From 87a7fdf220141883b04772c767d769935d6804f2 Mon Sep 17 00:00:00 2001 From: alexgigliotti Date: Fri, 3 May 2019 15:59:02 -0500 Subject: [PATCH 1/3] Implement unit testing --- .travis.yml | 17 + geostatspy/tests/__init__.py | 0 .../tests/__pycache__/__init__.cpython-37.pyc | Bin 0 -> 176 bytes .../tests/__pycache__/test.cpython-37.pyc | Bin 0 -> 4083 bytes geostatspy/tests/sample_data.csv | 263 +++++++++ geostatspy/tests/test.py | 515 ++++++++++++++++++ 6 files changed, 795 insertions(+) create mode 100644 .travis.yml create mode 100644 geostatspy/tests/__init__.py create mode 100644 geostatspy/tests/__pycache__/__init__.cpython-37.pyc create mode 100644 geostatspy/tests/__pycache__/test.cpython-37.pyc create mode 100644 geostatspy/tests/sample_data.csv create mode 100644 geostatspy/tests/test.py diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..1605632 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,17 @@ +sudo: false + +language: python + +install: + - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; + - 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 + - conda info -a + - conda install numpy pandas numba scipy + +script: + - python -m unittest discover + diff --git a/geostatspy/tests/__init__.py b/geostatspy/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/geostatspy/tests/__pycache__/__init__.cpython-37.pyc b/geostatspy/tests/__pycache__/__init__.cpython-37.pyc new file mode 100644 index 0000000000000000000000000000000000000000..2dc989ab820021a54bef74199bad489cb9ea3401 GIT binary patch literal 176 zcmZ?b<>g`kf&CzY8p|EZgkPv}`nLV(bP?Ht}cJARDo=P^s-xQ&Th5 zUFEIn*`2m3qC3X;K#Va45@XnXFiJv*Q6G#UM2I2~9*hr)1w0sDSQ8Z=e30 z?uHlATb28rd(S;}zk5&JpL6f6R7w&)Z-4RN!k;%J=`AW8J{o4)n1Xu|Kmys7bXiD6 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Any inputs go here + + this_dir = os.path.dirname(os.path.abspath(__file__)) # Get current directory + sample_data_path = this_dir + '/sample_data.csv' # Set data file path + self.sample_data = pd.read_csv(sample_data_path, sep=',') + + return + + def test_locate(self): + # Inputs + # xx = + # iis = + # iie = + # x = + + # Test answers + # j_test = + + # Call function + # j_output = geostats.locate(xx, iis, iie, x) + + # Testing + # np.testing.assert_allclose(j_output, j_test, atol=0.01) + + return + + def test_dlocate(self): + # Inputs + # xx = + # iis = + # iie = + # x = + + # Test answers + # j_test = + + # Call function + # j_output = geostats.locate(xx, iis, iie, x) + + # Testing + # np.testing.assert_allclose(j_output, j_test, atol=0.01) + + return + + def test_powint(self): + # Inputs + # xlow = + # xhigh = + # ylow = + # yhigh = + # xval = + # power = + + # Test answers + # powint_test = + + # Call function + # powint_output = geostats.powint(self, xlow, xhigh, ylow, yhigh, xval, power) + + # Testing + # np.testing.assert_allclose(powint_output, powint_test, atol=0.01) + + return + + def test_dsortem(self): + # Inputs + # ib = + # ie = + # a = + # iperm = + + # Test answers + # a_test = + # b_test = + # c_test = + # d_test = + # e_test = + # f_test = + # g_test = + # h_test = + # dsortem_test = [a_test, b_test, c_test, d_test, e_test, f_test, g_test, h_test] + + # Call function + # dsortem_output = geostats.dsortem(ib, ie, a, iperm, b=0, c=0, d=0, e=0, f=0, g=0, h=0) + + # Testing + # np.testing.assert_allclose(dsortem_output, dsortem_test, atol=0.01) + + return + + def test_gauinv(self): + # Inputs + # p = + + # Test answers + # xp_test = + + # Call function + # xp_output = geostats.gauinv(p) + + # Testing + # np.testing.assert_allclose(xp_output, xp_test, atol=0.01) + + return + + def test_gcum(self): + # Inputs + # x = + + # Test answers + # gcum_test = + + # Call function + # gcum_output = geostats.gcum(x) + + # Testing + # np.testing.assert_allclose(gcum_output, gcum_test, atol=0.01) + + return + + def test_dpowint(self): + # Inputs + # xlow = + # xhigh = + # ylow = + # yhigh = + # xval = + # pwr = + + # Test answers + # dpowint_test = + + # Call function + # dpowint_output = geostats.dpowint(xlow, xhigh, ylow, yhigh, xval, pwr) + + # Testing + # np.testing.assert_allclose(lag_output, lag_test, atol=0.01) + + return + + def test_setup_rotmat(self): + # Inputs + # c0 = + # nst = + # it = + # cc = + # ang = + # pmx = + + # Test answers + # rotmat_test = + # maxcov_test = + + # Call function + # rotmat_output, maxcov_output = geostats.setup_rotmat(c0, nst, it, cc, ang, pmx) + + # Testing + # np.testing.assert_allclose(rotmat_output, rotmat_test, atol=0.01) + # np.testing.assert_allclose(maxcov_output, maxcov_test, atol=0.01) + + return + + def test_cova2(self): + # Inputs + # x1 = + # y1 = + # x2 = + # y2 = + # nst = + # c0 = + # pmx = + # cc = + # aa = + # it = + # ang = + # anis = + # rotmat = + # maxcov = + + # Test answers + # cova2_test = + + # Call function + # cova2_output = geostats.cova2(x1, y1, x2, y2, nst, c0, pmx, cc, aa, it, ang, anis, rotmat, maxcov) + + # Testing + # np.testing.assert_allclose(cova2_output, cova2_test, atol=0.01) + + return + + def test_ksol_numpy(self): + # Inputs + # neq = + # a = + # r = + + # Test answers + # s_test = + + # Call function + # s_output = geostats.ksol_numpy(neq, a, r) + + # Testing + # np.testing.assert_allclose(s_output, s_test, atol=0.01) + + return + + def test_correct_trend(self): + # Inputs + # trend = + + # Test answers + # trend_test = + + # Call function + # trend_output = geostats.correct_trend(trend) + + # Testing + # np.testing.assert_allclose(trend_output, trend_test, atol=0.01) + + return + + def test_ordrel(self): + # Inputs + # ivtype = + + # Test answers + # ccdfo_test = + + # Call function + # ccdfo_output = geostats.ordrel(ivtype) + + # Testing + # np.testing.assert_allclose(ccdfo_output, ccdfo_test, atol=0.01) + + return + + def test_declus(self): + # Inputs + # df = + # xcol = + # ycol = + # vcol = + # iminmax = + # noff = + # ncell = + # cmin = + # cmax = + + # Test answers + # wtopt_test = + # xcs_mat_test = + # vrcr_mat_test = + + # Call function + # wtopt_output, xcs_mat_output, vrcr_mat_output = geostats.declus(df, xcol, ycol, vcol, iminmax, noff, ncell, cmin, cmax) + + # Testing + # np.testing.assert_allclose(wtopt_output, wtopt_test, atol=0.01) + # np.testing.assert_allclose(xcs_mat_output, xcs_mat_test, atol=0.01) + # np.testing.assert_allclose(vrcr_mat_output, vrcr_mat_test, atol=0.01) + + return + + def test_gam(self): + # Inputs + # array = + # tmin = + # tmax = + # xsiz = + # ysiz = + # ixd = + # iyd = + # nlag = + # isill = + + # Test answers + # lag_test = + # vario_test = + # npp_test = + + # Call function + # lag_output, vario_output, npp_output = geostats.gam(array, tmin, tmax, xsiz, ysiz, ixd, iyd, isill) + + # Testing + # np.testing.assert_allclose(lag_output, lag_test, atol=0.01) + # np.testing.assert_allclose(vario_output, vario_test, atol=0.01) + # np.testing.assert_allclose(npp_output, npp_test, atol=0.01) + + return + + def test_gamv(self): + # Inputs + df = self.sample_data + xcol = "X" + ycol = "Y" + vcol = "Porosity" + tmin = 0 + tmax = 1500 + xlag = 100 + xltol = 25 + nlag = 7 + azm = 0 + atol = 90 + bandwh = 25 + isill = 1 + + # Test answers + dis_test = [0.0, 17.31, 93.002, 199.258, 300.349, 400.174, 501.166, 600.773, 0.0] + vario_test = [0.0, 0.056, 0.139, 0.201, 0.381, 0.357, 1.058, 0.172, 0.0] + npp_test = [522.0, 5032.0, 2168.0, 504.0, 372.0, 376.0, 312.0, 116.0, 0.0] + + # Call function + dis_output, vario_output, npp_output = geostats.gamv(df, xcol, ycol, vcol, tmin, tmax, xlag, xltol, nlag, azm, + atol, bandwh, isill) + + # Testing + np.testing.assert_allclose(dis_output, dis_test, atol=0.01) + np.testing.assert_allclose(vario_output, vario_test, atol=0.01) + np.testing.assert_allclose(npp_output, npp_test, atol=0.01) + + return + + def test_variogram_loop(self): + # Inputs + # x = + # y = + # vr = + # xlag = + # xltol = + # nlag = + # azm = + # atol = + # bandwh = + + # Test answers + # dis_test = + # vario_test = + # npp_test = + + # Call function + # dis_output, vario_output, npp_output = geostats.variogram_loop(x, y, vr, xlag, xltol, nlag, azm, atol, bandwh) + + # Testing + # np.testing.assert_allclose(dis_output, dis_test, atol=0.01) + # np.testing.assert_allclose(vario_output, vario_test, atol=0.01) + # np.testing.assert_allclose(npp_output, npp_test, atol=0.01) + + return + + def test_varmapv(self): + # Inputs + # df = + # xcol = + # ycol = + # tmin = + # tmax = + # nxlag = + # nylag = + # dxlag = + # dylag = + # minnp = + # isill = + + # Test answers + # gamf_test = + # nppf_test = + + # Call function + # gamf_output, nppf_output = geostats.varmapv(df, xcol, ycol, vcol, tmin, tmax, nxlag, nylag, dxlag, dylag, minnp, isill) + + # Testing + # np.testing.assert_allclose(gamf_output, gamf_test, atol=0.01) + # np.testing.assert_allclose(nppf_output, nppf_test, atol=0.01) + + return + + def test_vmodel(self): + # Inputs + # nlag = + # xlag = + # azm = + # vario = + + # Test answers + # index_test = + # h_test = + # gam_test = + # cov_test = + # ro_test = + + # Call function + # index_output, h_output, gam_output, cov_output, ro_output = geostats.vmodel(nlag, xlag, azm, vario) + + # Testing + # np.testing.assert_allclose(index_output, index_test, atol=0.01) + # np.testing.assert_allclose(h_output, h_test, atol=0.01) + # np.testing.assert_allclose(gam_output, gam_test, atol=0.01) + # np.testing.assert_allclose(cov_output, cov_test, atol=0.01) + # np.testing.assert_allclose(ro_output, ro_test, atol=0.01) + + return + + def test_nscore(self): + # Inputs + # df = + # vcol = + # wcol = None + # ismooth = False + # dfsmooth = None + # smcol = 0 + # smwcol = 0 + + # Test answers + # ns_test = + # vr_test = + # wt_ns_test = + + # Call function + # ns_output, vr_output, wt_ns_output = geostats.nscore(df, vcol, wcol=None, ismooth=False, dfsmooth=None, smcol=0, smwcol=0) + + # Testing + # np.testing.assert_allclose(ns_output, ns_test, atol=0.01) + # np.testing.assert_allclose(vr_output, vr_test, atol=0.01) + # np.testing.assert_allclose(wt_ns_output, wt_ns_test, atol=0.01) + + return + + def test_kb2d(self): + # Inputs + # df = + # xcol = + # ycol = + # vcol = + # tmin = + # tmax = + # nx = + # xmn = + # xsiz = + # ny = + # ymn = + # ysiz = + # nxdis = + # nydis = + # ndmin = + # ndmax = + # radius = + # ktype = + # skmean = + # vario = + + # Test answers + # kmap_test = + # vmap_test = + + # Call function + # kmap_output, vmap_output = geostats.kb2d(df, xcol, ycol, vcol, tmin, tmax, nx, xmn, xsiz, ny, ymn, ysiz, nxdis, nydis, ndmin, ndmax, radius, ktype, skmean, vario) + + # Testing + # np.testing.assert_allclose(kmap_output, kmap_test, atol=0.01) + # np.testing.assert_allclose(vmap_output, vmap_test, atol=0.01) + + return + + def test_ik2d(self): + # Inputs + # df = + # xcol = + # ycol = + # vcol = + # ivtype = + # tmax = + # koption = + # ncut = + # thresh = + # gcdf = + # trend = + # tmin = + # tmax = + # nx = + # xmn = + # xsiz = + # ny = + # ymn = + # ysiz = + # ndmin = + # ndmax = + # radius = + # ktype = + # vario = + + # Test answers + # ikout_test = + + # Call function + # ikout_output = geostats.ik2d(df, xcol, ycol, vcol, ivtype, koption, ncut, thresh, gcdf, trend, tmin, tmax, nx, xmn, xsiz, ny, ymn, ysiz, ndmin, ndmax, radius, ktype, vario) + + # Testing + # np.testing.assert_allclose(ikout_output, ikout_test, atol=0.01) + + return + + if __name__ == '__main__': + unittest.main() From b7ad97c878b30023d18fb19d623b7316d190cf7b Mon Sep 17 00:00:00 2001 From: alexgigliotti Date: Fri, 3 May 2019 16:10:06 -0500 Subject: [PATCH 2/3] Add statsmodel install to .travis.yml --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 1605632..aa25161 100644 --- a/.travis.yml +++ b/.travis.yml @@ -10,7 +10,7 @@ install: - conda config --set always_yes yes --set changeps1 no - conda update -q conda - conda info -a - - conda install numpy pandas numba scipy + - conda install numpy pandas numba scipy statsmodels script: - python -m unittest discover From 8fe64f2bb97ef3f67d3314d30316f129f0207d63 Mon Sep 17 00:00:00 2001 From: alexgigliotti Date: Mon, 13 May 2019 19:28:57 -0500 Subject: [PATCH 3/3] update readme and add gitignore --- .gitignore | 9 +++++++++ README.md | 2 +- .../tests/__pycache__/__init__.cpython-37.pyc | Bin 176 -> 0 bytes geostatspy/tests/__pycache__/test.cpython-37.pyc | Bin 4083 -> 0 bytes 4 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 .gitignore delete mode 100644 geostatspy/tests/__pycache__/__init__.cpython-37.pyc delete mode 100644 geostatspy/tests/__pycache__/test.cpython-37.pyc diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..57ff732 --- /dev/null +++ b/.gitignore @@ -0,0 +1,9 @@ +# Unit test output and cache +__pycache__/ +*.pyc + +# Temporary files +*.*~ +*.swp +*.swo + diff --git a/README.md b/README.md index ecd6225..2ba7b75 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@

-## GeostatsPy Package +## GeostatsPy Package [![Build Status](https://travis-ci.org/GeostatsGuy/GeostatsPy.svg?branch=master)](https://travis-ci.org/GeostatsGuy/GeostatsPy) The GeostatsPy Package brings GSLIB: Geostatistical Library (Deutsch and Journel, 1998) functions to Python. GSLIB is extremely robust and practical set of code for building spatial modeling workflows. I need it in Python to support my students in my **Data Analytics**, **Geostatistics** and **Machine Learning** courses. diff --git a/geostatspy/tests/__pycache__/__init__.cpython-37.pyc b/geostatspy/tests/__pycache__/__init__.cpython-37.pyc deleted file mode 100644 index 2dc989ab820021a54bef74199bad489cb9ea3401..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 176 zcmZ?b<>g`kf&CzY8p|EZgkPv}`nLV(bP?Ht}cJARDo=P^s-xQ&Th5 zUFEIn*`2m3qC3X;K#Va45@XnXFiJv*Q6G#UM2I2~9*hr)1w0sDSQ8Z=e30 z?uHlATb28rd(S;}zk5&JpL6f6R7w&)Z-4RN!k;%J=`AW8J{o4)n1Xu|Kmys7bXiD6 zSB2DcO~{;{L#ep=Zb2`|(pd>q&<-TftlSQ}qUuGEzbZ9y*RdUGvmqzUw!9!T!=OW& z!$-kP8&mKqf+e_g1!PbTB;*qnf_!D*DsmIUj&3V+F3xw?8yk|o%{kv9`|zUPDwT0z*6ad7mg zm~xoz!xVf1A(VFHtBOE1)UL_bv&=4G{4|= z`dzCR2FAAW9seaqv!>$Ve)=$eP~!QXF&=%hg4hQFWW0xLZ4&ybH8f~3}ECRdfg z?4dt5ghA$2@-8LeRhq!UQ}U+hWJBf^REc~FRV*emL}|EQ#|*7HDgv5_Qgu+zI7SSn zVk(PSQ!x!k6?i1#^e-G_M70n3?gsp)c`+hf zFMZ$OUf4CmCo;nNV0CZjtF6Fj?t=Ni3!*WZ67 zBbys6kCT01G!cQ(7X=SiBPTKKC?55&P*MP@?Tkbzc2q*Td)Zhj% zfz@&Q!T&R+mC4nX8cfB+gfDHgTgTly-GEmH^Wz@G+KhwtX*zerKA&JFl6IsRPsPk?IXRus`Qe2^^fg%Qq7AR7H1-lr}QmjC60>uav z9|*085GXpJ$bg~(p{<5^W=C?QL~5i(xhNkMA{G^+QZy5lqsq0)1vQ?JYw<#;?r1x? zXg->yNa8V7mWG;IG&iAHh^mJgaeCdcnaB?%^4E2C&f{L-g!`P1IOh!vAFc!DuCEXj z2y_CfwK2VR`s{CBQuf>S`mcWapPxVQt+svXxhGefFMg*@?TE+TzkcFw_Vm*&`-xud%I{x! zzGeSAYJKXF-@V+j-+Su6fBDMA*IIU2IrY88zyGym-}+0w{lkB~)3SG-4S%$(z1T|I zIrr$W!C(A(n0e>wF!Lyq3ZnLDl_683Yy&4bycyt`}I1x(EU=vfR?O%N@_vwS9qm0>iG;(>2^2 zFJrB1+IsG?i!8dS)4ES1P6%})jGZ8SY433Vk*KxzCnA2kt8|<3?-p&Z+M2Io8n2Iai zUiZ2lSnhW-s^!T|FEzLUOuYb)2J6X;X=#!vHJFMiok_bF&%kdpp4%qp2UXty7H9Vi zypgdSpJbux1aBW*)9D$;W@C*CbT`4PND0**^u@KLY#86@n{Hae=W(j?8o>eqZU6iT z!6LyD!7>5ugnX4?jo>K3O$0X++(OVGxQpNv0j(;&PJs7ci8m1v*2mi#P4+~iZjP)= zI&(PP8n}v3#3b%+OkqV*&M!gw#bgMd68dZYwQ@NHLP1<$Jq%ci?16cJtsmH zeiGZ!^FHn^>7WHR{4g^(|qaOWpW+{0&k-H++WI JCVZ8$`aZ8Jje-CG