Simplify Travis CI setup and parts of Python tests

.travis.yml

@@ -1,128 +1,62 @@
-language: c
-os: linux
-dist: trusty
-sudo: required
-compiler: gcc
-cache:
- apt: true
- pip: true
- directories:
- - $HOME/.cache/pip
- - $HOME/.local
-
+dist: xenial
+language: python
+python: "3.7"
+cache: pip
+
 matrix:
  include:
- - env: CVER=gfortran4
- language: c
+ - env: FC=gfortran-4.9
  addons:
  apt:
- sources: 
- - ubuntu-toolchain-r-test
- packages: 
+ sources: ubuntu-toolchain-r-test
+ packages:
  - gfortran-4.9
- - dpkg
- - unzip
 
- - env: CVER=gfortran5
- language: c
+ - env: FC=gfortran-5
  addons:
  apt:
- sources: 
- - ubuntu-toolchain-r-test
- packages: 
+ sources: ubuntu-toolchain-r-test
+ packages:
  - gfortran-5
- - dpkg
- - unzip
 
- - env: CVER=gfortran6
- language: c
+ - env: FC=gfortran-6
  addons:
  apt:
- sources: 
- - ubuntu-toolchain-r-test
- packages: 
+ sources: ubuntu-toolchain-r-test
+ packages:
  - gfortran-6
- - dpkg
- - unzip
 
- - env: CVER=gfortran7
- language: c
+ - env: FC=gfortran-7
  addons:
  apt:
- sources: 
- - ubuntu-toolchain-r-test
- packages: 
+ sources: ubuntu-toolchain-r-test
+ packages:
  - gfortran-7
- - dpkg
- - unzip
 
- - env: CVER=gfortran8
- language: c
+ - env: FC=gfortran-8
  addons:
  apt:
- sources: 
- - ubuntu-toolchain-r-test
- packages: 
+ sources: ubuntu-toolchain-r-test
+ packages:
  - gfortran-8
- - dpkg
- - unzip
-
+
  # allowed failures - uncomment lines below to allow failure
  # of specific gfortran compilers
  #allow_failures:
- # - env: CVER=gfortran7
- # - env: CVER=gfortran8
-
-
+ # - env: FC=gfortran-7
+ # - env: FC=gfortran-8
 
 
 install:
  - if [[ ! -d "$HOME/.local/bin" ]]; then
  mkdir "$HOME/.local/bin";
  fi
  - export PATH="$HOME/.local/bin:$PATH"
- - if [[ $CVER == "gfortran4" ]]; then
- ln -fs /usr/bin/gfortran-4.9 "$HOME/.local/bin/gfortran";
- gfortran --version;
- ls -l /usr/bin/gfortran-4.9;
- fi
- - if [[ $CVER == "gfortran5" ]]; then
- ln -fs /usr/bin/gfortran-5 "$HOME/.local/bin/gfortran";
- gfortran --version;
- ls -l /usr/bin/gfortran-5;
- fi
- - if [[ $CVER == "gfortran6" ]]; then
- ln -fs /usr/bin/gfortran-6 "$HOME/.local/bin/gfortran";
- gfortran --version;
- ls -l /usr/bin/gfortran-6;
- fi
- - if [[ $CVER == "gfortran7" ]]; then
- ln -fs /usr/bin/gfortran-7 "$HOME/.local/bin/gfortran";
- gfortran --version;
- ls -l /usr/bin/gfortran-7;
- fi
- - if [[ $CVER == "gfortran8" ]]; then
- ln -fs /usr/bin/gfortran-8 "$HOME/.local/bin/gfortran";
- gfortran --version;
- ls -l /usr/bin/gfortran-8;
- fi
- # install anaconda
- - if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- fi
- - bash miniconda.sh -b -p $HOME/miniconda
- - export PATH="$HOME/miniconda/bin:$PATH"
- - hash -r
- - conda config --set always_yes yes --set changeps1 no
- - conda update -q conda
- # Useful for debugging any issues with conda
- - conda info -a
- - conda install nose
- - python --version
- - pip install numpy
+ - ln -fs /usr/bin/$FC "$HOME/.local/bin/gfortran"
+ - gfortran --version
+ - pip install nose-timer requests numpy matplotlib
  - pip install https://github.com/modflowpy/flopy/zipball/develop
  - pip install https://github.com/modflowpy/pymake/zipball/master
- - pip install nose-timer
 
 
 script:

autotest/t003_test.py

@@ -62,8 +62,8 @@ def run_mt3d(spth, comparison=True):
  # needs to be inserted into the linker file for simulating
  # a period of equilibration.
  print('running insert_stopflow_period.py...{}'.format(testname))
- insert_stopflow_period.InsStpFlw()
- 
+ insert_stopflow_period.InsStpFlw(testpth)
+
  print('running mt3d-usgs model...{}'.format(testname))
  nam = os.path.basename(mtnamefile)
  exe_name = os.path.abspath(config.target)

autotest/t004_test_mt3dms_p01.py

@@ -143,8 +143,7 @@ def test_mt3dmsp01a():
  retardation, zero_order_decay,
  mixelm, zeta, prsity2)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -169,8 +168,7 @@ def test_mt3dmsp01b():
  retardation, zero_order_decay,
  mixelm, zeta, prsity2)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -195,8 +193,7 @@ def test_mt3dmsp01c():
  retardation, zero_order_decay,
  mixelm, zeta, prsity2)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -221,8 +218,7 @@ def test_mt3dmsp01d():
  retardation, zero_order_decay,
  mixelm, zeta, prsity2)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -247,8 +243,7 @@ def test_mt3dmsp01e():
  retardation, zero_order_decay,
  mixelm, zeta, prsity2)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 

autotest/t005_test_mt3dms_p02.py

@@ -130,8 +130,7 @@ def test_mt3dmsp02a(): # Tests Freudlich
  mt3dms_ws, isothm,
  sp1, sp2, mixelm, zeta)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -153,8 +152,7 @@ def test_mt3dmsp02b(): # Tests Langmuir
  mt3dms_ws, isothm,
  sp1, sp2, mixelm, zeta)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 def test_mt3dmsp02c(): # Tests Nonequilibrium
@@ -176,8 +174,9 @@ def test_mt3dmsp02c(): # Tests Nonequilibrium
  mt3dms_ws, isothm,
  sp1, beta, mixelm, zeta)
 
- msg = 'concentrations not equal {} {} for beta {}'.format(conc_mt3dusgs, conc_mt3dms, str(beta))
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ msg = 'concentrations not equal for beta {}'.format(beta)
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4,
+ err_msg=msg)
 
  return
 

autotest/t006_test_mt3dms_p03.py

@@ -124,8 +124,7 @@ def test_mt3dmsp03a():
  mf, mt, conc_mt3dms, cvt, mvt = p03mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -141,8 +140,7 @@ def test_mt3dmsp03b(): # Tests Langmuir
  mf, mt, conc_mt3dms, cvt, mvt = p03mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 

autotest/t007_test_mt3dms_p04.py

@@ -133,8 +133,7 @@ def test_mt3dmsp04a():
  mf, mt, conc_mt3dms, cvt, mvt = p04mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=6.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=6.0e-4)
  return
 
 
@@ -150,8 +149,7 @@ def test_mt3dmsp04b():
  mf, mt, conc_mt3dms, cvt, mvt = p04mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 
@@ -166,8 +164,7 @@ def test_mt3dmsp04c():
  mf, mt, conc_mt3dms, cvt, mvt = p04mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1e-4)
  return
 
 

autotest/t008_test_mt3dms_p05.py

@@ -123,8 +123,7 @@ def test_mt3dmsp05a():
  mf, mt, conc_mt3dms, cvt, mvt = p05mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm, dt0, ttsmult)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4)
  return
 
 

autotest/t009_test_mt3dms_p06.py

@@ -124,8 +124,8 @@ def test_mt3dmsp06a():
  mf, mt, conc_mt3dms, cvt, mvt = p06mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm, dt0)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms,
+  rtol=1e-05, atol=1.0e-4)
  return
 
 
@@ -143,8 +143,8 @@ def test_mt3dmsp06b():
  mf, mt, conc_mt3dms, cvt, mvt = p06mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm, dt0)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms,
+  rtol=1e-05, atol=1.0e-4)
  return
 
 
@@ -162,8 +162,8 @@ def test_mt3dmsp06c():
  mf, mt, conc_mt3dms, cvt, mvt = p06mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm, dt0)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms,
+  rtol=1e-05, atol=1.0e-4)
  return
 
 

autotest/t010_test_mt3dms_p07.py

@@ -125,8 +125,7 @@ def test_mt3dmsp07a():
  mf, mt, conc_mt3dms, cvt, mvt = p07mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4)
  return
 
 

autotest/t011_crashes_tst_mt3dms_p08.py

@@ -140,8 +140,7 @@ def test_mt3dmsp08a():
  mf, mt, conc_mt3dms, cvt, mvt = p08mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1.0e-4)
  return
 
 

autotest/t012_test_mt3dms_p09.py

@@ -131,8 +131,7 @@ def test_mt3dmsp09a():
  mf, mt, conc_mt3dms, cvt, mvt = p09mt3d(exe_name_mf, exe_name_mt3dms,
  mt3dms_ws, mixelm, nadvfd)
 
- msg = 'concentrations not equal {} {}'.format(conc_mt3dusgs, conc_mt3dms)
- assert np.allclose(conc_mt3dusgs, conc_mt3dms, atol=1.5e-3), msg
+ np.testing.assert_allclose(conc_mt3dusgs, conc_mt3dms, atol=1.5e-3)
  return