refactor(dag): add NetworkX python package as DAG option (#98)

Modified makefile generation to remove date and time so that changes
to makefiles are limited to source file name and dependency changes.
Refactored setup.py to a more modern format. Bumped version number
to 1.2.1. Black formatting. Added test of standard installation.

.github/common/install-python.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
 python -m pip install --upgrade pip
+pip install wheel
 pip install .
 pip install pytest pytest-cov coverage
 pip install pydotplus appdirs

.github/workflows/main.yml

@@ -41,9 +41,42 @@ jobs:
       - name: Run pylint
         run: pylint --jobs=0 --errors-only ./pymake
 
+  pymake_setup:
+    name: standard installation
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+
+      # check out repo
+      - name: Checkout pymake repo
+        uses: actions/[email protected]
+
+      - name: Setup Python 3.9
+        uses: actions/[email protected]
+        with:
+          python-version: 3.9
+
+      - name: Upgrade pip and install wheel
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+
+      - name: Base pymake installation
+        run: |
+          pip install . --use-feature=in-tree-build
+
+      - name: Print pymake version
+        run: |
+          python -c "import pymake; print(pymake.__version__)"
+
   pymakeCI-os-gcc:
     name: pymake CI gcc on different OSs
-    needs: pymake_lint
+    needs: [pymake_lint, pymake_setup]
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -109,7 +142,7 @@ jobs:
 
   pymakeCI-os-intel:
     name: pymake CI intel on different OSs
-    needs: pymake_lint
+    needs: [pymake_lint, pymake_setup]
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -233,7 +266,7 @@ jobs:
 
   pymakeCI-gcc-prev:
     name: pymake CI GCC 9 and 8
-    needs: pymake_lint
+    needs: [pymake_lint, pymake_setup]
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -290,7 +323,7 @@ jobs:
 
   pymakeCI-requests:
     name: pymake CI requests
-    needs: pymake_lint
+    needs: [pymake_lint, pymake_setup]
     runs-on: ubuntu-latest
     defaults:
       run:
@@ -324,7 +357,7 @@ jobs:
 
   pymakeCI-python-prev:
     name: pymake CI with previous python versions
-    needs: pymake_lint
+    needs: [pymake_lint, pymake_setup]
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false

MANIFEST.in

@@ -1,6 +1,10 @@
 # Exclude files
-global-exclude .DS_Store *.pyc *.pyo *.pyd *.swp *.bak *~ .* *.sh *.yml
+global-exclude .DS_Store *.pyc *.pyo *.pyd *.swp *.bak *~ .* *.sh *.yml *.md *.toml
 prune */__pycache__
+# exclude directories
+exclude docs/*
+exclude autotest/*
 # include specific files
 include pymake/utils/usgsprograms.txt
-recursive-include example *.py *.bat
+include pymake/examples/*.bat
+include pymake/examples/*.py

README.md

@@ -2,10 +2,10 @@
 Python package for compiling MODFLOW-based programs.
 
 
-### Version 1.2
+### Version 1.2.2
 ![pymake continuous integration](https://github.com/modflowpy/pymake/workflows/pymake%20continuous%20integration/badge.svg)
 [![codecov](https://codecov.io/gh/modflowpy/pymake/branch/master/graph/badge.svg)](https://codecov.io/gh/modflowpy/pymake)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/ff198bf587524161ad2bc60b3ab15979)](https://app.codacy.com/manual/jdhughes-usgs/pymake?utm_source=github.com&utm_medium=referral&utm_content=modflowpy/pymake&utm_campaign=Badge_Grade_Dashboard)
+[![Codacy Badge](https://app.codacy.com/project/badge/Grade/fe4275a3cfb84acf9c84aba7b4ae2086)](https://www.codacy.com/gh/modflowpy/pymake/dashboard?utm_source=github.com&utm_medium=referral&utm_content=modflowpy/pymake&utm_campaign=Badge_Grade)
 [![Documentation Status](https://readthedocs.org/projects/mfpymake/badge/?version=latest)](https://mfpymake.readthedocs.io/en/latest/?badge=latest)
 
 This is a python package for compiling MODFLOW-based and other Fortran, C, and 
@@ -58,18 +58,12 @@ 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,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]
-                    [-cs COMMONSRC] [-ef EXTRAFILES] [-exf EXCLUDEFILES] [-so]
-                    [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--inplace]
-                    srcdir target
+usage: __main__.py [-h] [-fc {ifort,mpiifort,gfortran,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] [-cs COMMONSRC] [-ef EXTRAFILES] [-exf EXCLUDEFILES] [-so] [-ad APPDIR] [-v] [--keep] [--zip ZIP] [--inplace] [--networkx]
+                   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.
+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.
@@ -82,64 +76,42 @@ optional arguments:
   -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)
+                        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)
+  -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)
+                        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)
+                        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)
+                        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)
   -cs COMMONSRC, --commonsrc COMMONSRC
-                        Additional directory with common source files.
-                        (default is None)
+                        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)
+                        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)
+                        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)
+                        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)
+  --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)
+
+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 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 
@@ -200,22 +172,22 @@ downloaded from
 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
+* `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 
@@ -228,6 +200,12 @@ python make_mf6.py -fc=ifort --fflags='-O3'
 
 ## Installation
 
+To install pymake using pip type:
+
+```
+pip install mfpymake
+```
+
 To install pymake directly from the git repository type:
 
 ```

autotest/t008_test.py

@@ -45,6 +45,7 @@
 pm.appdir = dstpth
 pm.makefile = True
 pm.inplace = True
+pm.networkx = True
 
 
 def build_with_makefile():

autotest/t009_test.py

@@ -205,6 +205,7 @@ def test_download_exes():
 
 @pytest.mark.regression
 @pytest.mark.skipif(sys.platform == "darwin", reason="do not run on OSX")
+@pytest.mark.skipif(sys.platform == "win32", reason="do not run on OSX")
 @pytest.mark.parametrize("ws", sim_dirs)
 def test_mt3dusgs(ws):
     assert run_mt3dusgs(ws), "could not run {}".format(ws)

codecov.yml

@@ -0,0 +1,9 @@
+coverage:
+  precision: 3
+  round: down
+  range: "50...100"
+  status:
+    project: off
+    patch: off
+comment:
+  layout: "diff, files"

docs/conf.py

@@ -31,8 +31,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "pymake"
-copyright = u"2020, Joseph D. Hughes"
-author = u"Joseph D. Hughes"
+copyright = "2020, Joseph D. Hughes"
+author = "Joseph D. Hughes"
 
 # The version.
 version = __version__