Test python

.github/workflows/build_testing.yml

@@ -31,22 +31,120 @@ jobs:
      - name: Checkout
        uses: actions/[email protected]
 
-     - name: Set up compilers
-       run: |
-         sudo apt-get update
-         sudo apt-get -qq install gfortran
-
      - name: Get a docker image and set it running
        run: |
-         docker pull mitgcm/testreport-images:ubuntu_18_04_villon
-         docker run  -v `pwd`:/MITgcm --name ubuntu_18_04-testreport -t -d mitgcm/testreport-images:ubuntu_18_04_villon /bin/bash
+         docker pull oliverjahn/testreport-images:ubuntu_18_04_villon
+         docker run  -v `pwd`:/MITgcm --name ubuntu_18_04-testreport -t -d oliverjahn/testreport-images:ubuntu_18_04_villon /bin/bash
 
      - name: Run a test
        env:
         MITGCM_EXP: ${{ matrix.exp }}
        run: |
          . tools/ci/runtr.sh
 
+     - name: Upload diagstats
+       uses: actions/upload-artifact@v2
+       with:
+         name: diagstats
+         path: verification/*/*run*/*StDiag*
+         if-no-files-found: ignore
+
+     - name: Upload mds output
+       uses: actions/upload-artifact@v2
+       with:
+         name: mds
+         path: verification/global_ocean.90x40x15/run/pickup.ckptA*
+         if-no-files-found: ignore
+
+     - name: Upload mnc output
+       uses: actions/upload-artifact@v2
+       with:
+         name: mnc
+         path: verification/*/*run*/mnc_test_*/*.nc
+         if-no-files-found: ignore
+
+ python:
+   needs: forward
+   runs-on: ubuntu-latest
+   strategy:
+     matrix:
+       python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]
+       include:
+         - python: 2.7
+           env: py27
+         - python: 3.5
+           env: py35
+         - python: 3.6
+           env: py36
+         - python: 3.7
+           env: py37
+         - python: 3.8
+           env: py38
+         - python: 3.9
+           env: py39
+   continue-on-error: true
+   steps:
+     - name: Checkout
+       uses: actions/[email protected]
+     - name: Setup Python
+       uses: actions/setup-python@v2
+       with:
+         python-version: ${{ matrix.python }}
+     - name: Install Tox and other packages
+       run: |
+         pip install --upgrade pip
+         pip install tox
+     - name: Install netcdf tools
+       run: |
+         sudo apt-get update
+         sudo apt-get -qq install netcdf-bin
+     - name: Download diagstats output
+       uses: actions/download-artifact@v2
+       with:
+         name: diagstats
+         path: utils/python/MITgcmutils/diagstats
+     - name: Download mds output
+       uses: actions/download-artifact@v2
+       with:
+         name: mds
+         path: utils/python/MITgcmutils/tests/data/global_ocean.90x40x15
+     - name: Download mnc output
+       uses: actions/download-artifact@v2
+       with:
+         name: mnc
+         path: utils/python/MITgcmutils/tests/data
+     - name: Create download directories
+       run: mkdir -p baseline_images data/llc90 data/aste data/eccov3
+       working-directory: utils/python/MITgcmutils/tests
+     - name: Download baseline images
+       uses: wei/[email protected]
+       with:
+         args: https://engaging-web.mit.edu/~jahn/MITgcmutils/baseline_images/{cs_pcol,cs_pcol_sphere,cs_pcol_sphere_pre330,llc_contour,llc_contourf,llc_pcol,llc_pcol_basemap,llc_pcol_stere,llc_pcol_xg}.png -o utils/python/MITgcmutils/tests/baseline_images/#1.png
+     - name: Download mds test data
+       uses: wei/[email protected]
+       with:
+         args: https://engaging-web.mit.edu/~jahn/MITgcmutils/mds/llc90/{Eta.0000000008,hFacC,XC,XG,YC,YG}.{data,meta} -o utils/python/MITgcmutils/tests/data/llc90/#1.#2
+     - name: Download aste test data
+       uses: wei/[email protected]
+       with:
+         args: https://engaging-web.mit.edu/~jahn/MITgcmutils/mnc/aste/grid.t0{01,02,04,05,07,08,10,11,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,36,37,38,39,41,42,43,44,45}.nc -o utils/python/MITgcmutils/tests/data/aste/grid.t0#1.nc
+     - name: Download eccov3 test data
+       uses: wei/[email protected]
+       with:
+         args: https://engaging-web.mit.edu/~jahn/MITgcmutils/mnc/eccov3/dic_tave.0000025920.t[001-032].nc -o utils/python/MITgcmutils/tests/data/eccov3/dic_tave.0000025920.t#1.nc
+     - name: Run Tox
+       run: tox -e ${{ matrix.env }}
+       working-directory: utils/python/MITgcmutils
+     - name: Run scripts
+       run: tests/run-scripts ${{ matrix.env }}
+       working-directory: utils/python/MITgcmutils
+     - name: Upload gluemncbig output
+       uses: actions/upload-artifact@v2
+       with:
+         name: gluemncbig
+         path: utils/python/MITgcmutils/*.nc
+       if: ${{ always() }}
+
  openad:
    runs-on: ubuntu-latest
 

utils/python/MITgcmutils/tests/data/sose/UVEL.0000000060.meta

@@ -0,0 +1,9 @@
+ nDims = [   3 ];
+ dimList = [
+  2160,    1, 2160,
+   320,    1,  320,
+    42,    1,   42 
+ ];
+ dataprec = [ 'float32' ];
+ nrecords = [       40 ];
+ timeStepNumber = [    60 ];

utils/python/MITgcmutils/tests/md5/eccov3/dic_tave.0000025920.cdl

@@ -0,0 +1,50 @@
+netcdf dic_tave.0000025920 {
+dimensions:
+	T = UNLIMITED ; // (1 currently)
+	X = 360 ;
+	Y = 160 ;
+variables:
+	double X(X) ;
+		X:long_name = "longitude of cell center" ;
+		X:units = "degrees_east" ;
+	double Y(Y) ;
+		Y:long_name = "latitude of cell center" ;
+		Y:units = "degrees_north" ;
+	double T(T) ;
+		T:long_name = "model_time" ;
+		T:units = "s" ;
+	int iter(T) ;
+		iter:long_name = "iteration_count" ;
+	float dic_SUR_ave(T, Y, X) ;
+		dic_SUR_ave:units = "--" ;
+		dic_SUR_ave:description = "" ;
+	float dic_SURC_ave(T, Y, X) ;
+		dic_SURC_ave:units = "--" ;
+		dic_SURC_ave:description = "" ;
+	float dic_SURO_ave(T, Y, X) ;
+		dic_SURO_ave:units = "--" ;
+		dic_SURO_ave:description = "" ;
+	float dic_pH_ave(T, Y, X) ;
+		dic_pH_ave:units = "--" ;
+		dic_pH_ave:description = "" ;
+	float dic_pCO2_ave(T, Y, X) ;
+		dic_pCO2_ave:units = "--" ;
+		dic_pCO2_ave:description = "" ;
+
+// global attributes:
+		:MITgcm_version = "checkpoint63l" ;
+		:MITgcm_URL = "http://mitgcm.org" ;
+		:MITgcm_tag_id = "1.1645 2012/04/04" ;
+		:MITgcm_mnc_ver = 0.9 ;
+		:sNx = 45 ;
+		:sNy = 40 ;
+		:OLx = 4 ;
+		:OLy = 4 ;
+		:nSx = 1 ;
+		:nSy = 1 ;
+		:nPx = 8 ;
+		:nPy = 4 ;
+		:Nx = 360 ;
+		:Ny = 160 ;
+		:Nr = 23 ;
+}

utils/python/MITgcmutils/tests/md5/eccov3/dic_tave.0000025920.md5

@@ -0,0 +1 @@
+75932c55558af5a92c0644fc5ad0e02a  -

utils/python/MITgcmutils/tests/md5/global_ocean.cs32x15/run/mnc_test_0001/grid.cdl

@@ -0,0 +1,129 @@
+netcdf grid {
+dimensions:
+	Z = 15 ;
+	Zp1 = 16 ;
+	Zu = 15 ;
+	Zl = 15 ;
+	X = 384 ;
+	Y = 16 ;
+	Xp1 = 385 ;
+	Yp1 = 17 ;
+variables:
+	double Z(Z) ;
+		Z:long_name = "vertical coordinate of cell center" ;
+		Z:units = "meters" ;
+		Z:positive = "up" ;
+	double RC(Z) ;
+		RC:description = "R coordinate of cell center" ;
+		RC:units = "m" ;
+	double Zp1(Zp1) ;
+		Zp1:long_name = "vertical coordinate of cell interface" ;
+		Zp1:units = "meters" ;
+		Zp1:positive = "up" ;
+	double RF(Zp1) ;
+		RF:description = "R coordinate of cell interface" ;
+		RF:units = "m" ;
+	double Zu(Zu) ;
+		Zu:long_name = "vertical coordinate of lower cell interface" ;
+		Zu:units = "meters" ;
+		Zu:positive = "up" ;
+	double RU(Zu) ;
+		RU:description = "R coordinate of upper interface" ;
+		RU:units = "m" ;
+	double Zl(Zl) ;
+		Zl:long_name = "vertical coordinate of upper cell interface" ;
+		Zl:units = "meters" ;
+		Zl:positive = "up" ;
+	double RL(Zl) ;
+		RL:description = "R coordinate of lower interface" ;
+		RL:units = "m" ;
+	double drC(Zp1) ;
+		drC:description = "r cell center separation" ;
+	double drF(Z) ;
+		drF:description = "r cell face separation" ;
+	double X(X) ;
+		X:long_name = "i-index of cell center" ;
+		X:units = "none" ;
+	double Y(Y) ;
+		Y:long_name = "j-index of cell center" ;
+		Y:units = "none" ;
+	double XC(Y, X) ;
+		XC:description = "X coordinate of cell center (T-P point)" ;
+		XC:units = "degree_east" ;
+	double YC(Y, X) ;
+		YC:description = "Y coordinate of cell center (T-P point)" ;
+		YC:units = "degree_north" ;
+	double Xp1(Xp1) ;
+		Xp1:long_name = "i-index of cell corner" ;
+		Xp1:units = "none" ;
+	double Yp1(Yp1) ;
+		Yp1:long_name = "j-index of cell corner" ;
+		Yp1:units = "none" ;
+	double XG(Yp1, Xp1) ;
+		XG:description = "X coordinate of cell corner (Vorticity point)" ;
+		XG:units = "degree_east" ;
+	double YG(Yp1, Xp1) ;
+		YG:description = "Y coordinate of cell corner (Vorticity point)" ;
+		YG:units = "degree_north" ;
+	double dxC(Y, Xp1) ;
+		dxC:description = "x cell center separation" ;
+	double dyC(Yp1, X) ;
+		dyC:description = "y cell center separation" ;
+	double dxF(Y, X) ;
+		dxF:description = "x cell face separation" ;
+	double dyF(Y, X) ;
+		dyF:description = "y cell face separation" ;
+	double dxG(Yp1, X) ;
+		dxG:description = "x cell corner separation" ;
+	double dyG(Y, Xp1) ;
+		dyG:description = "y cell corner separation" ;
+	double dxV(Yp1, Xp1) ;
+		dxV:description = "x v-velocity separation" ;
+	double dyU(Yp1, Xp1) ;
+		dyU:description = "y u-velocity separation" ;
+	double rA(Y, X) ;
+		rA:description = "r-face area at cell center" ;
+	double rAw(Y, Xp1) ;
+		rAw:description = "r-face area at U point" ;
+	double rAs(Yp1, X) ;
+		rAs:description = "r-face area at V point" ;
+	double rAz(Yp1, Xp1) ;
+		rAz:description = "r-face area at cell corner" ;
+	double AngleCS(Y, X) ;
+		AngleCS:description = "Cos of grid orientation angle at cell center" ;
+	double AngleSN(Y, X) ;
+		AngleSN:description = "Sin of grid orientation angle at cell center" ;
+	double fCori(Y, X) ;
+		fCori:description = "Coriolis f at cell center" ;
+	double fCoriG(Yp1, Xp1) ;
+		fCoriG:description = "Coriolis f at cell corner" ;
+	double R_low(Y, X) ;
+		R_low:description = "base of fluid in r-units" ;
+	double Ro_surf(Y, X) ;
+		Ro_surf:description = "surface reference (at rest) position" ;
+	double Depth(Y, X) ;
+		Depth:description = "fluid thickness in r coordinates (at rest)" ;
+	double HFacC(Z, Y, X) ;
+		HFacC:description = "vertical fraction of open cell at cell center" ;
+	double HFacW(Z, Y, Xp1) ;
+		HFacW:description = "vertical fraction of open cell at West face" ;
+	double HFacS(Z, Yp1, X) ;
+		HFacS:description = "vertical fraction of open cell at South face" ;
+
+// global attributes:
+		:MITgcm_version = "checkpoint67u" ;
+		:MITgcm_URL = "http://mitgcm.org" ;
+		:MITgcm_tag_id = "" ;
+		:MITgcm_mnc_ver = 0.9 ;
+		:sNx = 32 ;
+		:sNy = 16 ;
+		:OLx = 4 ;
+		:OLy = 4 ;
+		:nSx = 12 ;
+		:nSy = 1 ;
+		:nPx = 1 ;
+		:nPy = 1 ;
+		:Nx = 384 ;
+		:Ny = 16 ;
+		:Nr = 15 ;
+}

utils/python/MITgcmutils/tests/md5/global_ocean.cs32x15/run/mnc_test_0001/grid.md5

@@ -0,0 +1 @@
+511a0016be635ca9b9c4b7bdb872a607  -

utils/python/MITgcmutils/tests/md5/global_ocean.cs32x15/run/mnc_test_0001/oceDiag.0000072000.cdl

@@ -0,0 +1,71 @@
+netcdf oceDiag.0000072000 {
+dimensions:
+	T = UNLIMITED ; // (2 currently)
+	Zmd000015 = 15 ;
+	X = 384 ;
+	Y = 16 ;
+	Zld000015 = 15 ;
+	Xp1 = 385 ;
+	Yp1 = 17 ;
+variables:
+	double diag_levels(Zmd000015) ;
+		diag_levels:description = "Idicies of vertical levels within the source arrays" ;
+	double X(X) ;
+		X:long_name = "i-index of cell center" ;
+		X:units = "none" ;
+	double Y(Y) ;
+		Y:long_name = "j-index of cell center" ;
+		Y:units = "none" ;
+	double Xp1(Xp1) ;
+		Xp1:long_name = "i-index of cell corner" ;
+		Xp1:units = "none" ;
+	double Yp1(Yp1) ;
+		Yp1:long_name = "j-index of cell corner" ;
+		Yp1:units = "none" ;
+	double T(T) ;
+		T:long_name = "model_time" ;
+		T:units = "s" ;
+	int iter(T) ;
+		iter:long_name = "iteration_count" ;
+	float DRHODR(T, Zld000015, Y, X) ;
+		DRHODR:description = "Stratification: d.Sigma/dr (kg/m3/r_unit)" ;
+		DRHODR:units = "kg/m^4" ;
+	float RHOAnoma(T, Zmd000015, Y, X) ;
+		RHOAnoma:description = "Density Anomaly (=Rho-rhoConst)" ;
+		RHOAnoma:units = "kg/m^3" ;
+	float CONVADJ(T, Zld000015, Y, X) ;
+		CONVADJ:description = "Convective Adjustment Index [0-1]" ;
+		CONVADJ:units = "fraction" ;
+	float GM_Kwx(T, Zld000015, Y, X) ;
+		GM_Kwx:description = "K_31 element (W.point, X.dir) of GM-Redi tensor" ;
+		GM_Kwx:units = "m^2/s" ;
+	float GM_Kwy(T, Zld000015, Y, X) ;
+		GM_Kwy:description = "K_32 element (W.point, Y.dir) of GM-Redi tensor" ;
+		GM_Kwy:units = "m^2/s" ;
+	float GM_Kwz(T, Zld000015, Y, X) ;
+		GM_Kwz:description = "K_33 element (W.point, Z.dir) of GM-Redi tensor" ;
+		GM_Kwz:units = "m^2/s" ;
+	float GM_PsiX(T, Zld000015, Y, Xp1) ;
+		GM_PsiX:description = "GM Bolus transport stream-function : U component" ;
+		GM_PsiX:units = "m^2/s" ;
+	float GM_PsiY(T, Zld000015, Yp1, X) ;
+		GM_PsiY:description = "GM Bolus transport stream-function : V component" ;
+		GM_PsiY:units = "m^2/s" ;
+
+// global attributes:
+		:MITgcm_version = "checkpoint67u" ;
+		:MITgcm_URL = "http://mitgcm.org" ;
+		:MITgcm_tag_id = "" ;
+		:MITgcm_mnc_ver = 0.9 ;
+		:sNx = 32 ;
+		:sNy = 16 ;
+		:OLx = 4 ;
+		:OLy = 4 ;
+		:nSx = 12 ;
+		:nSy = 1 ;
+		:nPx = 1 ;
+		:nPy = 1 ;
+		:Nx = 384 ;
+		:Ny = 16 ;
+		:Nr = 15 ;
+}

utils/python/MITgcmutils/tests/md5/global_ocean.cs32x15/run/mnc_test_0001/oceDiag.0000072000.md5

@@ -0,0 +1 @@
+b8e7e40ab7edadeb8f30ad08d9390887  -