fix: define int/float precision to prevent deprecation warning (#35)

feat: use try/except for retrieving netrc credentials
feat: add figshare secure FTP uploader to utilities
ci: use cartopy no-binary in build
fix: use first value in requirements in setup
ci: brew install `pkg-config`
ci: use older proj7 in brew install for cartopy
ci: add LD and CPP flags for proj7
ci: add cython to installations
ci: `ACCEPT_USE_OF_DEPRECATED_PROJ_API_H`
ci: set pkg-config path

Author: tsutterley

.github/workflows/python-request.yml

@@ -39,14 +39,19 @@ jobs:
     - name: Install dependencies for MacOS
       if: matrix.os == 'macos-latest'
       run: |
-        brew install proj
+        brew install proj@7
         brew install geos
         brew install hdf5
         brew install netcdf
         brew install libxml2
         brew install libxslt
+        brew install pkg-config
         pip install --upgrade pip
-        pip install flake8 pytest pytest-cov numpy
+        pip install flake8 pytest pytest-cov numpy cython
+        export LDFLAGS="-L/usr/local/opt/proj@7/lib"
+        export CPPFLAGS="-I/usr/local/opt/proj@7/include"
+        export ACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1
+        export PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/local/opt/proj@7/lib/pkgconfig"
         pip install git+https://github.com/tsutterley/geoid-toolkit.git
         pip install git+https://github.com/tsutterley/read-GRACE-geocenter.git
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

doc/source/user_guide/utilities.rst

@@ -343,6 +343,35 @@ General Methods
     .. _figshare: https://doi.org/10.6084/m9.figshare.7388540
 
 
+.. method:: gravity_toolkit.utilities.to_figshare(files,username=None,password=None,directory=None,timeout=None,context=ssl.SSLContext(ssl.PROTOCOL_TLS),get_ca_certs=False,verbose=False,chunk=8192)
+
+    Send files to `figshare`_ using secure `FTP uploader <https://help.figshare.com/article/upload-large-datasets-and-bulk-upload-using-the-ftp-uploader-desktop-uploader-or-api>`_
+
+    Arguments:
+
+      ``files``: list of files to upload
+
+    Keyword arguments:
+
+        ``username``: ftp username
+
+        ``password``: ftp password
+
+        ``directory``: figshare subdirectory for sending data
+
+        ``timeout``: timeout in seconds for blocking operations
+
+        ``context``: SSL context for ftp connection
+
+        ``get_ca_certs``: get list of loaded “certification authority” certificates
+
+        ``verbose``: print ftp transfer information
+
+        ``chunk``: chunk size for transfer encoding
+
+    .. _figshare: https://doi.org/10.6084/m9.figshare.7388540
+
+
 .. method:: gravity_toolkit.utilities.from_csr(directory,timeout=None,context=ssl.SSLContext(),chunk=16384,verbose=False,fid=sys.stdout,mode=0o775)
 
     Download `satellite laser ranging (SLR)`__ files from the University of Texas Center for Space Research (UTCSR)

gravity_toolkit/destripe_harmonics.py

@@ -3,7 +3,7 @@
 destripe_harmonics.py
 Original Fortran program remove_errors.f written by Isabella Velicogna
 Adapted by Chia-Wei Hsu (05/2018)
-Updated by Tyler Sutterley (02/2021)
+Updated by Tyler Sutterley (05/2021)
 
 Filters spherical harmonic coefficients for correlated "striping" errors
 
@@ -45,6 +45,7 @@
         http://dx.doi.org/10.1029/2005GL025285
 
 UPDATE HISTORY:
+    Updated 05/2021: define int/float precision to prevent deprecation warning
     Updated 02/2021: replaced numpy bool to prevent deprecation warning
     Updated 07/2020: added function docstrings
     Updated 03/2020: Updated for public release
@@ -135,8 +136,8 @@ def destripe_harmonics(clm1, slm1, LMIN=2, LMAX=60, MMAX=None,
         #-- put the even and odd l's into their own arrays
         ieven = -1
         iodd = -1
-        leven = np.zeros((LMAX), dtype=np.int)
-        lodd = np.zeros((LMAX), dtype=np.int)
+        leven = np.zeros((LMAX), dtype=np.int64)
+        lodd = np.zeros((LMAX), dtype=np.int64)
 
         for l in range(int(m),int(LMAX+1)):
             #-- check if degree is odd or even

gravity_toolkit/gen_harmonics.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 gen_harmonics.py
-Written by Tyler Sutterley (01/2021)
+Written by Tyler Sutterley (05/2021)
 Converts data from the spatial domain to spherical harmonic coefficients
 
 Differs from the gen_stokes() function as it does not
@@ -46,6 +46,7 @@
         Associated Legendre Functions", Journal of Geodesy (2002)
 
 UPDATE HISTORY:
+    Updated 05/2021: define int/float precision to prevent deprecation warning
     Updated 01/2021: use harmonics class for spherical harmonic operations
     Updated 07/2020: added function docstrings
     Updated 04/2020: include degrees and orders in output dictionary
@@ -86,8 +87,8 @@ def gen_harmonics(data, lon, lat, LMAX=60, MMAX=None, PLM=0):
         MMAX = np.copy(LMAX)
 
     #-- dimensions of the longitude and latitude arrays
-    nlon = np.int(len(lon))
-    nlat = np.int(len(lat))
+    nlon = np.int64(len(lon))
+    nlat = np.int64(len(lat))
 
     #-- grid step
     dlon = np.abs(lon[1]-lon[0])
@@ -98,8 +99,8 @@ def gen_harmonics(data, lon, lat, LMAX=60, MMAX=None, PLM=0):
     dth = dlat*np.pi/180.0
 
     #-- convert latitude and longitude to float if integers
-    lon = lon.astype(np.float)
-    lat = lat.astype(np.float)
+    lon = lon.astype(np.float64)
+    lat = lat.astype(np.float64)
     #-- reformatting longitudes to range 0:360 (if previously -180:180)
     if np.count_nonzero(lon < 0):
         lon[lon < 0] += 360.0

gravity_toolkit/gen_stokes.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 gen_stokes.py
-Written by Tyler Sutterley (01/2021)
+Written by Tyler Sutterley (05/2021)
 
 Converts data from the spatial domain to spherical harmonic coefficients
 
@@ -46,6 +46,7 @@
         hdf5_stokes.py: writes output spherical harmonic data to HDF5
 
 UPDATE HISTORY:
+    Updated 05/2021: define int/float precision to prevent deprecation warning
     Updated 01/2021: use harmonics class for spherical harmonic operations
     Updated 07/2020: added function docstrings
     Updated 04/2020: reading load love numbers outside of this function
@@ -103,13 +104,13 @@ def gen_stokes(data, lon, lat, LMIN=0, LMAX=60, MMAX=None, UNITS=1,
     """
 
     #-- converting LMIN and LMAX to integer
-    LMIN = np.int(LMIN)
-    LMAX = np.int(LMAX)
+    LMIN = np.int64(LMIN)
+    LMAX = np.int64(LMAX)
     #-- upper bound of spherical harmonic orders (default = LMAX)
     MMAX = np.copy(LMAX) if (MMAX is None) else MMAX
 
     #-- grid dimensions
-    nlat = np.int(len(lat))
+    nlat = np.int64(len(lat))
     #-- grid step
     dlon = np.abs(lon[1]-lon[0])
     dlat = np.abs(lat[1]-lat[0])

gravity_toolkit/grace_date.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 grace_date.py
-Written by Tyler Sutterley (02/2021)
+Written by Tyler Sutterley (05/2021)
 
 Reads index file from podaac_grace_sync.py or gfz_isdc_grace_ftp.py
 Parses dates of each GRACE/GRACE-FO file and assigns the month number
@@ -38,6 +38,7 @@
     time.py: utilities for calculating time operations
 
 UPDATE HISTORY:
+    Updated 05/2021: define int/float precision to prevent deprecation warning
     Updated 02/2021: use adjust_months function to fix special months cases
     Updated 12/2020: using utilities from time module
     Updated 10/2020: use argparse to set command line parameters
@@ -135,7 +136,7 @@ def grace_date(base_dir, PROC='', DREL='', DSET='', OUTPUT=True, MODE=0o775):
     mid_day = np.zeros((n_files))#-- mid-month day
     tot_days = np.zeros((n_files))#-- number of days since Jan 2002
     tdec = np.zeros((n_files))#-- tdec is the date in decimal form
-    mon = np.zeros((n_files,),dtype=np.int)#-- GRACE/GRACE-FO month number
+    mon = np.zeros((n_files,),dtype=np.int64)#-- GRACE/GRACE-FO month number
 
     #-- compile numerical expression operator for parameters from files
     #-- will work with previous releases and releases for GRACE-FO
@@ -153,10 +154,10 @@ def grace_date(base_dir, PROC='', DREL='', DSET='', OUTPUT=True, MODE=0o775):
         #-- extract parameters from input filename
         PFX,start_date,end_date,AUX,PRC,F1,DRL,F2,SFX = rx.findall(infile).pop()
         #-- find start date, end date and number of days
-        start_yr[t] = np.float(start_date[:4])
-        end_yr[t] = np.float(end_date[:4])
-        start_day[t] = np.float(start_date[4:])
-        end_day[t] = np.float(end_date[4:])
+        start_yr[t] = np.float64(start_date[:4])
+        end_yr[t] = np.float64(end_date[:4])
+        start_day[t] = np.float64(start_date[4:])
+        end_day[t] = np.float64(end_date[4:])
 
         #-- number of days in the starting year for leap and standard years
         dpy = gravity_toolkit.time.calendar_days(start_yr[t]).sum()
@@ -176,7 +177,7 @@ def grace_date(base_dir, PROC='', DREL='', DSET='', OUTPUT=True, MODE=0o775):
 
         #-- Calculation of total days since start of campaign
         count = 0
-        n_yrs = np.int(start_yr[t]-2002)
+        n_yrs = np.int64(start_yr[t]-2002)
         #-- for each of the GRACE years up to the file year
         for iyr in range(n_yrs):
             #-- year

gravity_toolkit/grace_find_months.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 grace_find_months.py
-Written by Tyler Sutterley (07/2020)
+Written by Tyler Sutterley (05/2021)
 
 Parses date index file from grace_date.py
 Finds the months available for a GRACE/GRACE-FO product
@@ -29,6 +29,7 @@
     grace_date.py: reads GRACE index file and calculates dates for each month
 
 UPDATE HISTORY:
+    Updated 05/2021: define int/float precision to prevent deprecation warning
     Updated 07/2020: added function docstrings
     Updated 03/2020: check that GRACE/GRACE-FO date file exists
     Updated 10/2019: using local() function to set subdirectories
@@ -91,18 +92,18 @@ def grace_find_months(base_dir, PROC, DREL, DSET='GSM'):
     #-- skip the header row and extract dates (decimal format) and months
     date_input = np.loadtxt(date_file, skiprows=1)
     tdec = date_input[:,0]
-    months = date_input[:,1].astype(np.int)
+    months = date_input[:,1].astype(np.int64)
 
     #-- array of all possible months (or in case of CNES RL01/2: 10-day sets)
-    all_months = np.arange(1,months.max(),dtype=np.int)
+    all_months = np.arange(1,months.max(),dtype=np.int64)
     #-- missing months (values in all_months but not in months)
     missing = sorted(set(all_months)-set(months))
     #-- If CNES RL01/2: simply convert into numpy array
     #-- else: remove months 1-3 and convert into numpy array
     if ((PROC == 'CNES') & (DREL in ('RL01','RL02'))):
-        missing = np.array(missing,dtype=np.int)
+        missing = np.array(missing,dtype=np.int64)
     else:
-        missing = np.array(missing[3:],dtype=np.int)
+        missing = np.array(missing[3:],dtype=np.int64)
 
     return {'time':tdec, 'start':months[0], 'end':months[-1], 'months':months,
         'missing':missing}

gravity_toolkit/grace_input_months.py

@@ -92,6 +92,7 @@
 
 UPDATE HISTORY:
     Updated 05/2021: can use SLR low-degree harmonic values produced by GFZ
+        define int/float precision to prevent deprecation warning
     Updated 04/2021: can replace figure axis and azimuthal dependence with SLR
     Updated 12/2020: updated SLR geocenter for new solutions from Minkang Cheng
     Updated 11/2020: set regress_model RELATIVE option to 2003.3 to match others
@@ -384,7 +385,7 @@ def grace_input_months(base_dir, PROC, DREL, DSET, LMAX, start_mon, end_mon,
     grace_clm = np.zeros((LMAX+1,MMAX+1,n_cons))
     grace_slm = np.zeros((LMAX+1,MMAX+1,n_cons))
     tdec = np.zeros((n_cons))
-    mon = np.zeros((n_cons),dtype=np.int)
+    mon = np.zeros((n_cons),dtype=np.int64)
     #-- output dimensions
     lout = np.arange(LMAX+1)
     mout = np.arange(MMAX+1)
@@ -400,7 +401,7 @@ def grace_input_months(base_dir, PROC, DREL, DSET, LMAX, start_mon, end_mon,
         grace_clm[:,:,i] = Ylms['clm'][0:LMAX+1,0:MMAX+1]
         grace_slm[:,:,i] = Ylms['slm'][0:LMAX+1,0:MMAX+1]
         tdec[i] = Ylms['time']
-        mon[i] = np.int(grace_month)
+        mon[i] = np.int64(grace_month)
 
     #-- Replace C20 with SLR coefficients
     if SLR_C20 in ('CSR','GFZ','GSFC'):
@@ -580,12 +581,12 @@ def read_ecmwf_corrections(base_dir, LMAX, months, MMAX=None):
                 #-- split the line into individual components
                 line_contents = line.split()
                 #-- degree and order for the line
-                l1 = np.int(line_contents[1])
-                m1 = np.int(line_contents[2])
+                l1 = np.int64(line_contents[1])
+                m1 = np.int64(line_contents[2])
                 #-- if degree and order are below the truncation limits
                 if ((l1 <= LMAX) and (m1 <= MMAX)):
-                    atm_corr_clm[key][l1,m1] = np.float(line_contents[3])
-                    atm_corr_slm[key][l1,m1] = np.float(line_contents[4])
+                    atm_corr_clm[key][l1,m1] = np.float64(line_contents[3])
+                    atm_corr_slm[key][l1,m1] = np.float64(line_contents[4])
 
     #-- create output atmospheric corrections to be removed/added to data
     atm_corr = {}
@@ -647,10 +648,10 @@ def regress_model(t_in, d_in, t_out, ORDER=2, CYCLES=None, RELATIVE=0.0):
         MMAT.append((t_out-RELATIVE)**o)
     #-- add cyclical terms (0.5=semi-annual, 1=annual)
     for c in CYCLES:
-        DMAT.append(np.sin(2.0*np.pi*t_in/np.float(c)))
-        DMAT.append(np.cos(2.0*np.pi*t_in/np.float(c)))
-        MMAT.append(np.sin(2.0*np.pi*t_out/np.float(c)))
-        MMAT.append(np.cos(2.0*np.pi*t_out/np.float(c)))
+        DMAT.append(np.sin(2.0*np.pi*t_in/np.float64(c)))
+        DMAT.append(np.cos(2.0*np.pi*t_in/np.float64(c)))
+        MMAT.append(np.sin(2.0*np.pi*t_out/np.float64(c)))
+        MMAT.append(np.cos(2.0*np.pi*t_out/np.float64(c)))
     #-- Calculating Least-Squares Coefficients
     #-- Standard Least-Squares fitting (the [0] denotes coefficients output)
     beta_mat = np.linalg.lstsq(np.transpose(DMAT), d_in, rcond=-1)[0]

gravity_toolkit/grace_months_index.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 grace_months_index.py
-Written by Tyler Sutterley (10/2020)
+Written by Tyler Sutterley (05/2021)
 
 Creates a file with the start and end days for each dataset
 Shows the range of each month for (CSR/GFZ/JPL) (RL04/RL05/RL06)
@@ -33,6 +33,7 @@
     numpy: Scientific Computing Tools For Python (https://numpy.org)
 
 UPDATE HISTORY:
+    Updated 05/2021: define int/float precision to prevent deprecation warning
     Updated 10/2020: use argparse to set command line parameters
     Updated 09/2020: add column for GSFC v02.4 GRACE mascons
     Updated 07/2020: added function docstrings
@@ -112,20 +113,20 @@ def grace_months_index(base_dir, DREL=['RL06','v02.4'], MODE=None):
                 #-- Adding data to dictionary for data processing and release
                 var_info[var_name] = {}
                 #-- allocate for output variables
-                var_info[var_name]['mon'] = np.zeros((nmon),dtype=np.int)
-                var_info[var_name]['styr'] = np.zeros((nmon),dtype=np.int)
-                var_info[var_name]['stday'] = np.zeros((nmon),dtype=np.int)
-                var_info[var_name]['endyr'] = np.zeros((nmon),dtype=np.int)
-                var_info[var_name]['endday'] = np.zeros((nmon),dtype=np.int)
+                var_info[var_name]['mon'] = np.zeros((nmon),dtype=np.int64)
+                var_info[var_name]['styr'] = np.zeros((nmon),dtype=np.int64)
+                var_info[var_name]['stday'] = np.zeros((nmon),dtype=np.int64)
+                var_info[var_name]['endyr'] = np.zeros((nmon),dtype=np.int64)
+                var_info[var_name]['endday'] = np.zeros((nmon),dtype=np.int64)
                 #-- place output variables in dictionary
                 for i,key in enumerate(['mon','styr','stday','endyr','endday']):
                     #-- first column is date in decimal form (start at 1 not 0)
-                    var_info[var_name][key] = date_input[:,i+1].astype(np.int)
+                    var_info[var_name][key] = date_input[:,i+1].astype(np.int64)
                 #-- Finding the maximum month measured
                 if (var_info[var_name]['mon'].max() > max_mon):
                     #-- if the maximum month in this dataset is greater
                     #-- than the previously read datasets
-                    max_mon = np.int(var_info[var_name]['mon'].max())
+                    max_mon = np.int64(var_info[var_name]['mon'].max())
 
     #-- sort datasets alphanumerically
     var_name = sorted(var_info.keys())