fix: prevent overwriting ATLAS compact x and y coordinates to address #…

…238 (#240)

ci: update versions to prevent deprecations

.github/workflows/auto-update-bulletin-a.yml

@@ -24,7 +24,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up mamba ${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@v1
       with:
@@ -66,7 +66,7 @@ jobs:
         python -c "import pyTMD.time; pyTMD.time.append_delta_time(verbose=True)"
     - name: Create pull request
       if: steps.changes.outputs.DETECTED == 'true'
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v5
       with:
         assignees: ${{ github.actor }}
         title: "data: automatic bulletin updates"

.github/workflows/auto-update-files.yml

@@ -24,7 +24,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up mamba ${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@v1
       with:
@@ -64,7 +64,7 @@ jobs:
         fi
     - name: Create pull request
       if: steps.changes.outputs.DETECTED == 'true'
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v5
       with:
         assignees: ${{ github.actor }}
         title: "data: automatic time updates"

.github/workflows/python-publish.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/python-request.yml

@@ -25,7 +25,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up mamba ${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@v1
       with:
@@ -52,7 +52,7 @@ jobs:
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Checkout Matlab TMD Toolbox
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: tsutterley/TMD_Matlab_Toolbox_v2.5
         path: TMD_Matlab_Toolbox

doc/source/release_notes/release-v2.0.8.rst

@@ -0,0 +1,11 @@
+##################
+`Release v2.0.8`__
+##################
+
+* ``feat``: add option to run with parquet tabular files (`#236 <https://github.com/tsutterley/pyTMD/pull/236>`_)
+* ``feat``: add function to invert field mapping keys and values  (`#235 <https://github.com/tsutterley/pyTMD/pull/235>`_)
+* ``fix``: prevent overwriting ATLAS compact x and y coordinates to address `#238 <https://github.com/tsutterley/pyTMD/issues/238>`_ (`#240 <https://github.com/tsutterley/pyTMD/pull/240>`_)
+* ``docs``: use micromamba for builds  (`#235 <https://github.com/tsutterley/pyTMD/pull/235>`_)
+* ``ci``: bump versions of imports to prevent deprecation errors (`#235 <https://github.com/tsutterley/pyTMD/pull/235>`_)
+
+.. __: https://github.com/tsutterley/pyTMD/releases/tag/2.0.8

pyTMD/calc_astrol_longitudes.py

@@ -88,9 +88,7 @@ def calc_astrol_longitudes(*args, **kwargs):
     ----------
     .. [1] J. Meeus, *Astronomical Algorithms*, 2nd edition, 477 pp., (1998).
     """
-    warnings.filterwarnings("module")
     warnings.warn("Deprecated. Please use pyTMD.astro instead",
         DeprecationWarning)
-    warnings.filterwarnings("ignore")
     # call updated function to not break current workflows
     return pyTMD.astro.mean_longitudes(*args, **kwargs)

pyTMD/convert_ll_xy.py

@@ -74,9 +74,7 @@ def convert_ll_xy(*args, **kwargs):
     o2: float
         Projected y-coordinates (``'F'``) or latitude (``'B``')
     """
-    warnings.filterwarnings("module")
     warnings.warn("Deprecated. Please use pyTMD.convert_crs instead",
         DeprecationWarning)
-    warnings.filterwarnings("ignore")
     # call updated function to not break current workflows
     return pyTMD.convert_crs(*args, **kwargs)

pyTMD/io/OTIS.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 OTIS.py
-Written by Tyler Sutterley (08/2023)
+Written by Tyler Sutterley (09/2023)
 
 Reads files for a tidal model and makes initial calculations to run tide program
 Includes functions to extract tidal harmonic constants from OTIS tide models for
@@ -59,6 +59,7 @@
     interpolate.py: interpolation routines for spatial data
 
 UPDATE HISTORY:
+    Updated 09/2023: prevent overwriting ATLAS compact x and y coordinates
     Updated 08/2023: changed ESR netCDF4 format to TMD3 format
     Updated 04/2023: using pathlib to define and expand tide model paths
     Updated 03/2023: add basic variable typing to function inputs
@@ -353,7 +354,7 @@ def extract_constants(
             # read z constituent from elevation file
             if (kwargs['grid'] == 'ATLAS'):
                 z0,zlocal = read_atlas_elevation(model_file, i, c)
-                xi,yi,hc = combine_atlas_model(x0, y0, z0, pmask, zlocal,
+                _,_,hc = combine_atlas_model(x0, y0, z0, pmask, zlocal,
                     variable='z')
             elif (kwargs['grid'] == 'TMD3'):
                 hc = read_netcdf_file(model_file, i, variable='z')
@@ -368,7 +369,7 @@ def extract_constants(
             # read u constituent from transport file
             if (kwargs['grid'] == 'ATLAS'):
                 u0,v0,uvlocal = read_atlas_transport(model_file, i, c)
-                xi,yi,hc = combine_atlas_model(x0, y0, u0, pmask, uvlocal,
+                _,_,hc = combine_atlas_model(x0, y0, u0, pmask, uvlocal,
                     variable='u')
             elif (kwargs['grid'] == 'TMD3'):
                 hc = read_netcdf_file(model_file, i, variable='u')
@@ -380,7 +381,7 @@ def extract_constants(
             # read v constituent from transport file
             if (kwargs['grid'] == 'ATLAS'):
                 u0,v0,uvlocal = read_atlas_transport(model_file, i, c)
-                xi,yi,hc = combine_atlas_model(x0, y0, v0, pmask, uvlocal,
+                _,_,hc = combine_atlas_model(x0, y0, v0, pmask, uvlocal,
                     variable='v')
             elif (kwargs['grid'] == 'TMD3'):
                 hc = read_netcdf_file(model_file, i, type='v')
@@ -392,7 +393,7 @@ def extract_constants(
         # replace original values with extend matrices
         if global_grid:
             hc = extend_matrix(hc)
-        # copy mask to elevation
+        # copy mask to constituent
         hc.mask |= bathymetry.mask
 
         # interpolate amplitude and phase of the constituent
@@ -587,64 +588,49 @@ def read_constants(
             # read constituent from elevation file
             if (kwargs['grid'] == 'ATLAS'):
                 z0,zlocal = read_atlas_elevation(model_file, i, c)
-                xi,yi,z = combine_atlas_model(x0, y0, z0, pmask, zlocal,
+                _,_,hc = combine_atlas_model(x0, y0, z0, pmask, zlocal,
                     variable='z')
             elif (kwargs['grid'] == 'TMD3'):
-                z = read_netcdf_file(model_file, i, variable='z')
+                hc = read_netcdf_file(model_file, i, variable='z')
                 # apply flexure scaling
                 if kwargs['apply_flexure']:
-                    z *= sf
+                    hc *= sf
             elif isinstance(model_file,list):
-                z = read_otis_elevation(model_file[i], 0)
+                hc = read_otis_elevation(model_file[i], 0)
             else:
-                z = read_otis_elevation(model_file, i)
-            # replace original values with extend matrices
-            if global_grid:
-                z = extend_matrix(z)
-            # copy mask to elevation
-            z.mask |= mz.astype(bool)
-            # append extended constituent
-            constituents.append(c, z)
-
+                hc = read_otis_elevation(model_file, i)
         elif kwargs['type'] in ('U','u'):
             # read constituent from transport file
             if (kwargs['grid'] == 'ATLAS'):
                 u0,v0,uvlocal = read_atlas_transport(model_file, i, c)
-                xi,yi,u = combine_atlas_model(x0, y0, u0, pmask, uvlocal,
+                _,_,hc = combine_atlas_model(x0, y0, u0, pmask, uvlocal,
                     variable='u')
             elif (kwargs['grid'] == 'TMD3'):
-                u = read_netcdf_file(model_file, i, variable='u')
+                hc = read_netcdf_file(model_file, i, variable='u')
             elif isinstance(model_file,list):
-                u,v = read_otis_transport(model_file[i], 0)
+                hc,v = read_otis_transport(model_file[i], 0)
             else:
-                u,v = read_otis_transport(model_file, i)
-            # replace original values with extend matrices
-            if global_grid:
-                u = extend_matrix(u)
-            # copy mask to u transports
-            u.mask |= mu.astype(bool)
-            # append extended constituent
-            constituents.append(c, u)
-
+                hc,v = read_otis_transport(model_file, i)
         elif kwargs['type'] in ('V','v'):
             # read constituent from transport file
             if (kwargs['grid'] == 'ATLAS'):
                 u0,v0,uvlocal = read_atlas_transport(model_file, i, c)
-                xi,yi,v = combine_atlas_model(x0, y0, v0, pmask, uvlocal,
+                _,_,hc = combine_atlas_model(x0, y0, v0, pmask, uvlocal,
                     variable='v')
             elif (kwargs['grid'] == 'TMD3'):
-                v = read_netcdf_file(model_file, i, type='v')
+                hc = read_netcdf_file(model_file, i, type='v')
             elif isinstance(model_file,list):
-                u,v = read_otis_transport(model_file[i], 0)
+                u,hc = read_otis_transport(model_file[i], 0)
             else:
-                u,v = read_otis_transport(model_file, i)
-            # replace original values with extend matrices
-            if global_grid:
-                v = extend_matrix(v)
-            # copy mask to v transports
-            v.mask |= mv.astype(bool)
-            # append extended constituent
-            constituents.append(c, v)
+                u,hc = read_otis_transport(model_file, i)
+
+        # replace original values with extend matrices
+        if global_grid:
+            hc = extend_matrix(hc)
+        # copy mask to constituent
+        hc.mask |= bathymetry.mask
+        # append extended constituent
+        constituents.append(c, hc)
 
     # return the complex form of the model constituents
     return constituents

pyTMD/load_nodal_corrections.py

@@ -105,7 +105,6 @@ def load_nodal_corrections(*args, **kwargs):
     .. __: https://doi.org/10.1175/1520-0426(2002)019<0183:EIMOBO>2.0.CO;2
     """
     # raise warning for deprecated function call
-    warnings.filterwarnings("module")
     warnings.warn("Deprecated. Please use pyTMD.arguments instead",
         DeprecationWarning)
     # raise warnings for deprecated keyword arguments
@@ -116,6 +115,5 @@ def load_nodal_corrections(*args, **kwargs):
                 Changed to '{new}'""", DeprecationWarning)
             # set renamed argument to not break workflows
             kwargs[new] = copy.copy(kwargs[old])
-    warnings.filterwarnings("ignore")
     # call updated function to not break current workflows
     return pyTMD.arguments(*args, **kwargs)

scripts/usap_cats_tides.py

@@ -126,9 +126,7 @@ def main():
     args,_ = parser.parse_known_args()
 
     # warn user that USAP requires a reCAPTCHA check
-    warnings.filterwarnings("module")
     warnings.warn("Deprecated. USAP now requires captcha", DeprecationWarning)
-    warnings.filterwarnings("ignore")
     # check internet connection before attempting to run program
     if pyTMD.utilities.check_connection('https://www.usap-dc.org'):
         for m in args.tide: