Updates to dev following PR#65

.github/workflows/development-pipeline.yml

@@ -33,7 +33,7 @@ jobs:
             python-version: 3.12
             python: xvfb-run python3
             pip_arg: ""
-          - os: macos-13
+          - os: macos-15
             python-version: 3.12
             python: python3
             pip_arg: ""

openfast_toolbox/case_generation/runner.py

@@ -368,7 +368,8 @@ def writeBatch(batchfile, fastfiles, fastExe=None, nBatches=1, pause=False, flag
     - nBatches: split into nBatches files.
     - pause: insert a pause statement at the end so that batch file is not closed after execution
     - flags: flags (string) to be placed between the executable and the filename
-    - flags_after: flags (string) to be placed after the filename
+    - flags_after: flags to be placed after the filename (single string if the same for every file,
+                   or a list of strings if different for each file)
     - run_if_ext_missing: add a line in the batch file so that the command is only run if
                           the file `f.EXT` is missing, where .EXT is specified in run_if_ext_missing
                           If None, the command is always run
@@ -394,8 +395,11 @@ def writeBatch(batchfile, fastfiles, fastExe=None, nBatches=1, pause=False, flag
     fastExe_rel   = os.path.relpath(fastExe_abs, batchdir)
     if len(flags)>0:
         flags=' '+flags
-    if len(flags_after)>0:
-        flags_after=' '+flags_after
+    if isinstance(flags_after, str):
+        if len(flags_after)>0:
+            flags_after=' '+flags_after
+    elif isinstance(flags_after, list):
+        flags_after = [' '+f if len(f)>0 else f for f in flags_after]
 
     # Remove commandlines if outputs are already present
     if discard_if_ext_present:
@@ -414,10 +418,11 @@ def writeb(batchfile, fastfiles):
                     f.write('@echo off\n')
             if preCommands is not None:
                 f.write(preCommands+'\n')
-            for ff in fastfiles:
+            for i, ff in enumerate(fastfiles):
                 ff_abs = os.path.abspath(ff)
                 ff_rel = os.path.relpath(ff_abs, batchdir)
-                cmd = fastExe_rel + flags + ' '+ ff_rel + flags_after
+                cmd = fastExe_rel + flags + ' '+ ff_rel
+                cmd += flags_after[i] if isinstance(flags_after, list) else flags_after
                 if stdOutToFile:
                     stdout = os.path.splitext(ff_rel)[0]+'.stdout'
                     cmd += ' > ' +stdout

openfast_toolbox/fastfarm/examples/Ex1_FASTFarm_discretization.py

@@ -136,7 +136,7 @@ def main(test=False):
     # --- 1.2 Getting the default resolution and plotting the layout
     # --------------------------------------------------------------------------------
     # Below we provide the minimal set of arguments needed to compute the resolution automatically.
-    ffcase = FFCaseCreation(wts=wts, vhub=vhub, 
+    ffcase = FFCaseCreation(path=path, wts=wts, vhub=vhub, 
                           mod_wake=mod_wake,
                           inflowType=inflowType)
 
@@ -151,7 +151,7 @@ def main(test=False):
     dt_high = 0.50 # [s]
     dt_low  = 2.00 # [s]
     ds_low  = 25   # [m]
-    ffcase2 = FFCaseCreation(wts=wts, vhub=vhub,
+    ffcase2 = FFCaseCreation(path=path, wts=wts, vhub=vhub,
                          dt_high=dt_high,
                          dt_low=dt_low,   ds_low=ds_low,
                          mod_wake=mod_wake,
@@ -187,8 +187,6 @@ def main(test=False):
 
     """
 
-
-
     return ffcase, ffcase2
 
 
@@ -200,9 +198,9 @@ def main(test=False):
 
 if __name__=='__test__':
     ffcase, ffcase2 = main(test=True)
-    np.testing.assert_equal(ffcase.ds_low, 0.9)
+    np.testing.assert_equal(ffcase.ds_low, 20)
     np.testing.assert_equal(ffcase.dt_low, 0.9)
-    np.testing.assert_equal(ffcase.ds_high, 0.3)
+    np.testing.assert_equal(ffcase.ds_high, 5)
     np.testing.assert_equal(ffcase.dt_high, 0.3)
     np.testing.assert_array_equal(ffcase.extent_low, [3, 6, 3, 3, 2] )
     np.testing.assert_equal(ffcase.vhub    , [8])
@@ -211,9 +209,9 @@ def main(test=False):
     np.testing.assert_equal(ffcase.shear   , [0])
     np.testing.assert_equal(ffcase.TIvalue, [10])
 
-    np.testing.assert_equal(ffcase2.ds_low, 2.0)
+    np.testing.assert_equal(ffcase2.ds_low, 25)
     np.testing.assert_equal(ffcase2.dt_low, 2.0)
-    np.testing.assert_equal(ffcase2.ds_high, 0.5)
+    np.testing.assert_equal(ffcase2.ds_high, 5)
     np.testing.assert_equal(ffcase2.dt_high, 0.5)
     np.testing.assert_array_equal(ffcase2.extent_low, [3, 6, 3, 3, 2] )
 

openfast_toolbox/fastfarm/examples/Ex2a_FASTFarm_TurbSim_driven.py

@@ -46,8 +46,8 @@
 
 from openfast_toolbox.fastfarm.FASTFarmCaseCreation import FFCaseCreation
 
-from openfast_toolbox.fastfarm.FASTFarmCaseCreation import check_files_exist, check_discon_library # Helper functions 
-from openfast_toolbox.fastfarm.fastfarm import plotFastFarmSetup # Low level FAST.Farm functions 
+from openfast_toolbox.fastfarm.FASTFarmCaseCreation import check_files_exist, check_discon_library, modifyProperty
+from openfast_toolbox.fastfarm.fastfarm import plotFastFarmSetup
 
 scriptDir = os.path.dirname(__file__)
 
@@ -177,11 +177,11 @@ def main(test=False):
     # END OF USER INPUT
     # -----------------------------------------------------------------------------
 
-	# Plot turbines locations
+    # Plot turbines locations
     fig = plotFastFarmSetup(wts)
     if not test:
-    	check_files_exist(ffbin, tsbin, templateFSTF, templateFiles)
-    	check_discon_library(libdisconfilepath);
+        check_files_exist(ffbin, tsbin, templateFSTF, templateFiles)
+        check_discon_library(libdiscon)
 
     # -----------------------------------------------------------------------------
     # -------------------- FAST.Farm initial setup --------------------------------

openfast_toolbox/fastfarm/fastfarm.py

@@ -353,7 +353,7 @@ def writeFastFarm(outputFile, templateFile, xWT, yWT, zWT, FFTS=None, OutListT1=
             if isinstance(FFTS[k],int):
                 fst[k] = FFTS[k] 
             else:
-                fst[k] = np.around(FFTS[k],3)
+                fst[k] = np.around(FFTS[k],5)
         fst['WrDisDT'] = FFTS['DT_Low']
 
     # --- Set turbine names, position, and box extent

openfast_toolbox/modules/elastodyn.py

@@ -108,8 +108,12 @@
 def RotMat_AxisAngle(u,theta):
     """ Returns the rotation matrix for a rotation around an axis u, with an angle theta """
     R=np.zeros((3,3))
-    ux,uy,uz=u
+    u = np.asarray(u).ravel()  # Ensure 1D array
+    ux,uy,uz = u[0], u[1], u[2]
     c,s=np.cos(theta),np.sin(theta)
+    # Ensure scalar values to avoid numpy deprecation warnings
+    ux, uy, uz = float(ux), float(uy), float(uz)
+    c, s = float(c), float(s)
     R[0,0]=ux**2*(1-c)+c    ; R[0,1]=ux*uy*(1-c)-uz*s; R[0,2]=ux*uz*(1-c)+uy*s;
     R[1,0]=uy*ux*(1-c)+uz*s ; R[1,1]=uy**2*(1-c)+c   ; R[1,2]=uy*uz*(1-c)-ux*s
     R[2,0]=uz*ux*(1-c)-uy*s ; R[2,1]=uz*uy*(1-c)+ux*s; R[2,2]=uz**2*(1-c)+c;

openfast_toolbox/postpro/postpro.py

@@ -4,10 +4,13 @@
 import numpy as np
 import re
 try:
-    from scipy.integrate import cumulative_trapezoid 
-    from numpy import trapezoid
-except:
+    from scipy.integrate import cumulative_trapezoid
+except ImportError:
     from scipy.integrate import cumtrapz as cumulative_trapezoid
+
+try:
+    from numpy import trapezoid
+except ImportError:
     from numpy import trapz as trapezoid
 
 import openfast_toolbox.io as weio

setup.py

@@ -40,6 +40,7 @@
         "chardet",
         "xarray",  # for netcdf files
         "pytest",
+        "dill",
     ],
     test_suite="pytest",
     tests_require=["pytest"],