args (Namespace object) – reset self.variables using command line arguments

build(target=None, srcdir=None, modify_exe_name=False)[source]¶

Build the target

Parameters

target (str) – target name. If target is None self.target is used. (default is None)
srcdir (str) – path to directory with source files. (default is None)
modify_exe_name (bool) – boolean that determines if the target name can be modified to include precision (dbl) and debugging (d) indicators.

compress_targets()[source]¶: Compress targets in build_targets list.

download_setup(target, url=None, download_path='.', verify=True, timeout=30)[source]¶

Setup download

Parameters

target (str) – target name
url (str) – url of asset
download_path (str) – path where the asset will be saved
verify (bool) – boolean defining ssl verification
timeout (int) – download timeout in seconds (default is 30)

download_target(target, url=None, download_path='.', verify=True, timeout=30)[source]¶

Setup and download url

Parameters

target (str) – target name
url (str) – url of asset
download_path (str) – path where the asset will be saved
verify (bool) – boolean defining ssl verification
timeout (int) – download timeout in seconds (default is 30)

Returns

success – boolean flag indicating download success

Return type

bool

download_url()[source]¶

Download files from the url

Returns: success – boolean flag indicating download success
Return type: bool

finalize()[source]¶: Finalize Pymake class

reset(target)[source]¶

Reset PyMake object variables for a target

Parameters: target (str) – target name

set_build_target_bool(target=None)[source]¶

Evaluate if the executable exists and if so and the command line argument –keep is specified then the executable is not built.

Parameters: target (str) – target name. If target is None self.target will be used. (default is None)
Returns: build – boolean indicating if the executable should be built
Return type: bool

update_build_targets()[source]¶: Add target to build_targets list if it is not in the list

update_target(target, modify_target=False)[source]¶

Update target name with executable extension on Windows and based on pymake settings.

Parameters

target (str) – target name
modify_target (bool) – boolean indicating if the target name can be modified based on pymake double and debug settings (default is False)

Returns

target – updated target name

Return type

str

pymake.pymake_build_apps module¶

Function to build MODFLOW-based models and other utility software based on targets defined in the usgsprograms database (usgsprograms.txt). The usgsprograms database can be queried using functions in the usgsprograms module. An example of using pymake.build_apps() to build MODFLOW 6 is:

import pymake
pymake.build_apps(["mf6",])

which will download the latest MODFLOW 6 software release, compile the code, and delete the downloaded files after successfully building the application. Multiple applications can be built by adding additional targets to the tuple in pymake.build_apps(). For example, MODFLOW 6 and MODFLOW-2005 could be built by specifying:

import pymake
pymake.build_apps(["mf6","mf2005"]))

Applications are built in the order they are listed in the list. All valid USGS applications are built if no list is passed to pymake.build_apps().

build_apps(targets=None, pymake_object=None, download_dir=None, appdir=None, verbose=None, release_precision=True, meson=False, mesondir='.', clean=True)[source]¶

Build all of the current targets or a subset of targets.

Parameters

targets (str or list of str) – targets to build. If targets is None, all current targets will be build. Default is None
pymake_object (Pymake()) – Pymake object created outside of build_apps
download_dir (str) – download directory path
appdir (str) – target path
release_precision (bool) – boolean indicating if only the release precision version should be build. If release_precision is False, then the release precision version will be compiled along with a double precision version of the program for programs where the standard_switch and double_switch in usgsprograms.txt is True. default is True.
meson (bool) – boolean indicating that the executable should be built using the meson build system. (default is False)
mesondir (str) – Main meson.build file path
clean (bool) – boolean determining of final download should be removed

Returns

returncode – integer value indicating successful completion (0) or failure (>0)

Return type

int

pymake.pymake_base module¶

Main pymake function, pymake.main(), that is called when pymake is run from the command line. pymake.main() can also be called directly from a script in combination with pymake.parser().

import pymake
args = pymake.parser()
pymake.main(
    args.srcdir,
    args.target,
    fc=args.fc,
    cc=args.cc,
    makeclean=args.makeclean,
    expedite=args.expedite,
    dryrun=args.dryrun,
    double=args.double,
    debug=args.debug,
    include_subdirs=args.subdirs,
    fflags=args.fflags,
    cflags=args.cflags,
    arch=args.arch,
    syslibs=args.syslibs,
    makefile=args.makefile,
    srcdir2=args.commonsrc,
    extrafiles=args.extrafiles,
    excludefiles=args.excludefiles,
    sharedobject=args.sharedobject,
    appdir=args.appdir,
    verbose=args.verbose,
    inplace=args.inplace,
)

The script could be run from the command line using:

python myscript.py ../src myapp -fc=ifort -cc=icc

get_temporary_directories(appdir=None)[source]¶

Get paths to temporary object, module, and source files

Parameters

appdir (str) – path for executable

Returns

obj_temp (str) – path to temporary object files
mod_temp (str) – path to temporary module files
src_temp (str) – path to temporary source files

main(srcdir=None, target=None, fc='gfortran', cc='gcc', makeclean=True, expedite=False, dryrun=False, double=False, debug=False, include_subdirs=False, fflags=None, cflags=None, syslibs=None, arch='intel64', makefile=False, makefiledir='.', srcdir2=None, extrafiles=None, excludefiles=None, sharedobject=False, appdir=None, verbose=False, inplace=False, networkx=False, meson=False, mesondir='.')[source]¶

Main pymake function.

Parameters

srcdir (str) – path for directory containing source files
target (str) – executable name or path for executable to create
fc (str) – fortran compiler
cc (str) – c or cpp compiler
makeclean (bool) – boolean indicating if intermediate files should be cleaned up after successful build
expedite (bool) – boolean indicating if only out of date source files will be compiled. Clean must not have been used on previous build.
dryrun (bool) – boolean indicating if source files should be compiled. Files will be deleted, if makeclean is True.
double (bool) – boolean indicating a compiler switch will be used to create an executable with double precision real variables.
debug (bool) – boolean indicating is a debug executable will be built
include_subdirs (bool) – boolean indicating source files in srcdir subdirectories should be included in the build
fflags (list) – user provided list of fortran compiler flags
cflags (list) – user provided list of c or cpp compiler flags
syslibs (list) – user provided syslibs
arch (str) – Architecture to use for Intel Compilers on Windows (default is intel64)
makefile (bool) – boolean indicating if a GNU make makefile should be created
makefiledir (str) – GNU make makefile path
srcdir2 (str) – additional directory with common source files.
extrafiles (str) – path for extrafiles file that contains paths to additional source files to include
excludefiles (str) – path for excludefiles file that contains filename of source files to exclude from the build
sharedobject (bool) – boolean indicating a shared object will be built
appdir (str) – path for executable
verbose (bool) – boolean indicating if output will be printed to the terminal
inplace (bool) – boolean indicating that the source files in srcdir, srcdir2, and defined in extrafiles will be used directly. If inplace is False, source files will be copied to a directory named srcdir_temp. (default is False)
networkx (bool) – boolean indicating that the NetworkX python package will be used to create the Directed Acyclic Graph (DAG) used to determine the order source files are compiled in. The NetworkX package tends to result in a unique DAG more often than the standard algorithm used in pymake. (default is False)
meson (bool) – boolean indicating that the executable should be built using the meson build system. (default is False)
mesondir (str) – Main meson.build file path

Returns

returncode – return code

Return type

int

pymake.pymake_parser module¶

Parser used to process command line arguments when running pymake directly from the command line or in a script. The standard argparse module is used to parse command line arguments. Available command line arguments are programmatically developed by a protected dictionary. The parser can be accessed using:

import pymake
args = pymake.parser()

parser()[source]¶

Construct the parser and return argument values.

Returns: args – Namespace with command line arguments
Return type: Namespace object

pymake.plot package¶

Submodules¶

pymake.plot.dependency_graphs module¶

Dependency graphs for applications can be created using:

import os
import pymake

srcpth = os.path.join("..", "src")
deppth = "dependencies"
if not os.path.exists(deppth):
    os.makedirs(deppth)

pymake.visualize.make_plots(srcpth, deppth, include_subdir=True)

make_plots(srcdir, outdir, include_subdir=False, level=3, extension='.png', verbose=False, networkx=False)[source]¶

Create plots of module dependencies.

Parameters

srcdir (str) – path for source files
outdir (str) – path for output images
include_subdir (bool) – boolean indicating is subdirectories in the source file directory should be included
level (int) – dependency level (1 is the minimum)
extension (str) – output extension (default is .png)
verbose (bool) – boolean indicating if output will be printed to the terminal
networkx (bool) – boolean indicating that the NetworkX python package will be used to create the Directed Acyclic Graph (DAG) used to determine the order source files are compiled in. The NetworkX package tends to result in a unique DAG more often than the standard algorithm used in pymake. (default is False)

to_pydot(dag, filename='mygraph.png')[source]¶

Create a png file of a Directed Acyclic Graph

Parameters

dag (object) – directed acyclic graph
filename (str) – path of the graph png

Module contents¶

Functions to plot source code dependencies determined using a directed acyclic graph (DAG). pydotplus is used to plot the DAG.

pymake.autotest package¶

Submodules¶

pymake.autotest.autotest module¶

A typical example of using the autotest functionality for MODFLOW-2005 and comparing the MODFLOW-2005 results to MODFLOW-2000 results is:

import pymake

# Setup
testpth = "../test/mytest"
nam1 = "model1.nam"
pymake.setup(nam1, testpth)

# run test models
success, buff = flopy.run_model(
        "mf2005", nam1, model_ws=testpth, silent=True
    )
if success:
    testpth_reg = os.path.join(testpth, "mf2000")
    nam2 = "model2.name"
    pymake.setup(nam2, testpth_reg)
    success_reg, buff = flopy.run_model(
            "mf2000", nam2, model_ws=testpth_reg, silent=True
        )

# compare results
if success and success_reg:
    fpth = os.path.split(os.path.join(testpth, nam1))[0]
    outfile1 = os.path.join(fpth, "bud.cmp")
    fpth = os.path.split(os.path.join(testpth, nam2))[0]
    outfile2 = os.path.join(fpth, "hds.cmp")
    success_reg = pymake.compare(
        os.path.join(testpth, nam1),
        os.path.join(testpth_reg, nam2),
        max_cumpd=0.01,
        max_incpd=0.01,
        htol=0.001,
        outfile1=outfile1,
        outfile2=outfile2,
    )

# Clean things up
if success_reg:
    pymake.teardown(testpth)

Note: autotest functionality will likely be removed from pymake in the future to a dedicated GitHub repository.

compare(namefile1, namefile2, precision='auto', max_cumpd=0.01, max_incpd=0.01, htol=0.001, outfile1=None, outfile2=None, files1=None, files2=None)[source]¶

Compare the budget and head results for two MODFLOW-based model simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
max_cumpd (float) – maximum percent discrepancy allowed for cumulative budget terms (default is 0.01)
max_incpd (float) – maximum percent discrepancy allowed for incremental budget terms (default is 0.01)
htol (float) – maximum allowed head difference (default is 0.001)
outfile1 (str) – budget comparison output file name. If outfile1 is None, no budget comparison output is saved. (default is None)
outfile2 (str) – head comparison output file name. If outfile2 is None, no head comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)

Returns

success – boolean indicating if the budget and head differences are less than max_cumpd, max_incpd, and htol.

Return type

bool

compare_budget(namefile1, namefile2, max_cumpd=0.01, max_incpd=0.01, outfile=None, files1=None, files2=None)[source]¶

Compare the budget results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
max_cumpd (float) – maximum percent discrepancy allowed for cumulative budget terms (default is 0.01)
max_incpd (float) – maximum percent discrepancy allowed for incremental budget terms (default is 0.01)
outfile (str) – budget comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)

Returns

success – boolean indicating if the difference between budgets are less than max_cumpd and max_incpd

Return type

bool

compare_concs(namefile1, namefile2, precision='auto', ctol=0.001, outfile=None, files1=None, files2=None, difftol=False, verbose=False)[source]¶

Compare the mt3dms and mt3dusgs concentration results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
ctol (float) – maximum allowed concentration difference (default is 0.001)
outfile (str) – concentration comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)
difftol (bool) – boolean determining if the absolute value of the concentration difference greater than ctol should be evaluated (default is False)
verbose (bool) – boolean indicating if verbose output should be written to the terminal (default is False)

Returns

success – boolean indicating if the concentration differences are less than ctol.

Return type

bool

compare_heads(namefile1, namefile2, precision='auto', text='head', text2=None, htol=0.001, outfile=None, files1=None, files2=None, difftol=False, verbose=False, exfile=None, exarr=None, maxerr=None)[source]¶

Compare the head results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
htol (float) – maximum allowed head difference (default is 0.001)
outfile (str) – head comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)
difftol (bool) – boolean determining if the absolute value of the head difference greater than htol should be evaluated (default is False)
verbose (bool) – boolean indicating if verbose output should be written to the terminal (default is False)
exfile (str) – path to a file with exclusion array data. Head differences will not be evaluated where exclusion array values are greater than zero. (default is None)
exarr (numpy.ndarry) – exclusion array. Head differences will not be evaluated where exclusion array values are greater than zero. (default is None).
maxerr (int) – maximum number of head difference greater than htol that should be reported. If maxerr is None, all head difference greater than htol will be reported. (default is None)

Returns

success – boolean indicating if the head differences are less than htol.

Return type

bool

compare_stages(namefile1=None, namefile2=None, files1=None, files2=None, htol=0.001, outfile=None, difftol=False, verbose=False)[source]¶

Compare SWR process stage results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
htol (float) – maximum allowed stage difference (default is 0.001)
outfile (str) – head comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)
difftol (bool) – boolean determining if the absolute value of the stage difference greater than htol should be evaluated (default is False)
verbose (bool) – boolean indicating if verbose output should be written to the terminal (default is False)

Returns

success – boolean indicating if the stage differences are less than htol.

Return type

bool

compare_swrbudget(namefile1, namefile2, max_cumpd=0.01, max_incpd=0.01, outfile=None, files1=None, files2=None)[source]¶

Compare the SWR budget results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
max_cumpd (float) – maximum percent discrepancy allowed for cumulative budget terms (default is 0.01)
max_incpd (float) – maximum percent discrepancy allowed for incremental budget terms (default is 0.01)
outfile (str) – budget comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)

Returns

success – boolean indicating if the difference between budgets are less than max_cumpd and max_incpd

Return type

bool

get_entries_from_namefile(namefile, ftype=None, unit=None, extension=None)[source]¶

Get entries from a namefile. Can select using FTYPE, UNIT, or file extension.

Parameters

namefile (str) – path to a MODFLOW-based model name file
ftype (str) – package type
unit (int) – file unit number
extension (str) – file extension

Returns

entries – list of tuples containing FTYPE, UNIT, FNAME, STATUS for each namefile entry that meets a user-specified value.

Return type

list of tuples

get_input_files(namefile)[source]¶

Return a list of all the input files in this model.

Parameters: namefile (str) – path to a MODFLOW-based model name file
Returns: filelist – list of MODFLOW-based model input files
Return type: list

get_mf6_blockdata(f, blockstr)[source]¶

Return list with all non comments between start and end of block specified by blockstr.

Parameters

f (file object) – open file object
blockstr (str) – name of block to search

Returns

data – list of data in specified block

Return type

list

get_mf6_comparison(src)[source]¶

Determine comparison type for MODFLOW 6 simulation.

Parameters: src (str) – directory path to search for comparison types
Returns: action – comparison type
Return type: str

get_mf6_files(mfnamefile)[source]¶

Return a list of all the MODFLOW 6 input and output files in this model.

Parameters

mfnamefile (str) – path to the MODFLOW 6 simulation name file

Returns

filelist (list) – list of MODFLOW 6 input files in a simulation
outplist (list) – list of MODFLOW 6 output files in a simulation

get_mf6_ftypes(namefile, ftypekeys)[source]¶

Return a list of FTYPES that are in the name file and in ftypekeys.

Parameters

namefile (str) – path to a MODFLOW 6 name file
ftypekeys (list) – list of desired FTYPEs

Returns

ftypes – list of FTYPES that match ftypekeys in namefile

Return type

list

get_mf6_mshape(disfile)[source]¶

Return the shape of the MODFLOW 6 model.

Parameters: disfile (str) – path to a MODFLOW 6 discretization file
Returns: mshape – tuple with the shape of the MODFLOW 6 model.
Return type: tuple

get_mf6_nper(tdisfile)[source]¶

Return the number of stress periods in the MODFLOW 6 model.

Parameters: tdisfile (str) – path to the TDIS file
Returns: nper – number of stress periods in the simulation
Return type: int

get_namefiles(pth, exclude=None)[source]¶

Search through a path (pth) for all .nam files.

Parameters

pth (str) – path to model files
exclude (str or lst) – File or list of files to exclude from the search (default is None)

Returns

namefiles – List of namefiles with paths

Return type

lst

get_sim_name(namefiles, rootpth=None)[source]¶

Get simulation name.

Parameters

namefiles (str or list of strings) – path(s) to MODFLOW-based model name files
rootpth (str) – optional root directory path (default is None)

Returns

simname – list of namefiles without the file extension

Return type

list

setup(namefile, dst, remove_existing=True, extrafiles=None)[source]¶

Setup MODFLOW-based model files for autotests.

Parameters

namefile (str) – MODFLOW-based model name file.
dst (str) – destination path for comparison model or file(s)
remove_existing (bool) – boolean indicating if an existing comparision model or file(s) should be replaced (default is True)
extrafiles (str or list of str) – list of extra files to include in the comparision

setup_comparison(namefile, dst, remove_existing=True)[source]¶

Setup a comparison model or comparision file(s) for a MODFLOW-based model.

Parameters

namefile (str) – MODFLOW-based model name file.
dst (str) – destination path for comparison model or file(s)
remove_existing (bool) – boolean indicating if an existing comparision model or file(s) should be replaced (default is True)

setup_mf6(src, dst, mfnamefile='mfsim.nam', extrafiles=None, remove_existing=True)[source]¶

Copy all of the MODFLOW 6 input files from the src directory to the dst directory.

Parameters

src (src) – directory path with original MODFLOW 6 input files
dst (str) – directory path that original MODFLOW 6 input files will be copied to
mfnamefile (str) – optional MODFLOW 6 simulation name file (default is mfsim.nam)
extrafiles (bool) – boolean indicating if extra files should be included (default is None)
remove_existing (bool) – boolean indicating if existing file in dst should be removed (default is True)

Returns

mf6inp (list) – list of MODFLOW 6 input files
mf6outp (list) – list of MODFLOW 6 output files

setup_mf6_comparison(src, dst, remove_existing=True)[source]¶

Setup comparision for MODFLOW 6 simulation.

Parameters

src (src) – directory path with original MODFLOW 6 input files
dst (str) – directory path that original MODFLOW 6 input files will be copied to
remove_existing (bool) – boolean indicating if existing file in dst should be removed (default is True)

Returns

action – comparison type

Return type

str

teardown(src)[source]¶

Teardown a autotest directory.

Parameters: src (str) – autotest directory to teardown

Module contents¶

Autotest functionality for MODFLOW-based models. Includes functionality for copying existing model and comparision files, comparing results, and tearing down test and comparison models.

pymake.utils package¶

Submodules¶

pymake.utils.download module¶

Utility functions to:

download and unzip software releases from the USGS and other organizations (triangle, MT3DMS).
download the latest MODFLOW-based applications and utilities for MacOS, Linux, and Windows from https://github.com/MODFLOW-USGS/executables
determine the latest version (GitHub tag) of a GitHub repository and a dictionary containing the file name and the link to a asset on contained in a github repository
compress all files in a list, files in a list of directories

download_and_unzip(url, pth='./', delete_zip=True, verify=True, timeout=30, max_requests=10, chunk_size=2048000, verbose=False)[source]¶

Download and unzip a zip file from a url.

Parameters

url (str) – url address for the zip file
pth (str) – path where the zip file will be saved (default is the current path)
delete_zip (bool) – boolean indicating if the zip file should be deleted after it is unzipped (default is True)
verify (bool) – boolean indicating if the url request should be verified
timeout (int) – url request time out length (default is 30 seconds)
max_requests (int) – number of url download request attempts (default is 10)
chunk_size (int) – maximum url download request chunk size (default is 2048000 bytes)
verbose (bool) – boolean indicating if output will be printed to the terminal

get_repo_assets(github_repo=None, version=None, error_return=False, verify=True)[source]¶

Return a dictionary containing the file name and the link to the asset contained in a github repository.

Parameters

github_repo (str) – Repository name, such as MODFLOW-USGS/modflow6. If github_repo is None set to ‘MODFLOW-USGS/executables’
version (str) – github repository release tag
error_return (bool) – boolean indicating if None will be returned if there are GitHub API issues
verify (bool) – boolean indicating if the url request should be verified

Returns

result_dict – dictionary of file names and links

Return type

dict

getmfexes(pth='.', version=None, platform=None, exes=None, verbose=False, verify=True)[source]¶

Get the latest MODFLOW binary executables from a github site (https://github.com/MODFLOW-USGS/executables) for the specified operating system and put them in the specified path.

Parameters

pth (str) – Location to put the executables (default is current working directory)
version (str) – Version of the MODFLOW-USGS/executables release to use. If version is None the github repo will be queried for the version number.
platform (str) – Platform that will run the executables. Valid values include mac, linux, win32 and win64. If platform is None, then routine will download the latest asset from the github repository.
exes (str or list of strings) – executable or list of executables to retain
verbose (bool) – boolean indicating if output will be printed to the terminal
verify (bool) – boolean indicating if the url request should be verified

getmfnightly(pth='.', platform=None, exes=None, verbose=False, verify=True)[source]¶

Get the latest MODFLOW 6 binary nightly-build executables from github (https://github.com/MODFLOW-USGS/modflow6-nightly-build/) for the specified operating system and put them in the specified path.

Parameters

pth (str) – Location to put the executables (default is current working directory)
platform (str) – Platform that will run the executables. Valid values include mac, linux, win32 and win64. If platform is None, then routine will download the latest asset from the github repository.
exes (str or list of strings) – executable or list of executables to retain
verbose (bool) – boolean indicating if output will be printed to the terminal
verify (bool) – boolean indicating if the url request should be verified

class pymakeZipFile(file, mode='r', compression=0, allowZip64=True, compresslevel=None)[source]¶

Bases: zipfile.ZipFile

ZipFile file attributes are not being preserved. This class preserves file attributes as described on StackOverflow at https://stackoverflow.com/questions/39296101/python-zipfile-removes-execute-permissions-from-binaries

static compressall(path, file_pths=None, dir_pths=None, patterns=None)[source]¶

Compress selected files or files in selected directories.

Parameters

path (str) – output zip file path
file_pths (str or list of str) – file paths to include in the output zip file (default is None)
dir_pths (str or list of str) – directory paths to include in the output zip file (default is None)
patterns (str or list of str) – file patterns to include in the output zip file (default is None)

Returns

success – boolean indicating if the output zip file was created

Return type

bool

extract(member, path=None, pwd=None)[source]¶

Parameters

member (str) – individual file to extract. If member does not exist, all files are extracted.
path (str) – directory path to extract file in a zip file (default is None, which results in files being extracted in the current directory)
pwd (str) – zip file password (default is None)

Returns

ret_val – return value indicating status of file extraction

Return type

int

extractall(path=None, members=None, pwd=None)[source]¶

Extract all files in the zipfile.

Parameters

path (str) – directory path to extract files in a zip file (default is None, which results in files being extracted in the current directory)
members (str) – individual files to extract (default is None, which extracts all members)
pwd (str) – zip file password (default is None)

repo_latest_version(github_repo=None, verify=True)[source]¶

Return a string of the latest version number (tag) contained in a github repository release.

Parameters: github_repo (str) – Repository name, such as MODFLOW-USGS/modflow6. If github_repo is None set to ‘MODFLOW-USGS/executables’
Returns: version – string with the latest version/tag number
Return type: str

zip_all(path, file_pths=None, dir_pths=None, patterns=None)[source]¶

Compress all files in the user-provided list of file paths and directory paths that match the provided file patterns.

Parameters

path (str) – path of the zip file that will be created
file_pths (str or list) – file path or list of file paths to be compressed
dir_pths (str or list) – directory path or list of directory paths to search for files that will be compressed
patterns (str or list) – file pattern or list of file patterns s to match to when creating a list of files that will be compressed

pymake.utils.usgsprograms module¶

Utility functions to extract information for a target from the USGS application database. Available functionality includes:

Get a list of available targets
Get data for a specific target
Get a dictionary with the data for all targets
Get the current version of a target
Get a list indicating if single and double precsion versions of the target application should be built
Functions to load, update, and export a USGS-style “code.json” json file containing information in the USGS application database

A table listing the available pymake targets is included below:

Available pymake targets¶
target	version	current	url	dirname	srcdir	standard_switch	double_switch	shared_object
mf6	6.3.0	True	https://github.com/MODFLOW-USGS/modflow6/releases/download/6.3.0/mf6.3.0_linux.zip	mf6.3.0_linux	src	True	False	False
zbud6	6.3.0	True	https://github.com/MODFLOW-USGS/modflow6/releases/download/6.3.0/mf6.3.0_linux.zip	mf6.3.0_linux	utils/zonebudget/src	True	False	False
libmf6	6.3.0	True	https://github.com/MODFLOW-USGS/modflow6/releases/download/6.3.0/mf6.3.0_linux.zip	mf6.3.0_linux	srcbmi	True	False	True
mp7	7.2.001	True	https://water.usgs.gov/water-resources/software/MODPATH/modpath_7_2_001.zip	modpath_7_2_001	source	True	False	False
mt3dms	5.3.0	True	https://hydro.geo.ua.edu/mt3d/mt3dms_530.exe	mt3dms5.3.0	src/true-binary	True	False	False
mt3dusgs	1.1.0	True	https://water.usgs.gov/water-resources/software/MT3D-USGS/mt3dusgs1.1.0.zip	mt3dusgs1.1.0	src	True	False	False
vs2dt	3.3	True	https://water.usgs.gov/water-resources/software/VS2DI/vs2dt3_3.zip	vs2dt3_3	include	True	False	False
triangle	1.6	True	https://www.netlib.org/voronoi/triangle.zip	triangle1.6	src	True	False	False
gridgen	1.0.02	True	https://water.usgs.gov/water-resources/software/GRIDGEN/gridgen.1.0.02.zip	gridgen.1.0.02	src	True	False	False
crt	1.3.1	True	https://water.usgs.gov/ogw/CRT/CRT_1.3.1.zip	CRT_1.3.1	SOURCE	True	False	False
gsflow	2.2.0	True	https://water.usgs.gov/water-resources/software/gsflow/gsflow_2.2.0_linux.zip	gsflow_2.2.0_linux	src	True	False	False
sutra	3.0	True	https://water.usgs.gov/water-resources/software/sutra/SUTRA_3_0_0.zip	SutraSuite	SUTRA_3_0/source	True	False	False
mf2000	1.19.01	True	https://water.usgs.gov/nrp/gwsoftware/modflow2000/mf2k1_19_01.tar.gz	mf2k.1_19	src	True	False	False
mf2005	1.12.00	True	https://github.com/MODFLOW-USGS/mf2005/releases/download/v.1.12.00/MF2005.1_12u.zip	MF2005.1_12u	src	True	True	False
mf2005.1.11	1.11.00	False	https://water.usgs.gov/ogw/modflow/archive-mf2005/MODFLOW-2005_v1.11.00/mf2005v1_11_00_unix.zip	Unix	src	True	False	False
mfusg	1.5	True	https://water.usgs.gov/water-resources/software/MODFLOW-USG/mfusg1_5.zip	mfusg1_5	src	True	True	False
zonbudusg	1.5	True	https://water.usgs.gov/water-resources/software/MODFLOW-USG/mfusg1_5.zip	mfusg1_5	src/zonebudusg	True	False	False
swtv4	4.00.05	True	https://water.usgs.gov/water-resources/software/SEAWAT/swt_v4_00_05.zip	swt_v4_00_05	source	False	True	False
mp6	6.0.1	True	https://water.usgs.gov/water-resources/software/MODPATH/modpath.6_0_01.zip	modpath.6_0	src	True	False	False
mflgr	2.0.0	True	https://water.usgs.gov/ogw/modflow-lgr/modflow-lgr-v2.0.0/mflgrv2_0_00.zip	mflgr.2_0	src	True	True	False
zonbud3	3.01	True	https://water.usgs.gov/water-resources/software/ZONEBUDGET/zonbud3_01.exe	Zonbud.3_01	Src	True	False	False
mfnwt1.1.4	1.1.4	False	https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.1.4.zip	MODFLOW-NWT_1.1.4	src	True	False	False
mfnwt	1.2.0	True	https://water.usgs.gov/water-resources/software/MODFLOW-NWT/MODFLOW-NWT_1.2.0.zip	MODFLOW-NWT_1.2.0	src	True	True	False
prms	5.2.1	True	https://water.usgs.gov/water-resources/software/PRMS/prms_5.2.1_linux.zip	prms_5.2.1_linux	src	True	False	False

class dotdict[source]¶

Bases: dict

dot.notation access to dictionary attributes.

class usgs_program_data[source]¶

Bases: object

USGS program database class.

static export_json(fpth='code.json', prog_data=None, current=False, update=True, write_markdown=False, verbose=False)[source]¶

Export USGS program data as a json file.

Parameters

fpth (str) – Path for the json file to be created. Default is “code.json”
prog_data (dict) – User-specified program database. If prog_data is None, it will be created from the USGS program database
current (bool) – If False, all USGS program targets are listed. If True, only USGS program targets that are defined as current are listed. Default is False.
update (bool) – If True, existing targets in the user-specified program database with values in the USGS program database. If False, existing targets in the user-specified program database will not be updated. Default is True.
write_markdown (bool) – If True, write markdown file that includes the target name, version, and the last-modified date of the download asset (url). Default is False.
verbose (bool) – boolean for verbose output to terminal

static get_keys(current=False)[source]¶

Get target keys from the USGS program database.

Parameters: current (bool) – If False, all USGS program targets are listed. If True, only USGS program targets that are defined as current are listed. Default is False.
Returns: keys – list of USGS program targets
Return type: list

static get_precision(key)[source]¶

Get the dictionary for a specified target.

Parameters: key (str) – Target USGS program
Returns: precision – List
Return type: list

static get_program_dict()[source]¶

Get the complete USGS program database.

Returns: program_dict – Dictionary with USGS program attributes for all targets
Return type: dict

static get_target(key)[source]¶

Get the dictionary for a specified target.

Parameters: key (str) – Target USGS program that may have a path and an extension
Returns: program_dict – Dictionary with USGS program attributes for the specified key
Return type: dict

static get_version(key)[source]¶

Get the current version of the specified target.

Parameters: key (str) – Target USGS program
Returns: version – current version of the specified target
Return type: str

static list_json(fpth='code.json')[source]¶

List an existing code json file.

Parameters: fpth (str) – Path for the json file to be listed. Default is “code.json”

static list_targets(current=False)[source]¶

Print a list of the available USGS program targets.

Parameters: current (bool) – If False, all USGS program targets are listed. If True, only USGS program targets that are defined as current are listed. Default is False.

static load_json(fpth='code.json')[source]¶

Load an existing code json file. Basic error checking is done to make sure the file contains the correct keys.

Parameters: fpth (str) – Path for the json file to be created. Default is “code.json”
Returns: json_dict – Valid USGS program database
Return type: dict

static update_json(fpth='code.json', temp_dict=None)[source]¶

UPDATE an existing code json file.

Parameters

fpth (str) – Path for the json file to be listed. Default is “code.json”
temp_dict (dict) – Dictionary with USGS program data for a target

Module contents¶

Utility functions to 1) download and uncompress software releases containing source code or executables, 2) zip files, 3) query a USGS software and utility program database for information on current software releases.

pymake package¶

Subpackages¶

Submodules¶

pymake.config module¶

Module contents¶

pymake is a python package for compiling MODFLOW-based and other Fortran, C, and C++ programs. The package determines the build order using a directed acyclic graph and then compiles the source files using GNU compilers (gcc, g++, gfortran) or Intel compilers (ifort, icc).

class Pymake(name='pymake', verbose=None)[source]¶

Bases: object

Pymake class for interacting with pymake functionality. This is essentially a wrapper for all of the pymake functions needed to download and build a target.

argv_reset_settings(args)[source]¶

Reset settings using command line arguments

Parameters: args (Namespace object) – reset self.variables using command line arguments

build(target=None, srcdir=None, modify_exe_name=False)[source]¶

Build the target

Parameters

target (str) – target name. If target is None self.target is used. (default is None)
srcdir (str) – path to directory with source files. (default is None)
modify_exe_name (bool) – boolean that determines if the target name can be modified to include precision (dbl) and debugging (d) indicators.

compress_targets()[source]¶: Compress targets in build_targets list.

download_setup(target, url=None, download_path='.', verify=True, timeout=30)[source]¶

Setup download

Parameters

target (str) – target name
url (str) – url of asset
download_path (str) – path where the asset will be saved
verify (bool) – boolean defining ssl verification
timeout (int) – download timeout in seconds (default is 30)

download_target(target, url=None, download_path='.', verify=True, timeout=30)[source]¶

Setup and download url

Parameters

target (str) – target name
url (str) – url of asset
download_path (str) – path where the asset will be saved
verify (bool) – boolean defining ssl verification
timeout (int) – download timeout in seconds (default is 30)

Returns

success – boolean flag indicating download success

Return type

bool

download_url()[source]¶

Download files from the url

Returns: success – boolean flag indicating download success
Return type: bool

finalize()[source]¶: Finalize Pymake class

reset(target)[source]¶

Reset PyMake object variables for a target

Parameters: target (str) – target name

set_build_target_bool(target=None)[source]¶

Evaluate if the executable exists and if so and the command line argument –keep is specified then the executable is not built.

Parameters: target (str) – target name. If target is None self.target will be used. (default is None)
Returns: build – boolean indicating if the executable should be built
Return type: bool

update_build_targets()[source]¶: Add target to build_targets list if it is not in the list

update_target(target, modify_target=False)[source]¶

Update target name with executable extension on Windows and based on pymake settings.

Parameters

target (str) – target name
modify_target (bool) – boolean indicating if the target name can be modified based on pymake double and debug settings (default is False)

Returns

target – updated target name

Return type

str

build_apps(targets=None, pymake_object=None, download_dir=None, appdir=None, verbose=None, release_precision=True, meson=False, mesondir='.', clean=True)[source]¶

Build all of the current targets or a subset of targets.

Parameters

targets (str or list of str) – targets to build. If targets is None, all current targets will be build. Default is None
pymake_object (Pymake()) – Pymake object created outside of build_apps
download_dir (str) – download directory path
appdir (str) – target path
release_precision (bool) – boolean indicating if only the release precision version should be build. If release_precision is False, then the release precision version will be compiled along with a double precision version of the program for programs where the standard_switch and double_switch in usgsprograms.txt is True. default is True.
meson (bool) – boolean indicating that the executable should be built using the meson build system. (default is False)
mesondir (str) – Main meson.build file path
clean (bool) – boolean determining of final download should be removed

Returns

returncode – integer value indicating successful completion (0) or failure (>0)

Return type

int

compare(namefile1, namefile2, precision='auto', max_cumpd=0.01, max_incpd=0.01, htol=0.001, outfile1=None, outfile2=None, files1=None, files2=None)[source]¶

Compare the budget and head results for two MODFLOW-based model simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
max_cumpd (float) – maximum percent discrepancy allowed for cumulative budget terms (default is 0.01)
max_incpd (float) – maximum percent discrepancy allowed for incremental budget terms (default is 0.01)
htol (float) – maximum allowed head difference (default is 0.001)
outfile1 (str) – budget comparison output file name. If outfile1 is None, no budget comparison output is saved. (default is None)
outfile2 (str) – head comparison output file name. If outfile2 is None, no head comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)

Returns

success – boolean indicating if the budget and head differences are less than max_cumpd, max_incpd, and htol.

Return type

bool

compare_budget(namefile1, namefile2, max_cumpd=0.01, max_incpd=0.01, outfile=None, files1=None, files2=None)[source]¶

Compare the budget results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
max_cumpd (float) – maximum percent discrepancy allowed for cumulative budget terms (default is 0.01)
max_incpd (float) – maximum percent discrepancy allowed for incremental budget terms (default is 0.01)
outfile (str) – budget comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)

Returns

success – boolean indicating if the difference between budgets are less than max_cumpd and max_incpd

Return type

bool

compare_concs(namefile1, namefile2, precision='auto', ctol=0.001, outfile=None, files1=None, files2=None, difftol=False, verbose=False)[source]¶

Compare the mt3dms and mt3dusgs concentration results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
ctol (float) – maximum allowed concentration difference (default is 0.001)
outfile (str) – concentration comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)
difftol (bool) – boolean determining if the absolute value of the concentration difference greater than ctol should be evaluated (default is False)
verbose (bool) – boolean indicating if verbose output should be written to the terminal (default is False)

Returns

success – boolean indicating if the concentration differences are less than ctol.

Return type

bool

compare_heads(namefile1, namefile2, precision='auto', text='head', text2=None, htol=0.001, outfile=None, files1=None, files2=None, difftol=False, verbose=False, exfile=None, exarr=None, maxerr=None)[source]¶

Compare the head results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
htol (float) – maximum allowed head difference (default is 0.001)
outfile (str) – head comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)
difftol (bool) – boolean determining if the absolute value of the head difference greater than htol should be evaluated (default is False)
verbose (bool) – boolean indicating if verbose output should be written to the terminal (default is False)
exfile (str) – path to a file with exclusion array data. Head differences will not be evaluated where exclusion array values are greater than zero. (default is None)
exarr (numpy.ndarry) – exclusion array. Head differences will not be evaluated where exclusion array values are greater than zero. (default is None).
maxerr (int) – maximum number of head difference greater than htol that should be reported. If maxerr is None, all head difference greater than htol will be reported. (default is None)

Returns

success – boolean indicating if the head differences are less than htol.

Return type

bool

compare_stages(namefile1=None, namefile2=None, files1=None, files2=None, htol=0.001, outfile=None, difftol=False, verbose=False)[source]¶

Compare SWR process stage results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
precision (str) – precision for binary head file (“auto”, “single”, or “double”) default is “auto”
htol (float) – maximum allowed stage difference (default is 0.001)
outfile (str) – head comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)
difftol (bool) – boolean determining if the absolute value of the stage difference greater than htol should be evaluated (default is False)
verbose (bool) – boolean indicating if verbose output should be written to the terminal (default is False)

Returns

success – boolean indicating if the stage differences are less than htol.

Return type

bool

compare_swrbudget(namefile1, namefile2, max_cumpd=0.01, max_incpd=0.01, outfile=None, files1=None, files2=None)[source]¶

Compare the SWR budget results from two simulations.

Parameters

namefile1 (str) – namefile path for base model
namefile2 (str) – namefile path for comparison model
max_cumpd (float) – maximum percent discrepancy allowed for cumulative budget terms (default is 0.01)
max_incpd (float) – maximum percent discrepancy allowed for incremental budget terms (default is 0.01)
outfile (str) – budget comparison output file name. If outfile is None, no comparison output is saved. (default is None)
files1 (str) – base model output file. If files1 is not None, results will be extracted from files1 and namefile1 will not be used. (default is None)
files2 (str) – comparison model output file. If files2 is not None, results will be extracted from files2 and namefile2 will not be used. (default is None)

Returns

success – boolean indicating if the difference between budgets are less than max_cumpd and max_incpd

Return type

bool

download_and_unzip(url, pth='./', delete_zip=True, verify=True, timeout=30, max_requests=10, chunk_size=2048000, verbose=False)[source]¶

Download and unzip a zip file from a url.

Parameters

url (str) – url address for the zip file
pth (str) – path where the zip file will be saved (default is the current path)
delete_zip (bool) – boolean indicating if the zip file should be deleted after it is unzipped (default is True)
verify (bool) – boolean indicating if the url request should be verified
timeout (int) – url request time out length (default is 30 seconds)
max_requests (int) – number of url download request attempts (default is 10)
chunk_size (int) – maximum url download request chunk size (default is 2048000 bytes)
verbose (bool) – boolean indicating if output will be printed to the terminal

get_entries_from_namefile(namefile, ftype=None, unit=None, extension=None)[source]¶

Get entries from a namefile. Can select using FTYPE, UNIT, or file extension.

Parameters

namefile (str) – path to a MODFLOW-based model name file
ftype (str) – package type
unit (int) – file unit number
extension (str) – file extension

Returns

entries – list of tuples containing FTYPE, UNIT, FNAME, STATUS for each namefile entry that meets a user-specified value.

Return type

list of tuples

get_input_files(namefile)[source]¶

Return a list of all the input files in this model.

Parameters: namefile (str) – path to a MODFLOW-based model name file
Returns: filelist – list of MODFLOW-based model input files
Return type: list

get_mf6_blockdata(f, blockstr)[source]¶

Return list with all non comments between start and end of block specified by blockstr.

Parameters

f (file object) – open file object
blockstr (str) – name of block to search

Returns

data – list of data in specified block

Return type

list

get_mf6_comparison(src)[source]¶

Determine comparison type for MODFLOW 6 simulation.

Parameters: src (str) – directory path to search for comparison types
Returns: action – comparison type
Return type: str

get_mf6_files(mfnamefile)[source]¶

Return a list of all the MODFLOW 6 input and output files in this model.

Parameters

mfnamefile (str) – path to the MODFLOW 6 simulation name file

Returns

filelist (list) – list of MODFLOW 6 input files in a simulation
outplist (list) – list of MODFLOW 6 output files in a simulation

get_mf6_ftypes(namefile, ftypekeys)[source]¶

Return a list of FTYPES that are in the name file and in ftypekeys.

Parameters

namefile (str) – path to a MODFLOW 6 name file
ftypekeys (list) – list of desired FTYPEs

Returns

ftypes – list of FTYPES that match ftypekeys in namefile

Return type

list

get_mf6_mshape(disfile)[source]¶

Return the shape of the MODFLOW 6 model.

Parameters: disfile (str) – path to a MODFLOW 6 discretization file
Returns: mshape – tuple with the shape of the MODFLOW 6 model.
Return type: tuple

get_mf6_nper(tdisfile)[source]¶

Return the number of stress periods in the MODFLOW 6 model.

Parameters: tdisfile (str) – path to the TDIS file
Returns: nper – number of stress periods in the simulation
Return type: int

get_namefiles(pth, exclude=None)[source]¶

Search through a path (pth) for all .nam files.

Parameters

pth (str) – path to model files
exclude (str or lst) – File or list of files to exclude from the search (default is None)

Returns

namefiles – List of namefiles with paths

Return type

lst

get_repo_assets(github_repo=None, version=None, error_return=False, verify=True)[source]¶

Return a dictionary containing the file name and the link to the asset contained in a github repository.

Parameters

github_repo (str) – Repository name, such as MODFLOW-USGS/modflow6. If github_repo is None set to ‘MODFLOW-USGS/executables’
version (str) – github repository release tag
error_return (bool) – boolean indicating if None will be returned if there are GitHub API issues
verify (bool) – boolean indicating if the url request should be verified

Returns

result_dict – dictionary of file names and links

Return type

dict

get_sim_name(namefiles, rootpth=None)[source]¶

Get simulation name.

Parameters

namefiles (str or list of strings) – path(s) to MODFLOW-based model name files
rootpth (str) – optional root directory path (default is None)

Returns

simname – list of namefiles without the file extension

Return type

list

getmfexes(pth='.', version=None, platform=None, exes=None, verbose=False, verify=True)[source]¶

Get the latest MODFLOW binary executables from a github site (https://github.com/MODFLOW-USGS/executables) for the specified operating system and put them in the specified path.

Parameters

pth (str) – Location to put the executables (default is current working directory)
version (str) – Version of the MODFLOW-USGS/executables release to use. If version is None the github repo will be queried for the version number.
platform (str) – Platform that will run the executables. Valid values include mac, linux, win32 and win64. If platform is None, then routine will download the latest asset from the github repository.
exes (str or list of strings) – executable or list of executables to retain
verbose (bool) – boolean indicating if output will be printed to the terminal
verify (bool) – boolean indicating if the url request should be verified

main(srcdir=None, target=None, fc='gfortran', cc='gcc', makeclean=True, expedite=False, dryrun=False, double=False, debug=False, include_subdirs=False, fflags=None, cflags=None, syslibs=None, arch='intel64', makefile=False, makefiledir='.', srcdir2=None, extrafiles=None, excludefiles=None, sharedobject=False, appdir=None, verbose=False, inplace=False, networkx=False, meson=False, mesondir='.')[source]¶

Main pymake function.

Parameters

srcdir (str) – path for directory containing source files
target (str) – executable name or path for executable to create
fc (str) – fortran compiler
cc (str) – c or cpp compiler
makeclean (bool) – boolean indicating if intermediate files should be cleaned up after successful build
expedite (bool) – boolean indicating if only out of date source files will be compiled. Clean must not have been used on previous build.
dryrun (bool) – boolean indicating if source files should be compiled. Files will be deleted, if makeclean is True.
double (bool) – boolean indicating a compiler switch will be used to create an executable with double precision real variables.
debug (bool) – boolean indicating is a debug executable will be built
include_subdirs (bool) – boolean indicating source files in srcdir subdirectories should be included in the build
fflags (list) – user provided list of fortran compiler flags
cflags (list) – user provided list of c or cpp compiler flags
syslibs (list) – user provided syslibs
arch (str) – Architecture to use for Intel Compilers on Windows (default is intel64)
makefile (bool) – boolean indicating if a GNU make makefile should be created
makefiledir (str) – GNU make makefile path
srcdir2 (str) – additional directory with common source files.
extrafiles (str) – path for extrafiles file that contains paths to additional source files to include
excludefiles (str) – path for excludefiles file that contains filename of source files to exclude from the build
sharedobject (bool) – boolean indicating a shared object will be built
appdir (str) – path for executable
verbose (bool) – boolean indicating if output will be printed to the terminal
inplace (bool) – boolean indicating that the source files in srcdir, srcdir2, and defined in extrafiles will be used directly. If inplace is False, source files will be copied to a directory named srcdir_temp. (default is False)
networkx (bool) – boolean indicating that the NetworkX python package will be used to create the Directed Acyclic Graph (DAG) used to determine the order source files are compiled in. The NetworkX package tends to result in a unique DAG more often than the standard algorithm used in pymake. (default is False)
meson (bool) – boolean indicating that the executable should be built using the meson build system. (default is False)
mesondir (str) – Main meson.build file path

Returns

returncode – return code

Return type

int

make_plots(srcdir, outdir, include_subdir=False, level=3, extension='.png', verbose=False, networkx=False)[source]¶

Create plots of module dependencies.

Parameters

srcdir (str) – path for source files
outdir (str) – path for output images
include_subdir (bool) – boolean indicating is subdirectories in the source file directory should be included
level (int) – dependency level (1 is the minimum)
extension (str) – output extension (default is .png)
verbose (bool) – boolean indicating if output will be printed to the terminal
networkx (bool) – boolean indicating that the NetworkX python package will be used to create the Directed Acyclic Graph (DAG) used to determine the order source files are compiled in. The NetworkX package tends to result in a unique DAG more often than the standard algorithm used in pymake. (default is False)

parser()[source]¶

Construct the parser and return argument values.

Returns: args – Namespace with command line arguments
Return type: Namespace object

repo_latest_version(github_repo=None, verify=True)[source]¶

Return a string of the latest version number (tag) contained in a github repository release.

Parameters: github_repo (str) – Repository name, such as MODFLOW-USGS/modflow6. If github_repo is None set to ‘MODFLOW-USGS/executables’
Returns: version – string with the latest version/tag number
Return type: str

setup(namefile, dst, remove_existing=True, extrafiles=None)[source]¶

Setup MODFLOW-based model files for autotests.

Parameters

namefile (str) – MODFLOW-based model name file.
dst (str) – destination path for comparison model or file(s)
remove_existing (bool) – boolean indicating if an existing comparision model or file(s) should be replaced (default is True)
extrafiles (str or list of str) – list of extra files to include in the comparision

setup_comparison(namefile, dst, remove_existing=True)[source]¶

Setup a comparison model or comparision file(s) for a MODFLOW-based model.

Parameters

namefile (str) – MODFLOW-based model name file.
dst (str) – destination path for comparison model or file(s)
remove_existing (bool) – boolean indicating if an existing comparision model or file(s) should be replaced (default is True)

setup_mf6(src, dst, mfnamefile='mfsim.nam', extrafiles=None, remove_existing=True)[source]¶

Copy all of the MODFLOW 6 input files from the src directory to the dst directory.

Parameters

src (src) – directory path with original MODFLOW 6 input files
dst (str) – directory path that original MODFLOW 6 input files will be copied to
mfnamefile (str) – optional MODFLOW 6 simulation name file (default is mfsim.nam)
extrafiles (bool) – boolean indicating if extra files should be included (default is None)
remove_existing (bool) – boolean indicating if existing file in dst should be removed (default is True)

Returns

mf6inp (list) – list of MODFLOW 6 input files
mf6outp (list) – list of MODFLOW 6 output files

setup_mf6_comparison(src, dst, remove_existing=True)[source]¶

Setup comparision for MODFLOW 6 simulation.

Parameters

src (src) – directory path with original MODFLOW 6 input files
dst (str) – directory path that original MODFLOW 6 input files will be copied to
remove_existing (bool) – boolean indicating if existing file in dst should be removed (default is True)

Returns

action – comparison type

Return type

str

teardown(src)[source]¶

Teardown a autotest directory.

Parameters: src (str) – autotest directory to teardown

to_pydot(dag, filename='mygraph.png')[source]¶

Create a png file of a Directed Acyclic Graph

Parameters

dag (object) – directed acyclic graph
filename (str) – path of the graph png

class usgs_program_data[source]¶

Bases: object

USGS program database class.

static export_json(fpth='code.json', prog_data=None, current=False, update=True, write_markdown=False, verbose=False)[source]¶

Export USGS program data as a json file.

Parameters

fpth (str) – Path for the json file to be created. Default is “code.json”
prog_data (dict) – User-specified program database. If prog_data is None, it will be created from the USGS program database
current (bool) – If False, all USGS program targets are listed. If True, only USGS program targets that are defined as current are listed. Default is False.
update (bool) – If True, existing targets in the user-specified program database with values in the USGS program database. If False, existing targets in the user-specified program database will not be updated. Default is True.
write_markdown (bool) – If True, write markdown file that includes the target name, version, and the last-modified date of the download asset (url). Default is False.
verbose (bool) – boolean for verbose output to terminal

static get_keys(current=False)[source]¶

Get target keys from the USGS program database.

Parameters: current (bool) – If False, all USGS program targets are listed. If True, only USGS program targets that are defined as current are listed. Default is False.
Returns: keys – list of USGS program targets
Return type: list

static get_precision(key)[source]¶

Get the dictionary for a specified target.

Parameters: key (str) – Target USGS program
Returns: precision – List
Return type: list

static get_program_dict()[source]¶

Get the complete USGS program database.

Returns: program_dict – Dictionary with USGS program attributes for all targets
Return type: dict

static get_target(key)[source]¶

Get the dictionary for a specified target.

Parameters: key (str) – Target USGS program that may have a path and an extension
Returns: program_dict – Dictionary with USGS program attributes for the specified key
Return type: dict

static get_version(key)[source]¶

Get the current version of the specified target.

Parameters: key (str) – Target USGS program
Returns: version – current version of the specified target
Return type: str

static list_json(fpth='code.json')[source]¶

List an existing code json file.

Parameters: fpth (str) – Path for the json file to be listed. Default is “code.json”

static list_targets(current=False)[source]¶

Print a list of the available USGS program targets.

Parameters: current (bool) – If False, all USGS program targets are listed. If True, only USGS program targets that are defined as current are listed. Default is False.

static load_json(fpth='code.json')[source]¶

Load an existing code json file. Basic error checking is done to make sure the file contains the correct keys.

Parameters: fpth (str) – Path for the json file to be created. Default is “code.json”
Returns: json_dict – Valid USGS program database
Return type: dict

static update_json(fpth='code.json', temp_dict=None)[source]¶

UPDATE an existing code json file.

Parameters

fpth (str) – Path for the json file to be listed. Default is “code.json”
temp_dict (dict) – Dictionary with USGS program data for a target

zip_all(path, file_pths=None, dir_pths=None, patterns=None)[source]¶

Compress all files in the user-provided list of file paths and directory paths that match the provided file patterns.

Parameters

path (str) – path of the zip file that will be created
file_pths (str or list) – file path or list of file paths to be compressed
dir_pths (str or list) – directory path or list of directory paths to search for files that will be compressed
patterns (str or list) – file pattern or list of file patterns s to match to when creating a list of files that will be compressed

pymake Documentation¶

Getting Started¶

Command Line Usage¶

From Python¶

Script to compile MODFLOW 6¶

Notes¶

pymake Installation¶

Building Applications¶

API-docs¶

pymake.pymake module¶

pymake.pymake_build_apps module¶

pymake.pymake_base module¶

pymake.pymake_parser module¶

pymake.plot package¶

Submodules¶

pymake.plot.dependency_graphs module¶

Module contents¶

pymake.autotest package¶

Submodules¶

pymake.autotest.autotest module¶

Module contents¶

pymake.utils package¶

Submodules¶

pymake.utils.download module¶

pymake.utils.usgsprograms module¶

Module contents¶

pymake package¶

Subpackages¶

Submodules¶

pymake.config module¶

Module contents¶

Indices and tables¶